A FRAMEWORK FOR FINE-SCALE COMPUTATIONAL FLUID DYNAMICS AIR QUALITY MODELING AND ANALYSIS

EPA Science Inventory

Fine-scale Computational Fluid Dynamics (CFD) simulation of pollutant concentrations within roadway and building microenvironments is feasible using high performance computing. Unlike currently used regulatory air quality models, fine-scale CFD simulations are able to account rig...

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

NASA Technical Reports Server (NTRS)

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

2016-01-01

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

Computational Particle Dynamic Simulations on Multicore Processors (CPDMu) Final Report Phase I

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

Schmalz, Mark S

2011-07-24

Statement of Problem - Department of Energy has many legacy codes for simulation of computational particle dynamics and computational fluid dynamics applications that are designed to run on sequential processors and are not easily parallelized. Emerging high-performance computing architectures employ massively parallel multicore architectures (e.g., graphics processing units) to increase throughput. Parallelization of legacy simulation codes is a high priority, to achieve compatibility, efficiency, accuracy, and extensibility. General Statement of Solution - A legacy simulation application designed for implementation on mainly-sequential processors has been represented as a graph G. Mathematical transformations, applied to G, produce a graph representation {und G}more » for a high-performance architecture. Key computational and data movement kernels of the application were analyzed/optimized for parallel execution using the mapping G {yields} {und G}, which can be performed semi-automatically. This approach is widely applicable to many types of high-performance computing systems, such as graphics processing units or clusters comprised of nodes that contain one or more such units. Phase I Accomplishments - Phase I research decomposed/profiled computational particle dynamics simulation code for rocket fuel combustion into low and high computational cost regions (respectively, mainly sequential and mainly parallel kernels), with analysis of space and time complexity. Using the research team's expertise in algorithm-to-architecture mappings, the high-cost kernels were transformed, parallelized, and implemented on Nvidia Fermi GPUs. Measured speedups (GPU with respect to single-core CPU) were approximately 20-32X for realistic model parameters, without final optimization. Error analysis showed no loss of computational accuracy. Commercial Applications and Other Benefits - The proposed research will constitute a breakthrough in solution of problems related to efficient parallel computation of particle and fluid dynamics simulations. These problems occur throughout DOE, military and commercial sectors: the potential payoff is high. We plan to license or sell the solution to contractors for military and domestic applications such as disaster simulation (aerodynamic and hydrodynamic), Government agencies (hydrological and environmental simulations), and medical applications (e.g., in tomographic image reconstruction). Keywords - High-performance Computing, Graphic Processing Unit, Fluid/Particle Simulation. Summary for Members of Congress - Department of Energy has many simulation codes that must compute faster, to be effective. The Phase I research parallelized particle/fluid simulations for rocket combustion, for high-performance computing systems.« less

High frequency dynamic engine simulation. [TF-30 engine

NASA Technical Reports Server (NTRS)

Schuerman, J. A.; Fischer, K. E.; Mclaughlin, P. W.

1977-01-01

A digital computer simulation of a mixed flow, twin spool turbofan engine was assembled to evaluate and improve the dynamic characteristics of the engine simulation to disturbance frequencies of at least 100 Hz. One dimensional forms of the dynamic mass, momentum and energy equations were used to model the engine. A TF30 engine was simulated so that dynamic characteristics could be evaluated against results obtained from testing of the TF30 engine at the NASA Lewis Research Center. Dynamic characteristics of the engine simulation were improved by modifying the compression system model. Modifications to the compression system model were established by investigating the influence of size and number of finite dynamic elements. Based on the results of this program, high frequency engine simulations using finite dynamic elements can be assembled so that the engine dynamic configuration is optimum with respect to dynamic characteristics and computer execution time. Resizing of the compression systems finite elements improved the dynamic characteristics of the engine simulation but showed that additional refinements are required to obtain close agreement simulation and actual engine dynamic characteristics.

Improved Pyrolysis Micro reactor Design via Computational Fluid Dynamics Simulations

DTIC Science & Technology

2017-05-23

Dynamics Simulations Ghanshyam L. Vaghjiani Air Force Research Laboratory (AFMC) AFRL/RQRS 1 Ara Drive Edwards AFB, CA 93524-7013 Air Force...Aerospace Systems Directorate Air Force Research Laboratory AFRL/RQRS 1 Ara Road Edwards AFB, CA 93524 *Email: ghanshyam.vaghjiani@us.af.mil IMPROVED...PYROLYSIS MICRO-REACTOR DESIGN VIA COMPUTATIONAL FLUID DYNAMICS SIMULATIONS Ghanshyam L. Vaghjiani* DISTRIBUTION A: Approved for public release

Combat Simulation Using Breach Computer Language

DTIC Science & Technology

1979-09-01

simulation and weapon system analysis computer language Two types of models were constructed: a stochastic duel and a dynamic engagement model The... duel model validates the BREACH approach by comparing results with mathematical solutions. The dynamic model shows the capability of the BREACH...BREACH 2 Background 2 The Language 3 Static Duel 4 Background and Methodology 4 Validation 5 Results 8 Tank Duel Simulation 8 Dynamic Assault Model

Physical Principle for Generation of Randomness

NASA Technical Reports Server (NTRS)

Zak, Michail

2009-01-01

A physical principle (more precisely, a principle that incorporates mathematical models used in physics) has been conceived as the basis of a method of generating randomness in Monte Carlo simulations. The principle eliminates the need for conventional random-number generators. The Monte Carlo simulation method is among the most powerful computational methods for solving high-dimensional problems in physics, chemistry, economics, and information processing. The Monte Carlo simulation method is especially effective for solving problems in which computational complexity increases exponentially with dimensionality. The main advantage of the Monte Carlo simulation method over other methods is that the demand on computational resources becomes independent of dimensionality. As augmented by the present principle, the Monte Carlo simulation method becomes an even more powerful computational method that is especially useful for solving problems associated with dynamics of fluids, planning, scheduling, and combinatorial optimization. The present principle is based on coupling of dynamical equations with the corresponding Liouville equation. The randomness is generated by non-Lipschitz instability of dynamics triggered and controlled by feedback from the Liouville equation. (In non-Lipschitz dynamics, the derivatives of solutions of the dynamical equations are not required to be bounded.)

Surface Modification Engineered Assembly of Novel Quantum Dot Architectures for Advanced Applications

DTIC Science & Technology

2008-02-09

Campbell, S. Ogata, and F. Shimojo, “ Multimillion atom simulations of nanosystems on parallel computers,” in Proceedings of the International...nanomesas: multimillion -atom molecular dynamics simulations on parallel computers,” J. Appl. Phys. 94, 6762 (2003). 21. P. Vashishta, R. K. Kalia...and A. Nakano, “ Multimillion atom molecular dynamics simulations of nanoparticles on parallel computers,” Journal of Nanoparticle Research 5, 119-135

Fast Dynamic Simulation-Based Small Signal Stability Assessment and Control

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

Acharya, Naresh; Baone, Chaitanya; Veda, Santosh

2014-12-31

Power grid planning and operation decisions are made based on simulation of the dynamic behavior of the system. Enabling substantial energy savings while increasing the reliability of the aging North American power grid through improved utilization of existing transmission assets hinges on the adoption of wide-area measurement systems (WAMS) for power system stabilization. However, adoption of WAMS alone will not suffice if the power system is to reach its full entitlement in stability and reliability. It is necessary to enhance predictability with "faster than real-time" dynamic simulations that will enable the dynamic stability margins, proactive real-time control, and improve gridmore » resiliency to fast time-scale phenomena such as cascading network failures. Present-day dynamic simulations are performed only during offline planning studies, considering only worst case conditions such as summer peak, winter peak days, etc. With widespread deployment of renewable generation, controllable loads, energy storage devices and plug-in hybrid electric vehicles expected in the near future and greater integration of cyber infrastructure (communications, computation and control), monitoring and controlling the dynamic performance of the grid in real-time would become increasingly important. The state-of-the-art dynamic simulation tools have limited computational speed and are not suitable for real-time applications, given the large set of contingency conditions to be evaluated. These tools are optimized for best performance of single-processor computers, but the simulation is still several times slower than real-time due to its computational complexity. With recent significant advances in numerical methods and computational hardware, the expectations have been rising towards more efficient and faster techniques to be implemented in power system simulators. This is a natural expectation, given that the core solution algorithms of most commercial simulators were developed decades ago, when High Performance Computing (HPC) resources were not commonly available.« less

Good coupling for the multiscale patch scheme on systems with microscale heterogeneity

NASA Astrophysics Data System (ADS)

Bunder, J. E.; Roberts, A. J.; Kevrekidis, I. G.

2017-05-01

Computational simulation of microscale detailed systems is frequently only feasible over spatial domains much smaller than the macroscale of interest. The 'equation-free' methodology couples many small patches of microscale computations across space to empower efficient computational simulation over macroscale domains of interest. Motivated by molecular or agent simulations, we analyse the performance of various coupling schemes for patches when the microscale is inherently 'rough'. As a canonical problem in this universality class, we systematically analyse the case of heterogeneous diffusion on a lattice. Computer algebra explores how the dynamics of coupled patches predict the large scale emergent macroscale dynamics of the computational scheme. We determine good design for the coupling of patches by comparing the macroscale predictions from patch dynamics with the emergent macroscale on the entire domain, thus minimising the computational error of the multiscale modelling. The minimal error on the macroscale is obtained when the coupling utilises averaging regions which are between a third and a half of the patch. Moreover, when the symmetry of the inter-patch coupling matches that of the underlying microscale structure, patch dynamics predicts the desired macroscale dynamics to any specified order of error. The results confirm that the patch scheme is useful for macroscale computational simulation of a range of systems with microscale heterogeneity.

The investigation of tethered satellite system dynamics

NASA Technical Reports Server (NTRS)

Lorenzini, E.

1985-01-01

Progress in tethered satellite system dynamics research is reported. A retrieval rate control law with no angular feedback to investigate the system's dynamic response was studied. The initial conditions for the computer code which simulates the satellite's rotational dynamics were extended to a generic orbit. The model of the satellite thrusters was modified to simulate a pulsed thrust, by making the SKYHOOK integrator suitable for dealing with delta functions without loosing computational efficiency. Tether breaks were simulated with the high resolution computer code SLACK3. Shuttle's maneuvers were tested. The electric potential around a severed conductive tether with insulator, in the case of a tether breakage at 20 km from the Shuttle, was computed. The electrodynamic hazards due to the breakage of the TSS electrodynamic tether in a plasma are evaluated.

Multiple shooting shadowing for sensitivity analysis of chaotic dynamical systems

NASA Astrophysics Data System (ADS)

Blonigan, Patrick J.; Wang, Qiqi

2018-02-01

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

The DYNAMO Simulation Language--An Alternate Approach to Computer Science Education.

ERIC Educational Resources Information Center

Bronson, Richard

1986-01-01

Suggests the use of computer simulation of continuous systems as a problem solving approach to computer languages. Outlines the procedures that the system dynamics approach employs in computer simulations. Explains the advantages of the special purpose language, DYNAMO. (ML)

Protocols for Molecular Dynamics Simulations of RNA Nanostructures.

PubMed

Kim, Taejin; Kasprzak, Wojciech K; Shapiro, Bruce A

2017-01-01

Molecular dynamics (MD) simulations have been used as one of the main research tools to study a wide range of biological systems and bridge the gap between X-ray crystallography or NMR structures and biological mechanism. In the field of RNA nanostructures, MD simulations have been used to fix steric clashes in computationally designed RNA nanostructures, characterize the dynamics, and investigate the interaction between RNA and other biomolecules such as delivery agents and membranes.In this chapter we present examples of computational protocols for molecular dynamics simulations in explicit and implicit solvent using the Amber Molecular Dynamics Package. We also show examples of post-simulation analysis steps and briefly mention selected tools beyond the Amber package. Limitations of the methods, tools, and protocols are also discussed. Most of the examples are illustrated for a small RNA duplex (helix), but the protocols are applicable to any nucleic acid structure, subject only to the computational speed and memory limitations of the hardware available to the user.

Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations

PubMed Central

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

2012-01-01

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

Guidelines for Computing Longitudinal Dynamic Stability Characteristics of a Subsonic Transport

NASA Technical Reports Server (NTRS)

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

2010-01-01

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

An efficient formulation of robot arm dynamics for control and computer simulation

NASA Astrophysics Data System (ADS)

Lee, C. S. G.; Nigam, R.

This paper describes an efficient formulation of the dynamic equations of motion of industrial robots based on the Lagrange formulation of d'Alembert's principle. This formulation, as applied to a PUMA robot arm, results in a set of closed form second order differential equations with cross product terms. They are not as efficient in computation as those formulated by the Newton-Euler method, but provide a better analytical model for control analysis and computer simulation. Computational complexities of this dynamic model together with other models are tabulated for discussion.

Mesoscopic modelling and simulation of soft matter.

PubMed

Schiller, Ulf D; Krüger, Timm; Henrich, Oliver

2017-12-20

The deformability of soft condensed matter often requires modelling of hydrodynamical aspects to gain quantitative understanding. This, however, requires specialised methods that can resolve the multiscale nature of soft matter systems. We review a number of the most popular simulation methods that have emerged, such as Langevin dynamics, dissipative particle dynamics, multi-particle collision dynamics, sometimes also referred to as stochastic rotation dynamics, and the lattice-Boltzmann method. We conclude this review with a short glance at current compute architectures for high-performance computing and community codes for soft matter simulation.

AceCloud: Molecular Dynamics Simulations in the Cloud.

PubMed

Harvey, M J; De Fabritiis, G

2015-05-26

We present AceCloud, an on-demand service for molecular dynamics simulations. AceCloud is designed to facilitate the secure execution of large ensembles of simulations on an external cloud computing service (currently Amazon Web Services). The AceCloud client, integrated into the ACEMD molecular dynamics package, provides an easy-to-use interface that abstracts all aspects of interaction with the cloud services. This gives the user the experience that all simulations are running on their local machine, minimizing the learning curve typically associated with the transition to using high performance computing services.

Dynamic Fracture Simulations of Explosively Loaded Cylinders

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

Arthur, Carly W.; Goto, D. M.

2015-11-30

This report documents the modeling results of high explosive experiments investigating dynamic fracture of steel (AerMet® 100 alloy) cylinders. The experiments were conducted at Lawrence Livermore National Laboratory (LLNL) during 2007 to 2008 [10]. A principal objective of this study was to gain an understanding of dynamic material failure through the analysis of hydrodynamic computer code simulations. Two-dimensional and three-dimensional computational cylinder models were analyzed using the ALE3D multi-physics computer code.

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

NASA Astrophysics Data System (ADS)

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

2016-04-01

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

Computer-aided Instructional System for Transmission Line Simulation.

ERIC Educational Resources Information Center

Reinhard, Erwin A.; Roth, Charles H., Jr.

A computer-aided instructional system has been developed which utilizes dynamic computer-controlled graphic displays and which requires student interaction with a computer simulation in an instructional mode. A numerical scheme has been developed for digital simulation of a uniform, distortionless transmission line with resistive terminations and…

The Development and Comparison of Molecular Dynamics Simulation and Monte Carlo Simulation

NASA Astrophysics Data System (ADS)

Chen, Jundong

2018-03-01

Molecular dynamics is an integrated technology that combines physics, mathematics and chemistry. Molecular dynamics method is a computer simulation experimental method, which is a powerful tool for studying condensed matter system. This technique not only can get the trajectory of the atom, but can also observe the microscopic details of the atomic motion. By studying the numerical integration algorithm in molecular dynamics simulation, we can not only analyze the microstructure, the motion of particles and the image of macroscopic relationship between them and the material, but can also study the relationship between the interaction and the macroscopic properties more conveniently. The Monte Carlo Simulation, similar to the molecular dynamics, is a tool for studying the micro-molecular and particle nature. In this paper, the theoretical background of computer numerical simulation is introduced, and the specific methods of numerical integration are summarized, including Verlet method, Leap-frog method and Velocity Verlet method. At the same time, the method and principle of Monte Carlo Simulation are introduced. Finally, similarities and differences of Monte Carlo Simulation and the molecular dynamics simulation are discussed.

Computational Methods for Structural Mechanics and Dynamics

NASA Technical Reports Server (NTRS)

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

1989-01-01

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

A High Performance Computing Approach to the Simulation of Fluid Solid Interaction Problems with Rigid and Flexible Components (Open Access Publisher’s Version)

DTIC Science & Technology

2014-08-01

performance computing, smoothed particle hydrodynamics, rigid body dynamics, flexible body dynamics ARMAN PAZOUKI ∗, RADU SERBAN ∗, DAN NEGRUT ∗ A...HIGH PERFORMANCE COMPUTING APPROACH TO THE SIMULATION OF FLUID-SOLID INTERACTION PROBLEMS WITH RIGID AND FLEXIBLE COMPONENTS This work outlines a unified...are implemented to model rigid and flexible multibody dynamics. The two- way coupling of the fluid and solid phases is supported through use of

Physics Computing '92: Proceedings of the 4th International Conference

NASA Astrophysics Data System (ADS)

de Groot, Robert A.; Nadrchal, Jaroslav

1993-04-01

The Table of Contents for the book is as follows: * Preface * INVITED PAPERS * Ab Initio Theoretical Approaches to the Structural, Electronic and Vibrational Properties of Small Clusters and Fullerenes: The State of the Art * Neural Multigrid Methods for Gauge Theories and Other Disordered Systems * Multicanonical Monte Carlo Simulations * On the Use of the Symbolic Language Maple in Physics and Chemistry: Several Examples * Nonequilibrium Phase Transitions in Catalysis and Population Models * Computer Algebra, Symmetry Analysis and Integrability of Nonlinear Evolution Equations * The Path-Integral Quantum Simulation of Hydrogen in Metals * Digital Optical Computing: A New Approach of Systolic Arrays Based on Coherence Modulation of Light and Integrated Optics Technology * Molecular Dynamics Simulations of Granular Materials * Numerical Implementation of a K.A.M. Algorithm * Quasi-Monte Carlo, Quasi-Random Numbers and Quasi-Error Estimates * What Can We Learn from QMC Simulations * Physics of Fluctuating Membranes * Plato, Apollonius, and Klein: Playing with Spheres * Steady States in Nonequilibrium Lattice Systems * CONVODE: A REDUCE Package for Differential Equations * Chaos in Coupled Rotators * Symplectic Numerical Methods for Hamiltonian Problems * Computer Simulations of Surfactant Self Assembly * High-dimensional and Very Large Cellular Automata for Immunological Shape Space * A Review of the Lattice Boltzmann Method * Electronic Structure of Solids in the Self-interaction Corrected Local-spin-density Approximation * Dedicated Computers for Lattice Gauge Theory Simulations * Physics Education: A Survey of Problems and Possible Solutions * Parallel Computing and Electronic-Structure Theory * High Precision Simulation Techniques for Lattice Field Theory * CONTRIBUTED PAPERS * Case Study of Microscale Hydrodynamics Using Molecular Dynamics and Lattice Gas Methods * Computer Modelling of the Structural and Electronic Properties of the Supported Metal Catalysis * Ordered Particle Simulations for Serial and MIMD Parallel Computers * "NOLP" -- Program Package for Laser Plasma Nonlinear Optics * Algorithms to Solve Nonlinear Least Square Problems * Distribution of Hydrogen Atoms in Pd-H Computed by Molecular Dynamics * A Ray Tracing of Optical System for Protein Crystallography Beamline at Storage Ring-SIBERIA-2 * Vibrational Properties of a Pseudobinary Linear Chain with Correlated Substitutional Disorder * Application of the Software Package Mathematica in Generalized Master Equation Method * Linelist: An Interactive Program for Analysing Beam-foil Spectra * GROMACS: A Parallel Computer for Molecular Dynamics Simulations * GROMACS Method of Virial Calculation Using a Single Sum * The Interactive Program for the Solution of the Laplace Equation with the Elimination of Singularities for Boundary Functions * Random-Number Generators: Testing Procedures and Comparison of RNG Algorithms * Micro-TOPIC: A Tokamak Plasma Impurities Code * Rotational Molecular Scattering Calculations * Orthonormal Polynomial Method for Calibrating of Cryogenic Temperature Sensors * Frame-based System Representing Basis of Physics * The Role of Massively Data-parallel Computers in Large Scale Molecular Dynamics Simulations * Short-range Molecular Dynamics on a Network of Processors and Workstations * An Algorithm for Higher-order Perturbation Theory in Radiative Transfer Computations * Hydrostochastics: The Master Equation Formulation of Fluid Dynamics * HPP Lattice Gas on Transputers and Networked Workstations * Study on the Hysteresis Cycle Simulation Using Modeling with Different Functions on Intervals * Refined Pruning Techniques for Feed-forward Neural Networks * Random Walk Simulation of the Motion of Transient Charges in Photoconductors * The Optical Hysteresis in Hydrogenated Amorphous Silicon * Diffusion Monte Carlo Analysis of Modern Interatomic Potentials for He * A Parallel Strategy for Molecular Dynamics Simulations of Polar Liquids on Transputer Arrays * Distribution of Ions Reflected on Rough Surfaces * The Study of Step Density Distribution During Molecular Beam Epitaxy Growth: Monte Carlo Computer Simulation * Towards a Formal Approach to the Construction of Large-scale Scientific Applications Software * Correlated Random Walk and Discrete Modelling of Propagation through Inhomogeneous Media * Teaching Plasma Physics Simulation * A Theoretical Determination of the Au-Ni Phase Diagram * Boson and Fermion Kinetics in One-dimensional Lattices * Computational Physics Course on the Technical University * Symbolic Computations in Simulation Code Development and Femtosecond-pulse Laser-plasma Interaction Studies * Computer Algebra and Integrated Computing Systems in Education of Physical Sciences * Coordinated System of Programs for Undergraduate Physics Instruction * Program Package MIRIAM and Atomic Physics of Extreme Systems * High Energy Physics Simulation on the T_Node * The Chapman-Kolmogorov Equation as Representation of Huygens' Principle and the Monolithic Self-consistent Numerical Modelling of Lasers * Authoring System for Simulation Developments * Molecular Dynamics Study of Ion Charge Effects in the Structure of Ionic Crystals * A Computational Physics Introductory Course * Computer Calculation of Substrate Temperature Field in MBE System * Multimagnetical Simulation of the Ising Model in Two and Three Dimensions * Failure of the CTRW Treatment of the Quasicoherent Excitation Transfer * Implementation of a Parallel Conjugate Gradient Method for Simulation of Elastic Light Scattering * Algorithms for Study of Thin Film Growth * Algorithms and Programs for Physics Teaching in Romanian Technical Universities * Multicanonical Simulation of 1st order Transitions: Interface Tension of the 2D 7-State Potts Model * Two Numerical Methods for the Calculation of Periodic Orbits in Hamiltonian Systems * Chaotic Behavior in a Probabilistic Cellular Automata? * Wave Optics Computing by a Networked-based Vector Wave Automaton * Tensor Manipulation Package in REDUCE * Propagation of Electromagnetic Pulses in Stratified Media * The Simple Molecular Dynamics Model for the Study of Thermalization of the Hot Nucleon Gas * Electron Spin Polarization in PdCo Alloys Calculated by KKR-CPA-LSD Method * Simulation Studies of Microscopic Droplet Spreading * A Vectorizable Algorithm for the Multicolor Successive Overrelaxation Method * Tetragonality of the CuAu I Lattice and Its Relation to Electronic Specific Heat and Spin Susceptibility * Computer Simulation of the Formation of Metallic Aggregates Produced by Chemical Reactions in Aqueous Solution * Scaling in Growth Models with Diffusion: A Monte Carlo Study * The Nucleus as the Mesoscopic System * Neural Network Computation as Dynamic System Simulation * First-principles Theory of Surface Segregation in Binary Alloys * Data Smooth Approximation Algorithm for Estimating the Temperature Dependence of the Ice Nucleation Rate * Genetic Algorithms in Optical Design * Application of 2D-FFT in the Study of Molecular Exchange Processes by NMR * Advanced Mobility Model for Electron Transport in P-Si Inversion Layers * Computer Simulation for Film Surfaces and its Fractal Dimension * Parallel Computation Techniques and the Structure of Catalyst Surfaces * Educational SW to Teach Digital Electronics and the Corresponding Text Book * Primitive Trinomials (Mod 2) Whose Degree is a Mersenne Exponent * Stochastic Modelisation and Parallel Computing * Remarks on the Hybrid Monte Carlo Algorithm for the ∫4 Model * An Experimental Computer Assisted Workbench for Physics Teaching * A Fully Implicit Code to Model Tokamak Plasma Edge Transport * EXPFIT: An Interactive Program for Automatic Beam-foil Decay Curve Analysis * Mapping Technique for Solving General, 1-D Hamiltonian Systems * Freeway Traffic, Cellular Automata, and Some (Self-Organizing) Criticality * Photonuclear Yield Analysis by Dynamic Programming * Incremental Representation of the Simply Connected Planar Curves * Self-convergence in Monte Carlo Methods * Adaptive Mesh Technique for Shock Wave Propagation * Simulation of Supersonic Coronal Streams and Their Interaction with the Solar Wind * The Nature of Chaos in Two Systems of Ordinary Nonlinear Differential Equations * Considerations of a Window-shopper * Interpretation of Data Obtained by RTP 4-Channel Pulsed Radar Reflectometer Using a Multi Layer Perceptron * Statistics of Lattice Bosons for Finite Systems * Fractal Based Image Compression with Affine Transformations * Algorithmic Studies on Simulation Codes for Heavy-ion Reactions * An Energy-Wise Computer Simulation of DNA-Ion-Water Interactions Explains the Abnormal Structure of Poly[d(A)]:Poly[d(T)] * Computer Simulation Study of Kosterlitz-Thouless-Like Transitions * Problem-oriented Software Package GUN-EBT for Computer Simulation of Beam Formation and Transport in Technological Electron-Optical Systems * Parallelization of a Boundary Value Solver and its Application in Nonlinear Dynamics * The Symbolic Classification of Real Four-dimensional Lie Algebras * Short, Singular Pulses Generation by a Dye Laser at Two Wavelengths Simultaneously * Quantum Monte Carlo Simulations of the Apex-Oxygen-Model * Approximation Procedures for the Axial Symmetric Static Einstein-Maxwell-Higgs Theory * Crystallization on a Sphere: Parallel Simulation on a Transputer Network * FAMULUS: A Software Product (also) for Physics Education * MathCAD vs. FAMULUS -- A Brief Comparison * First-principles Dynamics Used to Study Dissociative Chemisorption * A Computer Controlled System for Crystal Growth from Melt * A Time Resolved Spectroscopic Method for Short Pulsed Particle Emission * Green's Function Computation in Radiative Transfer Theory * Random Search Optimization Technique for One-criteria and Multi-criteria Problems * Hartley Transform Applications to Thermal Drift Elimination in Scanning Tunneling Microscopy * Algorithms of Measuring, Processing and Interpretation of Experimental Data Obtained with Scanning Tunneling Microscope * Time-dependent Atom-surface Interactions * Local and Global Minima on Molecular Potential Energy Surfaces: An Example of N3 Radical * Computation of Bifurcation Surfaces * Symbolic Computations in Quantum Mechanics: Energies in Next-to-solvable Systems * A Tool for RTP Reactor and Lamp Field Design * Modelling of Particle Spectra for the Analysis of Solid State Surface * List of Participants

Computational plasticity algorithm for particle dynamics simulations

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

The investigation of tethered satellite system dynamics

NASA Technical Reports Server (NTRS)

Lorenzini, E.

1985-01-01

The tether control law to retrieve the satellite was modified in order to have a smooth retrieval trajectory of the satellite that minimizes the thruster activation. The satellite thrusters were added to the rotational dynamics computer code and a preliminary control logic was implemented to simulate them during the retrieval maneuver. The high resolution computer code for modelling the three dimensional dynamics of untensioned tether, SLACK3, was made fully operative and a set of computer simulations of possible tether breakages was run. The distribution of the electric field around an electrodynamic tether in vacuo severed at some length from the shuttle was computed with a three dimensional electrodynamic computer code.

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.

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.

Displaying Computer Simulations Of Physical Phenomena

NASA Technical Reports Server (NTRS)

Watson, Val

1991-01-01

Paper discusses computer simulation as means of experiencing and learning to understand physical phenomena. Covers both present simulation capabilities and major advances expected in near future. Visual, aural, tactile, and kinesthetic effects used to teach such physical sciences as dynamics of fluids. Recommends classrooms in universities, government, and industry be linked to advanced computing centers so computer simulations integrated into education process.

Using stroboscopic flow imaging to validate large-scale computational fluid dynamics simulations

NASA Astrophysics Data System (ADS)

Laurence, Ted A.; Ly, Sonny; Fong, Erika; Shusteff, Maxim; Randles, Amanda; Gounley, John; Draeger, Erik

2017-02-01

The utility and accuracy of computational modeling often requires direct validation against experimental measurements. The work presented here is motivated by taking a combined experimental and computational approach to determine the ability of large-scale computational fluid dynamics (CFD) simulations to understand and predict the dynamics of circulating tumor cells in clinically relevant environments. We use stroboscopic light sheet fluorescence imaging to track the paths and measure the velocities of fluorescent microspheres throughout a human aorta model. Performed over complex physiologicallyrealistic 3D geometries, large data sets are acquired with microscopic resolution over macroscopic distances.

Applying Parallel Adaptive Methods with GeoFEST/PYRAMID to Simulate Earth Surface Crustal Dynamics

NASA Technical Reports Server (NTRS)

Norton, Charles D.; Lyzenga, Greg; Parker, Jay; Glasscoe, Margaret; Donnellan, Andrea; Li, Peggy

2006-01-01

This viewgraph presentation reviews the use Adaptive Mesh Refinement (AMR) in simulating the Crustal Dynamics of Earth's Surface. AMR simultaneously improves solution quality, time to solution, and computer memory requirements when compared to generating/running on a globally fine mesh. The use of AMR in simulating the dynamics of the Earth's Surface is spurred by future proposed NASA missions, such as InSAR for Earth surface deformation and other measurements. These missions will require support for large-scale adaptive numerical methods using AMR to model observations. AMR was chosen because it has been successful in computation fluid dynamics for predictive simulation of complex flows around complex structures.

Efficient Computation Of Manipulator Inertia Matrix

NASA Technical Reports Server (NTRS)

Fijany, Amir; Bejczy, Antal K.

1991-01-01

Improved method for computation of manipulator inertia matrix developed, based on concept of spatial inertia of composite rigid body. Required for implementation of advanced dynamic-control schemes as well as dynamic simulation of manipulator motion. Motivated by increasing demand for fast algorithms to provide real-time control and simulation capability and, particularly, need for faster-than-real-time simulation capability, required in many anticipated space teleoperation applications.

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.

Data-driven train set crash dynamics simulation

NASA Astrophysics Data System (ADS)

Tang, Zhao; Zhu, Yunrui; Nie, Yinyu; Guo, Shihui; Liu, Fengjia; Chang, Jian; Zhang, Jianjun

2017-02-01

Traditional finite element (FE) methods are arguably expensive in computation/simulation of the train crash. High computational cost limits their direct applications in investigating dynamic behaviours of an entire train set for crashworthiness design and structural optimisation. On the contrary, multi-body modelling is widely used because of its low computational cost with the trade-off in accuracy. In this study, a data-driven train crash modelling method is proposed to improve the performance of a multi-body dynamics simulation of train set crash without increasing the computational burden. This is achieved by the parallel random forest algorithm, which is a machine learning approach that extracts useful patterns of force-displacement curves and predicts a force-displacement relation in a given collision condition from a collection of offline FE simulation data on various collision conditions, namely different crash velocities in our analysis. Using the FE simulation results as a benchmark, we compared our method with traditional multi-body modelling methods and the result shows that our data-driven method improves the accuracy over traditional multi-body models in train crash simulation and runs at the same level of efficiency.

International benchmarking of longitudinal train dynamics simulators: results

NASA Astrophysics Data System (ADS)

Wu, Qing; Spiryagin, Maksym; Cole, Colin; Chang, Chongyi; Guo, Gang; Sakalo, Alexey; Wei, Wei; Zhao, Xubao; Burgelman, Nico; Wiersma, Pier; Chollet, Hugues; Sebes, Michel; Shamdani, Amir; Melzi, Stefano; Cheli, Federico; di Gialleonardo, Egidio; Bosso, Nicola; Zampieri, Nicolò; Luo, Shihui; Wu, Honghua; Kaza, Guy-Léon

2018-03-01

This paper presents the results of the International Benchmarking of Longitudinal Train Dynamics Simulators which involved participation of nine simulators (TABLDSS, UM, CRE-LTS, TDEAS, PoliTo, TsDyn, CARS, BODYSIM and VOCO) from six countries. Longitudinal train dynamics results and computing time of four simulation cases are presented and compared. The results show that all simulators had basic agreement in simulations of locomotive forces, resistance forces and track gradients. The major differences among different simulators lie in the draft gear models. TABLDSS, UM, CRE-LTS, TDEAS, TsDyn and CARS had general agreement in terms of the in-train forces; minor differences exist as reflections of draft gear model variations. In-train force oscillations were observed in VOCO due to the introduction of wheel-rail contact. In-train force instabilities were sometimes observed in PoliTo and BODYSIM due to the velocity controlled transitional characteristics which could have generated unreasonable transitional stiffness. Regarding computing time per train operational second, the following list is in order of increasing computing speed: VOCO, TsDyn, PoliTO, CARS, BODYSIM, UM, TDEAS, CRE-LTS and TABLDSS (fastest); all simulators except VOCO, TsDyn and PoliTo achieved faster speeds than real-time simulations. Similarly, regarding computing time per integration step, the computing speeds in order are: CRE-LTS, VOCO, CARS, TsDyn, UM, TABLDSS and TDEAS (fastest).

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

NASA Technical Reports Server (NTRS)

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

1978-01-01

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

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.

Molecular Dynamics, Monte Carlo Simulations, and Langevin Dynamics: A Computational Review

PubMed Central

Paquet, Eric; Viktor, Herna L.

2015-01-01

Macromolecular structures, such as neuraminidases, hemagglutinins, and monoclonal antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is the result of the interaction and collective motion of their constituent atoms. This conformational diversity has a significant impact on their physicochemical and biological properties. Among these are their structural stability, the transport of ions through the M2 channel, drug resistance, macromolecular docking, binding energy, and rational epitope design. To assess these properties and to calculate the associated thermodynamical observables, the conformational space must be efficiently sampled and the dynamic of the constituent atoms must be simulated. This paper presents algorithms and techniques that address the abovementioned issues. To this end, a computational review of molecular dynamics, Monte Carlo simulations, Langevin dynamics, and free energy calculation is presented. The exposition is made from first principles to promote a better understanding of the potentialities, limitations, applications, and interrelations of these computational methods. PMID:25785262

Transient Solid Dynamics Simulations on the Sandia/Intel Teraflop Computer

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

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

1997-12-31

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

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

Hybrid computers and simulation languages in the study of dynamics of continuous systems

NASA Technical Reports Server (NTRS)

Acaccia, G. M.; Lucifredi, A. L.

1970-01-01

A comparison is presented of the use of hybrid computers and simulation languages as a means of studying the behavior of dynamic systems. Both procedures are defined and their advantages and disadvantages at the present state of the art are discussed. Some comparison and evaluation criteria are presented.

Dynamic CFD Simulations of the Supersonic Inflatable Aerodynamic Decelerator (SIAD) Ballistic Range Tests

NASA Technical Reports Server (NTRS)

Brock, Joseph M; Stern, Eric

2016-01-01

Dynamic CFD simulations of the SIAD ballistic test model were performed using US3D flow solver. Motivation for performing these simulations is for the purpose of validation and verification of the US3D flow solver as a viable computational tool for predicting dynamic coefficients.

More reliable forecasts with less precise computations: a fast-track route to cloud-resolved weather and climate simulators?

PubMed Central

Palmer, T. N.

2014-01-01

This paper sets out a new methodological approach to solving the equations for simulating and predicting weather and climate. In this approach, the conventionally hard boundary between the dynamical core and the sub-grid parametrizations is blurred. This approach is motivated by the relatively shallow power-law spectrum for atmospheric energy on scales of hundreds of kilometres and less. It is first argued that, because of this, the closure schemes for weather and climate simulators should be based on stochastic–dynamic systems rather than deterministic formulae. Second, as high-wavenumber elements of the dynamical core will necessarily inherit this stochasticity during time integration, it is argued that the dynamical core will be significantly over-engineered if all computations, regardless of scale, are performed completely deterministically and if all variables are represented with maximum numerical precision (in practice using double-precision floating-point numbers). As the era of exascale computing is approached, an energy- and computationally efficient approach to cloud-resolved weather and climate simulation is described where determinism and numerical precision are focused on the largest scales only. PMID:24842038

More reliable forecasts with less precise computations: a fast-track route to cloud-resolved weather and climate simulators?

PubMed

Palmer, T N

2014-06-28

This paper sets out a new methodological approach to solving the equations for simulating and predicting weather and climate. In this approach, the conventionally hard boundary between the dynamical core and the sub-grid parametrizations is blurred. This approach is motivated by the relatively shallow power-law spectrum for atmospheric energy on scales of hundreds of kilometres and less. It is first argued that, because of this, the closure schemes for weather and climate simulators should be based on stochastic-dynamic systems rather than deterministic formulae. Second, as high-wavenumber elements of the dynamical core will necessarily inherit this stochasticity during time integration, it is argued that the dynamical core will be significantly over-engineered if all computations, regardless of scale, are performed completely deterministically and if all variables are represented with maximum numerical precision (in practice using double-precision floating-point numbers). As the era of exascale computing is approached, an energy- and computationally efficient approach to cloud-resolved weather and climate simulation is described where determinism and numerical precision are focused on the largest scales only.

Efficient Conformational Sampling in Explicit Solvent Using a Hybrid Replica Exchange Molecular Dynamics Method

DTIC Science & Technology

2011-12-01

REMD while reproducing the energy landscape of explicit solvent simulations . ’ INTRODUCTION Molecular dynamics (MD) simulations of proteins can pro...Mongan, J.; McCammon, J. A. Accelerated molecular dynamics : a promising and efficient simulation method for biomolecules. J. Chem. Phys. 2004, 120 (24...Chemical Theory and Computation ARTICLE (8) Abraham,M. J.; Gready, J. E. Ensuringmixing efficiency of replica- exchange molecular dynamics simulations . J

Computer simulation of multigrid body dynamics and control

NASA Technical Reports Server (NTRS)

Swaminadham, M.; Moon, Young I.; Venkayya, V. B.

1990-01-01

The objective is to set up and analyze benchmark problems on multibody dynamics and to verify the predictions of two multibody computer simulation codes. TREETOPS and DISCOS have been used to run three example problems - one degree-of-freedom spring mass dashpot system, an inverted pendulum system, and a triple pendulum. To study the dynamics and control interaction, an inverted planar pendulum with an external body force and a torsional control spring was modeled as a hinge connected two-rigid body system. TREETOPS and DISCOS affected the time history simulation of this problem. System state space variables and their time derivatives from two simulation codes were compared.

Cinema Fire Modelling by FDS

NASA Astrophysics Data System (ADS)

Glasa, J.; Valasek, L.; Weisenpacher, P.; Halada, L.

2013-02-01

Recent advances in computer fluid dynamics (CFD) and rapid increase of computational power of current computers have led to the development of CFD models capable to describe fire in complex geometries incorporating a wide variety of physical phenomena related to fire. In this paper, we demonstrate the use of Fire Dynamics Simulator (FDS) for cinema fire modelling. FDS is an advanced CFD system intended for simulation of the fire and smoke spread and prediction of thermal flows, toxic substances concentrations and other relevant parameters of fire. The course of fire in a cinema hall is described focusing on related safety risks. Fire properties of flammable materials used in the simulation were determined by laboratory measurements and validated by fire tests and computer simulations

Aeroelastic analysis of bridge girder section using computer modeling

DOT National Transportation Integrated Search

2001-05-01

This report describes the numerical simulation of wind flow around bridges using the Finite Element Method (FEM) and the principles of Computational Fluid Dynamics (CFD) and Computational Structural Dynamics (CSD). Since, the suspension bridges are p...

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.

Understanding Islamist political violence through computational social simulation

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

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

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

Computer animation challenges for computational fluid dynamics

NASA Astrophysics Data System (ADS)

Vines, Mauricio; Lee, Won-Sook; Mavriplis, Catherine

2012-07-01

Computer animation requirements differ from those of traditional computational fluid dynamics (CFD) investigations in that visual plausibility and rapid frame update rates trump physical accuracy. We present an overview of the main techniques for fluid simulation in computer animation, starting with Eulerian grid approaches, the Lattice Boltzmann method, Fourier transform techniques and Lagrangian particle introduction. Adaptive grid methods, precomputation of results for model reduction, parallelisation and computation on graphical processing units (GPUs) are reviewed in the context of accelerating simulation computations for animation. A survey of current specific approaches for the application of these techniques to the simulation of smoke, fire, water, bubbles, mixing, phase change and solid-fluid coupling is also included. Adding plausibility to results through particle introduction, turbulence detail and concentration on regions of interest by level set techniques has elevated the degree of accuracy and realism of recent animations. Basic approaches are described here. Techniques to control the simulation to produce a desired visual effect are also discussed. Finally, some references to rendering techniques and haptic applications are mentioned to provide the reader with a complete picture of the challenges of simulating fluids in computer animation.

An iterative method for hydrodynamic interactions in Brownian dynamics simulations of polymer dynamics

NASA Astrophysics Data System (ADS)

Miao, Linling; Young, Charles D.; Sing, Charles E.

2017-07-01

Brownian Dynamics (BD) simulations are a standard tool for understanding the dynamics of polymers in and out of equilibrium. Quantitative comparison can be made to rheological measurements of dilute polymer solutions, as well as direct visual observations of fluorescently labeled DNA. The primary computational challenge with BD is the expensive calculation of hydrodynamic interactions (HI), which are necessary to capture physically realistic dynamics. The full HI calculation, performed via a Cholesky decomposition every time step, scales with the length of the polymer as O(N3). This limits the calculation to a few hundred simulated particles. A number of approximations in the literature can lower this scaling to O(N2 - N2.25), and explicit solvent methods scale as O(N); however both incur a significant constant per-time step computational cost. Despite this progress, there remains a need for new or alternative methods of calculating hydrodynamic interactions; large polymer chains or semidilute polymer solutions remain computationally expensive. In this paper, we introduce an alternative method for calculating approximate hydrodynamic interactions. Our method relies on an iterative scheme to establish self-consistency between a hydrodynamic matrix that is averaged over simulation and the hydrodynamic matrix used to run the simulation. Comparison to standard BD simulation and polymer theory results demonstrates that this method quantitatively captures both equilibrium and steady-state dynamics after only a few iterations. The use of an averaged hydrodynamic matrix allows the computationally expensive Brownian noise calculation to be performed infrequently, so that it is no longer the bottleneck of the simulation calculations. We also investigate limitations of this conformational averaging approach in ring polymers.

Supercomputing in Aerospace

NASA Technical Reports Server (NTRS)

Kutler, Paul; Yee, Helen

1987-01-01

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

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.

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.

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

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

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

The Australian Computational Earth Systems Simulator

NASA Astrophysics Data System (ADS)

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

2001-12-01

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

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.

Modeling Education on the Real World.

ERIC Educational Resources Information Center

Hunter, Beverly

1983-01-01

Offers and discusses three suggestions to capitalize on two developments related to system dynamics modeling and simulation. These developments are a junior/senior high textbook called "Introduction to Computer Simulation" and Micro-DYNAMO, a computer simulation language for microcomputers. (Author/JN)

HYDES: A generalized hybrid computer program for studying turbojet or turbofan engine dynamics

NASA Technical Reports Server (NTRS)

Szuch, J. R.

1974-01-01

This report describes HYDES, a hybrid computer program capable of simulating one-spool turbojet, two-spool turbojet, or two-spool turbofan engine dynamics. HYDES is also capable of simulating two- or three-stream turbofans with or without mixing of the exhaust streams. The program is intended to reduce the time required for implementing dynamic engine simulations. HYDES was developed for running on the Lewis Research Center's Electronic Associates (EAI) 690 Hybrid Computing System and satisfies the 16384-word core-size and hybrid-interface limits of that machine. The program could be modified for running on other computing systems. The use of HYDES to simulate a single-spool turbojet and a two-spool, two-stream turbofan engine is demonstrated. The form of the required input data is shown and samples of output listings (teletype) and transient plots (x-y plotter) are provided. HYDES is shown to be capable of performing both steady-state design and off-design analyses and transient analyses.

Absolute comparison of simulated and experimental protein-folding dynamics

NASA Astrophysics Data System (ADS)

Snow, Christopher D.; Nguyen, Houbi; Pande, Vijay S.; Gruebele, Martin

2002-11-01

Protein folding is difficult to simulate with classical molecular dynamics. Secondary structure motifs such as α-helices and β-hairpins can form in 0.1-10µs (ref. 1), whereas small proteins have been shown to fold completely in tens of microseconds. The longest folding simulation to date is a single 1-µs simulation of the villin headpiece; however, such single runs may miss many features of the folding process as it is a heterogeneous reaction involving an ensemble of transition states. Here, we have used a distributed computing implementation to produce tens of thousands of 5-20-ns trajectories (700µs) to simulate mutants of the designed mini-protein BBA5. The fast relaxation dynamics these predict were compared with the results of laser temperature-jump experiments. Our computational predictions are in excellent agreement with the experimentally determined mean folding times and equilibrium constants. The rapid folding of BBA5 is due to the swift formation of secondary structure. The convergence of experimentally and computationally accessible timescales will allow the comparison of absolute quantities characterizing in vitro and in silico (computed) protein folding.

Architectural Improvements and New Processing Tools for the Open XAL Online Model

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

Allen, Christopher K; Pelaia II, Tom; Freed, Jonathan M

The online model is the component of Open XAL providing accelerator modeling, simulation, and dynamic synchronization to live hardware. Significant architectural changes and feature additions have been recently made in two separate areas: 1) the managing and processing of simulation data, and 2) the modeling of RF cavities. Simulation data and data processing have been completely decoupled. A single class manages all simulation data while standard tools were developed for processing the simulation results. RF accelerating cavities are now modeled as composite structures where parameter and dynamics computations are distributed. The beam and hardware models both maintain their relative phasemore » information, which allows for dynamic phase slip and elapsed time computation.« less

BeeSim: Leveraging Wearable Computers in Participatory Simulations with Young Children

ERIC Educational Resources Information Center

Peppler, Kylie; Danish, Joshua; Zaitlen, Benjamin; Glosson, Diane; Jacobs, Alexander; Phelps, David

2010-01-01

New technologies have enabled students to become active participants in computational simulations of dynamic and complex systems (called Participatory Simulations), providing a "first-person"perspective on complex systems. However, most existing Participatory Simulations have targeted older children, teens, and adults assuming that such concepts…

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.

Computational fluid dynamics uses in fluid dynamics/aerodynamics education

NASA Technical Reports Server (NTRS)

Holst, Terry L.

1994-01-01

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

Adjoint Sensitivity Analysis for Scale-Resolving Turbulent Flow Solvers

NASA Astrophysics Data System (ADS)

Blonigan, Patrick; Garai, Anirban; Diosady, Laslo; Murman, Scott

2017-11-01

Adjoint-based sensitivity analysis methods are powerful design tools for engineers who use computational fluid dynamics. In recent years, these engineers have started to use scale-resolving simulations like large-eddy simulations (LES) and direct numerical simulations (DNS), which resolve more scales in complex flows with unsteady separation and jets than the widely-used Reynolds-averaged Navier-Stokes (RANS) methods. However, the conventional adjoint method computes large, unusable sensitivities for scale-resolving simulations, which unlike RANS simulations exhibit the chaotic dynamics inherent in turbulent flows. Sensitivity analysis based on least-squares shadowing (LSS) avoids the issues encountered by conventional adjoint methods, but has a high computational cost even for relatively small simulations. The following talk discusses a more computationally efficient formulation of LSS, ``non-intrusive'' LSS, and its application to turbulent flows simulated with a discontinuous-Galkerin spectral-element-method LES/DNS solver. Results are presented for the minimal flow unit, a turbulent channel flow with a limited streamwise and spanwise domain.

Dynamic analysis of astronaut motions in microgravity: Applications for Extravehicular Activity (EVA)

NASA Technical Reports Server (NTRS)

Newman, Dava J.

1995-01-01

Simulations of astronaut motions during extravehicular activity (EVA) tasks were performed using computational multibody dynamics methods. The application of computational dynamic simulation to EVA was prompted by the realization that physical microgravity simulators have inherent limitations: viscosity in neutral buoyancy tanks; friction in air bearing floors; short duration for parabolic aircraft; and inertia and friction in suspension mechanisms. These limitations can mask critical dynamic effects that later cause problems during actual EVA's performed in space. Methods of formulating dynamic equations of motion for multibody systems are discussed with emphasis on Kane's method, which forms the basis of the simulations presented herein. Formulation of the equations of motion for a two degree of freedom arm is presented as an explicit example. The four basic steps in creating the computational simulations were: system description, in which the geometry, mass properties, and interconnection of system bodies are input to the computer; equation formulation based on the system description; inverse kinematics, in which the angles, velocities, and accelerations of joints are calculated for prescribed motion of the endpoint (hand) of the arm; and inverse dynamics, in which joint torques are calculated for a prescribed motion. A graphical animation and data plotting program, EVADS (EVA Dynamics Simulation), was developed and used to analyze the results of the simulations that were performed on a Silicon Graphics Indigo2 computer. EVA tasks involving manipulation of the Spartan 204 free flying astronomy payload, as performed during Space Shuttle mission STS-63 (February 1995), served as the subject for two dynamic simulations. An EVA crewmember was modeled as a seven segment system with an eighth segment representing the massive payload attached to the hand. For both simulations, the initial configuration of the lower body (trunk, upper leg, and lower leg) was a neutral microgravity posture. In the first simulation, the payload was manipulated around a circular trajectory of 0.15 m radius in 10 seconds. It was found that the wrist joint theoretically exceeded its ulnal deviation limit by as much as 49. 8 deg and was required to exert torques as high as 26 N-m to accomplish the task, well in excess of the wrist physiological limit of 12 N-m. The largest torque in the first simulation, 52 N-m, occurred in the ankle joint. To avoid these problems, the second simulation placed the arm in a more comfortable initial position and the radius and speed of the circular trajectory were reduced by half. As a result, the joint angles and torques were reduced to values well within their physiological limits. In particular, the maximum wrist torque for the second simulation was only 3 N-m and the maximum ankle torque was only 6 N-m.

Method for Identification of Results of Dynamic Overloads in Assessment of Safety Use of the Mine Auxiliary Transportation System

NASA Astrophysics Data System (ADS)

Tokarczyk, Jarosław

2016-12-01

Method for identification the effects of dynamic overload affecting the people, which may occur in the emergency state of suspended monorail is presented in the paper. The braking curve using MBS (Multi-Body System) simulation was determined. For this purpose a computational model (MBS) of suspended monorail was developed and two different variants of numerical calculations were carried out. An algorithm of conducting numerical simulations to assess the effects of dynamic overload acting on the suspended monorails' users is also posted in the paper. An example of computational model FEM (Finite Element Method) composed of technical mean and the anthropometrical model ATB (Articulated Total Body) is shown. The simulation results are presented: graph of HIC (Head Injury Criterion) parameter and successive phases of dislocation of ATB model. Generator of computational models for safety criterion, which enables preparation of input data and remote starting the simulation, is proposed.

Application of control theory to dynamic systems simulation

NASA Technical Reports Server (NTRS)

Auslander, D. M.; Spear, R. C.; Young, G. E.

1982-01-01

The application of control theory is applied to dynamic systems simulation. Theory and methodology applicable to controlled ecological life support systems are considered. Spatial effects on system stability, design of control systems with uncertain parameters, and an interactive computing language (PARASOL-II) designed for dynamic system simulation, report quality graphics, data acquisition, and simple real time control are discussed.

Real-time dynamic simulation of the Cassini spacecraft using DARTS. Part 2: Parallel/vectorized real-time implementation

NASA Technical Reports Server (NTRS)

Fijany, A.; Roberts, J. A.; Jain, A.; Man, G. K.

1993-01-01

Part 1 of this paper presented the requirements for the real-time simulation of Cassini spacecraft along with some discussion of the DARTS algorithm. Here, in Part 2 we discuss the development and implementation of parallel/vectorized DARTS algorithm and architecture for real-time simulation. Development of the fast algorithms and architecture for real-time hardware-in-the-loop simulation of spacecraft dynamics is motivated by the fact that it represents a hard real-time problem, in the sense that the correctness of the simulation depends on both the numerical accuracy and the exact timing of the computation. For a given model fidelity, the computation should be computed within a predefined time period. Further reduction in computation time allows increasing the fidelity of the model (i.e., inclusion of more flexible modes) and the integration routine.

Development of massive multilevel molecular dynamics simulation program, Platypus (PLATform for dYnamic Protein Unified Simulation), for the elucidation of protein functions.

PubMed

Takano, Yu; Nakata, Kazuto; Yonezawa, Yasushige; Nakamura, Haruki

2016-05-05

A massively parallel program for quantum mechanical-molecular mechanical (QM/MM) molecular dynamics simulation, called Platypus (PLATform for dYnamic Protein Unified Simulation), was developed to elucidate protein functions. The speedup and the parallelization ratio of Platypus in the QM and QM/MM calculations were assessed for a bacteriochlorophyll dimer in the photosynthetic reaction center (DIMER) on the K computer, a massively parallel computer achieving 10 PetaFLOPs with 705,024 cores. Platypus exhibited the increase in speedup up to 20,000 core processors at the HF/cc-pVDZ and B3LYP/cc-pVDZ, and up to 10,000 core processors by the CASCI(16,16)/6-31G** calculations. We also performed excited QM/MM-MD simulations on the chromophore of Sirius (SIRIUS) in water. Sirius is a pH-insensitive and photo-stable ultramarine fluorescent protein. Platypus accelerated on-the-fly excited-state QM/MM-MD simulations for SIRIUS in water, using over 4000 core processors. In addition, it also succeeded in 50-ps (200,000-step) on-the-fly excited-state QM/MM-MD simulations for the SIRIUS in water. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

The Computer Simulation of Liquids by Molecular Dynamics.

ERIC Educational Resources Information Center

Smith, W.

1987-01-01

Proposes a mathematical computer model for the behavior of liquids using the classical dynamic principles of Sir Isaac Newton and the molecular dynamics method invented by other scientists. Concludes that other applications will be successful using supercomputers to go beyond simple Newtonian physics. (CW)

Quantum Fragment Based ab Initio Molecular Dynamics for Proteins.

PubMed

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

2015-12-08

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

New Flutter Analysis Technique for Time-Domain Computational Aeroelasticity

NASA Technical Reports Server (NTRS)

Pak, Chan-Gi; Lung, Shun-Fat

2017-01-01

A new time-domain approach for computing flutter speed is presented. Based on the time-history result of aeroelastic simulation, the unknown unsteady aerodynamics model is estimated using a system identification technique. The full aeroelastic model is generated via coupling the estimated unsteady aerodynamic model with the known linear structure model. The critical dynamic pressure is computed and used in the subsequent simulation until the convergence of the critical dynamic pressure is achieved. The proposed method is applied to a benchmark cantilevered rectangular wing.

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

NASA Technical Reports Server (NTRS)

1989-01-01

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

Parallel computational fluid dynamics '91; Conference Proceedings, Stuttgart, Germany, Jun. 10-12, 1991

NASA Technical Reports Server (NTRS)

Reinsch, K. G. (Editor); Schmidt, W. (Editor); Ecer, A. (Editor); Haeuser, Jochem (Editor); Periaux, J. (Editor)

1992-01-01

A conference was held on parallel computational fluid dynamics and produced related papers. Topics discussed in these papers include: parallel implicit and explicit solvers for compressible flow, parallel computational techniques for Euler and Navier-Stokes equations, grid generation techniques for parallel computers, and aerodynamic simulation om massively parallel systems.

Simulating Vibrations in a Complex Loaded Structure

NASA Technical Reports Server (NTRS)

Cao, Tim T.

2005-01-01

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

[Automobile versus pedestrian accidents analysis by fixed-parameters computer simulation].

PubMed

Mao, Ming-Yuan; Chen, Yi-Jiu; Liu, Ning-Guo; Zou, Dong-Hua; Liu, Jun-Yong; Jin, Xian-Long

2008-04-01

Using computer simulation to analyze the effects of speed, type of automobile and impacted position on crash-course and injuries of pedestrians in automobile vs. pedestrian accidents. Automobiles (bus, minibus, car and truck) and pedestrian models were constructed with multi-body dynamics computing method. The crashes were simulated at different impact speeds (20, 30, 40, 50 and 60 km/h) and different positions (front, lateral and rear of pedestrians). Crash-courses and their biomechanical responses were studied. If the type of automobile and impact position were the same, the crash-courses were similar (impact speed < or = 60 km/h). There were some characteristics in the head acceleration, upper neck axial force and leg axial force. Multi-body dynamics computer simulation of crash can be applied to analyze crash-course and injuries (head, neck and leg) of pedestrians.

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

PubMed

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

2016-10-21

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

GPS synchronized power system phase angle measurements

NASA Astrophysics Data System (ADS)

Wilson, Robert E.; Sterlina, Patrick S.

1994-09-01

This paper discusses the use of Global Positioning System (GPS) synchronized equipment for the measurement and analysis of key power system quantities. Two GPS synchronized phasor measurement units (PMU) were installed before testing. It was indicated that PMUs recorded the dynamic response of the power system phase angles when the northern California power grid was excited by the artificial short circuits. Power system planning engineers perform detailed computer generated simulations of the dynamic response of the power system to naturally occurring short circuits. The computer simulations use models of transmission lines, transformers, circuit breakers, and other high voltage components. This work will compare computer simulations of the same event with field measurement.

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

NASA Astrophysics Data System (ADS)

Hoepfer, Matthias

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

Numerical Simulation Of Flow Through An Artificial Heart

NASA Technical Reports Server (NTRS)

Rogers, Stuart; Kutler, Paul; Kwak, Dochan; Kiris, Centin

1991-01-01

Research in both artificial hearts and fluid dynamics benefits from computational studies. Algorithm that implements Navier-Stokes equations of flow extended to simulate flow of viscous, incompressible blood through articifial heart. Ability to compute details of such flow important for two reasons: internal flows with moving boundaries of academic interest in their own right, and many of deficiencies of artificial hearts attributable to dynamics of flow.

MPI implementation of PHOENICS: A general purpose computational fluid dynamics code

NASA Astrophysics Data System (ADS)

Simunovic, S.; Zacharia, T.; Baltas, N.; Spalding, D. B.

1995-03-01

PHOENICS is a suite of computational analysis programs that are used for simulation of fluid flow, heat transfer, and dynamical reaction processes. The parallel version of the solver EARTH for the Computational Fluid Dynamics (CFD) program PHOENICS has been implemented using Message Passing Interface (MPI) standard. Implementation of MPI version of PHOENICS makes this computational tool portable to a wide range of parallel machines and enables the use of high performance computing for large scale computational simulations. MPI libraries are available on several parallel architectures making the program usable across different architectures as well as on heterogeneous computer networks. The Intel Paragon NX and MPI versions of the program have been developed and tested on massively parallel supercomputers Intel Paragon XP/S 5, XP/S 35, and Kendall Square Research, and on the multiprocessor SGI Onyx computer at Oak Ridge National Laboratory. The preliminary testing results of the developed program have shown scalable performance for reasonably sized computational domains.

MPI implementation of PHOENICS: A general purpose computational fluid dynamics code

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

Simunovic, S.; Zacharia, T.; Baltas, N.

1995-04-01

PHOENICS is a suite of computational analysis programs that are used for simulation of fluid flow, heat transfer, and dynamical reaction processes. The parallel version of the solver EARTH for the Computational Fluid Dynamics (CFD) program PHOENICS has been implemented using Message Passing Interface (MPI) standard. Implementation of MPI version of PHOENICS makes this computational tool portable to a wide range of parallel machines and enables the use of high performance computing for large scale computational simulations. MPI libraries are available on several parallel architectures making the program usable across different architectures as well as on heterogeneous computer networks. Themore » Intel Paragon NX and MPI versions of the program have been developed and tested on massively parallel supercomputers Intel Paragon XP/S 5, XP/S 35, and Kendall Square Research, and on the multiprocessor SGI Onyx computer at Oak Ridge National Laboratory. The preliminary testing results of the developed program have shown scalable performance for reasonably sized computational domains.« less

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

PubMed

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

2004-07-15

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

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

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

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

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

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.

ADDRESSING ENVIRONMENTAL ENGINEERING CHALLENGES WITH COMPUTATIONAL FLUID DYNAMICS

EPA Science Inventory

This paper discusses the status and application of Computational Fluid Dynamics )CFD) models to address environmental engineering challenges for more detailed understanding of air pollutant source emissions, atmospheric dispersion and resulting human exposure. CFD simulations ...

Model implementation for dynamic computation of system cost

NASA Astrophysics Data System (ADS)

Levri, J.; Vaccari, D.

The Advanced Life Support (ALS) Program metric is the ratio of the equivalent system mass (ESM) of a mission based on International Space Station (ISS) technology to the ESM of that same mission based on ALS technology. ESM is a mission cost analog that converts the volume, power, cooling and crewtime requirements of a mission into mass units to compute an estimate of the life support system emplacement cost. Traditionally, ESM has been computed statically, using nominal values for system sizing. However, computation of ESM with static, nominal sizing estimates cannot capture the peak sizing requirements driven by system dynamics. In this paper, a dynamic model for a near-term Mars mission is described. The model is implemented in Matlab/Simulink' for the purpose of dynamically computing ESM. This paper provides a general overview of the crew, food, biomass, waste, water and air blocks in the Simulink' model. Dynamic simulations of the life support system track mass flow, volume and crewtime needs, as well as power and cooling requirement profiles. The mission's ESM is computed, based upon simulation responses. Ultimately, computed ESM values for various system architectures will feed into an optimization search (non-derivative) algorithm to predict parameter combinations that result in reduced objective function values.

Integration of Computational Geometry, Finite Element, and Multibody System Algorithms for the Development of New Computational Methodology for High-Fidelity Vehicle Systems Modeling and Simulation. ADDENDUM

DTIC Science & Technology

2013-11-12

Dr. Paramsothy Jayakumar (586) 282-4896 Computational Dynamics Inc.   0    Name of Contractor Computational Dynamics Inc. (CDI) 1809...Dr. Paramsothy Jayakumar TARDEC Computational Dynamics Inc.   1    Project Summary This project aims at addressing and remedying the serious...Shabana, A.A., Jayakumar , P., and Letherwood, M., “Soil Models and Vehicle System Dynamics”, Applied Mechanics Reviews, Vol. 65(4), 2013, doi

Semi-physical Simulation Platform of a Parafoil Nonlinear Dynamic System

NASA Astrophysics Data System (ADS)

Gao, Hai-Tao; Yang, Sheng-Bo; Zhu, Er-Lin; Sun, Qing-Lin; Chen, Zeng-Qiang; Kang, Xiao-Feng

2013-11-01

Focusing on the problems in the process of simulation and experiment on a parafoil nonlinear dynamic system, such as limited methods, high cost and low efficiency we present a semi-physical simulation platform. It is designed by connecting parts of physical objects to a computer, and remedies the defect that a computer simulation is divorced from a real environment absolutely. The main components of the platform and its functions, as well as simulation flows, are introduced. The feasibility and validity are verified through a simulation experiment. The experimental results show that the platform has significance for improving the quality of the parafoil fixed-point airdrop system, shortening the development cycle and saving cost.

The SCEC/USGS dynamic earthquake rupture code verification exercise

USGS Publications Warehouse

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

2009-01-01

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

Experiments in cooperative-arm object manipulation with a two-armed free-flying robot. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Koningstein, Ross

1990-01-01

Developing computed-torque controllers for complex manipulator systems using current techniques and tools is difficult because they address the issues pertinent to simulation, as opposed to control. A new formulation of computed-torque (CT) control that leads to an automated computer-torque robot controller program is presented. This automated tool is used for simulations and experimental demonstrations of endpoint and object control from a free-flying robot. A new computed-torque formulation states the multibody control problem in an elegant, homogeneous, and practical form. A recursive dynamics algorithm is presented that numerically evaluates kinematics and dynamics terms for multibody systems given a topological description. Manipulators may be free-flying, and may have closed-chain constraints. With the exception of object squeeze-force control, the algorithm does not deal with actuator redundancy. The algorithm is used to implement an automated 2D computed-torque dynamics and control package that allows joint, endpoint, orientation, momentum, and object squeeze-force control. This package obviates the need for hand-derivation of kinematics and dynamics, and is used for both simulation and experimental control. Endpoint control experiments are performed on a laboratory robot that has two arms to manipulate payloads, and uses an air bearing to achieve very-low drag characteristics. Simulations and experimental data for endpoint and object controllers are presented for the experimental robot - a complex dynamic system. There is a certain rather wide set of conditions under which CT endpoint controllers can neglect robot base accelerations (but not motions) and achieve comparable performance including base accelerations in the model. The regime over which this simplification holds is explored by simulation and experiment.

Modeling and simulation of dense cloud dispersion in urban areas by means of computational fluid dynamics.

PubMed

Scargiali, F; Grisafi, F; Busciglio, A; Brucato, A

2011-12-15

The formation of toxic heavy clouds as a result of sudden accidental releases from mobile containers, such as road tankers or railway tank cars, may occur inside urban areas so the problem arises of their consequences evaluation. Due to the semi-confined nature of the dispersion site simplified models may often be inappropriate. As an alternative, computational fluid dynamics (CFD) has the potential to provide realistic simulations even for geometrically complex scenarios since the heavy gas dispersion process is described by basic conservation equations with a reduced number of approximations. In the present work a commercial general purpose CFD code (CFX 4.4 by Ansys(®)) is employed for the simulation of dense cloud dispersion in urban areas. The simulation strategy proposed involves a stationary pre-release flow field simulation followed by a dynamic after-release flow and concentration field simulations. In order to try a generalization of results, the computational domain is modeled as a simple network of straight roads with regularly distributed blocks mimicking the buildings. Results show that the presence of buildings lower concentration maxima and enlarge the side spread of the cloud. Dispersion dynamics is also found to be strongly affected by the quantity of heavy-gas released. Copyright © 2011 Elsevier B.V. All rights reserved.

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.

27ps DFT Molecular Dynamics Simulation of a-maltose: A Reduced Basis Set Study.

USDA-ARS?s Scientific Manuscript database

DFT molecular dynamics simulations are time intensive when carried out on carbohydrates such as alpha-maltose, requiring up to three or more weeks on a fast 16-processor computer to obtain just 5ps of constant energy dynamics. In a recent publication [1] forces for dynamics were generated from B3LY...

Conjugate Gradient Algorithms For Manipulator Simulation

NASA Technical Reports Server (NTRS)

Fijany, Amir; Scheid, Robert E.

1991-01-01

Report discusses applicability of conjugate-gradient algorithms to computation of forward dynamics of robotic manipulators. Rapid computation of forward dynamics essential to teleoperation and other advanced robotic applications. Part of continuing effort to find algorithms meeting requirements for increased computational efficiency and speed. Method used for iterative solution of systems of linear equations.

Scalable Cloning on Large-Scale GPU Platforms with Application to Time-Stepped Simulations on Grids

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

Yoginath, Srikanth B.; Perumalla, Kalyan S.

Cloning is a technique to efficiently simulate a tree of multiple what-if scenarios that are unraveled during the course of a base simulation. However, cloned execution is highly challenging to realize on large, distributed memory computing platforms, due to the dynamic nature of the computational load across clones, and due to the complex dependencies spanning the clone tree. In this paper, we present the conceptual simulation framework, algorithmic foundations, and runtime interface of CloneX, a new system we designed for scalable simulation cloning. It efficiently and dynamically creates whole logical copies of a dynamic tree of simulations across a largemore » parallel system without full physical duplication of computation and memory. The performance of a prototype implementation executed on up to 1,024 graphical processing units of a supercomputing system has been evaluated with three benchmarks—heat diffusion, forest fire, and disease propagation models—delivering a speed up of over two orders of magnitude compared to replicated runs. Finally, the results demonstrate a significantly faster and scalable way to execute many what-if scenario ensembles of large simulations via cloning using the CloneX interface.« less

Scalable Cloning on Large-Scale GPU Platforms with Application to Time-Stepped Simulations on Grids

DOE PAGES

Yoginath, Srikanth B.; Perumalla, Kalyan S.

2018-01-31

Cloning is a technique to efficiently simulate a tree of multiple what-if scenarios that are unraveled during the course of a base simulation. However, cloned execution is highly challenging to realize on large, distributed memory computing platforms, due to the dynamic nature of the computational load across clones, and due to the complex dependencies spanning the clone tree. In this paper, we present the conceptual simulation framework, algorithmic foundations, and runtime interface of CloneX, a new system we designed for scalable simulation cloning. It efficiently and dynamically creates whole logical copies of a dynamic tree of simulations across a largemore » parallel system without full physical duplication of computation and memory. The performance of a prototype implementation executed on up to 1,024 graphical processing units of a supercomputing system has been evaluated with three benchmarks—heat diffusion, forest fire, and disease propagation models—delivering a speed up of over two orders of magnitude compared to replicated runs. Finally, the results demonstrate a significantly faster and scalable way to execute many what-if scenario ensembles of large simulations via cloning using the CloneX interface.« less

Vortex Filaments in Grids for Scalable, Fine Smoke Simulation.

PubMed

Meng, Zhang; Weixin, Si; Yinling, Qian; Hanqiu, Sun; Jing, Qin; Heng, Pheng-Ann

2015-01-01

Vortex modeling can produce attractive visual effects of dynamic fluids, which are widely applicable for dynamic media, computer games, special effects, and virtual reality systems. However, it is challenging to effectively simulate intensive and fine detailed fluids such as smoke with fast increasing vortex filaments and smoke particles. The authors propose a novel vortex filaments in grids scheme in which the uniform grids dynamically bridge the vortex filaments and smoke particles for scalable, fine smoke simulation with macroscopic vortex structures. Using the vortex model, their approach supports the trade-off between simulation speed and scale of details. After computing the whole velocity, external control can be easily exerted on the embedded grid to guide the vortex-based smoke motion. The experimental results demonstrate the efficiency of using the proposed scheme for a visually plausible smoke simulation with macroscopic vortex structures.

Conservative boundary conditions for 3D gas dynamics problems

NASA Technical Reports Server (NTRS)

Gerasimov, B. P.; Karagichev, A. B.; Semushin, S. A.

1986-01-01

A method is described for 3D-gas dynamics computer simulation in regions of complicated shape by means of nonadjusted rectangular grids providing unified treatment of various problems. Some test problem computation results are given.

Math modeling and computer mechanization for real time simulation of rotary-wing aircraft

NASA Technical Reports Server (NTRS)

Howe, R. M.

1979-01-01

Mathematical modeling and computer mechanization for real time simulation of rotary wing aircraft is discussed. Error analysis in the digital simulation of dynamic systems, such as rotary wing aircraft is described. The method for digital simulation of nonlinearities with discontinuities, such as exist in typical flight control systems and rotor blade hinges, is discussed.

On efficiency of fire simulation realization: parallelization with greater number of computational meshes

NASA Astrophysics Data System (ADS)

Valasek, Lukas; Glasa, Jan

2017-12-01

Current fire simulation systems are capable to utilize advantages of high-performance computer (HPC) platforms available and to model fires efficiently in parallel. In this paper, efficiency of a corridor fire simulation on a HPC computer cluster is discussed. The parallel MPI version of Fire Dynamics Simulator is used for testing efficiency of selected strategies of allocation of computational resources of the cluster using a greater number of computational cores. Simulation results indicate that if the number of cores used is not equal to a multiple of the total number of cluster node cores there are allocation strategies which provide more efficient calculations.

Development of a Computer Simulation Game Using a Reverse Engineering Approach

ERIC Educational Resources Information Center

Ozkul, Ahmet

2012-01-01

Business simulation games are widely used in the classroom to provide students with experiential learning opportunities on business situations in a dynamic fashion. When properly designed and implemented, the computer simulation game can be a useful educational tool by integrating separate theoretical concepts and demonstrating the nature of…

Simulations of Probabilities for Quantum Computing

NASA Technical Reports Server (NTRS)

Zak, M.

1996-01-01

It has been demonstrated that classical probabilities, and in particular, probabilistic Turing machine, can be simulated by combining chaos and non-LIpschitz dynamics, without utilization of any man-made devices (such as random number generators). Self-organizing properties of systems coupling simulated and calculated probabilities and their link to quantum computations are discussed.

Research in Distance Education: A System Modeling Approach.

ERIC Educational Resources Information Center

Saba, Farhad; Twitchell, David

1988-01-01

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

Molecular dynamics simulations through GPU video games technologies

PubMed Central

Loukatou, Styliani; Papageorgiou, Louis; Fakourelis, Paraskevas; Filntisi, Arianna; Polychronidou, Eleftheria; Bassis, Ioannis; Megalooikonomou, Vasileios; Makałowski, Wojciech; Vlachakis, Dimitrios; Kossida, Sophia

2016-01-01

Bioinformatics is the scientific field that focuses on the application of computer technology to the management of biological information. Over the years, bioinformatics applications have been used to store, process and integrate biological and genetic information, using a wide range of methodologies. One of the most de novo techniques used to understand the physical movements of atoms and molecules is molecular dynamics (MD). MD is an in silico method to simulate the physical motions of atoms and molecules under certain conditions. This has become a state strategic technique and now plays a key role in many areas of exact sciences, such as chemistry, biology, physics and medicine. Due to their complexity, MD calculations could require enormous amounts of computer memory and time and therefore their execution has been a big problem. Despite the huge computational cost, molecular dynamics have been implemented using traditional computers with a central memory unit (CPU). A graphics processing unit (GPU) computing technology was first designed with the goal to improve video games, by rapidly creating and displaying images in a frame buffer such as screens. The hybrid GPU-CPU implementation, combined with parallel computing is a novel technology to perform a wide range of calculations. GPUs have been proposed and used to accelerate many scientific computations including MD simulations. Herein, we describe the new methodologies developed initially as video games and how they are now applied in MD simulations. PMID:27525251

USAF/SCEEE Summer Faculty Research Program (1982). Management Report.

DTIC Science & Technology

1982-10-01

Patrick J. Sweeney, Ph.D., P.E. Mary Doddy, M.S. ABSTRACT This dynamic simulation computer model demonstrates the affects of C-forces upon the eyeball...Assistant Professor Specialty: Numerical Modeling and University of Lowell Computer Simulation of Mathematics Department Geophysical Problems Lowell...Problems And Promises 25 Modeling And Tracking Saccadic Dr. John D. Enderle Eye Movements 26 Dynamic Response Of Doubly Curved Dr. Fernando E. Fagundo

A Computer Simulation of the Trophic Dynamics of an Aquatic System.

ERIC Educational Resources Information Center

Bowker, D. W.; Randerson, P. F.

1989-01-01

Described is a computer program, AQUASIM, which simulates interaction between environmental factors, phytoplankton, zooplankton, and fish in an aquatic ecosystem. The conceptual flow, equations, variables, rate processes, and parameter manipulations are discussed. (CW)

Reference Computational Meshing Strategy for Computational Fluid Dynamics Simulation of Departure from Nucleate BoilingReference Computational Meshing Strategy for Computational Fluid Dynamics Simulation of Departure from Nucleate Boiling

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

Pointer, William David

The objective of this effort is to establish a strategy and process for generation of suitable computational mesh for computational fluid dynamics simulations of departure from nucleate boiling in a 5 by 5 fuel rod assembly held in place by PWR mixing vane spacer grids. This mesh generation process will support ongoing efforts to develop, demonstrate and validate advanced multi-phase computational fluid dynamics methods that enable more robust identification of dryout conditions and DNB occurrence.Building upon prior efforts and experience, multiple computational meshes were developed using the native mesh generation capabilities of the commercial CFD code STAR-CCM+. These meshes weremore » used to simulate two test cases from the Westinghouse 5 by 5 rod bundle facility. The sensitivity of predicted quantities of interest to the mesh resolution was then established using two evaluation methods, the Grid Convergence Index method and the Least Squares method. This evaluation suggests that the Least Squares method can reliably establish the uncertainty associated with local parameters such as vector velocity components at a point in the domain or surface averaged quantities such as outlet velocity magnitude. However, neither method is suitable for characterization of uncertainty in global extrema such as peak fuel surface temperature, primarily because such parameters are not necessarily associated with a fixed point in space. This shortcoming is significant because the current generation algorithm for identification of DNB event conditions relies on identification of such global extrema. Ongoing efforts to identify DNB based on local surface conditions will address this challenge« less

Towards data warehousing and mining of protein unfolding simulation data.

PubMed

Berrar, Daniel; Stahl, Frederic; Silva, Candida; Rodrigues, J Rui; Brito, Rui M M; Dubitzky, Werner

2005-10-01

The prediction of protein structure and the precise understanding of protein folding and unfolding processes remains one of the greatest challenges in structural biology and bioinformatics. Computer simulations based on molecular dynamics (MD) are at the forefront of the effort to gain a deeper understanding of these complex processes. Currently, these MD simulations are usually on the order of tens of nanoseconds, generate a large amount of conformational data and are computationally expensive. More and more groups run such simulations and generate a myriad of data, which raises new challenges in managing and analyzing these data. Because the vast range of proteins researchers want to study and simulate, the computational effort needed to generate data, the large data volumes involved, and the different types of analyses scientists need to perform, it is desirable to provide a public repository allowing researchers to pool and share protein unfolding data. To adequately organize, manage, and analyze the data generated by unfolding simulation studies, we designed a data warehouse system that is embedded in a grid environment to facilitate the seamless sharing of available computer resources and thus enable many groups to share complex molecular dynamics simulations on a more regular basis. To gain insight into the conformational fluctuations and stability of the monomeric forms of the amyloidogenic protein transthyretin (TTR), molecular dynamics unfolding simulations of the monomer of human TTR have been conducted. Trajectory data and meta-data of the wild-type (WT) protein and the highly amyloidogenic variant L55P-TTR represent the test case for the data warehouse. Web and grid services, especially pre-defined data mining services that can run on or 'near' the data repository of the data warehouse, are likely to play a pivotal role in the analysis of molecular dynamics unfolding data.

Real-time simulation of the TF30-P-3 turbofan engine using a hybrid computer

NASA Technical Reports Server (NTRS)

Szuch, J. R.; Bruton, W. M.

1974-01-01

A real-time, hybrid-computer simulation of the TF30-P-3 turbofan engine was developed. The simulation was primarily analog in nature but used the digital portion of the hybrid computer to perform bivariate function generation associated with the performance of the engine's rotating components. FORTRAN listings and analog patching diagrams are provided. The hybrid simulation was controlled by a digital computer programmed to simulate the engine's standard hydromechanical control. Both steady-state and dynamic data obtained from the digitally controlled engine simulation are presented. Hybrid simulation data are compared with data obtained from a digital simulation provided by the engine manufacturer. The comparisons indicate that the real-time hybrid simulation adequately matches the baseline digital simulation.

Full Quantum Dynamics Simulation of a Realistic Molecular System Using the Adaptive Time-Dependent Density Matrix Renormalization Group Method.

PubMed

Yao, Yao; Sun, Ke-Wei; Luo, Zhen; Ma, Haibo

2018-01-18

The accurate theoretical interpretation of ultrafast time-resolved spectroscopy experiments relies on full quantum dynamics simulations for the investigated system, which is nevertheless computationally prohibitive for realistic molecular systems with a large number of electronic and/or vibrational degrees of freedom. In this work, we propose a unitary transformation approach for realistic vibronic Hamiltonians, which can be coped with using the adaptive time-dependent density matrix renormalization group (t-DMRG) method to efficiently evolve the nonadiabatic dynamics of a large molecular system. We demonstrate the accuracy and efficiency of this approach with an example of simulating the exciton dissociation process within an oligothiophene/fullerene heterojunction, indicating that t-DMRG can be a promising method for full quantum dynamics simulation in large chemical systems. Moreover, it is also shown that the proper vibronic features in the ultrafast electronic process can be obtained by simulating the two-dimensional (2D) electronic spectrum by virtue of the high computational efficiency of the t-DMRG method.

Overcoming time scale and finite size limitations to compute nucleation rates from small scale well tempered metadynamics simulations.

PubMed

Salvalaglio, Matteo; Tiwary, Pratyush; Maggioni, Giovanni Maria; Mazzotti, Marco; Parrinello, Michele

2016-12-07

Condensation of a liquid droplet from a supersaturated vapour phase is initiated by a prototypical nucleation event. As such it is challenging to compute its rate from atomistic molecular dynamics simulations. In fact at realistic supersaturation conditions condensation occurs on time scales that far exceed what can be reached with conventional molecular dynamics methods. Another known problem in this context is the distortion of the free energy profile associated to nucleation due to the small, finite size of typical simulation boxes. In this work the problem of time scale is addressed with a recently developed enhanced sampling method while contextually correcting for finite size effects. We demonstrate our approach by studying the condensation of argon, and showing that characteristic nucleation times of the order of magnitude of hours can be reliably calculated. Nucleation rates spanning a range of 10 orders of magnitude are computed at moderate supersaturation levels, thus bridging the gap between what standard molecular dynamics simulations can do and real physical systems.

A spectral approach for discrete dislocation dynamics simulations of nanoindentation

NASA Astrophysics Data System (ADS)

Bertin, Nicolas; Glavas, Vedran; Datta, Dibakar; Cai, Wei

2018-07-01

We present a spectral approach to perform nanoindentation simulations using three-dimensional nodal discrete dislocation dynamics. The method relies on a two step approach. First, the contact problem between an indenter of arbitrary shape and an isotropic elastic half-space is solved using a spectral iterative algorithm, and the contact pressure is fully determined on the half-space surface. The contact pressure is then used as a boundary condition of the spectral solver to determine the resulting stress field produced in the simulation volume. In both stages, the mechanical fields are decomposed into Fourier modes and are efficiently computed using fast Fourier transforms. To further improve the computational efficiency, the method is coupled with a subcycling integrator and a special approach is devised to approximate the displacement field associated with surface steps. As a benchmark, the method is used to compute the response of an elastic half-space using different types of indenter. An example of a dislocation dynamics nanoindentation simulation with complex initial microstructure is presented.

Overcoming time scale and finite size limitations to compute nucleation rates from small scale well tempered metadynamics simulations

NASA Astrophysics Data System (ADS)

Salvalaglio, Matteo; Tiwary, Pratyush; Maggioni, Giovanni Maria; Mazzotti, Marco; Parrinello, Michele

2016-12-01

Condensation of a liquid droplet from a supersaturated vapour phase is initiated by a prototypical nucleation event. As such it is challenging to compute its rate from atomistic molecular dynamics simulations. In fact at realistic supersaturation conditions condensation occurs on time scales that far exceed what can be reached with conventional molecular dynamics methods. Another known problem in this context is the distortion of the free energy profile associated to nucleation due to the small, finite size of typical simulation boxes. In this work the problem of time scale is addressed with a recently developed enhanced sampling method while contextually correcting for finite size effects. We demonstrate our approach by studying the condensation of argon, and showing that characteristic nucleation times of the order of magnitude of hours can be reliably calculated. Nucleation rates spanning a range of 10 orders of magnitude are computed at moderate supersaturation levels, thus bridging the gap between what standard molecular dynamics simulations can do and real physical systems.

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

Predicting Flows of Rarefied Gases

NASA Technical Reports Server (NTRS)

LeBeau, Gerald J.; Wilmoth, Richard G.

2005-01-01

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

Computer modeling and simulation of human movement. Applications in sport and rehabilitation.

PubMed

Neptune, R R

2000-05-01

Computer modeling and simulation of human movement plays an increasingly important role in sport and rehabilitation, with applications ranging from sport equipment design to understanding pathologic gait. The complex dynamic interactions within the musculoskeletal and neuromuscular systems make analyzing human movement with existing experimental techniques difficult but computer modeling and simulation allows for the identification of these complex interactions and causal relationships between input and output variables. This article provides an overview of computer modeling and simulation and presents an example application in the field of rehabilitation.

Computer simulation of the coffee leaf miner using sexual Penna aging model

NASA Astrophysics Data System (ADS)

de Oliveira, A. C. S.; Martins, S. G. F.; Zacarias, M. S.

2008-01-01

Forecast models based on climatic conditions are of great interest in Integrated Pest Management (IPM) programs. The success of these models depends, among other factors, on the knowledge of the temperature effect on the pests’ population dynamics. In this direction, a computer simulation was made for the population dynamics of the coffee leaf miner, L. coffeella, at different temperatures, considering experimental data relative to the pest. The age structure was inserted into the dynamics through sexual Penna Model. The results obtained, such as life expectancy, growth rate and annual generations’ number, in agreement to those in laboratory and field conditions, show that the simulation can be used as a forecast model for controlling L. coffeella.

Crowding in Cellular Environments at an Atomistic Level from Computer Simulations

PubMed Central

2017-01-01

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

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.

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

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

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

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

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

DOE PAGES

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

2016-10-17

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

Analysis of dynamics and fit of diving suits

NASA Astrophysics Data System (ADS)

Mahnic Naglic, M.; Petrak, S.; Gersak, J.; Rolich, T.

2017-10-01

Paper presents research on dynamical behaviour and fit analysis of customised diving suits. Diving suits models are developed using the 3D flattening method, which enables the construction of a garment model directly on the 3D computer body model and separation of discrete 3D surfaces as well as transformation into 2D cutting parts. 3D body scanning of male and female test subjects was performed with the purpose of body measurements analysis in static and dynamic postures and processed body models were used for construction and simulation of diving suits prototypes. All necessary parameters, for 3D simulation were applied on obtained cutting parts, as well as parameters values for mechanical properties of neoprene material. Developed computer diving suits prototypes were used for stretch analysis on areas relevant for body dimensional changes according to dynamic anthropometrics. Garment pressures against the body in static and dynamic conditions was also analysed. Garments patterns for which the computer prototype verification was conducted were used for real prototype production. Real prototypes were also used for stretch and pressure analysis in static and dynamic conditions. Based on the obtained results, correlation analysis between body changes in dynamic positions and dynamic stress, determined on computer and real prototypes, was performed.

Modelling the spread of innovation in wild birds.

PubMed

Shultz, Thomas R; Montrey, Marcel; Aplin, Lucy M

2017-06-01

We apply three plausible algorithms in agent-based computer simulations to recent experiments on social learning in wild birds. Although some of the phenomena are simulated by all three learning algorithms, several manifestations of social conformity bias are simulated by only the approximate majority (AM) algorithm, which has roots in chemistry, molecular biology and theoretical computer science. The simulations generate testable predictions and provide several explanatory insights into the diffusion of innovation through a population. The AM algorithm's success raises the possibility of its usefulness in studying group dynamics more generally, in several different scientific domains. Our differential-equation model matches simulation results and provides mathematical insights into the dynamics of these algorithms. © 2017 The Author(s).

Generalized image charge solvation model for electrostatic interactions in molecular dynamics simulations of aqueous solutions

PubMed Central

Deng, Shaozhong; Xue, Changfeng; Baumketner, Andriy; Jacobs, Donald; Cai, Wei

2013-01-01

This paper extends the image charge solvation model (ICSM) [J. Chem. Phys. 131, 154103 (2009)], a hybrid explicit/implicit method to treat electrostatic interactions in computer simulations of biomolecules formulated for spherical cavities, to prolate spheroidal and triaxial ellipsoidal cavities, designed to better accommodate non-spherical solutes in molecular dynamics (MD) simulations. In addition to the utilization of a general truncated octahedron as the MD simulation box, central to the proposed extension is an image approximation method to compute the reaction field for a point charge placed inside such a non-spherical cavity by using a single image charge located outside the cavity. The resulting generalized image charge solvation model (GICSM) is tested in simulations of liquid water, and the results are analyzed in comparison with those obtained from the ICSM simulations as a reference. We find that, for improved computational efficiency due to smaller simulation cells and consequently a less number of explicit solvent molecules, the generalized model can still faithfully reproduce known static and dynamic properties of liquid water at least for systems considered in the present paper, indicating its great potential to become an accurate but more efficient alternative to the ICSM when bio-macromolecules of irregular shapes are to be simulated. PMID:23913979

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

NASA Technical Reports Server (NTRS)

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

1993-01-01

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

A Series of Molecular Dynamics and Homology Modeling Computer Labs for an Undergraduate Molecular Modeling Course

ERIC Educational Resources Information Center

Elmore, Donald E.; Guayasamin, Ryann C.; Kieffer, Madeleine E.

2010-01-01

As computational modeling plays an increasingly central role in biochemical research, it is important to provide students with exposure to common modeling methods in their undergraduate curriculum. This article describes a series of computer labs designed to introduce undergraduate students to energy minimization, molecular dynamics simulations,…

Efficient dynamic simulation for multiple chain robotic mechanisms

NASA Technical Reports Server (NTRS)

Lilly, Kathryn W.; Orin, David E.

1989-01-01

An efficient O(mN) algorithm for dynamic simulation of simple closed-chain robotic mechanisms is presented, where m is the number of chains, and N is the number of degrees of freedom for each chain. It is based on computation of the operational space inertia matrix (6 x 6) for each chain as seen by the body, load, or object. Also, computation of the chain dynamics, when opened at one end, is required, and the most efficient algorithm is used for this purpose. Parallel implementation of the dynamics for each chain results in an O(N) + O(log sub 2 m+1) algorithm.

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

Physically Based Modeling and Simulation with Dynamic Spherical Volumetric Simplex Splines

PubMed Central

Tan, Yunhao; Hua, Jing; Qin, Hong

2009-01-01

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

The investigation of tethered satellite system dynamics

NASA Technical Reports Server (NTRS)

Lorenzini, E.

1985-01-01

A progress report is presented that deals with three major topics related to Tethered Satellite System Dynamics. The SAO rotational dynamics computer code was updated. The program is now suitable to deal with inclined orbits. The output has been also modified in order to show the satellite Euler angles referred to the rotating orbital frame. The three-dimensional high resolution computer program SLACK3 was developed. The code simulates the three-dimensional dynamics of a tether going slack taking into account the effect produced by boom rotations. Preliminary simulations on the three-dimensional dynamics of a recoiling slack tether are shown in this report. A program to evaluate the electric potential around a severed tether is immersed in a plasma. The potential is computed on a three-dimensional grid axially symmetric with respect to the tether longitudinal axis. The electric potential variations due to the plasma are presently under investigation.

Development of a Computational Assay for the Estrogen Receptor

DTIC Science & Technology

2006-07-01

University Ashley Deline, Senior Thesis in chemistry, " Molecular Dynamic Simulations of a Glycoform and its Constituent Parts Related to Rheumatoid Arthritis...involves running a long molecular dynamics (MD) simulation of the uncoupled receptor in order to sample the protein’s unique conformations. The second...Receptor binding domain. * Performed several long molecular dynamics simulations (800 ps - 3 ns) on the ligand-ER system using ligands with known

Solving Equations of Multibody Dynamics

NASA Technical Reports Server (NTRS)

Jain, Abhinandan; Lim, Christopher

2007-01-01

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

Quantum decision-maker theory and simulation

NASA Astrophysics Data System (ADS)

Zak, Michail; Meyers, Ronald E.; Deacon, Keith S.

2000-07-01

A quantum device simulating the human decision making process is introduced. It consists of quantum recurrent nets generating stochastic processes which represent the motor dynamics, and of classical neural nets describing the evolution of probabilities of these processes which represent the mental dynamics. The autonomy of the decision making process is achieved by a feedback from the mental to motor dynamics which changes the stochastic matrix based upon the probability distribution. This feedback replaces unavailable external information by an internal knowledge- base stored in the mental model in the form of probability distributions. As a result, the coupled motor-mental dynamics is described by a nonlinear version of Markov chains which can decrease entropy without an external source of information. Applications to common sense based decisions as well as to evolutionary games are discussed. An example exhibiting self-organization is computed using quantum computer simulation. Force on force and mutual aircraft engagements using the quantum decision maker dynamics are considered.

Integration of Computational Geometry, Finite Element, and Multibody System Algorithms for the Development of New Computational Methodology for High-Fidelity Vehicle Systems Modeling and Simulation

DTIC Science & Technology

2013-04-11

vehicle dynamics. Unclassified Unclassified Unclassified UU 9 Dr. Paramsothy Jayakumar (586) 282-4896 Computational Dynamics Inc.   0    Name of...Technical Representative Dr. Paramsothy Jayakumar TARDEC Computational Dynamics Inc.   1    Project Summary This project aims at addressing and...applications. This literature review is being summarized and incorporated into the paper. The commentary provided by Dr. Jayakumar was addressed and

Dissertation Defense Computational Fluid Dynamics Uncertainty Analysis for Payload Fairing Spacecraft Environmental Control Systems

NASA Technical Reports Server (NTRS)

Groves, Curtis Edward

2014-01-01

Spacecraft thermal protection systems are at risk of being damaged due to airflow produced from Environmental Control Systems. There are inherent uncertainties and errors associated with using Computational Fluid Dynamics to predict the airflow field around a spacecraft from the Environmental Control System. This paper describes an approach to quantify the uncertainty in using Computational Fluid Dynamics to predict airflow speeds around an encapsulated spacecraft without the use of test data. Quantifying the uncertainty in analytical predictions is imperative to the success of any simulation-based product. The method could provide an alternative to traditional "validation by test only" mentality. This method could be extended to other disciplines and has potential to provide uncertainty for any numerical simulation, thus lowering the cost of performing these verifications while increasing the confidence in those predictions. Spacecraft requirements can include a maximum airflow speed to protect delicate instruments during ground processing. Computational Fluid Dynamics can be used to verify these requirements; however, the model must be validated by test data. This research includes the following three objectives and methods. Objective one is develop, model, and perform a Computational Fluid Dynamics analysis of three (3) generic, non-proprietary, environmental control systems and spacecraft configurations. Several commercially available and open source solvers have the capability to model the turbulent, highly three-dimensional, incompressible flow regime. The proposed method uses FLUENT, STARCCM+, and OPENFOAM. Objective two is to perform an uncertainty analysis of the Computational Fluid Dynamics model using the methodology found in "Comprehensive Approach to Verification and Validation of Computational Fluid Dynamics Simulations". This method requires three separate grids and solutions, which quantify the error bars around Computational Fluid Dynamics predictions. The method accounts for all uncertainty terms from both numerical and input variables. Objective three is to compile a table of uncertainty parameters that could be used to estimate the error in a Computational Fluid Dynamics model of the Environmental Control System /spacecraft system. Previous studies have looked at the uncertainty in a Computational Fluid Dynamics model for a single output variable at a single point, for example the re-attachment length of a backward facing step. For the flow regime being analyzed (turbulent, three-dimensional, incompressible), the error at a single point can propagate into the solution both via flow physics and numerical methods. Calculating the uncertainty in using Computational Fluid Dynamics to accurately predict airflow speeds around encapsulated spacecraft in is imperative to the success of future missions.

Dissertation Defense: Computational Fluid Dynamics Uncertainty Analysis for Payload Fairing Spacecraft Environmental Control Systems

NASA Technical Reports Server (NTRS)

Groves, Curtis Edward

2014-01-01

Spacecraft thermal protection systems are at risk of being damaged due to airflow produced from Environmental Control Systems. There are inherent uncertainties and errors associated with using Computational Fluid Dynamics to predict the airflow field around a spacecraft from the Environmental Control System. This paper describes an approach to quantify the uncertainty in using Computational Fluid Dynamics to predict airflow speeds around an encapsulated spacecraft without the use of test data. Quantifying the uncertainty in analytical predictions is imperative to the success of any simulation-based product. The method could provide an alternative to traditional validation by test only mentality. This method could be extended to other disciplines and has potential to provide uncertainty for any numerical simulation, thus lowering the cost of performing these verifications while increasing the confidence in those predictions.Spacecraft requirements can include a maximum airflow speed to protect delicate instruments during ground processing. Computational Fluid Dynamics can be used to verify these requirements; however, the model must be validated by test data. This research includes the following three objectives and methods. Objective one is develop, model, and perform a Computational Fluid Dynamics analysis of three (3) generic, non-proprietary, environmental control systems and spacecraft configurations. Several commercially available and open source solvers have the capability to model the turbulent, highly three-dimensional, incompressible flow regime. The proposed method uses FLUENT, STARCCM+, and OPENFOAM. Objective two is to perform an uncertainty analysis of the Computational Fluid Dynamics model using the methodology found in Comprehensive Approach to Verification and Validation of Computational Fluid Dynamics Simulations. This method requires three separate grids and solutions, which quantify the error bars around Computational Fluid Dynamics predictions. The method accounts for all uncertainty terms from both numerical and input variables. Objective three is to compile a table of uncertainty parameters that could be used to estimate the error in a Computational Fluid Dynamics model of the Environmental Control System spacecraft system.Previous studies have looked at the uncertainty in a Computational Fluid Dynamics model for a single output variable at a single point, for example the re-attachment length of a backward facing step. For the flow regime being analyzed (turbulent, three-dimensional, incompressible), the error at a single point can propagate into the solution both via flow physics and numerical methods. Calculating the uncertainty in using Computational Fluid Dynamics to accurately predict airflow speeds around encapsulated spacecraft in is imperative to the success of future missions.

Computational Fluid Dynamics Uncertainty Analysis for Payload Fairing Spacecraft Environmental Control Systems

NASA Technical Reports Server (NTRS)

Groves, Curtis E.

2013-01-01

Spacecraft thermal protection systems are at risk of being damaged due to airflow produced from Environmental Control Systems. There are inherent uncertainties and errors associated with using Computational Fluid Dynamics to predict the airflow field around a spacecraft from the Environmental Control System. This proposal describes an approach to validate the uncertainty in using Computational Fluid Dynamics to predict airflow speeds around an encapsulated spacecraft. The research described here is absolutely cutting edge. Quantifying the uncertainty in analytical predictions is imperative to the success of any simulation-based product. The method could provide an alternative to traditional"validation by test only'' mentality. This method could be extended to other disciplines and has potential to provide uncertainty for any numerical simulation, thus lowering the cost of performing these verifications while increasing the confidence in those predictions. Spacecraft requirements can include a maximum airflow speed to protect delicate instruments during ground processing. Computationaf Fluid Dynamics can be used to veritY these requirements; however, the model must be validated by test data. The proposed research project includes the following three objectives and methods. Objective one is develop, model, and perform a Computational Fluid Dynamics analysis of three (3) generic, non-proprietary, environmental control systems and spacecraft configurations. Several commercially available solvers have the capability to model the turbulent, highly three-dimensional, incompressible flow regime. The proposed method uses FLUENT and OPEN FOAM. Objective two is to perform an uncertainty analysis of the Computational Fluid . . . Dynamics model using the methodology found in "Comprehensive Approach to Verification and Validation of Computational Fluid Dynamics Simulations". This method requires three separate grids and solutions, which quantify the error bars around Computational Fluid Dynamics predictions. The method accounts for all uncertainty terms from both numerical and input variables. Objective three is to compile a table of uncertainty parameters that could be used to estimate the error in a Computational Fluid Dynamics model of the Environmental Control System /spacecraft system. Previous studies have looked at the uncertainty in a Computational Fluid Dynamics model for a single output variable at a single point, for example the re-attachment length of a backward facing step. To date, the author is the only person to look at the uncertainty in the entire computational domain. For the flow regime being analyzed (turbulent, threedimensional, incompressible), the error at a single point can propagate into the solution both via flow physics and numerical methods. Calculating the uncertainty in using Computational Fluid Dynamics to accurately predict airflow speeds around encapsulated spacecraft in is imperative to the success of future missions.

How Science Students Can Learn about Unobservable Phenomena Using Computer-Based Analogies

ERIC Educational Resources Information Center

Trey, L.; Khan, S.

2008-01-01

A novel instructional computer simulation that incorporates a dynamic analogy to represent Le Chatelier's Principle was designed to investigate the contribution of this feature to students' understanding. Two groups of 12th grade Chemistry students (n=15) interacted with the computer simulation during the study. Both groups did the same…

Optimising the Parallelisation of OpenFOAM Simulations

DTIC Science & Technology

2014-06-01

UNCLASSIFIED UNCLASSIFIED Optimising the Parallelisation of OpenFOAM Simulations Shannon Keough Maritime Division Defence...Science and Technology Organisation DSTO-TR-2987 ABSTRACT The OpenFOAM computational fluid dynamics toolbox allows parallel computation of...performance of a given high performance computing cluster with several OpenFOAM cases, running using a combination of MPI libraries and corresponding MPI

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.

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

PubMed

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

2018-04-05

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

Constraint methods that accelerate free-energy simulations of biomolecules.

PubMed

Perez, Alberto; MacCallum, Justin L; Coutsias, Evangelos A; Dill, Ken A

2015-12-28

Atomistic molecular dynamics simulations of biomolecules are critical for generating narratives about biological mechanisms. The power of atomistic simulations is that these are physics-based methods that satisfy Boltzmann's law, so they can be used to compute populations, dynamics, and mechanisms. But physical simulations are computationally intensive and do not scale well to the sizes of many important biomolecules. One way to speed up physical simulations is by coarse-graining the potential function. Another way is to harness structural knowledge, often by imposing spring-like restraints. But harnessing external knowledge in physical simulations is problematic because knowledge, data, or hunches have errors, noise, and combinatoric uncertainties. Here, we review recent principled methods for imposing restraints to speed up physics-based molecular simulations that promise to scale to larger biomolecules and motions.

Methods for simulation-based analysis of fluid-structure interaction.

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

Barone, Matthew Franklin; Payne, Jeffrey L.

2005-10-01

Methods for analysis of fluid-structure interaction using high fidelity simulations are critically reviewed. First, a literature review of modern numerical techniques for simulation of aeroelastic phenomena is presented. The review focuses on methods contained within the arbitrary Lagrangian-Eulerian (ALE) framework for coupling computational fluid dynamics codes to computational structural mechanics codes. The review treats mesh movement algorithms, the role of the geometric conservation law, time advancement schemes, wetted surface interface strategies, and some representative applications. The complexity and computational expense of coupled Navier-Stokes/structural dynamics simulations points to the need for reduced order modeling to facilitate parametric analysis. The proper orthogonalmore » decomposition (POD)/Galerkin projection approach for building a reduced order model (ROM) is presented, along with ideas for extension of the methodology to allow construction of ROMs based on data generated from ALE simulations.« less

Thermalized Drude Oscillators with the LAMMPS Molecular Dynamics Simulator.

PubMed

Dequidt, Alain; Devémy, Julien; Pádua, Agílio A H

2016-01-25

LAMMPS is a very customizable molecular dynamics simulation software, which can be used to simulate a large diversity of systems. We introduce a new package for simulation of polarizable systems with LAMMPS using thermalized Drude oscillators. The implemented functionalities are described and are illustrated by examples. The implementation was validated by comparing simulation results with published data and using a reference software. Computational performance is also analyzed.

G189A analytical simulation of the RITE Integrated Waste Management-Water System

NASA Technical Reports Server (NTRS)

Coggi, J. V.; Clonts, S. E.

1974-01-01

This paper discusses the computer simulation of the Integrated Waste Management-Water System Using Radioisotopes for Thermal Energy (RITE) and applications of the simulation. Variations in the system temperature and flows due to particular operating conditions and variations in equipment heating loads imposed on the system were investigated with the computer program. The results were assessed from the standpoint of the computed dynamic characteristics of the system and the potential applications of the simulation to system development and vehicle integration.

Real-time simulation of an automotive gas turbine using the hybrid computer

NASA Technical Reports Server (NTRS)

Costakis, W.; Merrill, W. C.

1984-01-01

A hybrid computer simulation of an Advanced Automotive Gas Turbine Powertrain System is reported. The system consists of a gas turbine engine, an automotive drivetrain with four speed automatic transmission, and a control system. Generally, dynamic performance is simulated on the analog portion of the hybrid computer while most of the steady state performance characteristics are calculated to run faster than real time and makes this simulation a useful tool for a variety of analytical studies.

Computer Science Techniques Applied to Parallel Atomistic Simulation

NASA Astrophysics Data System (ADS)

Nakano, Aiichiro

1998-03-01

Recent developments in parallel processing technology and multiresolution numerical algorithms have established large-scale molecular dynamics (MD) simulations as a new research mode for studying materials phenomena such as fracture. However, this requires large system sizes and long simulated times. We have developed: i) Space-time multiresolution schemes; ii) fuzzy-clustering approach to hierarchical dynamics; iii) wavelet-based adaptive curvilinear-coordinate load balancing; iv) multilevel preconditioned conjugate gradient method; and v) spacefilling-curve-based data compression for parallel I/O. Using these techniques, million-atom parallel MD simulations are performed for the oxidation dynamics of nanocrystalline Al. The simulations take into account the effect of dynamic charge transfer between Al and O using the electronegativity equalization scheme. The resulting long-range Coulomb interaction is calculated efficiently with the fast multipole method. Results for temperature and charge distributions, residual stresses, bond lengths and bond angles, and diffusivities of Al and O will be presented. The oxidation of nanocrystalline Al is elucidated through immersive visualization in virtual environments. A unique dual-degree education program at Louisiana State University will also be discussed in which students can obtain a Ph.D. in Physics & Astronomy and a M.S. from the Department of Computer Science in five years. This program fosters interdisciplinary research activities for interfacing High Performance Computing and Communications with large-scale atomistic simulations of advanced materials. This work was supported by NSF (CAREER Program), ARO, PRF, and Louisiana LEQSF.

Man-in-the-control-loop simulation of manipulators

NASA Technical Reports Server (NTRS)

Chang, J. L.; Lin, Tsung-Chieh; Yae, K. Harold

1989-01-01

A method to achieve man-in-the-control-loop simulation is presented. Emerging real-time dynamics simulation suggests a potential for creating an interactive design workstation with a human operator in the control loop. The recursive formulation for multibody dynamics simulation is studied to determine requirements for man-in-the-control-loop simulation. High speed computer graphics techniques provides realistic visual cues for the simulator. Backhoe and robot arm simulations are implemented to demonstrate the capability of man-in-the-control-loop simulation.

Model structure identification for wastewater treatment simulation based on computational fluid dynamics.

PubMed

Alex, J; Kolisch, G; Krause, K

2002-01-01

The objective of this presented project is to use the results of an CFD simulation to automatically, systematically and reliably generate an appropriate model structure for simulation of the biological processes using CSTR activated sludge compartments. Models and dynamic simulation have become important tools for research but also increasingly for the design and optimisation of wastewater treatment plants. Besides the biological models several cases are reported about the application of computational fluid dynamics ICFD) to wastewater treatment plants. One aim of the presented method to derive model structures from CFD results is to exclude the influence of empirical structure selection to the result of dynamic simulations studies of WWTPs. The second application of the approach developed is the analysis of badly performing treatment plants where the suspicion arises that bad flow behaviour such as short cut flows is part of the problem. The method suggested requires as the first step the calculation of fluid dynamics of the biological treatment step at different loading situations by use of 3-dimensional CFD simulation. The result of this information is used to generate a suitable model structure for conventional dynamic simulation of the treatment plant by use of a number of CSTR modules with a pattern of exchange flows between the tanks automatically. The method is explained in detail and the application to the WWTP Wuppertal Buchenhofen is presented.

Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics.

PubMed

Erban, Radek

2016-02-01

Molecular dynamics (MD) simulations of ions (K + , Na + , Ca 2+ and Cl - ) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parametrized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.

MCC level C formulation requirements. Shuttle TAEM guidance and flight control, STS-1 baseline

NASA Technical Reports Server (NTRS)

Carman, G. L.; Montez, M. N.

1980-01-01

The TAEM guidance and body rotational dynamics models required for the MCC simulation of the TAEM mission phase are defined. This simulation begins at the end of the entry phase and terminates at TAEM autoland interface. The logic presented is the required configuration for the first shuttle orbital flight (STS-1). The TAEM guidance is simulated in detail. The rotational dynamics simulation is a simplified model that assumes that the commanded rotational rates can be achieved in the integration interval. Thus, the rotational dynamics simulation is essentially a simulation of the autopilot commanded rates and integration of these rates to determine orbiter attitude. The rotational dynamics simulation also includes a simulation of the speedbrake deflection. The body flap and elevon deflections are computed in the orbiter aerodynamic simulation.

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.

Molecular dynamics simulations of collision-induced absorption: Implementation in LAMMPS

NASA Astrophysics Data System (ADS)

Fakhardji, W.; Gustafsson, M.

2017-02-01

We pursue simulations of collision-induced absorption in a mixture of argon and xenon gas at room temperature by means of classical molecular dynamics. The established theoretical approach (Hartmann et al. 2011 J. Chem. Phys. 134 094316) is implemented with the molecular dynamics package LAMMPS. The bound state features in the absorption spectrum are well reproduced with the molecular dynamics simulation in comparison with a laboratory measurement. The magnitude of the computed absorption, however, is underestimated in a large part of the spectrum. We suggest some aspects of the simulation that could be improved.

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

PubMed

Salis, Howard; Kaznessis, Yiannis

2005-02-01

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

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

NASA Technical Reports Server (NTRS)

Brown, S. C.

1973-01-01

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

Methods for Computationally Efficient Structured CFD Simulations of Complex Turbomachinery Flows

NASA Technical Reports Server (NTRS)

Herrick, Gregory P.; Chen, Jen-Ping

2012-01-01

This research presents more efficient computational methods by which to perform multi-block structured Computational Fluid Dynamics (CFD) simulations of turbomachinery, thus facilitating higher-fidelity solutions of complicated geometries and their associated flows. This computational framework offers flexibility in allocating resources to balance process count and wall-clock computation time, while facilitating research interests of simulating axial compressor stall inception with more complete gridding of the flow passages and rotor tip clearance regions than is typically practiced with structured codes. The paradigm presented herein facilitates CFD simulation of previously impractical geometries and flows. These methods are validated and demonstrate improved computational efficiency when applied to complicated geometries and flows.

A fast recursive algorithm for molecular dynamics simulation

NASA Technical Reports Server (NTRS)

Jain, A.; Vaidehi, N.; Rodriguez, G.

1993-01-01

The present recursive algorithm for solving molecular systems' dynamical equations of motion employs internal variable models that reduce such simulations' computation time by an order of magnitude, relative to Cartesian models. Extensive use is made of spatial operator methods recently developed for analysis and simulation of the dynamics of multibody systems. A factor-of-450 speedup over the conventional O(N-cubed) algorithm is demonstrated for the case of a polypeptide molecule with 400 residues.

Potential application of artificial concepts to aerodynamic simulation

NASA Technical Reports Server (NTRS)

Kutler, P.; Mehta, U. B.; Andrews, A.

1984-01-01

The concept of artificial intelligence as it applies to computational fluid dynamics simulation is investigated. How expert systems can be adapted to speed the numerical aerodynamic simulation process is also examined. A proposed expert grid generation system is briefly described which, given flow parameters, configuration geometry, and simulation constraints, uses knowledge about the discretization process to determine grid point coordinates, computational surface information, and zonal interface parameters.

Parallel Dynamics Simulation Using a Krylov-Schwarz Linear Solution Scheme

DOE PAGES

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

2016-11-07

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

Parallel Dynamics Simulation Using a Krylov-Schwarz Linear Solution Scheme

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

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

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

Gamma Ray Observatory (GRO) dynamics simulator requirements and mathematical specifications, revision 1

NASA Technical Reports Server (NTRS)

Harman, R.; Blejer, D.

1990-01-01

The requirements and mathematical specifications for the Gamma Ray Observatory (GRO) Dynamics Simulator are presented. The complete simulator system, which consists of the profie subsystem, simulation control and input/output subsystem, truth model subsystem, onboard computer model subsystem, and postprocessor, is described. The simulator will be used to evaluate and test the attitude determination and control models to be used on board GRO under conditions that simulate the expected in-flight environment.

Numerical simulation of dynamics of brushless dc motors for aerospace and other applications. Volume 2: User's guide to computer EMA model

NASA Technical Reports Server (NTRS)

Demerdash, N. A. O.; Nehl, T. W.

1979-01-01

A description and user's guide of the computer program developed to simulate the dynamics of an electromechanical actuator for aerospace applications are presented. The effects of the stator phase currents on the permanent magnets of the rotor are examined. The voltage and current waveforms present in the power conditioner network during the motoring, regenerative braking, and plugging modes of operation are presented and discussed.

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.

Use of computational fluid dynamics in respiratory medicine.

PubMed

Fernández Tena, Ana; Casan Clarà, Pere

2015-06-01

Computational Fluid Dynamics (CFD) is a computer-based tool for simulating fluid movement. The main advantages of CFD over other fluid mechanics studies include: substantial savings in time and cost, the analysis of systems or conditions that are very difficult to simulate experimentally (as is the case of the airways), and a practically unlimited level of detail. We used the Ansys-Fluent CFD program to develop a conducting airway model to simulate different inspiratory flow rates and the deposition of inhaled particles of varying diameters, obtaining results consistent with those reported in the literature using other procedures. We hope this approach will enable clinicians to further individualize the treatment of different respiratory diseases. Copyright © 2014 SEPAR. Published by Elsevier Espana. All rights reserved.

Parallel Simulation of Subsonic Fluid Dynamics on a Cluster of Workstations.

DTIC Science & Technology

1994-11-01

inside wind musical instruments. Typical simulations achieve $80\\%$ parallel efficiency (speedup/processors) using 20 HP-Apollo workstations. Detailed...TERMS AI, MIT, Artificial Intelligence, Distributed Computing, Workstation Cluster, Network, Fluid Dynamics, Musical Instruments 17. SECURITY...for example, the flow of air inside wind musical instruments. Typical simulations achieve 80% parallel efficiency (speedup/processors) using 20 HP

Efficient electron open boundaries for simulating electrochemical cells

NASA Astrophysics Data System (ADS)

Zauchner, Mario G.; Horsfield, Andrew P.; Todorov, Tchavdar N.

2018-01-01

Nonequilibrium electrochemistry raises new challenges for atomistic simulation: we need to perform molecular dynamics for the nuclear degrees of freedom with an explicit description of the electrons, which in turn must be free to enter and leave the computational cell. Here we present a limiting form for electron open boundaries that we expect to apply when the magnitude of the electric current is determined by the drift and diffusion of ions in a solution and which is sufficiently computationally efficient to be used with molecular dynamics. We present tight-binding simulations of a parallel-plate capacitor with nothing, a dimer, or an atomic wire situated in the space between the plates. These simulations demonstrate that this scheme can be used to perform molecular dynamics simulations when there is an applied bias between two metal plates with, at most, weak electronic coupling between them. This simple system captures some of the essential features of an electrochemical cell, suggesting this approach might be suitable for simulations of electrochemical cells out of equilibrium.

The very local Hubble flow: Computer simulations of dynamical history

NASA Astrophysics Data System (ADS)

Chernin, A. D.; Karachentsev, I. D.; Valtonen, M. J.; Dolgachev, V. P.; Domozhilova, L. M.; Makarov, D. I.

2004-02-01

The phenomenon of the very local (≤3 Mpc) Hubble flow is studied on the basis of the data of recent precision observations. A set of computer simulations is performed to trace the trajectories of the flow galaxies back in time to the epoch of the formation of the Local Group. It is found that the ``initial conditions'' of the flow are drastically different from the linear velocity-distance relation. The simulations enable one also to recognize the major trends of the flow evolution and identify the dynamical role of universal antigravity produced by the cosmic vacuum.

Reflections from a Computer Simulations Program on Cell Division in Selected Kenyan Secondary Schools

ERIC Educational Resources Information Center

Ndirangu, Mwangi; Kiboss, Joel K.; Wekesa, Eric W.

2005-01-01

The application of computer technology in education is a relatively new approach that is trying to justify inclusion in the Kenyan school curriculum. Being abstract, with a dynamic nature that does not manifest itself visibly, the process of cell division has posed difficulties for teachers. Consequently, a computer simulation program, using…

Realization of planning design of mechanical manufacturing system by Petri net simulation model

NASA Astrophysics Data System (ADS)

Wu, Yanfang; Wan, Xin; Shi, Weixiang

1991-09-01

Planning design is to work out a more overall long-term plan. In order to guarantee a mechanical manufacturing system (MMS) designed to obtain maximum economical benefit, it is necessary to carry out a reasonable planning design for the system. First, some principles on planning design for MMS are introduced. Problems of production scheduling and their decision rules for computer simulation are presented. Realizable method of each production scheduling decision rule in Petri net model is discussed. Second, the solution of conflict rules for conflict problems during running Petri net is given. Third, based on the Petri net model of MMS which includes part flow and tool flow, according to the principle of minimum event time advance, a computer dynamic simulation of the Petri net model, that is, a computer dynamic simulation of MMS, is realized. Finally, the simulation program is applied to a simulation exmple, so the scheme of a planning design for MMS can be evaluated effectively.

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.

A high performance computing framework for physics-based modeling and simulation of military ground vehicles

NASA Astrophysics Data System (ADS)

Negrut, Dan; Lamb, David; Gorsich, David

2011-06-01

This paper describes a software infrastructure made up of tools and libraries designed to assist developers in implementing computational dynamics applications running on heterogeneous and distributed computing environments. Together, these tools and libraries compose a so called Heterogeneous Computing Template (HCT). The heterogeneous and distributed computing hardware infrastructure is assumed herein to be made up of a combination of CPUs and Graphics Processing Units (GPUs). The computational dynamics applications targeted to execute on such a hardware topology include many-body dynamics, smoothed-particle hydrodynamics (SPH) fluid simulation, and fluid-solid interaction analysis. The underlying theme of the solution approach embraced by HCT is that of partitioning the domain of interest into a number of subdomains that are each managed by a separate core/accelerator (CPU/GPU) pair. Five components at the core of HCT enable the envisioned distributed computing approach to large-scale dynamical system simulation: (a) the ability to partition the problem according to the one-to-one mapping; i.e., spatial subdivision, discussed above (pre-processing); (b) a protocol for passing data between any two co-processors; (c) algorithms for element proximity computation; and (d) the ability to carry out post-processing in a distributed fashion. In this contribution the components (a) and (b) of the HCT are demonstrated via the example of the Discrete Element Method (DEM) for rigid body dynamics with friction and contact. The collision detection task required in frictional-contact dynamics (task (c) above), is shown to benefit on the GPU of a two order of magnitude gain in efficiency when compared to traditional sequential implementations. Note: Reference herein to any specific commercial products, process, or service by trade name, trademark, manufacturer, or otherwise, does not imply its endorsement, recommendation, or favoring by the United States Army. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Army, and shall not be used for advertising or product endorsement purposes.

Efficient mapping algorithms for scheduling robot inverse dynamics computation on a multiprocessor system

NASA Technical Reports Server (NTRS)

Lee, C. S. G.; Chen, C. L.

1989-01-01

Two efficient mapping algorithms for scheduling the robot inverse dynamics computation consisting of m computational modules with precedence relationship to be executed on a multiprocessor system consisting of p identical homogeneous processors with processor and communication costs to achieve minimum computation time are presented. An objective function is defined in terms of the sum of the processor finishing time and the interprocessor communication time. The minimax optimization is performed on the objective function to obtain the best mapping. This mapping problem can be formulated as a combination of the graph partitioning and the scheduling problems; both have been known to be NP-complete. Thus, to speed up the searching for a solution, two heuristic algorithms were proposed to obtain fast but suboptimal mapping solutions. The first algorithm utilizes the level and the communication intensity of the task modules to construct an ordered priority list of ready modules and the module assignment is performed by a weighted bipartite matching algorithm. For a near-optimal mapping solution, the problem can be solved by the heuristic algorithm with simulated annealing. These proposed optimization algorithms can solve various large-scale problems within a reasonable time. Computer simulations were performed to evaluate and verify the performance and the validity of the proposed mapping algorithms. Finally, experiments for computing the inverse dynamics of a six-jointed PUMA-like manipulator based on the Newton-Euler dynamic equations were implemented on an NCUBE/ten hypercube computer to verify the proposed mapping algorithms. Computer simulation and experimental results are compared and discussed.

ADDRESSING HUMAN EXPOSURE TO AIR POLLUTANTS AROUND BUILDINGS IN URBAN AREAS WITH COMPUTATIONAL FLUID DYNAMICS (CFD) MODELS

EPA Science Inventory

Computational Fluid Dynamics (CFD) simulations provide a number of unique opportunities for expanding and improving capabilities for modeling exposures to environmental pollutants. The US Environmental Protection Agency's National Exposure Research Laboratory (NERL) has been c...

Understanding Emergency Care Delivery Through Computer Simulation Modeling.

PubMed

Laker, Lauren F; Torabi, Elham; France, Daniel J; Froehle, Craig M; Goldlust, Eric J; Hoot, Nathan R; Kasaie, Parastu; Lyons, Michael S; Barg-Walkow, Laura H; Ward, Michael J; Wears, Robert L

2018-02-01

In 2017, Academic Emergency Medicine convened a consensus conference entitled, "Catalyzing System Change through Health Care Simulation: Systems, Competency, and Outcomes." This article, a product of the breakout session on "understanding complex interactions through systems modeling," explores the role that computer simulation modeling can and should play in research and development of emergency care delivery systems. This article discusses areas central to the use of computer simulation modeling in emergency care research. The four central approaches to computer simulation modeling are described (Monte Carlo simulation, system dynamics modeling, discrete-event simulation, and agent-based simulation), along with problems amenable to their use and relevant examples to emergency care. Also discussed is an introduction to available software modeling platforms and how to explore their use for research, along with a research agenda for computer simulation modeling. Through this article, our goal is to enhance adoption of computer simulation, a set of methods that hold great promise in addressing emergency care organization and design challenges. © 2017 by the Society for Academic Emergency Medicine.

Transistor analogs of emergent iono-neuronal dynamics.

PubMed

Rachmuth, Guy; Poon, Chi-Sang

2008-06-01

Neuromorphic analog metal-oxide-silicon (MOS) transistor circuits promise compact, low-power, and high-speed emulations of iono-neuronal dynamics orders-of-magnitude faster than digital simulation. However, their inherently limited input voltage dynamic range vs power consumption and silicon die area tradeoffs makes them highly sensitive to transistor mismatch due to fabrication inaccuracy, device noise, and other nonidealities. This limitation precludes robust analog very-large-scale-integration (aVLSI) circuits implementation of emergent iono-neuronal dynamics computations beyond simple spiking with limited ion channel dynamics. Here we present versatile neuromorphic analog building-block circuits that afford near-maximum voltage dynamic range operating within the low-power MOS transistor weak-inversion regime which is ideal for aVLSI implementation or implantable biomimetic device applications. The fabricated microchip allowed robust realization of dynamic iono-neuronal computations such as coincidence detection of presynaptic spikes or pre- and postsynaptic activities. As a critical performance benchmark, the high-speed and highly interactive iono-neuronal simulation capability on-chip enabled our prompt discovery of a minimal model of chaotic pacemaker bursting, an emergent iono-neuronal behavior of fundamental biological significance which has hitherto defied experimental testing or computational exploration via conventional digital or analog simulations. These compact and power-efficient transistor analogs of emergent iono-neuronal dynamics open new avenues for next-generation neuromorphic, neuroprosthetic, and brain-machine interface applications.

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids.

PubMed

Aradi, Bálint; Niklasson, Anders M N; Frauenheim, Thomas

2015-07-14

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. For systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can be applied to a broad range of problems in materials science, chemistry, and biology.

Simulation of Power Collection Dynamics for Simply Supported Power Rail

DOT National Transportation Integrated Search

1972-11-01

The mathematical model of a sprung mass moving along a simply supported beam is used to analyze the dynamics of a power-collection system. A computer simulation of one-dimensional motion is used to demonstrate the phenomenon of collector-power rail i...

Flexible rotor dynamics analysis

NASA Technical Reports Server (NTRS)

Shen, F. A.

1973-01-01

A digital computer program was developed to analyze the general nonaxisymmetric and nonsynchronous transient and steady-state rotor dynamic performance of a bending- and shear-wise flexible rotor-bearing system under various operating conditions. The effects of rotor material mechanical hysteresis, rotor torsion flexibility, transverse effects of rotor axial and torsional loading and the anisotropic, in-phase and out-of-phase bearing stiffness and damping force and moment coefficients were included in the program to broaden its capability. An optimum solution method was found and incorporated in the computer program. Computer simulation of experimental data was made and qualitative agreements observed. The mathematical formulations, computer program verification, test data simulation, and user instruction was presented and discussed.

Closed-Loop HIRF Experiments Performed on a Fault Tolerant Flight Control Computer

NASA Technical Reports Server (NTRS)

Belcastro, Celeste M.

1997-01-01

ABSTRACT Closed-loop HIRF experiments were performed on a fault tolerant flight control computer (FCC) at the NASA Langley Research Center. The FCC used in the experiments was a quad-redundant flight control computer executing B737 Autoland control laws. The FCC was placed in one of the mode-stirred reverberation chambers in the HIRF Laboratory and interfaced to a computer simulation of the B737 flight dynamics, engines, sensors, actuators, and atmosphere in the Closed-Loop Systems Laboratory. Disturbances to the aircraft associated with wind gusts and turbulence were simulated during tests. Electrical isolation between the FCC under test and the simulation computer was achieved via a fiber optic interface for the analog and discrete signals. Closed-loop operation of the FCC enabled flight dynamics and atmospheric disturbances affecting the aircraft to be represented during tests. Upset was induced in the FCC as a result of exposure to HIRF, and the effect of upset on the simulated flight of the aircraft was observed and recorded. This paper presents a description of these closed- loop HIRF experiments, upset data obtained from the FCC during these experiments, and closed-loop effects on the simulated flight of the aircraft.

Quantum Spin Glasses, Annealing and Computation

NASA Astrophysics Data System (ADS)

Chakrabarti, Bikas K.; Inoue, Jun-ichi; Tamura, Ryo; Tanaka, Shu

2017-05-01

List of tables; List of figures, Preface; 1. Introduction; Part I. Quantum Spin Glass, Annealing and Computation: 2. Classical spin models from ferromagnetic spin systems to spin glasses; 3. Simulated annealing; 4. Quantum spin glass; 5. Quantum dynamics; 6. Quantum annealing; Part II. Additional Notes: 7. Notes on adiabatic quantum computers; 8. Quantum information and quenching dynamics; 9. A brief historical note on the studies of quantum glass, annealing and computation.

Dynamics of Numerics & Spurious Behaviors in CFD Computations. Revised

NASA Technical Reports Server (NTRS)

Yee, Helen C.; Sweby, Peter K.

1997-01-01

The global nonlinear behavior of finite discretizations for constant time steps and fixed or adaptive grid spacings is studied using tools from dynamical systems theory. Detailed analysis of commonly used temporal and spatial discretizations for simple model problems is presented. The role of dynamics in the understanding of long time behavior of numerical integration and the nonlinear stability, convergence, and reliability of using time-marching approaches for obtaining steady-state numerical solutions in computational fluid dynamics (CFD) is explored. The study is complemented with examples of spurious behavior observed in steady and unsteady CFD computations. The CFD examples were chosen to illustrate non-apparent spurious behavior that was difficult to detect without extensive grid and temporal refinement studies and some knowledge from dynamical systems theory. Studies revealed the various possible dangers of misinterpreting numerical simulation of realistic complex flows that are constrained by available computing power. In large scale computations where the physics of the problem under study is not well understood and numerical simulations are the only viable means of solution, extreme care must be taken in both computation and interpretation of the numerical data. The goal of this paper is to explore the important role that dynamical systems theory can play in the understanding of the global nonlinear behavior of numerical algorithms and to aid the identification of the sources of numerical uncertainties in CFD.

Workflow Management Systems for Molecular Dynamics on Leadership Computers

NASA Astrophysics Data System (ADS)

Wells, Jack; Panitkin, Sergey; Oleynik, Danila; Jha, Shantenu

Molecular Dynamics (MD) simulations play an important role in a range of disciplines from Material Science to Biophysical systems and account for a large fraction of cycles consumed on computing resources. Increasingly science problems require the successful execution of ''many'' MD simulations as opposed to a single MD simulation. There is a need to provide scalable and flexible approaches to the execution of the workload. We present preliminary results on the Titan computer at the Oak Ridge Leadership Computing Facility that demonstrate a general capability to manage workload execution agnostic of a specific MD simulation kernel or execution pattern, and in a manner that integrates disparate grid-based and supercomputing resources. Our results build upon our extensive experience of distributed workload management in the high-energy physics ATLAS project using PanDA (Production and Distributed Analysis System), coupled with recent conceptual advances in our understanding of workload management on heterogeneous resources. We will discuss how we will generalize these initial capabilities towards a more production level service on DOE leadership resources. This research is sponsored by US DOE/ASCR and used resources of the OLCF computing facility.

On the origin of the electrostatic potential difference at a liquid-vacuum interface.

PubMed

Harder, Edward; Roux, Benoît

2008-12-21

The microscopic origin of the interface potential calculated from computer simulations is elucidated by considering a simple model of molecules near an interface. The model posits that molecules are isotropically oriented and their charge density is Gaussian distributed. Molecules that have a charge density that is more negative toward their interior tend to give rise to a negative interface potential relative to the gaseous phase, while charge densities more positive toward their interior give rise to a positive interface potential. The interface potential for the model is compared to the interface potential computed from molecular dynamics simulations of the nonpolar vacuum-methane system and the polar vacuum-water interface system. The computed vacuum-methane interface potential from a molecular dynamics simulation (-220 mV) is captured with quantitative precision by the model. For the vacuum-water interface system, the model predicts a potential of -400 mV compared to -510 mV, calculated from a molecular dynamics simulation. The physical implications of this isotropic contribution to the interface potential is examined using the example of ion solvation in liquid methane.

Long range Debye-Hückel correction for computation of grid-based electrostatic forces between biomacromolecules

PubMed Central

2014-01-01

Background Brownian dynamics (BD) simulations can be used to study very large molecular systems, such as models of the intracellular environment, using atomic-detail structures. Such simulations require strategies to contain the computational costs, especially for the computation of interaction forces and energies. A common approach is to compute interaction forces between macromolecules by precomputing their interaction potentials on three-dimensional discretized grids. For long-range interactions, such as electrostatics, grid-based methods are subject to finite size errors. We describe here the implementation of a Debye-Hückel correction to the grid-based electrostatic potential used in the SDA BD simulation software that was applied to simulate solutions of bovine serum albumin and of hen egg white lysozyme. Results We found that the inclusion of the long-range electrostatic correction increased the accuracy of both the protein-protein interaction profiles and the protein diffusion coefficients at low ionic strength. Conclusions An advantage of this method is the low additional computational cost required to treat long-range electrostatic interactions in large biomacromolecular systems. Moreover, the implementation described here for BD simulations of protein solutions can also be applied in implicit solvent molecular dynamics simulations that make use of gridded interaction potentials. PMID:25045516

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

NASA Astrophysics Data System (ADS)

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

2003-12-01

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

Computing Optimal Stochastic Portfolio Execution Strategies: A Parametric Approach Using Simulations

NASA Astrophysics Data System (ADS)

Moazeni, Somayeh; Coleman, Thomas F.; Li, Yuying

2010-09-01

Computing optimal stochastic portfolio execution strategies under appropriate risk consideration presents great computational challenge. We investigate a parametric approach for computing optimal stochastic strategies using Monte Carlo simulations. This approach allows reduction in computational complexity by computing coefficients for a parametric representation of a stochastic dynamic strategy based on static optimization. Using this technique, constraints can be similarly handled using appropriate penalty functions. We illustrate the proposed approach to minimize the expected execution cost and Conditional Value-at-Risk (CVaR).

Computational fluid dynamics applications to improve crop production systems

USDA-ARS?s Scientific Manuscript database

Computational fluid dynamics (CFD), numerical analysis and simulation tools of fluid flow processes have emerged from the development stage and become nowadays a robust design tool. It is widely used to study various transport phenomena which involve fluid flow, heat and mass transfer, providing det...

Potential applications of computational fluid dynamics to biofluid analysis

NASA Technical Reports Server (NTRS)

Kwak, D.; Chang, J. L. C.; Rogers, S. E.; Rosenfeld, M.; Kwak, D.

1988-01-01

Computational fluid dynamics was developed to the stage where it has become an indispensable part of aerospace research and design. In view of advances made in aerospace applications, the computational approach can be used for biofluid mechanics research. Several flow simulation methods developed for aerospace problems are briefly discussed for potential applications to biofluids, especially to blood flow analysis.

Computer Simulation of the Elastic Properties of Titanium Alloys for Medical Applications

NASA Astrophysics Data System (ADS)

Estevez, Elsa Paz; Burganova, R. M.; Lysogorskii, Yu. V.

2016-09-01

Results of a computer simulation of the elastic properties of α+β- and β-titanium alloys, used for medical purposes, within the framework of the molecular-dynamics method are presented. It is shown that β-titanium alloys are best suited for the use as bone implants because of their small moduli of elasticity. The advisability of the use of the molecular-dynamics method for the study of the elastic properties of titanium alloys, serving as bone implants, is demonstrated.

ISCFD Nagoya 1989 - International Symposium on Computational Fluid Dynamics, 3rd, Nagoya, Japan, Aug. 28-31, 1989, Technical Papers

NASA Astrophysics Data System (ADS)

Recent advances in computational fluid dynamics are discussed in reviews and reports. Topics addressed include large-scale LESs for turbulent pipe and channel flows, numerical solutions of the Euler and Navier-Stokes equations on parallel computers, multigrid methods for steady high-Reynolds-number flow past sudden expansions, finite-volume methods on unstructured grids, supersonic wake flow on a blunt body, a grid-characteristic method for multidimensional gas dynamics, and CIC numerical simulation of a wave boundary layer. Consideration is given to vortex simulations of confined two-dimensional jets, supersonic viscous shear layers, spectral methods for compressible flows, shock-wave refraction at air/water interfaces, oscillatory flow in a two-dimensional collapsible channel, the growth of randomness in a spatially developing wake, and an efficient simplex algorithm for the finite-difference and dynamic linear-programming method in optimal potential control.

The use of computer graphic simulation in the development of on-orbit tele-robotic systems

NASA Technical Reports Server (NTRS)

Fernandez, Ken; Hinman, Elaine

1987-01-01

This paper describes the use of computer graphic simulation techniques to resolve critical design and operational issues for robotic systems used for on-orbit operations. These issues are robot motion control, robot path-planning/verification, and robot dynamics. The major design issues in developing effective telerobotic systems are discussed, and the use of ROBOSIM, a NASA-developed computer graphic simulation tool, to address these issues is presented. Simulation plans for the Space Station and the Orbital Maneuvering Vehicle are presented and discussed.

Effect of Turbulence Modeling on an Excited Jet

NASA Technical Reports Server (NTRS)

Brown, Clifford A.; Hixon, Ray

2010-01-01

The flow dynamics in a high-speed jet are dominated by unsteady turbulent flow structures in the plume. Jet excitation seeks to control these flow structures through the natural instabilities present in the initial shear layer of the jet. Understanding and optimizing the excitation input, for jet noise reduction or plume mixing enhancement, requires many trials that may be done experimentally or computationally at a significant cost savings. Numerical simulations, which model various parts of the unsteady dynamics to reduce the computational expense of the simulation, must adequately capture the unsteady flow dynamics in the excited jet for the results are to be used. Four CFD methods are considered for use in an excited jet problem, including two turbulence models with an Unsteady Reynolds Averaged Navier-Stokes (URANS) solver, one Large Eddy Simulation (LES) solver, and one URANS/LES hybrid method. Each method is used to simulate a simplified excited jet and the results are evaluated based on the flow data, computation time, and numerical stability. The knowledge gained about the effect of turbulence modeling and CFD methods from these basic simulations will guide and assist future three-dimensional (3-D) simulations that will be used to understand and optimize a realistic excited jet for a particular application.

Ensemble Sampling vs. Time Sampling in Molecular Dynamics Simulations of Thermal Conductivity

DOE PAGES

Gordiz, Kiarash; Singh, David J.; Henry, Asegun

2015-01-29

In this report we compare time sampling and ensemble averaging as two different methods available for phase space sampling. For the comparison, we calculate thermal conductivities of solid argon and silicon structures, using equilibrium molecular dynamics. We introduce two different schemes for the ensemble averaging approach, and show that both can reduce the total simulation time as compared to time averaging. It is also found that velocity rescaling is an efficient mechanism for phase space exploration. Although our methodology is tested using classical molecular dynamics, the ensemble generation approaches may find their greatest utility in computationally expensive simulations such asmore » first principles molecular dynamics. For such simulations, where each time step is costly, time sampling can require long simulation times because each time step must be evaluated sequentially and therefore phase space averaging is achieved through sequential operations. On the other hand, with ensemble averaging, phase space sampling can be achieved through parallel operations, since each ensemble is independent. For this reason, particularly when using massively parallel architectures, ensemble sampling can result in much shorter simulation times and exhibits similar overall computational effort.« less

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

PubMed

Kurczynska, Monika; Kotulska, Malgorzata

2014-01-01

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

Computational Fluid Dynamics Simulation of Transport and Retention of Nanoparticle in Saturated Sand Filters

EPA Science Inventory

Experimental and computational investigation of the transport parameters of nano particles flowing through porous media has been made. The objective of this work was to develop a simulation capability applicable to the transport and retention of nanoparticles (NPs) in saturated p...

STREAM TEMPERATURE SIMULATION OF FORESTED RIPARIAN AREAS: I. WATERSHED-SCALE MODEL DEVELOPMENT

EPA Science Inventory

To simulate stream temperatures on a watershed scale, shading dynamics of topography and riparian vegetation must be computed for estimating the amount of solar radiation that is actually absorbed by water for each stream reach. A series of computational procedures identifying th...

Simulation of spacecraft attitude dynamics using TREETOPS and model-specific computer Codes

NASA Technical Reports Server (NTRS)

Cochran, John E.; No, T. S.; Fitz-Coy, Norman G.

1989-01-01

The simulation of spacecraft attitude dynamics and control using the generic, multi-body code called TREETOPS and other codes written especially to simulate particular systems is discussed. Differences in the methods used to derive equations of motion--Kane's method for TREETOPS and the Lagrangian and Newton-Euler methods, respectively, for the other two codes--are considered. Simulation results from the TREETOPS code are compared with those from the other two codes for two example systems. One system is a chain of rigid bodies; the other consists of two rigid bodies attached to a flexible base body. Since the computer codes were developed independently, consistent results serve as a verification of the correctness of all the programs. Differences in the results are discussed. Results for the two-rigid-body, one-flexible-body system are useful also as information on multi-body, flexible, pointing payload dynamics.

High temperature phonon dispersion in graphene using classical molecular dynamics

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

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

2014-04-24

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

Heave-pitch-roll analysis and testing of air cushion landing systems

NASA Technical Reports Server (NTRS)

Boghani, A. B.; Captain, K. M.; Wormley, D. N.

1978-01-01

The analytical tools (analysis and computer simulation) needed to explain and predict the dynamic operation of air cushion landing systems (ACLS) is described. The following tasks were performed: the development of improved analytical models for the fan and the trunk; formulation of a heave pitch roll analysis for the complete ACLS; development of a general purpose computer simulation to evaluate landing and taxi performance of an ACLS equipped aircraft; and the verification and refinement of the analysis by comparison with test data obtained through lab testing of a prototype cushion. Demonstration of simulation capabilities through typical landing and taxi simulation of an ACLS aircraft are given. Initial results show that fan dynamics have a major effect on system performance. Comparison with lab test data (zero forward speed) indicates that the analysis can predict most of the key static and dynamic parameters (pressure, deflection, acceleration, etc.) within a margin of a 10 to 25 percent.

Fluid-Structure Interaction in Composite Structures

DTIC Science & Technology

2014-03-01

polymer composite structures. Some previous experimental observations were confirmed using the results from the computer simulations , which also...computer simulations , which also enhanced understanding the effect of FSI on dynamic responses of composite structures. vi THIS PAGE INTENTIONALLY...forces) are applied. A great amount of research has been made using the FEM to study and simulate the cases when the structures are surrounded by

Incremental update of electrostatic interactions in adaptively restrained particle simulations.

PubMed

Edorh, Semeho Prince A; Redon, Stéphane

2018-04-06

The computation of long-range potentials is one of the demanding tasks in Molecular Dynamics. During the last decades, an inventive panoply of methods was developed to reduce the CPU time of this task. In this work, we propose a fast method dedicated to the computation of the electrostatic potential in adaptively restrained systems. We exploit the fact that, in such systems, only some particles are allowed to move at each timestep. We developed an incremental algorithm derived from a multigrid-based alternative to traditional Fourier-based methods. Our algorithm was implemented inside LAMMPS, a popular molecular dynamics simulation package. We evaluated the method on different systems. We showed that the new algorithm's computational complexity scales with the number of active particles in the simulated system, and is able to outperform the well-established Particle Particle Particle Mesh (P3M) for adaptively restrained simulations. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Tensor-Train Split-Operator Fourier Transform (TT-SOFT) Method: Multidimensional Nonadiabatic Quantum Dynamics.

PubMed

Greene, Samuel M; Batista, Victor S

2017-09-12

We introduce the "tensor-train split-operator Fourier transform" (TT-SOFT) method for simulations of multidimensional nonadiabatic quantum dynamics. TT-SOFT is essentially the grid-based SOFT method implemented in dynamically adaptive tensor-train representations. In the same spirit of all matrix product states, the tensor-train format enables the representation, propagation, and computation of observables of multidimensional wave functions in terms of the grid-based wavepacket tensor components, bypassing the need of actually computing the wave function in its full-rank tensor product grid space. We demonstrate the accuracy and efficiency of the TT-SOFT method as applied to propagation of 24-dimensional wave packets, describing the S 1 /S 2 interconversion dynamics of pyrazine after UV photoexcitation to the S 2 state. Our results show that the TT-SOFT method is a powerful computational approach for simulations of quantum dynamics of polyatomic systems since it avoids the exponential scaling problem of full-rank grid-based representations.

Real-time physics-based 3D biped character animation using an inverted pendulum model.

PubMed

Tsai, Yao-Yang; Lin, Wen-Chieh; Cheng, Kuangyou B; Lee, Jehee; Lee, Tong-Yee

2010-01-01

We present a physics-based approach to generate 3D biped character animation that can react to dynamical environments in real time. Our approach utilizes an inverted pendulum model to online adjust the desired motion trajectory from the input motion capture data. This online adjustment produces a physically plausible motion trajectory adapted to dynamic environments, which is then used as the desired motion for the motion controllers to track in dynamics simulation. Rather than using Proportional-Derivative controllers whose parameters usually cannot be easily set, our motion tracking adopts a velocity-driven method which computes joint torques based on the desired joint angular velocities. Physically correct full-body motion of the 3D character is computed in dynamics simulation using the computed torques and dynamical model of the character. Our experiments demonstrate that tracking motion capture data with real-time response animation can be achieved easily. In addition, physically plausible motion style editing, automatic motion transition, and motion adaptation to different limb sizes can also be generated without difficulty.

Temperature for a dynamic spin ensemble

NASA Astrophysics Data System (ADS)

Ma, Pui-Wai; Dudarev, S. L.; Semenov, A. A.; Woo, C. H.

2010-09-01

In molecular dynamics simulations, temperature is evaluated, via the equipartition principle, by computing the mean kinetic energy of atoms. There is no similar recipe yet for evaluating temperature of a dynamic system of interacting spins. By solving semiclassical Langevin spin-dynamics equations, and applying the fluctuation-dissipation theorem, we derive an equation for the temperature of a spin ensemble, expressed in terms of dynamic spin variables. The fact that definitions for the kinetic and spin temperatures are fully consistent is illustrated using large-scale spin dynamics and spin-lattice dynamics simulations.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

A dynamical-systems approach for computing ice-affected streamflow

USGS Publications Warehouse

Holtschlag, David J.

1996-01-01

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

DYGABCD: A program for calculating linear A, B, C, and D matrices from a nonlinear dynamic engine simulation

NASA Technical Reports Server (NTRS)

Geyser, L. C.

1978-01-01

A digital computer program, DYGABCD, was developed that generates linearized, dynamic models of simulated turbofan and turbojet engines. DYGABCD is based on an earlier computer program, DYNGEN, that is capable of calculating simulated nonlinear steady-state and transient performance of one- and two-spool turbojet engines or two- and three-spool turbofan engines. Most control design techniques require linear system descriptions. For multiple-input/multiple-output systems such as turbine engines, state space matrix descriptions of the system are often desirable. DYGABCD computes the state space matrices commonly referred to as the A, B, C, and D matrices required for a linear system description. The report discusses the analytical approach and provides a users manual, FORTRAN listings, and a sample case.

Research Summary 3-D Computational Fluid Dynamics (CFD) Model Of The Human Respiratory System

EPA Science Inventory

The U.S. EPA’s Office of Research and Development (ORD) has developed a 3-D computational fluid dynamics (CFD) model of the human respiratory system that allows for the simulation of particulate based contaminant deposition and clearance, while being adaptable for age, ethnicity,...

Atomistic Computer Simulations of Water Interactions and Dissolution of Inorganic Glasses

DOE PAGES

Du, Jincheng; Rimsza, Jessica

2017-09-01

Computational simulations at the atomistic level play an increasing important role in understanding the structures, behaviors, and the structure-property relationships of glass and amorphous materials. In this paper, we reviewed atomistic simulation methods ranging from first principles calculations and ab initio molecular dynamics (AIMD), to classical molecular dynamics (MD) and meso-scale kinetic Monte Carlo (KMC) simulations and their applications to glass-water interactions and glass dissolutions. Particularly, the use of these simulation methods in understanding the reaction mechanisms of water with oxide glasses, water-glass interfaces, hydrated porous silica gels formation, the structure and properties of multicomponent glasses, and microstructure evolution aremore » reviewed. Here, the advantages and disadvantageous of these methods are discussed and the current challenges and future direction of atomistic simulations in glass dissolution are presented.« less

3D Reconstruction of Chick Embryo Vascular Geometries Using Non-invasive High-Frequency Ultrasound for Computational Fluid Dynamics Studies.

PubMed

Tan, Germaine Xin Yi; Jamil, Muhammad; Tee, Nicole Gui Zhen; Zhong, Liang; Yap, Choon Hwai

2015-11-01

Recent animal studies have provided evidence that prenatal blood flow fluid mechanics may play a role in the pathogenesis of congenital cardiovascular malformations. To further these researches, it is important to have an imaging technique for small animal embryos with sufficient resolution to support computational fluid dynamics studies, and that is also non-invasive and non-destructive to allow for subject-specific, longitudinal studies. In the current study, we developed such a technique, based on ultrasound biomicroscopy scans on chick embryos. Our technique included a motion cancelation algorithm to negate embryonic body motion, a temporal averaging algorithm to differentiate blood spaces from tissue spaces, and 3D reconstruction of blood volumes in the embryo. The accuracy of the reconstructed models was validated with direct stereoscopic measurements. A computational fluid dynamics simulation was performed to model fluid flow in the generated construct of a Hamburger-Hamilton (HH) stage 27 embryo. Simulation results showed that there were divergent streamlines and a low shear region at the carotid duct, which may be linked to the carotid duct's eventual regression and disappearance by HH stage 34. We show that our technique has sufficient resolution to produce accurate geometries for computational fluid dynamics simulations to quantify embryonic cardiovascular fluid mechanics.

Investigation on the forced response of a radial turbine under aerodynamic excitations

NASA Astrophysics Data System (ADS)

Ma, Chaochen; Huang, Zhi; Qi, Mingxu

2016-04-01

Rotor blades in a radial turbine with nozzle guide vanes typically experience harmonic aerodynamic excitations due to the rotor stator interaction. Dynamic stresses induced by the harmonic excitations can result in high cycle fatigue (HCF) of the blades. A reliable prediction method for forced response issue is essential to avoid the HCF problem. In this work, the forced response mechanisms were investigated based on a fluid structure interaction (FSI) method. Aerodynamic excitations were obtained by three-dimensional unsteady computational fluid dynamics (CFD) simulation with phase shifted periodic boundary conditions. The first two harmonic pressures were determined as the primary components of the excitation and applied to finite element (FE) model to conduct the computational structural dynamics (CSD) simulation. The computed results from the harmonic forced response analysis show good agreement with the predictions of Singh's advanced frequency evaluation (SAFE) diagram. Moreover, the mode superposition method used in FE simulation offers an efficient way to provide quantitative assessments of mode response levels and resonant strength.

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.

Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations

PubMed Central

Fogolari, Federico; Corazza, Alessandra; Fortuna, Sara; Soler, Miguel Angel; VanSchouwen, Bryan; Brancolini, Giorgia; Corni, Stefano; Melacini, Giuseppe; Esposito, Gennaro

2015-01-01

Estimation of configurational entropy from molecular dynamics trajectories is a difficult task which is often performed using quasi-harmonic or histogram analysis. An entirely different approach, proposed recently, estimates local density distribution around each conformational sample by measuring the distance from its nearest neighbors. In this work we show this theoretically well grounded the method can be easily applied to estimate the entropy from conformational sampling. We consider a set of systems that are representative of important biomolecular processes. In particular: reference entropies for amino acids in unfolded proteins are obtained from a database of residues not participating in secondary structure elements;the conformational entropy of folding of β2-microglobulin is computed from molecular dynamics simulations using reference entropies for the unfolded state;backbone conformational entropy is computed from molecular dynamics simulations of four different states of the EPAC protein and compared with order parameters (often used as a measure of entropy);the conformational and rototranslational entropy of binding is computed from simulations of 20 tripeptides bound to the peptide binding protein OppA and of β2-microglobulin bound to a citrate coated gold surface. This work shows the potential of the method in the most representative biological processes involving proteins, and provides a valuable alternative, principally in the shown cases, where other approaches are problematic. PMID:26177039

Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations.

PubMed

Fogolari, Federico; Corazza, Alessandra; Fortuna, Sara; Soler, Miguel Angel; VanSchouwen, Bryan; Brancolini, Giorgia; Corni, Stefano; Melacini, Giuseppe; Esposito, Gennaro

2015-01-01

Estimation of configurational entropy from molecular dynamics trajectories is a difficult task which is often performed using quasi-harmonic or histogram analysis. An entirely different approach, proposed recently, estimates local density distribution around each conformational sample by measuring the distance from its nearest neighbors. In this work we show this theoretically well grounded the method can be easily applied to estimate the entropy from conformational sampling. We consider a set of systems that are representative of important biomolecular processes. In particular: reference entropies for amino acids in unfolded proteins are obtained from a database of residues not participating in secondary structure elements;the conformational entropy of folding of β2-microglobulin is computed from molecular dynamics simulations using reference entropies for the unfolded state;backbone conformational entropy is computed from molecular dynamics simulations of four different states of the EPAC protein and compared with order parameters (often used as a measure of entropy);the conformational and rototranslational entropy of binding is computed from simulations of 20 tripeptides bound to the peptide binding protein OppA and of β2-microglobulin bound to a citrate coated gold surface. This work shows the potential of the method in the most representative biological processes involving proteins, and provides a valuable alternative, principally in the shown cases, where other approaches are problematic.

Computational Investigation of Fluidic Counterflow Thrust Vectoring

NASA Technical Reports Server (NTRS)

Hunter, Craig A.; Deere, Karen A.

1999-01-01

A computational study of fluidic counterflow thrust vectoring has been conducted. Two-dimensional numerical simulations were run using the computational fluid dynamics code PAB3D with two-equation turbulence closure and linear Reynolds stress modeling. For validation, computational results were compared to experimental data obtained at the NASA Langley Jet Exit Test Facility. In general, computational results were in good agreement with experimental performance data, indicating that efficient thrust vectoring can be obtained with low secondary flow requirements (less than 1% of the primary flow). An examination of the computational flowfield has revealed new details about the generation of a countercurrent shear layer, its relation to secondary suction, and its role in thrust vectoring. In addition to providing new information about the physics of counterflow thrust vectoring, this work appears to be the first documented attempt to simulate the counterflow thrust vectoring problem using computational fluid dynamics.

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.

On-Track Testing as a Validation Method of Computational Fluid Dynamic Simulations of a Formula SAE Vehicle

NASA Astrophysics Data System (ADS)

Weingart, Robert

This thesis is about the validation of a computational fluid dynamics simulation of a ground vehicle by means of a low-budget coast-down test. The vehicle is built to the standards of the 2014 Formula SAE rules. It is equipped with large wings in the front and rear of the car; the vertical loads on the tires are measured by specifically calibrated shock potentiometers. The coast-down test was performed on a runway of a local airport and is used to determine vehicle specific coefficients such as drag, downforce, aerodynamic balance, and rolling resistance for different aerodynamic setups. The test results are then compared to the respective simulated results. The drag deviates about 5% from the simulated to the measured results. The downforce numbers show a deviation up to 18% respectively. Moreover, a sensitivity analysis of inlet velocities, ride heights, and pitch angles was performed with the help of the computational simulation.

A versatile model for soft patchy particles with various patch arrangements.

PubMed

Li, Zhan-Wei; Zhu, You-Liang; Lu, Zhong-Yuan; Sun, Zhao-Yan

2016-01-21

We propose a simple and general mesoscale soft patchy particle model, which can felicitously describe the deformable and surface-anisotropic characteristics of soft patchy particles. This model can be used in dynamics simulations to investigate the aggregation behavior and mechanism of various types of soft patchy particles with tunable number, size, direction, and geometrical arrangement of the patches. To improve the computational efficiency of this mesoscale model in dynamics simulations, we give the simulation algorithm that fits the compute unified device architecture (CUDA) framework of NVIDIA graphics processing units (GPUs). The validation of the model and the performance of the simulations using GPUs are demonstrated by simulating several benchmark systems of soft patchy particles with 1 to 4 patches in a regular geometrical arrangement. Because of its simplicity and computational efficiency, the soft patchy particle model will provide a powerful tool to investigate the aggregation behavior of soft patchy particles, such as patchy micelles, patchy microgels, and patchy dendrimers, over larger spatial and temporal scales.

Tether Dynamics Simulation

NASA Technical Reports Server (NTRS)

1987-01-01

The proceedings of the conference are presented. The objective was to provide a forum for the discussion of the structure and status of existing computer programs which are used to simulate the dynamics of a variety of tether applications in space. A major topic was different simulation models and the process of validating them. Guidance on future work in these areas was obtained from a panel discussion; the panel was composed of resource and technical managers and dynamic analysts in the tether field. The conclusions of this panel are also presented.

The Use of Computer Simulation Techniques in Educational Planning.

ERIC Educational Resources Information Center

Wilson, Charles Z.

Computer simulations provide powerful models for establishing goals, guidelines, and constraints in educational planning. They are dynamic models that allow planners to examine logical descriptions of organizational behavior over time as well as permitting consideration of the large and complex systems required to provide realistic descriptions of…

Insights from molecular dynamics simulations for computational protein design.

PubMed

Childers, Matthew Carter; Daggett, Valerie

2017-02-01

A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures.

Insights from molecular dynamics simulations for computational protein design

PubMed Central

Childers, Matthew Carter; Daggett, Valerie

2017-01-01

A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures. PMID:28239489

How far in-silico computing meets real experiments. A study on the structure and dynamics of spin labeled vinculin tail protein by molecular dynamics simulations and EPR spectroscopy

PubMed Central

2013-01-01

Background Investigation of conformational changes in a protein is a prerequisite to understand its biological function. To explore these conformational changes in proteins we developed a strategy with the combination of molecular dynamics (MD) simulations and electron paramagnetic resonance (EPR) spectroscopy. The major goal of this work is to investigate how far computer simulations can meet the experiments. Methods Vinculin tail protein is chosen as a model system as conformational changes within the vinculin protein are believed to be important for its biological function at the sites of cell adhesion. MD simulations were performed on vinculin tail protein both in water and in vacuo environments. EPR experimental data is compared with those of the simulated data for corresponding spin label positions. Results The calculated EPR spectra from MD simulations trajectories of selected spin labelled positions are comparable to experimental EPR spectra. The results show that the information contained in the spin label mobility provides a powerful means of mapping protein folds and their conformational changes. Conclusions The results suggest the localization of dynamic and flexible regions of the vinculin tail protein. This study shows MD simulations can be used as a complementary tool to interpret experimental EPR data. PMID:23445506

An efficient approach to the analysis of rail surface irregularities accounting for dynamic train-track interaction and inelastic deformations

NASA Astrophysics Data System (ADS)

Andersson, Robin; Torstensson, Peter T.; Kabo, Elena; Larsson, Fredrik

2015-11-01

A two-dimensional computational model for assessment of rolling contact fatigue induced by discrete rail surface irregularities, especially in the context of so-called squats, is presented. Dynamic excitation in a wide frequency range is considered in computationally efficient time-domain simulations of high-frequency dynamic vehicle-track interaction accounting for transient non-Hertzian wheel-rail contact. Results from dynamic simulations are mapped onto a finite element model to resolve the cyclic, elastoplastic stress response in the rail. Ratcheting under multiple wheel passages is quantified. In addition, low cycle fatigue impact is quantified using the Jiang-Sehitoglu fatigue parameter. The functionality of the model is demonstrated by numerical examples.

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

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

Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materialsmore » science, chemistry, and biology.« less

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

DOE PAGES

Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

2015-06-26

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materialsmore » science, chemistry, and biology.« less

Computing Dynamics Of A Robot Of 6+n Degrees Of Freedom

NASA Technical Reports Server (NTRS)

Quiocho, Leslie J.; Bailey, Robert W.

1995-01-01

Improved formulation speeds and simplifies computation of dynamics of robot arm of n rotational degrees of freedom mounted on platform having three translational and three rotational degrees of freedom. Intended for use in dynamical modeling of robotic manipulators attached to such moving bases as spacecraft, aircraft, vessel, or land vehicle. Such modeling important part of simulation and control of robotic motions.

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.

Computationally efficient multibody simulations

NASA Technical Reports Server (NTRS)

Ramakrishnan, Jayant; Kumar, Manoj

1994-01-01

Computationally efficient approaches to the solution of the dynamics of multibody systems are presented in this work. The computational efficiency is derived from both the algorithmic and implementational standpoint. Order(n) approaches provide a new formulation of the equations of motion eliminating the assembly and numerical inversion of a system mass matrix as required by conventional algorithms. Computational efficiency is also gained in the implementation phase by the symbolic processing and parallel implementation of these equations. Comparison of this algorithm with existing multibody simulation programs illustrates the increased computational efficiency.

Investigations in Computer-Aided Instruction and Computer-Aided Controls. Final Report.

ERIC Educational Resources Information Center

Rosenberg, R.C.; And Others

These research projects, designed to delve into certain relationships between humans and computers, are focused on computer-assisted instruction and on man-computer interaction. One study demonstrates that within the limits of formal engineering theory, a computer simulated laboratory (Dynamic Systems Laboratory) can be built in which freshmen…

Construction of dynamic stochastic simulation models using knowledge-based techniques

NASA Technical Reports Server (NTRS)

Williams, M. Douglas; Shiva, Sajjan G.

1990-01-01

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

Adaptive hybrid simulations for multiscale stochastic reaction networks

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

Hepp, Benjamin; Gupta, Ankit; Khammash, Mustafa

2015-01-21

The probability distribution describing the state of a Stochastic Reaction Network (SRN) evolves according to the Chemical Master Equation (CME). It is common to estimate its solution using Monte Carlo methods such as the Stochastic Simulation Algorithm (SSA). In many cases, these simulations can take an impractical amount of computational time. Therefore, many methods have been developed that approximate sample paths of the underlying stochastic process and estimate the solution of the CME. A prominent class of these methods include hybrid methods that partition the set of species and the set of reactions into discrete and continuous subsets. Such amore » partition separates the dynamics into a discrete and a continuous part. Simulating such a stochastic process can be computationally much easier than simulating the exact discrete stochastic process with SSA. Moreover, the quasi-stationary assumption to approximate the dynamics of fast subnetworks can be applied for certain classes of networks. However, as the dynamics of a SRN evolves, these partitions may have to be adapted during the simulation. We develop a hybrid method that approximates the solution of a CME by automatically partitioning the reactions and species sets into discrete and continuous components and applying the quasi-stationary assumption on identifiable fast subnetworks. Our method does not require any user intervention and it adapts to exploit the changing timescale separation between reactions and/or changing magnitudes of copy-numbers of constituent species. We demonstrate the efficiency of the proposed method by considering examples from systems biology and showing that very good approximations to the exact probability distributions can be achieved in significantly less computational time. This is especially the case for systems with oscillatory dynamics, where the system dynamics change considerably throughout the time-period of interest.« less

Adaptive hybrid simulations for multiscale stochastic reaction networks.

PubMed

Hepp, Benjamin; Gupta, Ankit; Khammash, Mustafa

2015-01-21

The probability distribution describing the state of a Stochastic Reaction Network (SRN) evolves according to the Chemical Master Equation (CME). It is common to estimate its solution using Monte Carlo methods such as the Stochastic Simulation Algorithm (SSA). In many cases, these simulations can take an impractical amount of computational time. Therefore, many methods have been developed that approximate sample paths of the underlying stochastic process and estimate the solution of the CME. A prominent class of these methods include hybrid methods that partition the set of species and the set of reactions into discrete and continuous subsets. Such a partition separates the dynamics into a discrete and a continuous part. Simulating such a stochastic process can be computationally much easier than simulating the exact discrete stochastic process with SSA. Moreover, the quasi-stationary assumption to approximate the dynamics of fast subnetworks can be applied for certain classes of networks. However, as the dynamics of a SRN evolves, these partitions may have to be adapted during the simulation. We develop a hybrid method that approximates the solution of a CME by automatically partitioning the reactions and species sets into discrete and continuous components and applying the quasi-stationary assumption on identifiable fast subnetworks. Our method does not require any user intervention and it adapts to exploit the changing timescale separation between reactions and/or changing magnitudes of copy-numbers of constituent species. We demonstrate the efficiency of the proposed method by considering examples from systems biology and showing that very good approximations to the exact probability distributions can be achieved in significantly less computational time. This is especially the case for systems with oscillatory dynamics, where the system dynamics change considerably throughout the time-period of interest.

Computational Methods for Dynamic Stability and Control Derivatives

NASA Technical Reports Server (NTRS)

Green, Lawrence L.; Spence, Angela M.; Murphy, Patrick C.

2003-01-01

Force and moment measurements from an F-16XL during forced pitch oscillation tests result in dynamic stability derivatives, which are measured in combinations. Initial computational simulations of the motions and combined derivatives are attempted via a low-order, time-dependent panel method computational fluid dynamics code. The code dynamics are shown to be highly questionable for this application and the chosen configuration. However, three methods to computationally separate such combined dynamic stability derivatives are proposed. One of the separation techniques is demonstrated on the measured forced pitch oscillation data. Extensions of the separation techniques to yawing and rolling motions are discussed. In addition, the possibility of considering the angles of attack and sideslip state vector elements as distributed quantities, rather than point quantities, is introduced.

Computational Methods for Dynamic Stability and Control Derivatives

NASA Technical Reports Server (NTRS)

Green, Lawrence L.; Spence, Angela M.; Murphy, Patrick C.

2004-01-01

Force and moment measurements from an F-16XL during forced pitch oscillation tests result in dynamic stability derivatives, which are measured in combinations. Initial computational simulations of the motions and combined derivatives are attempted via a low-order, time-dependent panel method computational fluid dynamics code. The code dynamics are shown to be highly questionable for this application and the chosen configuration. However, three methods to computationally separate such combined dynamic stability derivatives are proposed. One of the separation techniques is demonstrated on the measured forced pitch oscillation data. Extensions of the separation techniques to yawing and rolling motions are discussed. In addition, the possibility of considering the angles of attack and sideslip state vector elements as distributed quantities, rather than point quantities, is introduced.

A multilevel-skin neighbor list algorithm for molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Zhang, Chenglong; Zhao, Mingcan; Hou, Chaofeng; Ge, Wei

2018-01-01

Searching of the interaction pairs and organization of the interaction processes are important steps in molecular dynamics (MD) algorithms and are critical to the overall efficiency of the simulation. Neighbor lists are widely used for these steps, where thicker skin can reduce the frequency of list updating but is discounted by more computation in distance check for the particle pairs. In this paper, we propose a new neighbor-list-based algorithm with a precisely designed multilevel skin which can reduce unnecessary computation on inter-particle distances. The performance advantages over traditional methods are then analyzed against the main simulation parameters on Intel CPUs and MICs (many integrated cores), and are clearly demonstrated. The algorithm can be generalized for various discrete simulations using neighbor lists.

Implementation of the force decomposition machine for molecular dynamics simulations.

PubMed

Borštnik, Urban; Miller, Benjamin T; Brooks, Bernard R; Janežič, Dušanka

2012-09-01

We present the design and implementation of the force decomposition machine (FDM), a cluster of personal computers (PCs) that is tailored to running molecular dynamics (MD) simulations using the distributed diagonal force decomposition (DDFD) parallelization method. The cluster interconnect architecture is optimized for the communication pattern of the DDFD method. Our implementation of the FDM relies on standard commodity components even for networking. Although the cluster is meant for DDFD MD simulations, it remains general enough for other parallel computations. An analysis of several MD simulation runs on both the FDM and a standard PC cluster demonstrates that the FDM's interconnect architecture provides a greater performance compared to a more general cluster interconnect. Copyright © 2012 Elsevier Inc. All rights reserved.

Documentation and user guides for SPBLOB: a computer simulation model of the join population dynamics for loblolly pine and the southern pine beetle

Treesearch

John Bishir; James Roberds; Brian Strom; Xiaohai Wan

2009-01-01

SPLOB is a computer simulation model for the interaction between loblolly pine (Pinus taeda L.), the economically most important forest crop in the United States, and the southern pine beetle (SPB: Dendroctonus frontalis Zimm.), the major insect pest for this species. The model simulates loblolly pine stands from time of planting...

Real-time dynamics simulation of the Cassini spacecraft using DARTS. Part 1: Functional capabilities and the spatial algebra algorithm

NASA Technical Reports Server (NTRS)

Jain, A.; Man, G. K.

1993-01-01

This paper describes the Dynamics Algorithms for Real-Time Simulation (DARTS) real-time hardware-in-the-loop dynamics simulator for the National Aeronautics and Space Administration's Cassini spacecraft. The spacecraft model consists of a central flexible body with a number of articulated rigid-body appendages. The demanding performance requirements from the spacecraft control system require the use of a high fidelity simulator for control system design and testing. The DARTS algorithm provides a new algorithmic and hardware approach to the solution of this hardware-in-the-loop simulation problem. It is based upon the efficient spatial algebra dynamics for flexible multibody systems. A parallel and vectorized version of this algorithm is implemented on a low-cost, multiprocessor computer to meet the simulation timing requirements.

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

NASA Astrophysics Data System (ADS)

Hu, Wei; Tian, Qiang; Hu, HaiYan

2018-04-01

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

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome.

PubMed

Šponer, Jiří; Banáš, Pavel; Jurečka, Petr; Zgarbová, Marie; Kührová, Petra; Havrila, Marek; Krepl, Miroslav; Stadlbauer, Petr; Otyepka, Michal

2014-05-15

We present a brief overview of explicit solvent molecular dynamics (MD) simulations of nucleic acids. We explain physical chemistry limitations of the simulations, namely, the molecular mechanics (MM) force field (FF) approximation and limited time scale. Further, we discuss relations and differences between simulations and experiments, compare standard and enhanced sampling simulations, discuss the role of starting structures, comment on different versions of nucleic acid FFs, and relate MM computations with contemporary quantum chemistry. Despite its limitations, we show that MD is a powerful technique for studying the structural dynamics of nucleic acids with a fast growing potential that substantially complements experimental results and aids their interpretation.

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

Molecular Dynamics Simulations of Supramolecular Anticancer Nanotubes.

PubMed

Kang, Myungshim; Chakraborty, Kaushik; Loverde, Sharon M

2018-06-25

We report here on long-time all-atomistic molecular dynamics simulations of functional supramolecular nanotubes composed by the self-assembly of peptide-drug amphiphiles (DAs). These DAs have been shown to possess an inherently high drug loading of the hydrophobic anticancer drug camptothecin. We probe the self-assembly mechanism from random with ∼0.4 μs molecular dynamics simulations. Furthermore, we also computationally characterize the interfacial structure, directionality of π-π stacking, and water dynamics within several peptide-drug nanotubes with diameters consistent with the reported experimental nanotube diameter. Insight gained should inform the future design of these novel anticancer drug delivery systems.

Marc Henry de Frahan | NREL

Science.gov Websites

Computing Project, Marc develops high-fidelity turbulence models to enhance simulation accuracy and efficient numerical algorithms for future high performance computing hardware architectures. Research Interests High performance computing High order numerical methods for computational fluid dynamics Fluid

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

NASA Astrophysics Data System (ADS)

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

2017-11-01

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

Blood flow in intracranial aneurysms treated with Pipeline embolization devices: computational simulation and verification with Doppler ultrasonography on phantom models

PubMed Central

2015-01-01

Purpose: The aim of this study was to validate a computational fluid dynamics (CFD) simulation of flow-diverter treatment through Doppler ultrasonography measurements in patient-specific models of intracranial bifurcation and side-wall aneurysms. Methods: Computational and physical models of patient-specific bifurcation and sidewall aneurysms were constructed from computed tomography angiography with use of stereolithography, a three-dimensional printing technology. Flow dynamics parameters before and after flow-diverter treatment were measured with pulse-wave and color Doppler ultrasonography, and then compared with CFD simulations. Results: CFD simulations showed drastic flow reduction after flow-diverter treatment in both aneurysms. The mean volume flow rate decreased by 90% and 85% for the bifurcation aneurysm and the side-wall aneurysm, respectively. Velocity contour plots from computer simulations before and after flow diversion closely resembled the patterns obtained by color Doppler ultrasonography. Conclusion: The CFD estimation of flow reduction in aneurysms treated with a flow-diverting stent was verified by Doppler ultrasonography in patient-specific phantom models of bifurcation and side-wall aneurysms. The combination of CFD and ultrasonography may constitute a feasible and reliable technique in studying the treatment of intracranial aneurysms with flow-diverting stents. PMID:25754367

REMOVAL OF TANK AND SEWER SEDIMENT BY GATE FLUSHING: COMPUTATIONAL FLUID DYNAMICS MODEL STUDIES

EPA Science Inventory

This presentation will discuss the application of a computational fluid dynamics 3D flow model to simulate gate flushing for removing tank/sewer sediments. The physical model of the flushing device was a tank fabricated and installed at the head-end of a hydraulic flume. The fl...

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.

Multiscale Reactive Molecular Dynamics

DTIC Science & Technology

2012-08-15

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

ESIM_DSN Web-Enabled Distributed Simulation Network

NASA Technical Reports Server (NTRS)

Bedrossian, Nazareth; Novotny, John

2002-01-01

In this paper, the eSim(sup DSN) approach to achieve distributed simulation capability using the Internet is presented. With this approach a complete simulation can be assembled from component subsystems that run on different computers. The subsystems interact with each other via the Internet The distributed simulation uses a hub-and-spoke type network topology. It provides the ability to dynamically link simulation subsystem models to different computers as well as the ability to assign a particular model to each computer. A proof-of-concept demonstrator is also presented. The eSim(sup DSN) demonstrator can be accessed at http://www.jsc.draper.com/esim which hosts various examples of Web enabled simulations.

A comparison between theoretical prediction and experimental measurement of the dynamic behavior of spur gears

NASA Technical Reports Server (NTRS)

Rebbechi, Brian; Forrester, B. David; Oswald, Fred B.; Townsend, Dennis P.

1992-01-01

A comparison was made between computer model predictions of gear dynamics behavior and experimental results. The experimental data were derived from the NASA gear noise rig, which was used to record dynamic tooth loads and vibration. The experimental results were compared with predictions from the DSTO Aeronautical Research Laboratory's gear dynamics code for a matrix of 28 load speed points. At high torque the peak dynamic load predictions agree with the experimental results with an average error of 5 percent in the speed range 800 to 6000 rpm. Tooth separation (or bounce), which was observed in the experimental data for light torque, high speed conditions, was simulated by the computer model. The model was also successful in simulating the degree of load sharing between gear teeth in the multiple tooth contact region.

A novel representation of groundwater dynamics in large-scale land surface modelling

NASA Astrophysics Data System (ADS)

Rahman, Mostaquimur; Rosolem, Rafael; Kollet, Stefan

2017-04-01

Land surface processes are connected to groundwater dynamics via shallow soil moisture. For example, groundwater affects evapotranspiration (by influencing the variability of soil moisture) and runoff generation mechanisms. However, contemporary Land Surface Models (LSM) generally consider isolated soil columns and free drainage lower boundary condition for simulating hydrology. This is mainly due to the fact that incorporating detailed groundwater dynamics in LSMs usually requires considerable computing resources, especially for large-scale applications (e.g., continental to global). Yet, these simplifications undermine the potential effect of groundwater dynamics on land surface mass and energy fluxes. In this study, we present a novel approach of representing high-resolution groundwater dynamics in LSMs that is computationally efficient for large-scale applications. This new parameterization is incorporated in the Joint UK Land Environment Simulator (JULES) and tested at the continental-scale.

A Computer Model for Teaching the Dynamic Behavior of AC Contactors

ERIC Educational Resources Information Center

Ruiz, J.-R. R.; Espinosa, A. G.; Romeral, L.

2010-01-01

Ac-powered contactors are extensively used in industry in applications such as automatic electrical devices, motor starters, and heaters. In this work, a practical session that allows students to model and simulate the dynamic behavior of ac-powered electromechanical contactors is presented. Simulation is carried out using a rigorous parametric…

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

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

Temperature specification in atomistic molecular dynamics and its impact on simulation efficacy

NASA Astrophysics Data System (ADS)

Ocaya, R. O.; Terblans, J. J.

2017-10-01

Temperature is a vital thermodynamical function for physical systems. Knowledge of system temperature permits assessment of system ergodicity, entropy, system state and stability. Rapid theoretical and computational developments in the fields of condensed matter physics, chemistry, material science, molecular biology, nanotechnology and others necessitate clarity in the temperature specification. Temperature-based materials simulations, both standalone and distributed computing, are projected to grow in prominence over diverse research fields. In this article we discuss the apparent variability of temperature modeling formalisms used currently in atomistic molecular dynamics simulations, with respect to system energetics,dynamics and structural evolution. Commercial simulation programs, which by nature are heuristic, do not openly discuss this fundamental question. We address temperature specification in the context of atomistic molecular dynamics. We define a thermostat at 400K relative to a heat bath at 300K firstly using a modified ab-initio Newtonian method, and secondly using a Monte-Carlo method. The thermostatic vacancy formation and cohesion energies, equilibrium lattice constant for FCC copper is then calculated. Finally we compare and contrast the results.

Ab initio molecular dynamics simulation of LiBr association in water

NASA Astrophysics Data System (ADS)

Izvekov, Sergei; Philpott, Michael R.

2000-12-01

A computationally economical scheme which unifies the density functional description of an ionic solute and the classical description of a solvent was developed. The density functional part of the scheme comprises Car-Parrinello and related formalisms. The substantial saving in the computer time is achieved by performing the ab initio molecular dynamics of the solute electronic structure in a relatively small basis set constructed from lowest energy Kohn-Sham orbitals calculated for a single anion in vacuum, instead of using plane wave basis. The methodology permits simulation of an ionic solution for longer time scales while keeping accuracy in the prediction of the solute electronic structure. As an example the association of the Li+-Br- ion-pair system in water is studied. The results of the combined molecular dynamics simulation are compared with that obtained from the classical simulation with ion-ion interaction described by the pair potential of Born-Huggins-Mayer type. The comparison reveals an important role played by the polarization of the Br- ion in the dynamics of ion pair association.

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

PubMed

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

2017-04-05

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

Modelling and simulation techniques for membrane biology.

PubMed

Burrage, Kevin; Hancock, John; Leier, André; Nicolau, Dan V

2007-07-01

One of the most important aspects of Computational Cell Biology is the understanding of the complicated dynamical processes that take place on plasma membranes. These processes are often so complicated that purely temporal models cannot always adequately capture the dynamics. On the other hand, spatial models can have large computational overheads. In this article, we review some of these issues with respect to chemistry, membrane microdomains and anomalous diffusion and discuss how to select appropriate modelling and simulation paradigms based on some or all the following aspects: discrete, continuous, stochastic, delayed and complex spatial processes.

A suite of exercises for verifying dynamic earthquake rupture codes

USGS Publications Warehouse

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

2018-01-01

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

Computational analysis of nonlinearities within dynamics of cable-based driving systems

NASA Astrophysics Data System (ADS)

Anghelache, G. D.; Nastac, S.

2017-08-01

This paper deals with computational nonlinear dynamics of mechanical systems containing some flexural parts within the actuating scheme, and, especially, the situations of the cable-based driving systems were treated. It was supposed both functional nonlinearities and the real characteristic of the power supply, in order to obtain a realistically computer simulation model being able to provide very feasible results regarding the system dynamics. It was taken into account the transitory and stable regimes during a regular exploitation cycle. The authors present a particular case of a lift system, supposed to be representatively for the objective of this study. The simulations were made based on the values of the essential parameters acquired from the experimental tests and/or the regular practice in the field. The results analysis and the final discussions reveal the correlated dynamic aspects within the mechanical parts, the driving system, and the power supply, whole of these supplying potential sources of particular resonances, within some transitory phases of the working cycle, and which can affect structural and functional dynamics. In addition, it was underlines the influences of computational hypotheses on the both quantitative and qualitative behaviour of the system. Obviously, the most significant consequence of this theoretical and computational research consist by developing an unitary and feasible model, useful to dignify the nonlinear dynamic effects into the systems with cable-based driving scheme, and hereby to help an optimization of the exploitation regime including a dynamics control measures.

High-performance computational fluid dynamics: a custom-code approach

NASA Astrophysics Data System (ADS)

Fannon, James; Loiseau, Jean-Christophe; Valluri, Prashant; Bethune, Iain; Náraigh, Lennon Ó.

2016-07-01

We introduce a modified and simplified version of the pre-existing fully parallelized three-dimensional Navier-Stokes flow solver known as TPLS. We demonstrate how the simplified version can be used as a pedagogical tool for the study of computational fluid dynamics (CFDs) and parallel computing. TPLS is at its heart a two-phase flow solver, and uses calls to a range of external libraries to accelerate its performance. However, in the present context we narrow the focus of the study to basic hydrodynamics and parallel computing techniques, and the code is therefore simplified and modified to simulate pressure-driven single-phase flow in a channel, using only relatively simple Fortran 90 code with MPI parallelization, but no calls to any other external libraries. The modified code is analysed in order to both validate its accuracy and investigate its scalability up to 1000 CPU cores. Simulations are performed for several benchmark cases in pressure-driven channel flow, including a turbulent simulation, wherein the turbulence is incorporated via the large-eddy simulation technique. The work may be of use to advanced undergraduate and graduate students as an introductory study in CFDs, while also providing insight for those interested in more general aspects of high-performance computing.

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.

Simulation of solid-liquid flows in a stirred bead mill based on computational fluid dynamics (CFD)

NASA Astrophysics Data System (ADS)

Winardi, S.; Widiyastuti, W.; Septiani, E. L.; Nurtono, T.

2018-05-01

The selection of simulation model is an important step in computational fluid dynamics (CFD) to obtain an agreement with experimental work. In addition, computational time and processor speed also influence the performance of the simulation results. Here, we report the simulation of solid-liquid flow in a bead mill using Eulerian model. Multiple Reference Frame (MRF) was also used to model the interaction between moving (shaft and disk) and stationary (chamber exclude shaft and disk) zones. Bead mill dimension was based on the experimental work of Yamada and Sakai (2013). The effect of shaft rotation speed of 1200 and 1800 rpm on the particle distribution and the flow field was discussed. For rotation speed of 1200 rpm, the particles spread evenly throughout the bead mill chamber. On the other hand, for the rotation speed of 1800 rpm, the particles tend to be thrown to the near wall region resulting in the dead zone and found no particle in the center region. The selected model agreed well to the experimental data with average discrepancies less than 10%. Furthermore, the simulation was run without excessive computational cost.

Computational Modeling and Numerical Methods for Spatiotemporal Calcium Cycling in Ventricular Myocytes

PubMed Central

Nivala, Michael; de Lange, Enno; Rovetti, Robert; Qu, Zhilin

2012-01-01

Intracellular calcium (Ca) cycling dynamics in cardiac myocytes is regulated by a complex network of spatially distributed organelles, such as sarcoplasmic reticulum (SR), mitochondria, and myofibrils. In this study, we present a mathematical model of intracellular Ca cycling and numerical and computational methods for computer simulations. The model consists of a coupled Ca release unit (CRU) network, which includes a SR domain and a myoplasm domain. Each CRU contains 10 L-type Ca channels and 100 ryanodine receptor channels, with individual channels simulated stochastically using a variant of Gillespie’s method, modified here to handle time-dependent transition rates. Both the SR domain and the myoplasm domain in each CRU are modeled by 5 × 5 × 5 voxels to maintain proper Ca diffusion. Advanced numerical algorithms implemented on graphical processing units were used for fast computational simulations. For a myocyte containing 100 × 20 × 10 CRUs, a 1-s heart time simulation takes about 10 min of machine time on a single NVIDIA Tesla C2050. Examples of simulated Ca cycling dynamics, such as Ca sparks, Ca waves, and Ca alternans, are shown. PMID:22586402

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.

Xyce

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

Thomquist, Heidi K.; Fixel, Deborah A.; Fett, David Brian

The Xyce Parallel Electronic Simulator simulates electronic circuit behavior in DC, AC, HB, MPDE and transient mode using standard analog (DAE) and/or device (PDE) device models including several age and radiation aware devices. It supports a variety of computing platforms (both serial and parallel) computers. Lastly, it uses a variety of modern solution algorithms dynamic parallel load-balancing and iterative solvers.

Computing fluid-particle interaction forces for nano-suspension droplet spreading: molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Zhou, Weizhou; Shi, Baiou; Webb, Edmund

2017-11-01

Recently, there are many experimental and theoretical studies to understand and control the dynamic spreading of nano-suspension droplets on solid surfaces. However, fundamental understanding of driving forces dictating the kinetics of nano-suspension wetting and spreading, especially capillary forces that manifest during the process, is lacking. Here, we present results from atomic scale simulations that were used to compute forces between suspended particles and advancing liquid fronts. The role of nano-particle size, particle loading, and interaction strength on forces computed from simulations will be discussed. Results demonstrate that increasing the particle size dramatically changes observed wetting behavior from depinning to pinning. From simulations on varying particle size, a relationship between computed forces and particle size is advanced and compared to existing expressions in the literature. High particle loading significantly slowed spreading kinetics, by introducing tortuous transport paths for liquid delivery to the advancing contact line. Lastly, we show how weakening the interaction between the particle and the underlying substrate can change a system from exhibiting pinning behavior to de-pinning.

Computing the binding affinity of Zn2+ in human carbonic anhydrase II on the basis of all-atom molecular dynamics simulations.

NASA Astrophysics Data System (ADS)

Wambo, Thierry; Rodriguez, Roberto

Human carbonic anhydrase II (hCAII) is a metalloenzyme with a Zinc cation at its binding site. The presence of the Zinc turns the protein into an efficient enzyme which catalyzes the reversible hydration of carbon dioxide into bicarbonate anion. Available X-ray structures of the apo-hCAII and holo-hCAII show no significant differences in the overall structure of these proteins. What difference, if any, is there between the structures of the hydrated apo-hCAII and holo? How can we use computer simulation to efficiently compute the binding affinity of Zinc to hCAII? We will present a scheme developed to compute the binding affinity of Zinc cation to hCAII on the basis of all-atom molecular dynamics simulation where Zinc is represented as a point charge and the CHARMM36 force field is used for running the dynamics of the system. Our computed binding affinity of the cation to hCAII is in good agreement with experiment, within the margin of error, while a look at the dynamics of the binding site suggests that in the absence of the Zinc, there is a re-organization of the nearby histidine residues which adopt a new distinct configuration. The authors are thankful for the NIH support through Grants GM084834 and GM060655. They also acknowledge the Texas Advanced Computing Center at the University of Texas at Austin for the supercomputing time. They thank Dr Liao Chen for his comments.

Computational dynamics of soft machines

NASA Astrophysics Data System (ADS)

Hu, Haiyan; Tian, Qiang; Liu, Cheng

2017-06-01

Soft machine refers to a kind of mechanical system made of soft materials to complete sophisticated missions, such as handling a fragile object and crawling along a narrow tunnel corner, under low cost control and actuation. Hence, soft machines have raised great challenges to computational dynamics. In this review article, recent studies of the authors on the dynamic modeling, numerical simulation, and experimental validation of soft machines are summarized in the framework of multibody system dynamics. The dynamic modeling approaches are presented first for the geometric nonlinearities of coupled overall motions and large deformations of a soft component, the physical nonlinearities of a soft component made of hyperelastic or elastoplastic materials, and the frictional contacts/impacts of soft components, respectively. Then the computation approach is outlined for the dynamic simulation of soft machines governed by a set of differential-algebraic equations of very high dimensions, with an emphasis on the efficient computations of the nonlinear elastic force vector of finite elements. The validations of the proposed approaches are given via three case studies, including the locomotion of a soft quadrupedal robot, the spinning deployment of a solar sail of a spacecraft, and the deployment of a mesh reflector of a satellite antenna, as well as the corresponding experimental studies. Finally, some remarks are made for future studies.

Communication: A method to compute the transport coefficient of pure fluids diffusing through planar interfaces from equilibrium molecular dynamics simulations.

PubMed

Vermorel, Romain; Oulebsir, Fouad; Galliero, Guillaume

2017-09-14

The computation of diffusion coefficients in molecular systems ranks among the most useful applications of equilibrium molecular dynamics simulations. However, when dealing with the problem of fluid diffusion through vanishingly thin interfaces, classical techniques are not applicable. This is because the volume of space in which molecules diffuse is ill-defined. In such conditions, non-equilibrium techniques allow for the computation of transport coefficients per unit interface width, but their weak point lies in their inability to isolate the contribution of the different physical mechanisms prone to impact the flux of permeating molecules. In this work, we propose a simple and accurate method to compute the diffusional transport coefficient of a pure fluid through a planar interface from equilibrium molecular dynamics simulations, in the form of a diffusion coefficient per unit interface width. In order to demonstrate its validity and accuracy, we apply our method to the case study of a dilute gas diffusing through a smoothly repulsive single-layer porous solid. We believe this complementary technique can benefit to the interpretation of the results obtained on single-layer membranes by means of complex non-equilibrium methods.

ODECS -- A computer code for the optimal design of S.I. engine control strategies

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

Arsie, I.; Pianese, C.; Rizzo, G.

1996-09-01

The computer code ODECS (Optimal Design of Engine Control Strategies) for the design of Spark Ignition engine control strategies is presented. This code has been developed starting from the author`s activity in this field, availing of some original contributions about engine stochastic optimization and dynamical models. This code has a modular structure and is composed of a user interface for the definition, the execution and the analysis of different computations performed with 4 independent modules. These modules allow the following calculations: (1) definition of the engine mathematical model from steady-state experimental data; (2) engine cycle test trajectory corresponding to amore » vehicle transient simulation test such as ECE15 or FTP drive test schedule; (3) evaluation of the optimal engine control maps with a steady-state approach; (4) engine dynamic cycle simulation and optimization of static control maps and/or dynamic compensation strategies, taking into account dynamical effects due to the unsteady fluxes of air and fuel and the influences of combustion chamber wall thermal inertia on fuel consumption and emissions. Moreover, in the last two modules it is possible to account for errors generated by a non-deterministic behavior of sensors and actuators and the related influences on global engine performances, and compute robust strategies, less sensitive to stochastic effects. In the paper the four models are described together with significant results corresponding to the simulation and the calculation of optimal control strategies for dynamic transient tests.« less

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.

Fluid Structural Analysis of Human Cerebral Aneurysm Using Their Own Wall Mechanical Properties

PubMed Central

Valencia, Alvaro; Burdiles, Patricio; Ignat, Miguel; Mura, Jorge; Rivera, Rodrigo; Sordo, Juan

2013-01-01

Computational Structural Dynamics (CSD) simulations, Computational Fluid Dynamics (CFD) simulation, and Fluid Structure Interaction (FSI) simulations were carried out in an anatomically realistic model of a saccular cerebral aneurysm with the objective of quantifying the effects of type of simulation on principal fluid and solid mechanics results. Eight CSD simulations, one CFD simulation, and four FSI simulations were made. The results allowed the study of the influence of the type of material elements in the solid, the aneurism's wall thickness, and the type of simulation on the modeling of a human cerebral aneurysm. The simulations use their own wall mechanical properties of the aneurysm. The more complex simulation was the FSI simulation completely coupled with hyperelastic Mooney-Rivlin material, normal internal pressure, and normal variable thickness. The FSI simulation coupled in one direction using hyperelastic Mooney-Rivlin material, normal internal pressure, and normal variable thickness is the one that presents the most similar results with respect to the more complex FSI simulation, requiring one-fourth of the calculation time. PMID:24151523

Parallel implementation of the particle simulation method with dynamic load balancing: Toward realistic geodynamical simulation

NASA Astrophysics Data System (ADS)

Furuichi, M.; Nishiura, D.

2015-12-01

Fully Lagrangian methods such as Smoothed Particle Hydrodynamics (SPH) and Discrete Element Method (DEM) have been widely used to solve the continuum and particles motions in the computational geodynamics field. These mesh-free methods are suitable for the problems with the complex geometry and boundary. In addition, their Lagrangian nature allows non-diffusive advection useful for tracking history dependent properties (e.g. rheology) of the material. These potential advantages over the mesh-based methods offer effective numerical applications to the geophysical flow and tectonic processes, which are for example, tsunami with free surface and floating body, magma intrusion with fracture of rock, and shear zone pattern generation of granular deformation. In order to investigate such geodynamical problems with the particle based methods, over millions to billion particles are required for the realistic simulation. Parallel computing is therefore important for handling such huge computational cost. An efficient parallel implementation of SPH and DEM methods is however known to be difficult especially for the distributed-memory architecture. Lagrangian methods inherently show workload imbalance problem for parallelization with the fixed domain in space, because particles move around and workloads change during the simulation. Therefore dynamic load balance is key technique to perform the large scale SPH and DEM simulation. In this work, we present the parallel implementation technique of SPH and DEM method utilizing dynamic load balancing algorithms toward the high resolution simulation over large domain using the massively parallel super computer system. Our method utilizes the imbalances of the executed time of each MPI process as the nonlinear term of parallel domain decomposition and minimizes them with the Newton like iteration method. In order to perform flexible domain decomposition in space, the slice-grid algorithm is used. Numerical tests show that our approach is suitable for solving the particles with different calculation costs (e.g. boundary particles) as well as the heterogeneous computer architecture. We analyze the parallel efficiency and scalability on the super computer systems (K-computer, Earth simulator 3, etc.).

Simulation of windblown dust transport from a mine tailings impoundment using a computational fluid dynamics model

NASA Astrophysics Data System (ADS)

Stovern, Michael; Felix, Omar; Csavina, Janae; Rine, Kyle P.; Russell, MacKenzie R.; Jones, Robert M.; King, Matt; Betterton, Eric A.; Sáez, A. Eduardo

2014-09-01

Mining operations are potential sources of airborne particulate metal and metalloid contaminants through both direct smelter emissions and wind erosion of mine tailings. The warmer, drier conditions predicted for the Southwestern US by climate models may make contaminated atmospheric dust and aerosols increasingly important, due to potential deleterious effects on human health and ecology. Dust emissions and dispersion of dust and aerosol from the Iron King Mine tailings in Dewey-Humboldt, Arizona, a Superfund site, are currently being investigated through in situ field measurements and computational fluid dynamics modeling. These tailings are heavily contaminated with lead and arsenic. Using a computational fluid dynamics model, we model dust transport from the mine tailings to the surrounding region. The model includes gaseous plume dispersion to simulate the transport of the fine aerosols, while individual particle transport is used to track the trajectories of larger particles and to monitor their deposition locations. In order to improve the accuracy of the dust transport simulations, both regional topographical features and local weather patterns have been incorporated into the model simulations. Results show that local topography and wind velocity profiles are the major factors that control deposition.

Simulation of windblown dust transport from a mine tailings impoundment using a computational fluid dynamics model.

PubMed

Stovern, Michael; Felix, Omar; Csavina, Janae; Rine, Kyle P; Russell, MacKenzie R; Jones, Robert M; King, Matt; Betterton, Eric A; Sáez, A Eduardo

2014-09-01

Mining operations are potential sources of airborne particulate metal and metalloid contaminants through both direct smelter emissions and wind erosion of mine tailings. The warmer, drier conditions predicted for the Southwestern US by climate models may make contaminated atmospheric dust and aerosols increasingly important, due to potential deleterious effects on human health and ecology. Dust emissions and dispersion of dust and aerosol from the Iron King Mine tailings in Dewey-Humboldt, Arizona, a Superfund site, are currently being investigated through in situ field measurements and computational fluid dynamics modeling. These tailings are heavily contaminated with lead and arsenic. Using a computational fluid dynamics model, we model dust transport from the mine tailings to the surrounding region. The model includes gaseous plume dispersion to simulate the transport of the fine aerosols, while individual particle transport is used to track the trajectories of larger particles and to monitor their deposition locations. In order to improve the accuracy of the dust transport simulations, both regional topographical features and local weather patterns have been incorporated into the model simulations. Results show that local topography and wind velocity profiles are the major factors that control deposition.

Simulation of windblown dust transport from a mine tailings impoundment using a computational fluid dynamics model

PubMed Central

Stovern, Michael; Felix, Omar; Csavina, Janae; Rine, Kyle P.; Russell, MacKenzie R.; Jones, Robert M.; King, Matt; Betterton, Eric A.; Sáez, A. Eduardo

2014-01-01

Mining operations are potential sources of airborne particulate metal and metalloid contaminants through both direct smelter emissions and wind erosion of mine tailings. The warmer, drier conditions predicted for the Southwestern US by climate models may make contaminated atmospheric dust and aerosols increasingly important, due to potential deleterious effects on human health and ecology. Dust emissions and dispersion of dust and aerosol from the Iron King Mine tailings in Dewey-Humboldt, Arizona, a Superfund site, are currently being investigated through in situ field measurements and computational fluid dynamics modeling. These tailings are heavily contaminated with lead and arsenic. Using a computational fluid dynamics model, we model dust transport from the mine tailings to the surrounding region. The model includes gaseous plume dispersion to simulate the transport of the fine aerosols, while individual particle transport is used to track the trajectories of larger particles and to monitor their deposition locations. In order to improve the accuracy of the dust transport simulations, both regional topographical features and local weather patterns have been incorporated into the model simulations. Results show that local topography and wind velocity profiles are the major factors that control deposition. PMID:25621085

Simulating chemistry using quantum computers.

PubMed

Kassal, Ivan; Whitfield, James D; Perdomo-Ortiz, Alejandro; Yung, Man-Hong; Aspuru-Guzik, Alán

2011-01-01

The difficulty of simulating quantum systems, well known to quantum chemists, prompted the idea of quantum computation. One can avoid the steep scaling associated with the exact simulation of increasingly large quantum systems on conventional computers, by mapping the quantum system to another, more controllable one. In this review, we discuss to what extent the ideas in quantum computation, now a well-established field, have been applied to chemical problems. We describe algorithms that achieve significant advantages for the electronic-structure problem, the simulation of chemical dynamics, protein folding, and other tasks. Although theory is still ahead of experiment, we outline recent advances that have led to the first chemical calculations on small quantum information processors.

Design of object-oriented distributed simulation classes

NASA Technical Reports Server (NTRS)

Schoeffler, James D. (Principal Investigator)

1995-01-01

Distributed simulation of aircraft engines as part of a computer aided design package is being developed by NASA Lewis Research Center for the aircraft industry. The project is called NPSS, an acronym for 'Numerical Propulsion Simulation System'. NPSS is a flexible object-oriented simulation of aircraft engines requiring high computing speed. It is desirable to run the simulation on a distributed computer system with multiple processors executing portions of the simulation in parallel. The purpose of this research was to investigate object-oriented structures such that individual objects could be distributed. The set of classes used in the simulation must be designed to facilitate parallel computation. Since the portions of the simulation carried out in parallel are not independent of one another, there is the need for communication among the parallel executing processors which in turn implies need for their synchronization. Communication and synchronization can lead to decreased throughput as parallel processors wait for data or synchronization signals from other processors. As a result of this research, the following have been accomplished. The design and implementation of a set of simulation classes which result in a distributed simulation control program have been completed. The design is based upon MIT 'Actor' model of a concurrent object and uses 'connectors' to structure dynamic connections between simulation components. Connectors may be dynamically created according to the distribution of objects among machines at execution time without any programming changes. Measurements of the basic performance have been carried out with the result that communication overhead of the distributed design is swamped by the computation time of modules unless modules have very short execution times per iteration or time step. An analytical performance model based upon queuing network theory has been designed and implemented. Its application to realistic configurations has not been carried out.

Design of Object-Oriented Distributed Simulation Classes

NASA Technical Reports Server (NTRS)

Schoeffler, James D.

1995-01-01

Distributed simulation of aircraft engines as part of a computer aided design package being developed by NASA Lewis Research Center for the aircraft industry. The project is called NPSS, an acronym for "Numerical Propulsion Simulation System". NPSS is a flexible object-oriented simulation of aircraft engines requiring high computing speed. It is desirable to run the simulation on a distributed computer system with multiple processors executing portions of the simulation in parallel. The purpose of this research was to investigate object-oriented structures such that individual objects could be distributed. The set of classes used in the simulation must be designed to facilitate parallel computation. Since the portions of the simulation carried out in parallel are not independent of one another, there is the need for communication among the parallel executing processors which in turn implies need for their synchronization. Communication and synchronization can lead to decreased throughput as parallel processors wait for data or synchronization signals from other processors. As a result of this research, the following have been accomplished. The design and implementation of a set of simulation classes which result in a distributed simulation control program have been completed. The design is based upon MIT "Actor" model of a concurrent object and uses "connectors" to structure dynamic connections between simulation components. Connectors may be dynamically created according to the distribution of objects among machines at execution time without any programming changes. Measurements of the basic performance have been carried out with the result that communication overhead of the distributed design is swamped by the computation time of modules unless modules have very short execution times per iteration or time step. An analytical performance model based upon queuing network theory has been designed and implemented. Its application to realistic configurations has not been carried out.

Toward prethreshold gate-based quantum simulation of chemical dynamics: using potential energy surfaces to simulate few-channel molecular collisions

DOE PAGES

Sornborger, Andrew Tyler; Stancil, Phillip; Geller, Michael R.

2018-03-22

Here, one of the most promising applications of an error-corrected universal quantum computer is the efficient simulation of complex quantum systems such as large molecular systems. In this application, one is interested in both the electronic structure such as the ground state energy and dynamical properties such as the scattering cross section and chemical reaction rates. However, most theoretical work and experimental demonstrations have focused on the quantum computation of energies and energy surfaces. In this work, we attempt to make the prethreshold (not error-corrected) quantum simulation of dynamical properties practical as well. We show that the use of precomputedmore » potential energy surfaces and couplings enables the gate-based simulation of few-channel but otherwise realistic molecular collisions. Our approach is based on the widely used Born–Oppenheimer approximation for the structure problem coupled with a semiclassical method for the dynamics. In the latter the electrons are treated quantum mechanically but the nuclei are classical, which restricts the collisions to high energy or temperature (typically above ≈10 eV). By using operator splitting techniques optimized for the resulting time-dependent Hamiltonian simulation problem, we give several physically realistic collision examples, with 3–8 channels and circuit depths < 1000.« less

Toward prethreshold gate-based quantum simulation of chemical dynamics: using potential energy surfaces to simulate few-channel molecular collisions

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

Sornborger, Andrew Tyler; Stancil, Phillip; Geller, Michael R.

Here, one of the most promising applications of an error-corrected universal quantum computer is the efficient simulation of complex quantum systems such as large molecular systems. In this application, one is interested in both the electronic structure such as the ground state energy and dynamical properties such as the scattering cross section and chemical reaction rates. However, most theoretical work and experimental demonstrations have focused on the quantum computation of energies and energy surfaces. In this work, we attempt to make the prethreshold (not error-corrected) quantum simulation of dynamical properties practical as well. We show that the use of precomputedmore » potential energy surfaces and couplings enables the gate-based simulation of few-channel but otherwise realistic molecular collisions. Our approach is based on the widely used Born–Oppenheimer approximation for the structure problem coupled with a semiclassical method for the dynamics. In the latter the electrons are treated quantum mechanically but the nuclei are classical, which restricts the collisions to high energy or temperature (typically above ≈10 eV). By using operator splitting techniques optimized for the resulting time-dependent Hamiltonian simulation problem, we give several physically realistic collision examples, with 3–8 channels and circuit depths < 1000.« less

Toward prethreshold gate-based quantum simulation of chemical dynamics: using potential energy surfaces to simulate few-channel molecular collisions

NASA Astrophysics Data System (ADS)

Sornborger, Andrew T.; Stancil, Phillip; Geller, Michael R.

2018-05-01

One of the most promising applications of an error-corrected universal quantum computer is the efficient simulation of complex quantum systems such as large molecular systems. In this application, one is interested in both the electronic structure such as the ground state energy and dynamical properties such as the scattering cross section and chemical reaction rates. However, most theoretical work and experimental demonstrations have focused on the quantum computation of energies and energy surfaces. In this work, we attempt to make the prethreshold (not error-corrected) quantum simulation of dynamical properties practical as well. We show that the use of precomputed potential energy surfaces and couplings enables the gate-based simulation of few-channel but otherwise realistic molecular collisions. Our approach is based on the widely used Born-Oppenheimer approximation for the structure problem coupled with a semiclassical method for the dynamics. In the latter the electrons are treated quantum mechanically but the nuclei are classical, which restricts the collisions to high energy or temperature (typically above ≈ 10 eV). By using operator splitting techniques optimized for the resulting time-dependent Hamiltonian simulation problem, we give several physically realistic collision examples, with 3-8 channels and circuit depths < 1000.

Oxygen transport properties estimation by DSMC-CT simulations

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

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

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

Application of a computationally efficient method to approximate gap model results with a probabilistic approach

NASA Astrophysics Data System (ADS)

Scherstjanoi, M.; Kaplan, J. O.; Lischke, H.

2014-07-01

To be able to simulate climate change effects on forest dynamics over the whole of Switzerland, we adapted the second-generation DGVM (dynamic global vegetation model) LPJ-GUESS (Lund-Potsdam-Jena General Ecosystem Simulator) to the Alpine environment. We modified model functions, tuned model parameters, and implemented new tree species to represent the potential natural vegetation of Alpine landscapes. Furthermore, we increased the computational efficiency of the model to enable area-covering simulations in a fine resolution (1 km) sufficient for the complex topography of the Alps, which resulted in more than 32 000 simulation grid cells. To this aim, we applied the recently developed method GAPPARD (approximating GAP model results with a Probabilistic Approach to account for stand Replacing Disturbances) (Scherstjanoi et al., 2013) to LPJ-GUESS. GAPPARD derives mean output values from a combination of simulation runs without disturbances and a patch age distribution defined by the disturbance frequency. With this computationally efficient method, which increased the model's speed by approximately the factor 8, we were able to faster detect the shortcomings of LPJ-GUESS functions and parameters. We used the adapted LPJ-GUESS together with GAPPARD to assess the influence of one climate change scenario on dynamics of tree species composition and biomass throughout the 21st century in Switzerland. To allow for comparison with the original model, we additionally simulated forest dynamics along a north-south transect through Switzerland. The results from this transect confirmed the high value of the GAPPARD method despite some limitations towards extreme climatic events. It allowed for the first time to obtain area-wide, detailed high-resolution LPJ-GUESS simulation results for a large part of the Alpine region.

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

NASA Astrophysics Data System (ADS)

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

2017-08-01

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

Using Molecular Dynamics Simulations as an Aid in the Prediction of Domain Swapping of Computationally Designed Protein Variants.

PubMed

Mou, Yun; Huang, Po-Ssu; Thomas, Leonard M; Mayo, Stephen L

2015-08-14

In standard implementations of computational protein design, a positive-design approach is used to predict sequences that will be stable on a given backbone structure. Possible competing states are typically not considered, primarily because appropriate structural models are not available. One potential competing state, the domain-swapped dimer, is especially compelling because it is often nearly identical with its monomeric counterpart, differing by just a few mutations in a hinge region. Molecular dynamics (MD) simulations provide a computational method to sample different conformational states of a structure. Here, we tested whether MD simulations could be used as a post-design screening tool to identify sequence mutations leading to domain-swapped dimers. We hypothesized that a successful computationally designed sequence would have backbone structure and dynamics characteristics similar to that of the input structure and that, in contrast, domain-swapped dimers would exhibit increased backbone flexibility and/or altered structure in the hinge-loop region to accommodate the large conformational change required for domain swapping. While attempting to engineer a homodimer from a 51-amino-acid fragment of the monomeric protein engrailed homeodomain (ENH), we had instead generated a domain-swapped dimer (ENH_DsD). MD simulations on these proteins showed increased B-factors derived from MD simulation in the hinge loop of the ENH_DsD domain-swapped dimer relative to monomeric ENH. Two point mutants of ENH_DsD designed to recover the monomeric fold were then tested with an MD simulation protocol. The MD simulations suggested that one of these mutants would adopt the target monomeric structure, which was subsequently confirmed by X-ray crystallography. Copyright © 2015. Published by Elsevier Ltd.

Consequences of nonclassical measurement for the algorithmic description of continuous dynamical systems

NASA Technical Reports Server (NTRS)

Fields, Chris

1989-01-01

Continuous dynamical systems intuitively seem capable of more complex behavior than discrete systems. If analyzed in the framework of the traditional theory of computation, a continuous dynamical system with countably many quasistable states has at least the computational power of a universal Turing machine. Such an analysis assumes, however, the classical notion of measurement. If measurement is viewed nonclassically, a continuous dynamical system cannot, even in principle, exhibit behavior that cannot be simulated by a universal Turing machine.

Consequences of nonclassical measurement for the algorithmic description of continuous dynamical systems

NASA Technical Reports Server (NTRS)

Fields, Chris

1989-01-01

Continuous dynamical systems intuitively seem capable of more complex behavior than discrete systems. If analyzed in the framework of the traditional theory of computation, a continuous dynamical system with countablely many quasistable states has at least the computational power of a universal Turing machine. Such an analyses assumes, however, the classical notion of measurement. If measurement is viewed nonclassically, a continuous dynamical system cannot, even in principle, exhibit behavior that cannot be simulated by a universal Turing machine.

Computer Series, 29: Bits and Pieces, 10.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1982-01-01

Describes computer programs (available from authors) including molecular input to computer, programs for quantum chemistry, library orientation to technical literature, plotting potentiometric titration data, simulating oscilloscope curves, organic qualitative analysis with dynamic graphics, extended Huckel calculations, and calculator programs…

Computational Modeling of the Dolphin Kick in Competitive Swimming

NASA Astrophysics Data System (ADS)

Loebbeck, A.; Mark, R.; Bhanot, G.

2005-11-01

Numerical simulations are being used to study the fluid dynamics of the dolphin kick in competitive swimming. This stroke is performed underwater after starts and turns and involves an undulatory motion of the body. Highly detailed laser body scans of elite swimmers are used and the kinematics of the dolphin kick is recreated from videos of Olympic level swimmers. We employ a parallelized immersed boundary method to simulate the flow associated with this stroke in all its complexity. The simulations provide a first of its kind glimpse of the fluid and vortex dynamics associated with this stroke and hydrodynamic force computations allow us to gain a better understanding of the thrust producing mechanisms.

Event- and Time-Driven Techniques Using Parallel CPU-GPU Co-processing for Spiking Neural Networks

PubMed Central

Naveros, Francisco; Garrido, Jesus A.; Carrillo, Richard R.; Ros, Eduardo; Luque, Niceto R.

2017-01-01

Modeling and simulating the neural structures which make up our central neural system is instrumental for deciphering the computational neural cues beneath. Higher levels of biological plausibility usually impose higher levels of complexity in mathematical modeling, from neural to behavioral levels. This paper focuses on overcoming the simulation problems (accuracy and performance) derived from using higher levels of mathematical complexity at a neural level. This study proposes different techniques for simulating neural models that hold incremental levels of mathematical complexity: leaky integrate-and-fire (LIF), adaptive exponential integrate-and-fire (AdEx), and Hodgkin-Huxley (HH) neural models (ranged from low to high neural complexity). The studied techniques are classified into two main families depending on how the neural-model dynamic evaluation is computed: the event-driven or the time-driven families. Whilst event-driven techniques pre-compile and store the neural dynamics within look-up tables, time-driven techniques compute the neural dynamics iteratively during the simulation time. We propose two modifications for the event-driven family: a look-up table recombination to better cope with the incremental neural complexity together with a better handling of the synchronous input activity. Regarding the time-driven family, we propose a modification in computing the neural dynamics: the bi-fixed-step integration method. This method automatically adjusts the simulation step size to better cope with the stiffness of the neural model dynamics running in CPU platforms. One version of this method is also implemented for hybrid CPU-GPU platforms. Finally, we analyze how the performance and accuracy of these modifications evolve with increasing levels of neural complexity. We also demonstrate how the proposed modifications which constitute the main contribution of this study systematically outperform the traditional event- and time-driven techniques under increasing levels of neural complexity. PMID:28223930

Quantum chemistry simulation on quantum computers: theories and experiments.

PubMed

Lu, Dawei; Xu, Boruo; Xu, Nanyang; Li, Zhaokai; Chen, Hongwei; Peng, Xinhua; Xu, Ruixue; Du, Jiangfeng

2012-07-14

It has been claimed that quantum computers can mimic quantum systems efficiently in the polynomial scale. Traditionally, those simulations are carried out numerically on classical computers, which are inevitably confronted with the exponential growth of required resources, with the increasing size of quantum systems. Quantum computers avoid this problem, and thus provide a possible solution for large quantum systems. In this paper, we first discuss the ideas of quantum simulation, the background of quantum simulators, their categories, and the development in both theories and experiments. We then present a brief introduction to quantum chemistry evaluated via classical computers followed by typical procedures of quantum simulation towards quantum chemistry. Reviewed are not only theoretical proposals but also proof-of-principle experimental implementations, via a small quantum computer, which include the evaluation of the static molecular eigenenergy and the simulation of chemical reaction dynamics. Although the experimental development is still behind the theory, we give prospects and suggestions for future experiments. We anticipate that in the near future quantum simulation will become a powerful tool for quantum chemistry over classical computations.

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

NASA Astrophysics Data System (ADS)

Andrade, Xavier

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

Solid-liquid phase coexistence of alkali nitrates from molecular dynamics simulations.

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

Jayaraman, Saivenkataraman

2010-03-01

Alkali nitrate eutectic mixtures are finding application as industrial heat transfer fluids in concentrated solar power generation systems. An important property for such applications is the melting point, or phase coexistence temperature. We have computed melting points for lithium, sodium and potassium nitrate from molecular dynamics simulations using a recently developed method, which uses thermodynamic integration to compute the free energy difference between the solid and liquid phases. The computed melting point for NaNO3 was within 15K of its experimental value, while for LiNO3 and KNO3, the computed melting points were within 100K of the experimental values [4]. We aremore » currently extending the approach to calculate melting temperatures for binary mixtures of lithium and sodium nitrate.« less

Substructured multibody molecular dynamics.

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

Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James

2006-11-01

We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

Non-linear quantum-classical scheme to simulate non-equilibrium strongly correlated fermionic many-body dynamics

PubMed Central

Kreula, J. M.; Clark, S. R.; Jaksch, D.

2016-01-01

We propose a non-linear, hybrid quantum-classical scheme for simulating non-equilibrium dynamics of strongly correlated fermions described by the Hubbard model in a Bethe lattice in the thermodynamic limit. Our scheme implements non-equilibrium dynamical mean field theory (DMFT) and uses a digital quantum simulator to solve a quantum impurity problem whose parameters are iterated to self-consistency via a classically computed feedback loop where quantum gate errors can be partly accounted for. We analyse the performance of the scheme in an example case. PMID:27609673

N-MODY: A Code for Collisionless N-body Simulations in Modified Newtonian Dynamics

NASA Astrophysics Data System (ADS)

Londrillo, Pasquale; Nipoti, Carlo

2011-02-01

N-MODY is a parallel particle-mesh code for collisionless N-body simulations in modified Newtonian dynamics (MOND). N-MODY is based on a numerical potential solver in spherical coordinates that solves the non-linear MOND field equation, and is ideally suited to simulate isolated stellar systems. N-MODY can be used also to compute the MOND potential of arbitrary static density distributions. A few applications of N-MODY indicate that some astrophysically relevant dynamical processes are profoundly different in MOND and in Newtonian gravity with dark matter.

Integration of scheduling and discrete event simulation systems to improve production flow planning

NASA Astrophysics Data System (ADS)

Krenczyk, D.; Paprocka, I.; Kempa, W. M.; Grabowik, C.; Kalinowski, K.

2016-08-01

The increased availability of data and computer-aided technologies such as MRPI/II, ERP and MES system, allowing producers to be more adaptive to market dynamics and to improve production scheduling. Integration of production scheduling and computer modelling, simulation and visualization systems can be useful in the analysis of production system constraints related to the efficiency of manufacturing systems. A integration methodology based on semi-automatic model generation method for eliminating problems associated with complexity of the model and labour-intensive and time-consuming process of simulation model creation is proposed. Data mapping and data transformation techniques for the proposed method have been applied. This approach has been illustrated through examples of practical implementation of the proposed method using KbRS scheduling system and Enterprise Dynamics simulation system.

First-principles simulations of heat transport

NASA Astrophysics Data System (ADS)

Puligheddu, Marcello; Gygi, Francois; Galli, Giulia

2017-11-01

Advances in understanding heat transport in solids were recently reported by both experiment and theory. However an efficient and predictive quantum simulation framework to investigate thermal properties of solids, with the same complexity as classical simulations, has not yet been developed. Here we present a method to compute the thermal conductivity of solids by performing ab initio molecular dynamics at close to equilibrium conditions, which only requires calculations of first-principles trajectories and atomic forces, thus avoiding direct computation of heat currents and energy densities. In addition the method requires much shorter sequential simulation times than ordinary molecular dynamics techniques, making it applicable within density functional theory. We discuss results for a representative oxide, MgO, at different temperatures and for ordered and nanostructured morphologies, showing the performance of the method in different conditions.

Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale.

PubMed

Chavent, Matthieu; Duncan, Anna L; Sansom, Mark Sp

2016-10-01

Molecular dynamics simulations provide a computational tool to probe membrane proteins and systems at length scales ranging from nanometers to close to a micrometer, and on microsecond timescales. All atom and coarse-grained simulations may be used to explore in detail the interactions of membrane proteins and specific lipids, yielding predictions of lipid binding sites in good agreement with available structural data. Building on the success of protein-lipid interaction simulations, larger scale simulations reveal crowding and clustering of proteins, resulting in slow and anomalous diffusional dynamics, within realistic models of cell membranes. Current methods allow near atomic resolution simulations of small membrane organelles, and of enveloped viruses to be performed, revealing key aspects of their structure and functionally important dynamics. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Model reduction for agent-based social simulation: coarse-graining a civil violence model.

PubMed

Zou, Yu; Fonoberov, Vladimir A; Fonoberova, Maria; Mezic, Igor; Kevrekidis, Ioannis G

2012-06-01

Agent-based modeling (ABM) constitutes a powerful computational tool for the exploration of phenomena involving emergent dynamic behavior in the social sciences. This paper demonstrates a computer-assisted approach that bridges the significant gap between the single-agent microscopic level and the macroscopic (coarse-grained population) level, where fundamental questions must be rationally answered and policies guiding the emergent dynamics devised. Our approach will be illustrated through an agent-based model of civil violence. This spatiotemporally varying ABM incorporates interactions between a heterogeneous population of citizens [active (insurgent), inactive, or jailed] and a population of police officers. Detailed simulations exhibit an equilibrium punctuated by periods of social upheavals. We show how to effectively reduce the agent-based dynamics to a stochastic model with only two coarse-grained degrees of freedom: the number of jailed citizens and the number of active ones. The coarse-grained model captures the ABM dynamics while drastically reducing the computation time (by a factor of approximately 20).

Model reduction for agent-based social simulation: Coarse-graining a civil violence model

NASA Astrophysics Data System (ADS)

Zou, Yu; Fonoberov, Vladimir A.; Fonoberova, Maria; Mezic, Igor; Kevrekidis, Ioannis G.

2012-06-01

Agent-based modeling (ABM) constitutes a powerful computational tool for the exploration of phenomena involving emergent dynamic behavior in the social sciences. This paper demonstrates a computer-assisted approach that bridges the significant gap between the single-agent microscopic level and the macroscopic (coarse-grained population) level, where fundamental questions must be rationally answered and policies guiding the emergent dynamics devised. Our approach will be illustrated through an agent-based model of civil violence. This spatiotemporally varying ABM incorporates interactions between a heterogeneous population of citizens [active (insurgent), inactive, or jailed] and a population of police officers. Detailed simulations exhibit an equilibrium punctuated by periods of social upheavals. We show how to effectively reduce the agent-based dynamics to a stochastic model with only two coarse-grained degrees of freedom: the number of jailed citizens and the number of active ones. The coarse-grained model captures the ABM dynamics while drastically reducing the computation time (by a factor of approximately 20).

A new physical model with multilayer architecture for facial expression animation using dynamic adaptive mesh.

PubMed

Zhang, Yu; Prakash, Edmond C; Sung, Eric

2004-01-01

This paper presents a new physically-based 3D facial model based on anatomical knowledge which provides high fidelity for facial expression animation while optimizing the computation. Our facial model has a multilayer biomechanical structure, incorporating a physically-based approximation to facial skin tissue, a set of anatomically-motivated facial muscle actuators, and underlying skull structure. In contrast to existing mass-spring-damper (MSD) facial models, our dynamic skin model uses the nonlinear springs to directly simulate the nonlinear visco-elastic behavior of soft tissue and a new kind of edge repulsion spring is developed to prevent collapse of the skin model. Different types of muscle models have been developed to simulate distribution of the muscle force applied on the skin due to muscle contraction. The presence of the skull advantageously constrain the skin movements, resulting in more accurate facial deformation and also guides the interactive placement of facial muscles. The governing dynamics are computed using a local semi-implicit ODE solver. In the dynamic simulation, an adaptive refinement automatically adapts the local resolution at which potential inaccuracies are detected depending on local deformation. The method, in effect, ensures the required speedup by concentrating computational time only where needed while ensuring realistic behavior within a predefined error threshold. This mechanism allows more pleasing animation results to be produced at a reduced computational cost.

Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide-and-conquer, density-functional tight-binding, and massively parallel computation.

PubMed

Nishizawa, Hiroaki; Nishimura, Yoshifumi; Kobayashi, Masato; Irle, Stephan; Nakai, Hiromi

2016-08-05

The linear-scaling divide-and-conquer (DC) quantum chemical methodology is applied to the density-functional tight-binding (DFTB) theory to develop a massively parallel program that achieves on-the-fly molecular reaction dynamics simulations of huge systems from scratch. The functions to perform large scale geometry optimization and molecular dynamics with DC-DFTB potential energy surface are implemented to the program called DC-DFTB-K. A novel interpolation-based algorithm is developed for parallelizing the determination of the Fermi level in the DC method. The performance of the DC-DFTB-K program is assessed using a laboratory computer and the K computer. Numerical tests show the high efficiency of the DC-DFTB-K program, a single-point energy gradient calculation of a one-million-atom system is completed within 60 s using 7290 nodes of the K computer. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Applications of Computational Methods for Dynamic Stability and Control Derivatives

NASA Technical Reports Server (NTRS)

Green, Lawrence L.; Spence, Angela M.

2004-01-01

Initial steps in the application o f a low-order panel method computational fluid dynamic (CFD) code to the calculation of aircraft dynamic stability and control (S&C) derivatives are documented. Several capabilities, unique to CFD but not unique to this particular demonstration, are identified and demonstrated in this paper. These unique capabilities complement conventional S&C techniques and they include the ability to: 1) perform maneuvers without the flow-kinematic restrictions and support interference commonly associated with experimental S&C facilities, 2) easily simulate advanced S&C testing techniques, 3) compute exact S&C derivatives with uncertainty propagation bounds, and 4) alter the flow physics associated with a particular testing technique from those observed in a wind or water tunnel test in order to isolate effects. Also presented are discussions about some computational issues associated with the simulation of S&C tests and selected results from numerous surface grid resolution studies performed during the course of the study.

Computational fluid dynamics - The coming revolution

NASA Technical Reports Server (NTRS)

Graves, R. A., Jr.

1982-01-01

The development of aerodynamic theory is traced from the days of Aristotle to the present, with the next stage in computational fluid dynamics dependent on superspeed computers for flow calculations. Additional attention is given to the history of numerical methods inherent in writing computer codes applicable to viscous and inviscid analyses for complex configurations. The advent of the superconducting Josephson junction is noted to place configurational demands on computer design to avoid limitations imposed by the speed of light, and a Japanese projection of a computer capable of several hundred billion operations/sec is mentioned. The NASA Numerical Aerodynamic Simulator is described, showing capabilities of a billion operations/sec with a memory of 240 million words using existing technology. Near-term advances in fluid dynamics are discussed.

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

PubMed

Marsalek, Ondrej; Markland, Thomas E

2016-02-07

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

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/.

A resilient and efficient CFD framework: Statistical learning tools for multi-fidelity and heterogeneous information fusion

NASA Astrophysics Data System (ADS)

Lee, Seungjoon; Kevrekidis, Ioannis G.; Karniadakis, George Em

2017-09-01

Exascale-level simulations require fault-resilient algorithms that are robust against repeated and expected software and/or hardware failures during computations, which may render the simulation results unsatisfactory. If each processor can share some global information about the simulation from a coarse, limited accuracy but relatively costless auxiliary simulator we can effectively fill-in the missing spatial data at the required times by a statistical learning technique - multi-level Gaussian process regression, on the fly; this has been demonstrated in previous work [1]. Based on the previous work, we also employ another (nonlinear) statistical learning technique, Diffusion Maps, that detects computational redundancy in time and hence accelerate the simulation by projective time integration, giving the overall computation a "patch dynamics" flavor. Furthermore, we are now able to perform information fusion with multi-fidelity and heterogeneous data (including stochastic data). Finally, we set the foundations of a new framework in CFD, called patch simulation, that combines information fusion techniques from, in principle, multiple fidelity and resolution simulations (and even experiments) with a new adaptive timestep refinement technique. We present two benchmark problems (the heat equation and the Navier-Stokes equations) to demonstrate the new capability that statistical learning tools can bring to traditional scientific computing algorithms. For each problem, we rely on heterogeneous and multi-fidelity data, either from a coarse simulation of the same equation or from a stochastic, particle-based, more "microscopic" simulation. We consider, as such "auxiliary" models, a Monte Carlo random walk for the heat equation and a dissipative particle dynamics (DPD) model for the Navier-Stokes equations. More broadly, in this paper we demonstrate the symbiotic and synergistic combination of statistical learning, domain decomposition, and scientific computing in exascale simulations.

Clustering molecular dynamics trajectories for optimizing docking experiments.

PubMed

De Paris, Renata; Quevedo, Christian V; Ruiz, Duncan D; Norberto de Souza, Osmar; Barros, Rodrigo C

2015-01-01

Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR) model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand.

Hybrid classical/quantum simulation for infrared spectroscopy of water

NASA Astrophysics Data System (ADS)

Maekawa, Yuki; Sasaoka, Kenji; Ube, Takuji; Ishiguro, Takashi; Yamamoto, Takahiro

2018-05-01

We have developed a hybrid classical/quantum simulation method to calculate the infrared (IR) spectrum of water. The proposed method achieves much higher accuracy than conventional classical molecular dynamics (MD) simulations at a much lower computational cost than ab initio MD simulations. The IR spectrum of water is obtained as an ensemble average of the eigenvalues of the dynamical matrix constructed by ab initio calculations, using the positions of oxygen atoms that constitute water molecules obtained from the classical MD simulation. The calculated IR spectrum is in excellent agreement with the experimental IR spectrum.

Structured Overlapping Grid Simulations of Contra-rotating Open Rotor Noise

NASA Technical Reports Server (NTRS)

Housman, Jeffrey A.; Kiris, Cetin C.

2015-01-01

Computational simulations using structured overlapping grids with the Launch Ascent and Vehicle Aerodynamics (LAVA) solver framework are presented for predicting tonal noise generated by a contra-rotating open rotor (CROR) propulsion system. A coupled Computational Fluid Dynamics (CFD) and Computational AeroAcoustics (CAA) numerical approach is applied. Three-dimensional time-accurate hybrid Reynolds Averaged Navier-Stokes/Large Eddy Simulation (RANS/LES) CFD simulations are performed in the inertial frame, including dynamic moving grids, using a higher-order accurate finite difference discretization on structured overlapping grids. A higher-order accurate free-stream preserving metric discretization with discrete enforcement of the Geometric Conservation Law (GCL) on moving curvilinear grids is used to create an accurate, efficient, and stable numerical scheme. The aeroacoustic analysis is based on a permeable surface Ffowcs Williams-Hawkings (FW-H) approach, evaluated in the frequency domain. A time-step sensitivity study was performed using only the forward row of blades to determine an adequate time-step. The numerical approach is validated against existing wind tunnel measurements.

Digital system for structural dynamics simulation

NASA Technical Reports Server (NTRS)

Krauter, A. I.; Lagace, L. J.; Wojnar, M. K.; Glor, C.

1982-01-01

State-of-the-art digital hardware and software for the simulation of complex structural dynamic interactions, such as those which occur in rotating structures (engine systems). System were incorporated in a designed to use an array of processors in which the computation for each physical subelement or functional subsystem would be assigned to a single specific processor in the simulator. These node processors are microprogrammed bit-slice microcomputers which function autonomously and can communicate with each other and a central control minicomputer over parallel digital lines. Inter-processor nearest neighbor communications busses pass the constants which represent physical constraints and boundary conditions. The node processors are connected to the six nearest neighbor node processors to simulate the actual physical interface of real substructures. Computer generated finite element mesh and force models can be developed with the aid of the central control minicomputer. The control computer also oversees the animation of a graphics display system, disk-based mass storage along with the individual processing elements.

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.

Atomic detail brownian dynamics simulations of concentrated protein solutions with a mean field treatment of hydrodynamic interactions.

PubMed

Mereghetti, Paolo; Wade, Rebecca C

2012-07-26

High macromolecular concentrations are a distinguishing feature of living organisms. Understanding how the high concentration of solutes affects the dynamic properties of biological macromolecules is fundamental for the comprehension of biological processes in living systems. In this paper, we describe the implementation of mean field models of translational and rotational hydrodynamic interactions into an atomically detailed many-protein brownian dynamics simulation method. Concentrated solutions (30-40% volume fraction) of myoglobin, hemoglobin A, and sickle cell hemoglobin S were simulated, and static structure factors, oligomer formation, and translational and rotational self-diffusion coefficients were computed. Good agreement of computed properties with available experimental data was obtained. The results show the importance of both solvent mediated interactions and weak protein-protein interactions for accurately describing the dynamics and the association properties of concentrated protein solutions. Specifically, they show a qualitative difference in the translational and rotational dynamics of the systems studied. Although the translational diffusion coefficient is controlled by macromolecular shape and hydrodynamic interactions, the rotational diffusion coefficient is affected by macromolecular shape, direct intermolecular interactions, and both translational and rotational hydrodynamic interactions.

Molecular Dynamics Simulations of Ion Transport and Mechanisms in Polymer Nanocomposites

NASA Astrophysics Data System (ADS)

Mogurampelly, Santosh; Ganesan, Venkat

2015-03-01

Using all atom molecular dynamics and trajectory-extending kinetic Monte Carlo simulations, we study the influence of Al2O3 nanoparticles on the transport properties of Li+ ions in polymer electrolytes consisting of polyethylene oxide (PEO) melt solvated with LiBF4 salt. We observe that the nanoparticles have a strong influence on polymer segmental dynamics which in turn correlates with the mobility of Li+ ions. Explicitly, polymer segmental relaxation times and Li+ ion residence times around polymer were found to increase with the addition of nanoparticles. We also observe that increasing short range repulsive interactions between nanoparticles and polymer membrane leads to increasing polymer dynamics and ion mobility. Overall, our simulation results suggest that nanoparticle induced changes in conformational and dynamic properties of the polymer influences the ion mobilities in polymer electrolytes and suggests possible directions for using such findings to improve the polymer matrix conductivity. The authors acknowledge the Texas Advanced Computing Center (TACC) at The University of Texas at Austin for providing computing resources that have contributed to the research.

Examining Extreme Events Using Dynamically Downscaled 12-km WRF Simulations

EPA Science Inventory

Continued improvements in the speed and availability of computational resources have allowed dynamical downscaling of global climate model (GCM) projections to be conducted at increasingly finer grid scales and over extended time periods. The implementation of dynamical downscal...

Visual Computing Environment Workshop

NASA Technical Reports Server (NTRS)

Lawrence, Charles (Compiler)

1998-01-01

The Visual Computing Environment (VCE) is a framework for intercomponent and multidisciplinary computational simulations. Many current engineering analysis codes simulate various aspects of aircraft engine operation. For example, existing computational fluid dynamics (CFD) codes can model the airflow through individual engine components such as the inlet, compressor, combustor, turbine, or nozzle. Currently, these codes are run in isolation, making intercomponent and complete system simulations very difficult to perform. In addition, management and utilization of these engineering codes for coupled component simulations is a complex, laborious task, requiring substantial experience and effort. To facilitate multicomponent aircraft engine analysis, the CFD Research Corporation (CFDRC) is developing the VCE system. This system, which is part of NASA's Numerical Propulsion Simulation System (NPSS) program, can couple various engineering disciplines, such as CFD, structural analysis, and thermal analysis.

1D-3D hybrid modeling-from multi-compartment models to full resolution models in space and time.

PubMed

Grein, Stephan; Stepniewski, Martin; Reiter, Sebastian; Knodel, Markus M; Queisser, Gillian

2014-01-01

Investigation of cellular and network dynamics in the brain by means of modeling and simulation has evolved into a highly interdisciplinary field, that uses sophisticated modeling and simulation approaches to understand distinct areas of brain function. Depending on the underlying complexity, these models vary in their level of detail, in order to cope with the attached computational cost. Hence for large network simulations, single neurons are typically reduced to time-dependent signal processors, dismissing the spatial aspect of each cell. For single cell or networks with relatively small numbers of neurons, general purpose simulators allow for space and time-dependent simulations of electrical signal processing, based on the cable equation theory. An emerging field in Computational Neuroscience encompasses a new level of detail by incorporating the full three-dimensional morphology of cells and organelles into three-dimensional, space and time-dependent, simulations. While every approach has its advantages and limitations, such as computational cost, integrated and methods-spanning simulation approaches, depending on the network size could establish new ways to investigate the brain. In this paper we present a hybrid simulation approach, that makes use of reduced 1D-models using e.g., the NEURON simulator-which couples to fully resolved models for simulating cellular and sub-cellular dynamics, including the detailed three-dimensional morphology of neurons and organelles. In order to couple 1D- and 3D-simulations, we present a geometry-, membrane potential- and intracellular concentration mapping framework, with which graph- based morphologies, e.g., in the swc- or hoc-format, are mapped to full surface and volume representations of the neuron and computational data from 1D-simulations can be used as boundary conditions for full 3D simulations and vice versa. Thus, established models and data, based on general purpose 1D-simulators, can be directly coupled to the emerging field of fully resolved, highly detailed 3D-modeling approaches. We present the developed general framework for 1D/3D hybrid modeling and apply it to investigate electrically active neurons and their intracellular spatio-temporal calcium dynamics.

Perspectives on the Future of CFD

NASA Technical Reports Server (NTRS)

Kwak, Dochan

2000-01-01

This viewgraph presentation gives an overview of the future of computational fluid dynamics (CFD), which in the past has pioneered the field of flow simulation. Over time CFD has progressed as computing power. Numerical methods have been advanced as CPU and memory capacity increases. Complex configurations are routinely computed now and direct numerical simulations (DNS) and large eddy simulations (LES) are used to study turbulence. As the computing resources changed to parallel and distributed platforms, computer science aspects such as scalability (algorithmic and implementation) and portability and transparent codings have advanced. Examples of potential future (or current) challenges include risk assessment, limitations of the heuristic model, and the development of CFD and information technology (IT) tools.

Discrete Event-based Performance Prediction for Temperature Accelerated Dynamics

NASA Astrophysics Data System (ADS)

Junghans, Christoph; Mniszewski, Susan; Voter, Arthur; Perez, Danny; Eidenbenz, Stephan

2014-03-01

We present an example of a new class of tools that we call application simulators, parameterized fast-running proxies of large-scale scientific applications using parallel discrete event simulation (PDES). We demonstrate our approach with a TADSim application simulator that models the Temperature Accelerated Dynamics (TAD) method, which is an algorithmically complex member of the Accelerated Molecular Dynamics (AMD) family. The essence of the TAD application is captured without the computational expense and resource usage of the full code. We use TADSim to quickly characterize the runtime performance and algorithmic behavior for the otherwise long-running simulation code. We further extend TADSim to model algorithm extensions to standard TAD, such as speculative spawning of the compute-bound stages of the algorithm, and predict performance improvements without having to implement such a method. 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 into the TAD algorithm behavior and suggested extensions to the TAD method.

Molecular dynamics simulations of thermally activated edge dislocation unpinning from voids in α -Fe

NASA Astrophysics Data System (ADS)

Byggmästar, J.; Granberg, F.; Nordlund, K.

2017-10-01

In this study, thermal unpinning of edge dislocations from voids in α -Fe is investigated by means of molecular dynamics simulations. The activation energy as a function of shear stress and temperature is systematically determined. Simulations with a constant applied stress are compared with dynamic simulations with a constant strain rate. We found that a constant applied stress results in a temperature-dependent activation energy. The temperature dependence is attributed to the elastic softening of iron. If the stress is normalized with the softening of the specific shear modulus, the activation energy is shown to be temperature-independent. From the dynamic simulations, the activation energy as a function of critical shear stress was determined using previously developed methods. The results from the dynamic simulations are in good agreement with the constant stress simulations, after the normalization. This indicates that the computationally more efficient dynamic method can be used to obtain the activation energy as a function of stress and temperature. The obtained relation between stress, temperature, and activation energy can be used to introduce a stochastic unpinning event in larger-scale simulation methods, such as discrete dislocation dynamics.

Computation of magnetic suspension of maglev systems using dynamic circuit theory

NASA Technical Reports Server (NTRS)

He, J. L.; Rote, D. M.; Coffey, H. T.

1992-01-01

Dynamic circuit theory is applied to several magnetic suspensions associated with maglev systems. These suspension systems are the loop-shaped coil guideway, the figure-eight-shaped null-flux coil guideway, and the continuous sheet guideway. Mathematical models, which can be used for the development of computer codes, are provided for each of these suspension systems. The differences and similarities of the models in using dynamic circuit theory are discussed in the paper. The paper emphasizes the transient and dynamic analysis and computer simulation of maglev systems. In general, the method discussed here can be applied to many electrodynamic suspension system design concepts. It is also suited for the computation of the performance of maglev propulsion systems. Numerical examples are presented in the paper.

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.

Computational Modeling and Simulations of Bioparticle Internalization Through Clathrin-mediated Endocytosis

NASA Astrophysics Data System (ADS)

Deng, Hua; Dutta, Prashanta; Liu, Jin

2016-11-01

Clathrin-mediated endocytosis (CME) is one of the most important endocytic pathways for the internalization of bioparticles at lipid membrane of cells, which plays crucial roles in fundamental understanding of viral infections and interacellular/transcelluar targeted drug delivery. During CME, highly dynamic clathrin-coated pit (CCP), formed by the growth of ordered clathrin lattices, is the key scaffolding component that drives the deformation of plasma membrane. Experimental studies have shown that CCP alone can provide sufficient membrane curvature for facilitating membrane invagination. However, currently there is no computational model that could couple cargo receptor binding with membrane invagination process, nor simulations of the dynamic growing process of CCP. We develop a stochastic computational model for the clathrin-mediated endocytosis based on Metropolis Monte Carlo simulations. In our model, the energetic costs of bending membrane and CCP are linked with antigen-antibody interactions. The assembly of clathrin lattices is a dynamic process that correlates with antigen-antibody bond formation. This model helps study the membrane deformation and the effects of CCP during functionalized bioparticles internalization through CME. This work is supported by NSF Grants: CBET-1250107 and CBET-1604211.

Simulations of High Speed Fragment Trajectories

NASA Astrophysics Data System (ADS)

Yeh, Peter; Attaway, Stephen; Arunajatesan, Srinivasan; Fisher, Travis

2017-11-01

Flying shrapnel from an explosion are capable of traveling at supersonic speeds and distances much farther than expected due to aerodynamic interactions. Predicting the trajectories and stable tumbling modes of arbitrary shaped fragments is a fundamental problem applicable to range safety calculations, damage assessment, and military technology. Traditional approaches rely on characterizing fragment flight using a single drag coefficient, which may be inaccurate for fragments with large aspect ratios. In our work we develop a procedure to simulate trajectories of arbitrary shaped fragments with higher fidelity using high performance computing. We employ a two-step approach in which the force and moment coefficients are first computed as a function of orientation using compressible computational fluid dynamics. The force and moment data are then input into a six-degree-of-freedom rigid body dynamics solver to integrate trajectories in time. Results of these high fidelity simulations allow us to further understand the flight dynamics and tumbling modes of a single fragment. Furthermore, we use these results to determine the validity and uncertainty of inexpensive methods such as the single drag coefficient model.

Composite mechanics for engine structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

1987-01-01

Recent research activities and accomplishments at Lewis Research Center on composite mechanics for engine structures are summarized. The activities focused mainly on developing procedures for the computational simulation of composite intrinsic and structural behavior. The computational simulation encompasses all aspects of composite mechanics, advanced three-dimensional finite-element methods, damage tolerance, composite structural and dynamic response, and structural tailoring and optimization.

Composite mechanics for engine structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

1989-01-01

Recent research activities and accomplishments at Lewis Research Center on composite mechanics for engine structures are summarized. The activities focused mainly on developing procedures for the computational simulation of composite intrinsic and structural behavior. The computational simulation encompasses all aspects of composite mechanics, advanced three-dimensional finite-element methods, damage tolerance, composite structural and dynamic response, and structural tailoring and optimization.

Interactive Computer Simulation and Animation for Improving Student Learning of Particle Kinetics

ERIC Educational Resources Information Center

Fang, N.; Guo, Y.

2016-01-01

Computer simulation and animation (CSA) has been receiving growing attention and wide application in engineering education in recent years. A new interactive CSA module was developed in the present study to improve student learning of particle kinetics in an undergraduate engineering dynamics course. The unique feature of this CSA module is that…

Dynamic stability experiment of Maglev systems

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

Cai, Y.; Mulcahy, T.M.; Chen, S.S.

1995-04-01

This report summarizes the research performed on Maglev vehicle dynamic stability at Argonne National Laboratory during the past few years. It also documents magnetic-force data obtained from both measurements and calculations. Because dynamic instability is not acceptable for any commercial Maglev system, it is important to consider this phenomenon in the development of all Maglev systems. This report presents dynamic stability experiments on Maglev systems and compares their numerical simulation with predictions calculated by a nonlinear dynamic computer code. Instabilities of an electrodynamic system (EDS)-type vehicle model were obtained from both experimental observations and computer simulations for a five-degree-of-freedom Maglevmore » vehicle moving on a guideway consisting of double L-shaped aluminum segments attached to a rotating wheel. The experimental and theoretical analyses developed in this study identify basic stability characteristics and future research needs of Maglev systems.« less

Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics.

PubMed

Zheng, Mo; Li, Xiaoxia; Guo, Li

2013-04-01

Reactive force field (ReaxFF), a recent and novel bond order potential, allows for reactive molecular dynamics (ReaxFF MD) simulations for modeling larger and more complex molecular systems involving chemical reactions when compared with computation intensive quantum mechanical methods. However, ReaxFF MD can be approximately 10-50 times slower than classical MD due to its explicit modeling of bond forming and breaking, the dynamic charge equilibration at each time-step, and its one order smaller time-step than the classical MD, all of which pose significant computational challenges in simulation capability to reach spatio-temporal scales of nanometers and nanoseconds. The very recent advances of graphics processing unit (GPU) provide not only highly favorable performance for GPU enabled MD programs compared with CPU implementations but also an opportunity to manage with the computing power and memory demanding nature imposed on computer hardware by ReaxFF MD. In this paper, we present the algorithms of GMD-Reax, the first GPU enabled ReaxFF MD program with significantly improved performance surpassing CPU implementations on desktop workstations. The performance of GMD-Reax has been benchmarked on a PC equipped with a NVIDIA C2050 GPU for coal pyrolysis simulation systems with atoms ranging from 1378 to 27,283. GMD-Reax achieved speedups as high as 12 times faster than Duin et al.'s FORTRAN codes in Lammps on 8 CPU cores and 6 times faster than the Lammps' C codes based on PuReMD in terms of the simulation time per time-step averaged over 100 steps. GMD-Reax could be used as a new and efficient computational tool for exploiting very complex molecular reactions via ReaxFF MD simulation on desktop workstations. Copyright © 2013 Elsevier Inc. All rights reserved.

GPU-accelerated computing for Lagrangian coherent structures of multi-body gravitational regimes

NASA Astrophysics Data System (ADS)

Lin, Mingpei; Xu, Ming; Fu, Xiaoyu

2017-04-01

Based on a well-established theoretical foundation, Lagrangian Coherent Structures (LCSs) have elicited widespread research on the intrinsic structures of dynamical systems in many fields, including the field of astrodynamics. Although the application of LCSs in dynamical problems seems straightforward theoretically, its associated computational cost is prohibitive. We propose a block decomposition algorithm developed on Compute Unified Device Architecture (CUDA) platform for the computation of the LCSs of multi-body gravitational regimes. In order to take advantage of GPU's outstanding computing properties, such as Shared Memory, Constant Memory, and Zero-Copy, the algorithm utilizes a block decomposition strategy to facilitate computation of finite-time Lyapunov exponent (FTLE) fields of arbitrary size and timespan. Simulation results demonstrate that this GPU-based algorithm can satisfy double-precision accuracy requirements and greatly decrease the time needed to calculate final results, increasing speed by approximately 13 times. Additionally, this algorithm can be generalized to various large-scale computing problems, such as particle filters, constellation design, and Monte-Carlo simulation.

Finite-element approach to Brownian dynamics of polymers.

PubMed

Cyron, Christian J; Wall, Wolfgang A

2009-12-01

In the last decades simulation tools for Brownian dynamics of polymers have attracted more and more interest. Such simulation tools have been applied to a large variety of problems and accelerated the scientific progress significantly. However, the currently most frequently used explicit bead models exhibit severe limitations, especially with respect to time step size, the necessity of artificial constraints and the lack of a sound mathematical foundation. Here we present a framework for simulations of Brownian polymer dynamics based on the finite-element method. This approach allows simulating a wide range of physical phenomena at a highly attractive computational cost on the basis of a far-developed mathematical background.

Simulation of wetlands forest vegetation dynamics

USGS Publications Warehouse

Phipps, R.L.

1979-01-01

A computer program, SWAMP, was designed to simulate the effects of flood frequency and depth to water table on southern wetlands forest vegetation dynamics. By incorporating these hydrologic characteristics into the model, forest vegetation and vegetation dynamics can be simulated. The model, based on data from the White River National Wildlife Refuge near De Witt, Arkansas, "grows" individual trees on a 20 x 20-m plot taking into account effects on the tree growth of flooding, depth to water table, shade tolerance, overtopping and crowding, and probability of death and reproduction. A potential application of the model is illustrated with simulations of tree fruit production following flood-control implementation and lumbering. ?? 1979.

Molecular dynamics simulations of methane hydrate decomposition.

PubMed

Myshakin, Evgeniy M; Jiang, Hao; Warzinski, Robert P; Jordan, Kenneth D

2009-03-12

Molecular dynamics simulations have been carried out to study decomposition of methane hydrate at different cage occupancies. The decomposition rate is found to depend sensitively on the hydration number. The rate of the destruction of the cages displays Arrhenius behavior, consistent with an activated mechanism. During the simulations, reversible formation of partial water cages around methane molecules in the liquid was observed at the interface at temperatures above the computed hydrate decomposition temperature.

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

DOE PAGES

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

2015-04-08

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

Accelerating Time Integration for the Shallow Water Equations on the Sphere Using GPUs

DOE PAGES

Archibald, R.; Evans, K. J.; Salinger, A.

2015-06-01

The push towards larger and larger computational platforms has made it possible for climate simulations to resolve climate dynamics across multiple spatial and temporal scales. This direction in climate simulation has created a strong need to develop scalable timestepping methods capable of accelerating throughput on high performance computing. This study details the recent advances in the implementation of implicit time stepping of the spectral element dynamical core within the United States Department of Energy (DOE) Accelerated Climate Model for Energy (ACME) on graphical processing units (GPU) based machines. We demonstrate how solvers in the Trilinos project are interfaced with ACMEmore » and GPU kernels to increase computational speed of the residual calculations in the implicit time stepping method for the atmosphere dynamics. We demonstrate the optimization gains and data structure reorganization that facilitates the performance improvements.« less

High-order hydrodynamic algorithms for exascale computing

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

Morgan, Nathaniel Ray

Hydrodynamic algorithms are at the core of many laboratory missions ranging from simulating ICF implosions to climate modeling. The hydrodynamic algorithms commonly employed at the laboratory and in industry (1) typically lack requisite accuracy for complex multi- material vortical flows and (2) are not well suited for exascale computing due to poor data locality and poor FLOP/memory ratios. Exascale computing requires advances in both computer science and numerical algorithms. We propose to research the second requirement and create a new high-order hydrodynamic algorithm that has superior accuracy, excellent data locality, and excellent FLOP/memory ratios. This proposal will impact a broadmore » range of research areas including numerical theory, discrete mathematics, vorticity evolution, gas dynamics, interface instability evolution, turbulent flows, fluid dynamics and shock driven flows. If successful, the proposed research has the potential to radically transform simulation capabilities and help position the laboratory for computing at the exascale.« less

A Non-Intrusive Algorithm for Sensitivity Analysis of Chaotic Flow Simulations

NASA Technical Reports Server (NTRS)

Blonigan, Patrick J.; Wang, Qiqi; Nielsen, Eric J.; Diskin, Boris

2017-01-01

We demonstrate a novel algorithm for computing the sensitivity of statistics in chaotic flow simulations to parameter perturbations. The algorithm is non-intrusive but requires exposing an interface. Based on the principle of shadowing in dynamical systems, this algorithm is designed to reduce the effect of the sampling error in computing sensitivity of statistics in chaotic simulations. We compare the effectiveness of this method to that of the conventional finite difference method.

Hierarchical optimization for neutron scattering problems

DOE PAGES

Bao, Feng; Archibald, Rick; Bansal, Dipanshu; ...

2016-03-14

In this study, we present a scalable optimization method for neutron scattering problems that determines confidence regions of simulation parameters in lattice dynamics models used to fit neutron scattering data for crystalline solids. The method uses physics-based hierarchical dimension reduction in both the computational simulation domain and the parameter space. We demonstrate for silicon that after a few iterations the method converges to parameters values (interatomic force-constants) computed with density functional theory simulations.

Hierarchical optimization for neutron scattering problems

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

Bao, Feng; Archibald, Rick; Bansal, Dipanshu

In this study, we present a scalable optimization method for neutron scattering problems that determines confidence regions of simulation parameters in lattice dynamics models used to fit neutron scattering data for crystalline solids. The method uses physics-based hierarchical dimension reduction in both the computational simulation domain and the parameter space. We demonstrate for silicon that after a few iterations the method converges to parameters values (interatomic force-constants) computed with density functional theory simulations.

Adjoint-Based Aerodynamic Design of Complex Aerospace Configurations

NASA Technical Reports Server (NTRS)

Nielsen, Eric J.

2016-01-01

An overview of twenty years of adjoint-based aerodynamic design research at NASA Langley Research Center is presented. Adjoint-based algorithms provide a powerful tool for efficient sensitivity analysis of complex large-scale computational fluid dynamics (CFD) simulations. Unlike alternative approaches for which computational expense generally scales with the number of design parameters, adjoint techniques yield sensitivity derivatives of a simulation output with respect to all input parameters at the cost of a single additional simulation. With modern large-scale CFD applications often requiring millions of compute hours for a single analysis, the efficiency afforded by adjoint methods is critical in realizing a computationally tractable design optimization capability for such applications.

Investigation of different modeling approaches for computational fluid dynamics simulation of high-pressure rocket combustors

NASA Astrophysics Data System (ADS)

Ivancic, B.; Riedmann, H.; Frey, M.; Knab, O.; Karl, S.; Hannemann, K.

2016-07-01

The paper summarizes technical results and first highlights of the cooperation between DLR and Airbus Defence and Space (DS) within the work package "CFD Modeling of Combustion Chamber Processes" conducted in the frame of the Propulsion 2020 Project. Within the addressed work package, DLR Göttingen and Airbus DS Ottobrunn have identified several test cases where adequate test data are available and which can be used for proper validation of the computational fluid dynamics (CFD) tools. In this paper, the first test case, the Penn State chamber (RCM1), is discussed. Presenting the simulation results from three different tools, it is shown that the test case can be computed properly with steady-state Reynolds-averaged Navier-Stokes (RANS) approaches. The achieved simulation results reproduce the measured wall heat flux as an important validation parameter very well but also reveal some inconsistencies in the test data which are addressed in this paper.

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.

Dynamic Systems for Individual Tracking via Heterogeneous Information Integration and Crowd Source Distributed Simulation

DTIC Science & Technology

2015-12-04

51   6.6   Power Consumption: Communications ...simulations executing on mobile computing platforms, an area not widely studied to date in the distributed simulation research community . A...simulation community . These initial studies focused on two conservative synchronization algorithms widely used in the distributed simulation field

A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein.

PubMed

Xu, Mingyuan; Zhu, Tong; Zhang, John Z H

2018-01-01

A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC) method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA) 9 -NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

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.

Cross-scale MD simulations of dynamic strength of tantalum

NASA Astrophysics Data System (ADS)

Bulatov, Vasily

2017-06-01

Dislocations are ubiquitous in metals where their motion presents the dominant and often the only mode of plastic response to straining. Over the last 25 years computational prediction of plastic response in metals has relied on Discrete Dislocation Dynamics (DDD) as the most fundamental method to account for collective dynamics of moving dislocations. Here we present first direct atomistic MD simulations of dislocation-mediated plasticity that are sufficiently large and long to compute plasticity response of single crystal tantalum while tracing the underlying dynamics of dislocations in all atomistic details. Where feasible, direct MD simulations sidestep DDD altogether thus reducing uncertainties of strength predictions to those of the interatomic potential. In the specific context of shock-induced material dynamics, the same MD models predict when, under what conditions and how dislocations interact and compete with other fundamental mechanisms of dynamic response, e.g. twinning, phase-transformations, fracture. In collaboration with: Luis Zepeda-Ruiz, Lawrence Livermore National Laboratory; Alexander Stukowski, Technische Universitat Darmstadt; Tomas Oppelstrup, Lawrence Livermore National Laboratory. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Volterra representation enables modeling of complex synaptic nonlinear dynamics in large-scale simulations.

PubMed

Hu, Eric Y; Bouteiller, Jean-Marie C; Song, Dong; Baudry, Michel; Berger, Theodore W

2015-01-01

Chemical synapses are comprised of a wide collection of intricate signaling pathways involving complex dynamics. These mechanisms are often reduced to simple spikes or exponential representations in order to enable computer simulations at higher spatial levels of complexity. However, these representations cannot capture important nonlinear dynamics found in synaptic transmission. Here, we propose an input-output (IO) synapse model capable of generating complex nonlinear dynamics while maintaining low computational complexity. This IO synapse model is an extension of a detailed mechanistic glutamatergic synapse model capable of capturing the input-output relationships of the mechanistic model using the Volterra functional power series. We demonstrate that the IO synapse model is able to successfully track the nonlinear dynamics of the synapse up to the third order with high accuracy. We also evaluate the accuracy of the IO synapse model at different input frequencies and compared its performance with that of kinetic models in compartmental neuron models. Our results demonstrate that the IO synapse model is capable of efficiently replicating complex nonlinear dynamics that were represented in the original mechanistic model and provide a method to replicate complex and diverse synaptic transmission within neuron network simulations.

Volterra representation enables modeling of complex synaptic nonlinear dynamics in large-scale simulations

PubMed Central

Hu, Eric Y.; Bouteiller, Jean-Marie C.; Song, Dong; Baudry, Michel; Berger, Theodore W.

2015-01-01

Chemical synapses are comprised of a wide collection of intricate signaling pathways involving complex dynamics. These mechanisms are often reduced to simple spikes or exponential representations in order to enable computer simulations at higher spatial levels of complexity. However, these representations cannot capture important nonlinear dynamics found in synaptic transmission. Here, we propose an input-output (IO) synapse model capable of generating complex nonlinear dynamics while maintaining low computational complexity. This IO synapse model is an extension of a detailed mechanistic glutamatergic synapse model capable of capturing the input-output relationships of the mechanistic model using the Volterra functional power series. We demonstrate that the IO synapse model is able to successfully track the nonlinear dynamics of the synapse up to the third order with high accuracy. We also evaluate the accuracy of the IO synapse model at different input frequencies and compared its performance with that of kinetic models in compartmental neuron models. Our results demonstrate that the IO synapse model is capable of efficiently replicating complex nonlinear dynamics that were represented in the original mechanistic model and provide a method to replicate complex and diverse synaptic transmission within neuron network simulations. PMID:26441622

Computations of Combustion-Powered Actuation for Dynamic Stall Suppression

NASA Technical Reports Server (NTRS)

Jee, Solkeun; Bowles, Patrick O.; Matalanis, Claude G.; Min, Byung-Young; Wake, Brian E.; Crittenden, Tom; Glezer, Ari

2016-01-01

A computational framework for the simulation of dynamic stall suppression with combustion-powered actuation (COMPACT) is validated against wind tunnel experimental results on a VR-12 airfoil. COMPACT slots are located at 10% chord from the leading edge of the airfoil and directed tangentially along the suction-side surface. Helicopter rotor-relevant flow conditions are used in the study. A computationally efficient two-dimensional approach, based on unsteady Reynolds-averaged Navier-Stokes (RANS), is compared in detail against the baseline and the modified airfoil with COMPACT, using aerodynamic forces, pressure profiles, and flow-field data. The two-dimensional RANS approach predicts baseline static and dynamic stall very well. Most of the differences between the computational and experimental results are within two standard deviations of the experimental data. The current framework demonstrates an ability to predict COMPACT efficacy across the experimental dataset. Enhanced aerodynamic lift on the downstroke of the pitching cycle due to COMPACT is well predicted, and the cycleaveraged lift enhancement computed is within 3% of the test data. Differences with experimental data are discussed with a focus on three-dimensional features not included in the simulations and the limited computational model for COMPACT.

1D-3D hybrid modeling—from multi-compartment models to full resolution models in space and time

PubMed Central

Grein, Stephan; Stepniewski, Martin; Reiter, Sebastian; Knodel, Markus M.; Queisser, Gillian

2014-01-01

Investigation of cellular and network dynamics in the brain by means of modeling and simulation has evolved into a highly interdisciplinary field, that uses sophisticated modeling and simulation approaches to understand distinct areas of brain function. Depending on the underlying complexity, these models vary in their level of detail, in order to cope with the attached computational cost. Hence for large network simulations, single neurons are typically reduced to time-dependent signal processors, dismissing the spatial aspect of each cell. For single cell or networks with relatively small numbers of neurons, general purpose simulators allow for space and time-dependent simulations of electrical signal processing, based on the cable equation theory. An emerging field in Computational Neuroscience encompasses a new level of detail by incorporating the full three-dimensional morphology of cells and organelles into three-dimensional, space and time-dependent, simulations. While every approach has its advantages and limitations, such as computational cost, integrated and methods-spanning simulation approaches, depending on the network size could establish new ways to investigate the brain. In this paper we present a hybrid simulation approach, that makes use of reduced 1D-models using e.g., the NEURON simulator—which couples to fully resolved models for simulating cellular and sub-cellular dynamics, including the detailed three-dimensional morphology of neurons and organelles. In order to couple 1D- and 3D-simulations, we present a geometry-, membrane potential- and intracellular concentration mapping framework, with which graph- based morphologies, e.g., in the swc- or hoc-format, are mapped to full surface and volume representations of the neuron and computational data from 1D-simulations can be used as boundary conditions for full 3D simulations and vice versa. Thus, established models and data, based on general purpose 1D-simulators, can be directly coupled to the emerging field of fully resolved, highly detailed 3D-modeling approaches. We present the developed general framework for 1D/3D hybrid modeling and apply it to investigate electrically active neurons and their intracellular spatio-temporal calcium dynamics. PMID:25120463

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.

Micromagnetic computer simulations of spin waves in nanometre-scale patterned magnetic elements

NASA Astrophysics Data System (ADS)

Kim, Sang-Koog

2010-07-01

Current needs for further advances in the nanotechnologies of information-storage and -processing devices have attracted a great deal of interest in spin (magnetization) dynamics in nanometre-scale patterned magnetic elements. For instance, the unique dynamic characteristics of non-uniform magnetic microstructures such as various types of domain walls, magnetic vortices and antivortices, as well as spin wave dynamics in laterally restricted thin-film geometries, have been at the centre of extensive and intensive researches. Understanding the fundamentals of their unique spin structure as well as their robust and novel dynamic properties allows us to implement new functionalities into existing or future devices. Although experimental tools and theoretical approaches are effective means of understanding the fundamentals of spin dynamics and of gaining new insights into them, the limitations of those same tools and approaches have left gaps of unresolved questions in the pertinent physics. As an alternative, however, micromagnetic modelling and numerical simulation has recently emerged as a powerful tool for the study of a variety of phenomena related to spin dynamics of nanometre-scale magnetic elements. In this review paper, I summarize the recent results of simulations of the excitation and propagation and other novel wave characteristics of spin waves, highlighting how the micromagnetic computer simulation approach contributes to an understanding of spin dynamics of nanomagnetism and considering some of the merits of numerical simulation studies. Many examples of micromagnetic modelling for numerical calculations, employing various dimensions and shapes of patterned magnetic elements, are given. The current limitations of continuum micromagnetic modelling and of simulations based on the Landau-Lifshitz-Gilbert equation of motion of magnetization are also discussed, along with further research directions for spin-wave studies.

Quick realization of a ship steering training simulation system by virtual reality

NASA Astrophysics Data System (ADS)

Sun, Jifeng; Zhi, Pinghua; Nie, Weiguo

2003-09-01

This paper addresses two problems of a ship handling simulator. Firstly, 360 scene generation, especially 3D dynamic sea wave modeling, is described. Secondly, a multi-computer complementation of ship handling simulator. This paper also gives the experimental results of the proposed ship handling simulator.

Molecular dynamics studies of a DNA-binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor.

PubMed Central

Guenot, J.; Kollman, P. A.

1992-01-01

Although aqueous simulations with periodic boundary conditions more accurately describe protein dynamics than in vacuo simulations, these are computationally intensive for most proteins. Trp repressor dynamic simulations with a small water shell surrounding the starting model yield protein trajectories that are markedly improved over gas phase, yet computationally efficient. Explicit water in molecular dynamics simulations maintains surface exposure of protein hydrophilic atoms and burial of hydrophobic atoms by opposing the otherwise asymmetric protein-protein forces. This properly orients protein surface side chains, reduces protein fluctuations, and lowers the overall root mean square deviation from the crystal structure. For simulations with crystallographic waters only, a linear or sigmoidal distance-dependent dielectric yields a much better trajectory than does a constant dielectric model. As more water is added to the starting model, the differences between using distance-dependent and constant dielectric models becomes smaller, although the linear distance-dependent dielectric yields an average structure closer to the crystal structure than does a constant dielectric model. Multiplicative constants greater than one, for the linear distance-dependent dielectric simulations, produced trajectories that are progressively worse in describing trp repressor dynamics. Simulations of bovine pancreatic trypsin were used to ensure that the trp repressor results were not protein dependent and to explore the effect of the nonbonded cutoff on the distance-dependent and constant dielectric simulation models. The nonbonded cutoff markedly affected the constant but not distance-dependent dielectric bovine pancreatic trypsin inhibitor simulations. As with trp repressor, the distance-dependent dielectric model with a shell of water surrounding the protein produced a trajectory in better agreement with the crystal structure than a constant dielectric model, and the physical properties of the trajectory average structure, both with and without a nonbonded cutoff, were comparable. PMID:1304396

A Computational Approach for Modeling Neutron Scattering Data from Lipid Bilayers

DOE PAGES

Carrillo, Jan-Michael Y.; Katsaras, John; Sumpter, Bobby G.; ...

2017-01-12

Biological cell membranes are responsible for a range of structural and dynamical phenomena crucial to a cell's well-being and its associated functions. Due to the complexity of cell membranes, lipid bilayer systems are often used as biomimetic models. These systems have led to signficant insights into vital membrane phenomena such as domain formation, passive permeation and protein insertion. Experimental observations of membrane structure and dynamics are, however, limited in resolution, both spatially and temporally. Importantly, computer simulations are starting to play a more prominent role in interpreting experimental results, enabling a molecular under- standing of lipid membranes. Particularly, the synergymore » between scattering experiments and simulations offers opportunities for new discoveries in membrane physics, as the length and time scales probed by molecular dynamics (MD) simulations parallel those of experiments. We also describe a coarse-grained MD simulation approach that mimics neutron scattering data from large unilamellar lipid vesicles over a range of bilayer rigidity. Specfically, we simulate vesicle form factors and membrane thickness fluctuations determined from small angle neutron scattering (SANS) and neutron spin echo (NSE) experiments, respectively. Our simulations accurately reproduce trends from experiments and lay the groundwork for investigations of more complex membrane systems.« less

Rapid communication: Computational simulation and analysis of a candidate for the design of a novel silk-based biopolymer.

PubMed

Golas, Ewa I; Czaplewski, Cezary

2014-09-01

This work theoretically investigates the mechanical properties of a novel silk-derived biopolymer as polymerized in silico from sericin and elastin-like monomers. Molecular Dynamics simulations and Steered Molecular Dynamics were the principal computational methods used, the latter of which applies an external force onto the system and thereby enables an observation of its response to stress. The models explored herein are single-molecule approximations, and primarily serve as tools in a rational design process for the preliminary assessment of properties in a new material candidate. © 2014 Wiley Periodicals, Inc.

Time Accurate Unsteady Pressure Loads Simulated for the Space Launch System at a Wind Tunnel Condition

NASA Technical Reports Server (NTRS)

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

2015-01-01

Using the Fully Unstructured Three-Dimensional (FUN3D) computational fluid dynamics code, an unsteady, time-accurate flow field about a Space Launch System configuration was simulated at a transonic wind tunnel condition (Mach = 0.9). Delayed detached eddy simulation combined with Reynolds Averaged Naiver-Stokes and a Spallart-Almaras turbulence model were employed for the simulation. Second order accurate time evolution scheme was used to simulate the flow field, with a minimum of 0.2 seconds of simulated time to as much as 1.4 seconds. Data was collected at 480 pressure taps at locations, 139 of which matched a 3% wind tunnel model, tested in the Transonic Dynamic Tunnel (TDT) facility at NASA Langley Research Center. Comparisons between computation and experiment showed agreement within 5% in terms of location for peak RMS levels, and 20% for frequency and magnitude of power spectral densities. Grid resolution and time step sensitivity studies were performed to identify methods for improved accuracy comparisons to wind tunnel data. With limited computational resources, accurate trends for reduced vibratory loads on the vehicle were observed. Exploratory methods such as determining minimized computed errors based on CFL number and sub-iterations, as well as evaluating frequency content of the unsteady pressures and evaluation of oscillatory shock structures were used in this study to enhance computational efficiency and solution accuracy. These techniques enabled development of a set of best practices, for the evaluation of future flight vehicle designs in terms of vibratory loads.

Computer considerations for real time simulation of a generalized rotor model

NASA Technical Reports Server (NTRS)

Howe, R. M.; Fogarty, L. E.

1977-01-01

Scaled equations were developed to meet requirements for real time computer simulation of the rotor system research aircraft. These equations form the basis for consideration of both digital and hybrid mechanization for real time simulation. For all digital simulation estimates of the required speed in terms of equivalent operations per second are developed based on the complexity of the equations and the required intergration frame rates. For both conventional hybrid simulation and hybrid simulation using time-shared analog elements the amount of required equipment is estimated along with a consideration of the dynamic errors. Conventional hybrid mechanization using analog simulation of those rotor equations which involve rotor-spin frequencies (this consititutes the bulk of the equations) requires too much analog equipment. Hybrid simulation using time-sharing techniques for the analog elements appears possible with a reasonable amount of analog equipment. All-digital simulation with affordable general-purpose computers is not possible because of speed limitations, but specially configured digital computers do have the required speed and consitute the recommended approach.

BlazeDEM3D-GPU A Large Scale DEM simulation code for GPUs

NASA Astrophysics Data System (ADS)

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

2017-06-01

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

Space station dynamics, attitude control and momentum management

NASA Technical Reports Server (NTRS)

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

1989-01-01

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

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

NASA Technical Reports Server (NTRS)

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

2009-01-01

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

New Challenges in Computational Thermal Hydraulics

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

Yadigaroglu, George; Lakehal, Djamel

New needs and opportunities drive the development of novel computational methods for the design and safety analysis of light water reactors (LWRs). Some new methods are likely to be three dimensional. Coupling is expected between system codes, computational fluid dynamics (CFD) modules, and cascades of computations at scales ranging from the macro- or system scale to the micro- or turbulence scales, with the various levels continuously exchanging information back and forth. The ISP-42/PANDA and the international SETH project provide opportunities for testing applications of single-phase CFD methods to LWR safety problems. Although industrial single-phase CFD applications are commonplace, computational multifluidmore » dynamics is still under development. However, first applications are appearing; the state of the art and its potential uses are discussed. The case study of condensation of steam/air mixtures injected from a downward-facing vent into a pool of water is a perfect illustration of a simulation cascade: At the top of the hierarchy of scales, system behavior can be modeled with a system code; at the central level, the volume-of-fluid method can be applied to predict large-scale bubbling behavior; at the bottom of the cascade, direct-contact condensation can be treated with direct numerical simulation, in which turbulent flow (in both the gas and the liquid), interfacial dynamics, and heat/mass transfer are directly simulated without resorting to models.« less

Wavelet-based surrogate time series for multiscale simulation of heterogeneous catalysis

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

Savara, Aditya Ashi; Daw, C. Stuart; Xiong, Qingang

We propose a wavelet-based scheme that encodes the essential dynamics of discrete microscale surface reactions in a form that can be coupled with continuum macroscale flow simulations with high computational efficiency. This makes it possible to simulate the dynamic behavior of reactor-scale heterogeneous catalysis without requiring detailed concurrent simulations at both the surface and continuum scales using different models. Our scheme is based on the application of wavelet-based surrogate time series that encodes the essential temporal and/or spatial fine-scale dynamics at the catalyst surface. The encoded dynamics are then used to generate statistically equivalent, randomized surrogate time series, which canmore » be linked to the continuum scale simulation. As a result, we illustrate an application of this approach using two different kinetic Monte Carlo simulations with different characteristic behaviors typical for heterogeneous chemical reactions.« less

Wavelet-based surrogate time series for multiscale simulation of heterogeneous catalysis

DOE PAGES

Savara, Aditya Ashi; Daw, C. Stuart; Xiong, Qingang; ...

2016-01-28

We propose a wavelet-based scheme that encodes the essential dynamics of discrete microscale surface reactions in a form that can be coupled with continuum macroscale flow simulations with high computational efficiency. This makes it possible to simulate the dynamic behavior of reactor-scale heterogeneous catalysis without requiring detailed concurrent simulations at both the surface and continuum scales using different models. Our scheme is based on the application of wavelet-based surrogate time series that encodes the essential temporal and/or spatial fine-scale dynamics at the catalyst surface. The encoded dynamics are then used to generate statistically equivalent, randomized surrogate time series, which canmore » be linked to the continuum scale simulation. As a result, we illustrate an application of this approach using two different kinetic Monte Carlo simulations with different characteristic behaviors typical for heterogeneous chemical reactions.« less

Hardware accelerator for molecular dynamics: MDGRAPE-2

NASA Astrophysics Data System (ADS)

Susukita, Ryutaro; Ebisuzaki, Toshikazu; Elmegreen, Bruce G.; Furusawa, Hideaki; Kato, Kenya; Kawai, Atsushi; Kobayashi, Yoshinao; Koishi, Takahiro; McNiven, Geoffrey D.; Narumi, Tetsu; Yasuoka, Kenji

2003-10-01

We developed MDGRAPE-2, a hardware accelerator that calculates forces at high speed in molecular dynamics (MD) simulations. MDGRAPE-2 is connected to a PC or a workstation as an extension board. The sustained performance of one MDGRAPE-2 board is 15 Gflops, roughly equivalent to the peak performance of the fastest supercomputer processing element. One board is able to calculate all forces between 10 000 particles in 0.28 s (i.e. 310000 time steps per day). If 16 boards are connected to one computer and operated in parallel, this calculation speed becomes ˜10 times faster. In addition to MD, MDGRAPE-2 can be applied to gravitational N-body simulations, the vortex method and smoothed particle hydrodynamics in computational fluid dynamics.

Cycle-averaged dynamics of a periodically driven, closed-loop circulation model

NASA Technical Reports Server (NTRS)

Heldt, T.; Chang, J. L.; Chen, J. J. S.; Verghese, G. C.; Mark, R. G.

2005-01-01

Time-varying elastance models have been used extensively in the past to simulate the pulsatile nature of cardiovascular waveforms. Frequently, however, one is interested in dynamics that occur over longer time scales, in which case a detailed simulation of each cardiac contraction becomes computationally burdensome. In this paper, we apply circuit-averaging techniques to a periodically driven, closed-loop, three-compartment recirculation model. The resultant cycle-averaged model is linear and time invariant, and greatly reduces the computational burden. It is also amenable to systematic order reduction methods that lead to further efficiencies. Despite its simplicity, the averaged model captures the dynamics relevant to the representation of a range of cardiovascular reflex mechanisms. c2004 Elsevier Ltd. All rights reserved.

A molecular dynamics simulation study of chloroform

NASA Astrophysics Data System (ADS)

Tironi, Ilario G.; van Gunsteren, Wilfred F.

Three different chloroform models have been investigated using molecular dynamics computer simulation. The thermodynamic, structural and dynamic properties of the various models were investigated in detail. In particular, the potential energies, diffusion coefficients and rotational correlation times obtained for each model are compared with experiment. It is found that the theory of rotational Brownian motion fails in describing the rotational diffusion of chloroform. The force field of Dietz and Heinzinger was found to give good overall agreement with experiment. An extended investigation of this chloroform model has been performed. Values are reported for the isothermal compressibility, the thermal expansion coefficient and the constant volume heat capacity. The values agree well with experiment. The static and frequency dependent dielectric permittivity were computed from a 1·2 ns simulation conducted under reaction field boundary conditions. Considering the fact that the model is rigid with fixed partial charges, the static dielectric constant and Debye relaxation time compare well with experiment. From the same simulation the shear viscosity was computed using the off-diagonal elements of the pressure tensor, both via an Einstein type relation and via a Green-Kubo equation. The calculated viscosities show good agreement with experimental values. The excess Helmholtz energy is calculated using the thermodynamic integration technique and simulations of 50 and 80 ps. The value obtained for the excess Helmholtz energy matches the theoretical value within a few per cent.

Dynamic adaptive chemistry for turbulent flame simulations

NASA Astrophysics Data System (ADS)

Yang, Hongtao; Ren, Zhuyin; Lu, Tianfeng; Goldin, Graham M.

2013-02-01

The use of large chemical mechanisms in flame simulations is computationally expensive due to the large number of chemical species and the wide range of chemical time scales involved. This study investigates the use of dynamic adaptive chemistry (DAC) for efficient chemistry calculations in turbulent flame simulations. DAC is achieved through the directed relation graph (DRG) method, which is invoked for each computational fluid dynamics cell/particle to obtain a small skeletal mechanism that is valid for the local thermochemical condition. Consequently, during reaction fractional steps, one needs to solve a smaller set of ordinary differential equations governing chemical kinetics. Test calculations are performed in a partially-stirred reactor (PaSR) involving both methane/air premixed and non-premixed combustion with chemistry described by the 53-species GRI-Mech 3.0 mechanism and the 129-species USC-Mech II mechanism augmented with recently updated NO x pathways, respectively. Results show that, in the DAC approach, the DRG reduction threshold effectively controls the incurred errors in the predicted temperature and species concentrations. The computational saving achieved by DAC increases with the size of chemical kinetic mechanisms. For the PaSR simulations, DAC achieves a speedup factor of up to three for GRI-Mech 3.0 and up to six for USC-Mech II in simulation time, while at the same time maintaining good accuracy in temperature and species concentration predictions.

Parallel Three-Dimensional Computation of Fluid Dynamics and Fluid-Structure Interactions of Ram-Air Parachutes

NASA Technical Reports Server (NTRS)

Tezduyar, Tayfun E.

1998-01-01

This is a final report as far as our work at University of Minnesota is concerned. The report describes our research progress and accomplishments in development of high performance computing methods and tools for 3D finite element computation of aerodynamic characteristics and fluid-structure interactions (FSI) arising in airdrop systems, namely ram-air parachutes and round parachutes. This class of simulations involves complex geometries, flexible structural components, deforming fluid domains, and unsteady flow patterns. The key components of our simulation toolkit are a stabilized finite element flow solver, a nonlinear structural dynamics solver, an automatic mesh moving scheme, and an interface between the fluid and structural solvers; all of these have been developed within a parallel message-passing paradigm.

Dynamic and rheological properties of soft biological cell suspensions

PubMed Central

Yazdani, Alireza; Li, Xuejin

2016-01-01

Quantifying dynamic and rheological properties of suspensions of soft biological particles such as vesicles, capsules, and red blood cells (RBCs) is fundamentally important in computational biology and biomedical engineering. In this review, recent studies on dynamic and rheological behavior of soft biological cell suspensions by computer simulations are presented, considering both unbounded and confined shear flow. Furthermore, the hemodynamic and hemorheological characteristics of RBCs in diseases such as malaria and sickle cell anemia are highlighted. PMID:27540271

Free Enthalpy Differences between α-, π-, and 310-Helices of an Atomic Level Fine-Grained Alanine Deca-Peptide Solvated in Supramolecular Coarse-Grained Water.

PubMed

Lin, Zhixiong; Riniker, Sereina; van Gunsteren, Wilfred F

2013-03-12

Atomistic molecular dynamics simulations of peptides or proteins in aqueous solution are still limited to the multi-nanosecond time scale and multi-nanometer range by computational cost. Combining atomic solutes with a supramolecular solvent model in hybrid fine-grained/coarse-grained (FG/CG) simulations allows atomic detail in the region of interest while being computationally more efficient. We used enveloping distribution sampling (EDS) to calculate the free enthalpy differences between different helical conformations, i.e., α-, π-, and 310-helices, of an atomic level FG alanine deca-peptide solvated in a supramolecular CG water solvent. The free enthalpy differences obtained show that by replacing the FG solvent by the CG solvent, the π-helix is destabilized with respect to the α-helix by about 2.5 kJ mol(-1), and the 310-helix is stabilized with respect to the α-helix by about 9 kJ mol(-1). In addition, the dynamics of the peptide becomes faster. By introducing a FG water layer of 0.8 nm around the peptide, both thermodynamic and dynamic properties are recovered, while the hybrid FG/CG simulations are still four times more efficient than the atomistic simulations, even when the cutoff radius for the nonbonded interactions is increased from 1.4 to 2.0 nm. Hence, the hybrid FG/CG model, which yields an appropriate balance between reduced accuracy and enhanced computational speed, is very suitable for molecular dynamics simulation investigations of biomolecules.

Computational Fluid Dynamics (CFD) simulations of a Heisenberg Vortex Tube

NASA Astrophysics Data System (ADS)

Bunge, Carl; Sitaraman, Hariswaran; Leachman, Jake

2017-11-01

A 3D Computational Fluid Dynamics (CFD) simulation of a Heisenberg Vortex Tube (HVT) is performed to estimate cooling potential with cryogenic hydrogen. The main mechanism driving operation of the vortex tube is the use of fluid power for enthalpy streaming in a highly turbulent swirl in a dual-outlet tube. This enthalpy streaming creates a temperature separation between the outer and inner regions of the flow. Use of a catalyst on the peripheral wall of the centrifuge enables endothermic conversion of para-ortho hydrogen to aid primary cooling. A κ- ɛ turbulence model is used with a cryogenic, non-ideal equation of state, and para-orthohydrogen species evolution. The simulations are validated with experiments and strategies for parametric optimization of this device are presented.

Progress and supercomputing in computational fluid dynamics; Proceedings of U.S.-Israel Workshop, Jerusalem, Israel, December 1984

NASA Technical Reports Server (NTRS)

Murman, E. M. (Editor); Abarbanel, S. S. (Editor)

1985-01-01

Current developments and future trends in the application of supercomputers to computational fluid dynamics are discussed in reviews and reports. Topics examined include algorithm development for personal-size supercomputers, a multiblock three-dimensional Euler code for out-of-core and multiprocessor calculations, simulation of compressible inviscid and viscous flow, high-resolution solutions of the Euler equations for vortex flows, algorithms for the Navier-Stokes equations, and viscous-flow simulation by FEM and related techniques. Consideration is given to marching iterative methods for the parabolized and thin-layer Navier-Stokes equations, multigrid solutions to quasi-elliptic schemes, secondary instability of free shear flows, simulation of turbulent flow, and problems connected with weather prediction.

Next Generation Extended Lagrangian Quantum-based Molecular Dynamics

NASA Astrophysics Data System (ADS)

Negre, Christian

2017-06-01

A new framework for extended Lagrangian first-principles molecular dynamics simulations is presented, which overcomes shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while maintaining important advantages of the unified extended Lagrangian formulation of density functional theory pioneered by Car and Parrinello three decades ago. The new framework allows, for the first time, energy conserving, linear-scaling Born-Oppenheimer molecular dynamics simulations, which is necessary to study larger and more realistic systems over longer simulation times than previously possible. Expensive, self-consinstent-field optimizations are avoided and normal integration time steps of regular, direct Born-Oppenheimer molecular dynamics can be used. Linear scaling electronic structure theory is presented using a graph-based approach that is ideal for parallel calculations on hybrid computer platforms. For the first time, quantum based Born-Oppenheimer molecular dynamics simulation is becoming a practically feasible approach in simulations of +100,000 atoms-representing a competitive alternative to classical polarizable force field methods. In collaboration with: Anders Niklasson, Los Alamos National Laboratory.

Communication interval selection in distributed heterogeneous simulation of large-scale dynamical systems

NASA Astrophysics Data System (ADS)

Lucas, Charles E.; Walters, Eric A.; Jatskevich, Juri; Wasynczuk, Oleg; Lamm, Peter T.

2003-09-01

In this paper, a new technique useful for the numerical simulation of large-scale systems is presented. This approach enables the overall system simulation to be formed by the dynamic interconnection of the various interdependent simulations, each representing a specific component or subsystem such as control, electrical, mechanical, hydraulic, or thermal. Each simulation may be developed separately using possibly different commercial-off-the-shelf simulation programs thereby allowing the most suitable language or tool to be used based on the design/analysis needs. These subsystems communicate the required interface variables at specific time intervals. A discussion concerning the selection of appropriate communication intervals is presented herein. For the purpose of demonstration, this technique is applied to a detailed simulation of a representative aircraft power system, such as that found on the Joint Strike Fighter (JSF). This system is comprised of ten component models each developed using MATLAB/Simulink, EASY5, or ACSL. When the ten component simulations were distributed across just four personal computers (PCs), a greater than 15-fold improvement in simulation speed (compared to the single-computer implementation) was achieved.

Modeling the dynamics of chromosomal alteration progression in cervical cancer: A computational model

PubMed Central

2017-01-01

Computational modeling has been applied to simulate the heterogeneity of cancer behavior. The development of Cervical Cancer (CC) is a process in which the cell acquires dynamic behavior from non-deleterious and deleterious mutations, exhibiting chromosomal alterations as a manifestation of this dynamic. To further determine the progression of chromosomal alterations in precursor lesions and CC, we introduce a computational model to study the dynamics of deleterious and non-deleterious mutations as an outcome of tumor progression. The analysis of chromosomal alterations mediated by our model reveals that multiple deleterious mutations are more frequent in precursor lesions than in CC. Cells with lethal deleterious mutations would be eliminated, which would mitigate cancer progression; on the other hand, cells with non-deleterious mutations would become dominant, which could predispose them to cancer progression. The study of somatic alterations through computer simulations of cancer progression provides a feasible pathway for insights into the transformation of cell mechanisms in humans. During cancer progression, tumors may acquire new phenotype traits, such as the ability to invade and metastasize or to become clinically important when they develop drug resistance. Non-deleterious chromosomal alterations contribute to this progression. PMID:28723940

Conformational landscapes of membrane proteins delineated by enhanced sampling molecular dynamics simulations.

PubMed

Harpole, Tyler J; Delemotte, Lucie

2018-04-01

The expansion of computational power, better parameterization of force fields, and the development of novel algorithms to enhance the sampling of the free energy landscapes of proteins have allowed molecular dynamics (MD) simulations to become an indispensable tool to understand the function of biomolecules. The temporal and spatial resolution of MD simulations allows for the study of a vast number of processes of interest. Here, we review the computational efforts to uncover the conformational free energy landscapes of a subset of membrane proteins: ion channels, transporters and G-protein coupled receptors. We focus on the various enhanced sampling techniques used to study these questions, how the conclusions come together to build a coherent picture, and the relationship between simulation outcomes and experimental observables. Copyright © 2017 Elsevier B.V. All rights reserved.

Lightweight computational steering of very large scale molecular dynamics simulations

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

Beazley, D.M.; Lomdahl, P.S.

1996-09-01

We present a computational steering approach for controlling, analyzing, and visualizing very large scale molecular dynamics simulations involving tens to hundreds of millions of atoms. Our approach relies on extensible scripting languages and an easy to use tool for building extensions and modules. The system is extremely easy to modify, works with existing C code, is memory efficient, and can be used from inexpensive workstations and networks. We demonstrate how we have used this system to manipulate data from production MD simulations involving as many as 104 million atoms running on the CM-5 and Cray T3D. We also show howmore » this approach can be used to build systems that integrate common scripting languages (including Tcl/Tk, Perl, and Python), simulation code, user extensions, and commercial data analysis packages.« less

An Interactive Simulation Program for Exploring Computational Models of Auto-Associative Memory.

PubMed

Fink, Christian G

2017-01-01

While neuroscience students typically learn about activity-dependent plasticity early in their education, they often struggle to conceptually connect modification at the synaptic scale with network-level neuronal dynamics, not to mention with their own everyday experience of recalling a memory. We have developed an interactive simulation program (based on the Hopfield model of auto-associative memory) that enables the user to visualize the connections generated by any pattern of neural activity, as well as to simulate the network dynamics resulting from such connectivity. An accompanying set of student exercises introduces the concepts of pattern completion, pattern separation, and sparse versus distributed neural representations. Results from a conceptual assessment administered before and after students worked through these exercises indicate that the simulation program is a useful pedagogical tool for illustrating fundamental concepts of computational models of memory.

Functional assessment of coronary artery disease by intravascular ultrasound and computational fluid dynamics simulation.

PubMed

Carrizo, Sebastián; Xie, Xinzhou; Peinado-Peinado, Rafael; Sánchez-Recalde, Angel; Jiménez-Valero, Santiago; Galeote-Garcia, Guillermo; Moreno, Raúl

2014-10-01

Clinical trials have shown that functional assessment of coronary stenosis by fractional flow reserve (FFR) improves clinical outcomes. Intravascular ultrasound (IVUS) complements conventional angiography, and is a powerful tool to assess atherosclerotic plaques and to guide percutaneous coronary intervention (PCI). Computational fluid dynamics (CFD) simulation represents a novel method for the functional assessment of coronary flow. A CFD simulation can be calculated from the data normally acquired by IVUS images. A case of coronary heart disease studied with FFR and IVUS, before and after PCI, is presented. A three-dimensional model was constructed based on IVUS images, to which CFD was applied. A discussion of the literature concerning the clinical utility of CFD simulation is provided. Copyright © 2014 Sociedade Portuguesa de Cardiologia. Published by Elsevier España. All rights reserved.

Realistic natural atmospheric phenomena and weather effects for interactive virtual environments

NASA Astrophysics Data System (ADS)

McLoughlin, Leigh

Clouds and the weather are important aspects of any natural outdoor scene, but existing dynamic techniques within computer graphics only offer the simplest of cloud representations. The problem that this work looks to address is how to provide a means of simulating clouds and weather features such as precipitation, that are suitable for virtual environments. Techniques for cloud simulation are available within the area of meteorology, but numerical weather prediction systems are computationally expensive, give more numerical accuracy than we require for graphics and are restricted to the laws of physics. Within computer graphics, we often need to direct and adjust physical features or to bend reality to meet artistic goals, which is a key difference between the subjects of computer graphics and physical science. Pure physically-based simulations, however, evolve their solutions according to pre-set rules and are notoriously difficult to control. The challenge then is for the solution to be computationally lightweight and able to be directed in some measure while at the same time producing believable results. This work presents a lightweight physically-based cloud simulation scheme that simulates the dynamic properties of cloud formation and weather effects. The system simulates water vapour, cloud water, cloud ice, rain, snow and hail. The water model incorporates control parameters and the cloud model uses an arbitrary vertical temperature profile, with a tool described to allow the user to define this. The result of this work is that clouds can now be simulated in near real-time complete with precipitation. The temperature profile and tool then provide a means of directing the resulting formation..

Computational Wear Simulation of Patellofemoral Articular Cartilage during In Vitro Testing

PubMed Central

Li, Lingmin; Patil, Shantanu; Steklov, Nick; Bae, Won; Temple-Wong, Michele; D'Lima, Darryl D.; Sah, Robert L.; Fregly, Benjamin J.

2011-01-01

Though changes in normal joint motions and loads (e.g., following anterior cruciate ligament injury) contribute to the development of knee osteoarthritis, the precise mechanism by which these changes induce osteoarthritis remains unknown. As a first step toward identifying this mechanism, this study evaluates computational wear simulations of a patellofemoral joint specimen wear tested on a knee simulator machine. A multi-body dynamic model of the specimen mounted in the simulator machine was constructed in commercial computer-aided engineering software. A custom elastic foundation contact model was used to calculate contact pressures and wear on the femoral and patellar articular surfaces using geometry created from laser scan and MR data. Two different wear simulation approaches were investigated – one that wore the surface geometries gradually over a sequence of 10 one-cycle dynamic simulations (termed the “progressive” approach), and one that wore the surface geometries abruptly using results from a single one-cycle dynamic simulation (termed the “non-progressive” approach). The progressive approach with laser scan geometry reproduced the experimentally measured wear depths and areas for both the femur and patella. The less costly non-progressive approach predicted deeper wear depths, especially on the patella, but had little influence on predicted wear areas. Use of MR data for creating the articular and subchondral bone geometry altered wear depth and area predictions by at most 13%. These results suggest that MR-derived geometry may be sufficient for simulating articular cartilage wear in vivo and that a progressive simulation approach may be needed for the patella and tibia since both remain in continuous contact with the femur. PMID:21453922

Computational wear simulation of patellofemoral articular cartilage during in vitro testing.

PubMed

Li, Lingmin; Patil, Shantanu; Steklov, Nick; Bae, Won; Temple-Wong, Michele; D'Lima, Darryl D; Sah, Robert L; Fregly, Benjamin J

2011-05-17

Though changes in normal joint motions and loads (e.g., following anterior cruciate ligament injury) contribute to the development of knee osteoarthritis, the precise mechanism by which these changes induce osteoarthritis remains unknown. As a first step toward identifying this mechanism, this study evaluates computational wear simulations of a patellofemoral joint specimen wear tested on a knee simulator machine. A multibody dynamic model of the specimen mounted in the simulator machine was constructed in commercial computer-aided engineering software. A custom elastic foundation contact model was used to calculate contact pressures and wear on the femoral and patellar articular surfaces using geometry created from laser scan and MR data. Two different wear simulation approaches were investigated--one that wore the surface geometries gradually over a sequence of 10 one-cycle dynamic simulations (termed the "progressive" approach), and one that wore the surface geometries abruptly using results from a single one-cycle dynamic simulation (termed the "non-progressive" approach). The progressive approach with laser scan geometry reproduced the experimentally measured wear depths and areas for both the femur and patella. The less costly non-progressive approach predicted deeper wear depths, especially on the patella, but had little influence on predicted wear areas. Use of MR data for creating the articular and subchondral bone geometry altered wear depth and area predictions by at most 13%. These results suggest that MR-derived geometry may be sufficient for simulating articular cartilage wear in vivo and that a progressive simulation approach may be needed for the patella and tibia since both remain in continuous contact with the femur. Copyright © 2011 Elsevier Ltd. All rights reserved.

Algorithmic trends in computational fluid dynamics; The Institute for Computer Applications in Science and Engineering (ICASE)/LaRC Workshop, NASA Langley Research Center, Hampton, VA, US, Sep. 15-17, 1991

NASA Technical Reports Server (NTRS)

Hussaini, M. Y. (Editor); Kumar, A. (Editor); Salas, M. D. (Editor)

1993-01-01

The purpose here is to assess the state of the art in the areas of numerical analysis that are particularly relevant to computational fluid dynamics (CFD), to identify promising new developments in various areas of numerical analysis that will impact CFD, and to establish a long-term perspective focusing on opportunities and needs. Overviews are given of discretization schemes, computational fluid dynamics, algorithmic trends in CFD for aerospace flow field calculations, simulation of compressible viscous flow, and massively parallel computation. Also discussed are accerelation methods, spectral and high-order methods, multi-resolution and subcell resolution schemes, and inherently multidimensional schemes.

Integrated Multiscale Modeling of Molecular Computing Devices. Final Report

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

Tim Schulze

2012-11-01

The general theme of this research has been to expand the capabilities of a simulation technique, Kinetic Monte Carlo (KMC) and apply it to study self-assembled nano-structures on epitaxial thin films. KMC simulates thin film growth and evolution by replacing the detailed dynamics of the system's evolution, which might otherwise be studied using molecular dynamics, with an appropriate stochastic process.

Computational fluid dynamics study of viscous fingering in supercritical fluid chromatography.

PubMed

Subraveti, Sai Gokul; Nikrityuk, Petr; Rajendran, Arvind

2018-01-26

Axi-symmetric numerical simulations are carried out to study the dynamics of a plug introduced through a mixed-stream injection in supercritical fluid chromatographic columns. The computational fluid dynamics model developed in this work takes into account both the hydrodynamics and adsorption equilibria to describe the phenomena of viscous fingering and plug effect that contribute to peak distortions in mixed-stream injections. The model was implemented into commercial computational fluid dynamics software using user-defined functions. The simulations describe the propagation of both the solute and modifier highlighting the interplay between the hydrodynamics and plug effect. The simulated peaks showed good agreement with experimental data published in the literature involving different injection volumes (5 μL, 50 μL, 1 mL and 2 mL) of flurbiprofen on Chiralpak AD-H column using a mobile phase of CO 2 and methanol. The study demonstrates that while viscous fingering is the main source of peak distortions for large-volume injections (1 mL and 2 mL) it has negligible impact on small-volume injections (5 μL and 50 μL). Band broadening in small-volume injections arise mainly due to the plug effect. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

Characterizing rare-event property distributions via replicate molecular dynamics simulations of proteins.

PubMed

Krishnan, Ranjani; Walton, Emily B; Van Vliet, Krystyn J

2009-11-01

As computational resources increase, molecular dynamics simulations of biomolecules are becoming an increasingly informative complement to experimental studies. In particular, it has now become feasible to use multiple initial molecular configurations to generate an ensemble of replicate production-run simulations that allows for more complete characterization of rare events such as ligand-receptor unbinding. However, there are currently no explicit guidelines for selecting an ensemble of initial configurations for replicate simulations. Here, we use clustering analysis and steered molecular dynamics simulations to demonstrate that the configurational changes accessible in molecular dynamics simulations of biomolecules do not necessarily correlate with observed rare-event properties. This informs selection of a representative set of initial configurations. We also employ statistical analysis to identify the minimum number of replicate simulations required to sufficiently sample a given biomolecular property distribution. Together, these results suggest a general procedure for generating an ensemble of replicate simulations that will maximize accurate characterization of rare-event property distributions in biomolecules.

Analysis of vehicle dynamics under sadden cross wind

NASA Astrophysics Data System (ADS)

Walczak, S.

2016-09-01

In this paper, the way of calculating aerodynamic forces acting on a vehicle passing in the region of sadden cross wind was presented. The CarDyn, a vehicle dynamics simulation program, developed by the author was used. The effects of the cross wind were studied with a fixed steering wheel simulation. On the base of computer simulations the car cross wind sensitivity were determined, and vehicle responses such as lateral offset, side acceleration and yaw angular velocity are presented.

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

PubMed

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

2018-05-06

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

Visualization of Dynamic Vortex Structures in Magnetic Films with Uniaxial Anisotropy (Micromagnetic Simulation)

NASA Astrophysics Data System (ADS)

Zverev, V. V.; Izmozherov, I. M.; Filippov, B. N.

2018-02-01

Three-dimensional computer simulation of dynamic processes in a moving domain boundary separating domains in a soft magnetic uniaxial film with planar anisotropy is performed by numerical solution of Landau-Lifshitz-Gilbert equations. The developed visualization methods are used to establish the connection between the motion of surface vortices and antivortices, singular (Bloch) points, and core lines of intrafilm vortex structures. A relation between the character of magnetization dynamics and the film thickness is found. The analytical models of spatial vortex structures for imitation of topological properties of the structures observed in micromagnetic simulation are constructed.

N-MODY: a code for collisionless N-body simulations in modified Newtonian dynamics.

NASA Astrophysics Data System (ADS)

Londrillo, P.; Nipoti, C.

We describe the numerical code N-MODY, a parallel particle-mesh code for collisionless N-body simulations in modified Newtonian dynamics (MOND). N-MODY is based on a numerical potential solver in spherical coordinates that solves the non-linear MOND field equation, and is ideally suited to simulate isolated stellar systems. N-MODY can be used also to compute the MOND potential of arbitrary static density distributions. A few applications of N-MODY indicate that some astrophysically relevant dynamical processes are profoundly different in MOND and in Newtonian gravity with dark matter.

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).

Subject-specific computer simulation model for determining elbow loading in one-handed tennis backhand groundstrokes.

PubMed

King, Mark A; Glynn, Jonathan A; Mitchell, Sean R

2011-11-01

A subject-specific angle-driven computer model of a tennis player, combined with a forward dynamics, equipment-specific computer model of tennis ball-racket impacts, was developed to determine the effect of ball-racket impacts on loading at the elbow for one-handed backhand groundstrokes. Matching subject-specific computer simulations of a typical topspin/slice one-handed backhand groundstroke performed by an elite tennis player were done with root mean square differences between performance and matching simulations of < 0.5 degrees over a 50 ms period starting from ball impact. Simulation results suggest that for similar ball-racket impact conditions, the difference in elbow loading for a topspin and slice one-handed backhand groundstroke is relatively small. In this study, the relatively small differences in elbow loading may be due to comparable angle-time histories at the wrist and elbow joints with the major kinematic differences occurring at the shoulder. Using a subject-specific angle-driven computer model combined with a forward dynamics, equipment-specific computer model of tennis ball-racket impacts allows peak internal loading, net impulse, and shock due to ball-racket impact to be calculated which would not otherwise be possible without impractical invasive techniques. This study provides a basis for further investigation of the factors that may increase elbow loading during tennis strokes.

Rating of Dynamic Coefficient for Simple Beam Bridge Design on High-Speed Railways

NASA Astrophysics Data System (ADS)

Diachenko, Leonid; Benin, Andrey; Smirnov, Vladimir; Diachenko, Anastasia

2018-06-01

The aim of the work is to improve the methodology for the dynamic computation of simple beam spans during the impact of high-speed trains. Mathematical simulation utilizing numerical and analytical methods of structural mechanics is used in the research. The article analyses parameters of the effect of high-speed trains on simple beam spanning bridge structures and suggests a technique of determining of the dynamic index to the live load. Reliability of the proposed methodology is confirmed by results of numerical simulation of high-speed train passage over spans with different speeds. The proposed algorithm of dynamic computation is based on a connection between maximum acceleration of the span in the resonance mode of vibrations and the main factors of stress-strain state. The methodology allows determining maximum and also minimum values of the main efforts in the construction that makes possible to perform endurance tests. It is noted that dynamic additions for the components of the stress-strain state (bending moments, transverse force and vertical deflections) are different. This condition determines the necessity for differentiated approach to evaluation of dynamic coefficients performing design verification of I and II groups of limiting state. The practical importance: the methodology of determining the dynamic coefficients allows making dynamic calculation and determining the main efforts in split beam spans without numerical simulation and direct dynamic analysis that significantly reduces the labour costs for design.

Multibody dynamics model building using graphical interfaces

NASA Technical Reports Server (NTRS)

Macala, Glenn A.

1989-01-01

In recent years, the extremely laborious task of manually deriving equations of motion for the simulation of multibody spacecraft dynamics has largely been eliminated. Instead, the dynamicist now works with commonly available general purpose dynamics simulation programs which generate the equations of motion either explicitly or implicitly via computer codes. The user interface to these programs has predominantly been via input data files, each with its own required format and peculiarities, causing errors and frustrations during program setup. Recent progress in a more natural method of data input for dynamics programs: the graphical interface, is described.

Computer Simulation of Protein-Protein and Protein-Peptide Interactions

DTIC Science & Technology

1983-12-08

a full molecular dynamic z simulation is performed, with resulting dipolar re - laxation. However, this is prohibitive when a large . number of...1993 Dr. Mike Marron Program Manager Molecular Biology Office of Naval Research 800 N. Quincy Street Arlington, VA 22217 Dear Mike, Here is the...rztnbutior is unLi--ited. , 93-30630 98 12 � 12/08/93 01/0/92-;03/31/93: Final Report, Computer Simulation of Protein-Protein and Protein-Peptide

Comparison of digital controllers used in magnetic suspension and balance systems

NASA Technical Reports Server (NTRS)

Kilgore, William A.

1990-01-01

Dynamic systems that were once controlled by analog circuits are now controlled by digital computers. Presented is a comparison of the digital controllers presently used with magnetic suspension and balance systems. The overall responses of the systems are compared using a computer simulation of the magnetic suspension and balance system and the digital controllers. The comparisons include responses to both simulated force and position inputs. A preferred digital controller is determined from the simulated responses.

Verifying a computational method for predicting extreme ground motion

USGS Publications Warehouse

Harris, R.A.; Barall, M.; Andrews, D.J.; Duan, B.; Ma, S.; Dunham, E.M.; Gabriel, A.-A.; Kaneko, Y.; Kase, Y.; Aagaard, Brad T.; Oglesby, D.D.; Ampuero, J.-P.; Hanks, T.C.; Abrahamson, N.

2011-01-01

In situations where seismological data is rare or nonexistent, computer simulations may be used to predict ground motions caused by future earthquakes. This is particularly practical in the case of extreme ground motions, where engineers of special buildings may need to design for an event that has not been historically observed but which may occur in the far-distant future. Once the simulations have been performed, however, they still need to be tested. The SCEC-USGS dynamic rupture code verification exercise provides a testing mechanism for simulations that involve spontaneous earthquake rupture. We have performed this examination for the specific computer code that was used to predict maximum possible ground motion near Yucca Mountain. Our SCEC-USGS group exercises have demonstrated that the specific computer code that was used for the Yucca Mountain simulations produces similar results to those produced by other computer codes when tackling the same science problem. We also found that the 3D ground motion simulations produced smaller ground motions than the 2D simulations.

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

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

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

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

Closed Environment Module - Modularization and extension of the Virtual Habitat

NASA Astrophysics Data System (ADS)

Plötner, Peter; Czupalla, Markus; Zhukov, Anton

2013-12-01

The Virtual Habitat (V-HAB), is a Life Support System (LSS) simulation, created to perform dynamic simulation of LSS's for future human spaceflight missions. It allows the testing of LSS robustness by means of computer simulations, e.g. of worst case scenarios.

Event-based simulation of networks with pulse delayed coupling

NASA Astrophysics Data System (ADS)

Klinshov, Vladimir; Nekorkin, Vladimir

2017-10-01

Pulse-mediated interactions are common in networks of different nature. Here we develop a general framework for simulation of networks with pulse delayed coupling. We introduce the discrete map governing the dynamics of such networks and describe the computation algorithm for its numerical simulation.

Dynamic properties of epidemic spreading on finite size complex networks

NASA Astrophysics Data System (ADS)

Li, Ying; Liu, Yang; Shan, Xiu-Ming; Ren, Yong; Jiao, Jian; Qiu, Ben

2005-11-01

The Internet presents a complex topological structure, on which computer viruses can easily spread. By using theoretical analysis and computer simulation methods, the dynamic process of disease spreading on finite size networks with complex topological structure is investigated. On the finite size networks, the spreading process of SIS (susceptible-infected-susceptible) model is a finite Markov chain with an absorbing state. Two parameters, the survival probability and the conditional infecting probability, are introduced to describe the dynamic properties of disease spreading on finite size networks. Our results can help understanding computer virus epidemics and other spreading phenomena on communication and social networks. Also, knowledge about the dynamic character of virus spreading is helpful for adopting immunity policy.

Accelerating population balance-Monte Carlo simulation for coagulation dynamics from the Markov jump model, stochastic algorithm and GPU parallel computing

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

Xu, Zuwei; Zhao, Haibo, E-mail: klinsmannzhb@163.com; Zheng, Chuguang

2015-01-15

This paper proposes a comprehensive framework for accelerating population balance-Monte Carlo (PBMC) simulation of particle coagulation dynamics. By combining Markov jump model, weighted majorant kernel and GPU (graphics processing unit) parallel computing, a significant gain in computational efficiency is achieved. The Markov jump model constructs a coagulation-rule matrix of differentially-weighted simulation particles, so as to capture the time evolution of particle size distribution with low statistical noise over the full size range and as far as possible to reduce the number of time loopings. Here three coagulation rules are highlighted and it is found that constructing appropriate coagulation rule providesmore » a route to attain the compromise between accuracy and cost of PBMC methods. Further, in order to avoid double looping over all simulation particles when considering the two-particle events (typically, particle coagulation), the weighted majorant kernel is introduced to estimate the maximum coagulation rates being used for acceptance–rejection processes by single-looping over all particles, and meanwhile the mean time-step of coagulation event is estimated by summing the coagulation kernels of rejected and accepted particle pairs. The computational load of these fast differentially-weighted PBMC simulations (based on the Markov jump model) is reduced greatly to be proportional to the number of simulation particles in a zero-dimensional system (single cell). Finally, for a spatially inhomogeneous multi-dimensional (multi-cell) simulation, the proposed fast PBMC is performed in each cell, and multiple cells are parallel processed by multi-cores on a GPU that can implement the massively threaded data-parallel tasks to obtain remarkable speedup ratio (comparing with CPU computation, the speedup ratio of GPU parallel computing is as high as 200 in a case of 100 cells with 10 000 simulation particles per cell). These accelerating approaches of PBMC are demonstrated in a physically realistic Brownian coagulation case. The computational accuracy is validated with benchmark solution of discrete-sectional method. The simulation results show that the comprehensive approach can attain very favorable improvement in cost without sacrificing computational accuracy.« less

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

PubMed

Curuksu, Jeremy; Zacharias, Martin

2009-03-14

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

High-Fidelity Dynamic Modeling of Spacecraft in the Continuum--Rarefied Transition Regime

NASA Astrophysics Data System (ADS)

Turansky, Craig P.

The state of the art of spacecraft rarefied aerodynamics seldom accounts for detailed rigid-body dynamics. In part because of computational constraints, simpler models based upon the ballistic and drag coefficients are employed. Of particular interest is the continuum-rarefied transition regime of Earth's thermosphere where gas dynamic simulation is difficult yet wherein many spacecraft operate. The feasibility of increasing the fidelity of modeling spacecraft dynamics is explored by coupling rarefied aerodynamics with rigid-body dynamics modeling similar to that traditionally used for aircraft in atmospheric flight. Presented is a framework of analysis and guiding principles which capitalize on the availability of increasing computational methods and resources. Aerodynamic force inputs for modeling spacecraft in two dimensions in a rarefied flow are provided by analytical equations in the free-molecular regime, and the direct simulation Monte Carlo method in the transition regime. The application of the direct simulation Monte Carlo method to this class of problems is examined in detail with a new code specifically designed for engineering-level rarefied aerodynamic analysis. Time-accurate simulations of two distinct geometries in low thermospheric flight and atmospheric entry are performed, demonstrating non-linear dynamics that cannot be predicted using simpler approaches. The results of this straightforward approach to the aero-orbital coupled-field problem highlight the possibilities for future improvements in drag prediction, control system design, and atmospheric science. Furthermore, a number of challenges for future work are identified in the hope of stimulating the development of a new subfield of spacecraft dynamics.

Future Computer Requirements for Computational Aerodynamics

NASA Technical Reports Server (NTRS)

1978-01-01

Recent advances in computational aerodynamics are discussed as well as motivations for and potential benefits of a National Aerodynamic Simulation Facility having the capability to solve fluid dynamic equations at speeds two to three orders of magnitude faster than presently possible with general computers. Two contracted efforts to define processor architectures for such a facility are summarized.

Application of Microsoft's ActiveX and DirectX technologies to the visulization of physical system dynamics

NASA Astrophysics Data System (ADS)

Mann, Christopher; Narasimhamurthi, Natarajan

1998-08-01

This paper discusses a specific implementation of a web and complement based simulation systems. The overall simulation container is implemented within a web page viewed with Microsoft's Internet Explorer 4.0 web browser. Microsoft's ActiveX/Distributed Component Object Model object interfaces are used in conjunction with the Microsoft DirectX graphics APIs to provide visualization functionality for the simulation. The MathWorks' Matlab computer aided control system design program is used as an ActiveX automation server to provide the compute engine for the simulations.

Development of an Output-based Adaptive Method for Multi-Dimensional Euler and Navier-Stokes Simulations

NASA Technical Reports Server (NTRS)

Darmofal, David L.

2003-01-01

The use of computational simulations in the prediction of complex aerodynamic flows is becoming increasingly prevalent in the design process within the aerospace industry. Continuing advancements in both computing technology and algorithmic development are ultimately leading to attempts at simulating ever-larger, more complex problems. However, by increasing the reliance on computational simulations in the design cycle, we must also increase the accuracy of these simulations in order to maintain or improve the reliability arid safety of the resulting aircraft. At the same time, large-scale computational simulations must be made more affordable so that their potential benefits can be fully realized within the design cycle. Thus, a continuing need exists for increasing the accuracy and efficiency of computational algorithms such that computational fluid dynamics can become a viable tool in the design of more reliable, safer aircraft. The objective of this research was the development of an error estimation and grid adaptive strategy for reducing simulation errors in integral outputs (functionals) such as lift or drag from from multi-dimensional Euler and Navier-Stokes simulations. In this final report, we summarize our work during this grant.

In vitro flow assessment: from PC-MRI to computational fluid dynamics including fluid-structure interaction

NASA Astrophysics Data System (ADS)

Kratzke, Jonas; Rengier, Fabian; Weis, Christian; Beller, Carsten J.; Heuveline, Vincent

2016-04-01

Initiation and development of cardiovascular diseases can be highly correlated to specific biomechanical parameters. To examine and assess biomechanical parameters, numerical simulation of cardiovascular dynamics has the potential to complement and enhance medical measurement and imaging techniques. As such, computational fluid dynamics (CFD) have shown to be suitable to evaluate blood velocity and pressure in scenarios, where vessel wall deformation plays a minor role. However, there is a need for further validation studies and the inclusion of vessel wall elasticity for morphologies being subject to large displacement. In this work, we consider a fluid-structure interaction (FSI) model including the full elasticity equation to take the deformability of aortic wall soft tissue into account. We present a numerical framework, in which either a CFD study can be performed for less deformable aortic segments or an FSI simulation for regions of large displacement such as the aortic root and arch. Both of the methods are validated by means of an aortic phantom experiment. The computational results are in good agreement with 2D phase-contrast magnetic resonance imaging (PC-MRI) velocity measurements as well as catheter-based pressure measurements. The FSI simulation shows a characteristic vessel compliance effect on the flow field induced by the elasticity of the vessel wall, which the CFD model is not capable of. The in vitro validated FSI simulation framework can enable the computation of complementary biomechanical parameters such as the stress distribution within the vessel wall.

Dynamic and fluid-structure interaction simulations of bioprosthetic heart valves using parametric design with T-splines and Fung-type material models

NASA Astrophysics Data System (ADS)

Hsu, Ming-Chen; Kamensky, David; Xu, Fei; Kiendl, Josef; Wang, Chenglong; Wu, Michael C. H.; Mineroff, Joshua; Reali, Alessandro; Bazilevs, Yuri; Sacks, Michael S.

2015-06-01

This paper builds on a recently developed immersogeometric fluid-structure interaction (FSI) methodology for bioprosthetic heart valve (BHV) modeling and simulation. It enhances the proposed framework in the areas of geometry design and constitutive modeling. With these enhancements, BHV FSI simulations may be performed with greater levels of automation, robustness and physical realism. In addition, the paper presents a comparison between FSI analysis and standalone structural dynamics simulation driven by prescribed transvalvular pressure, the latter being a more common modeling choice for this class of problems. The FSI computation achieved better physiological realism in predicting the valve leaflet deformation than its standalone structural dynamics counterpart.

Cost efficient CFD simulations: Proper selection of domain partitioning strategies

NASA Astrophysics Data System (ADS)

Haddadi, Bahram; Jordan, Christian; Harasek, Michael

2017-10-01

Computational Fluid Dynamics (CFD) is one of the most powerful simulation methods, which is used for temporally and spatially resolved solutions of fluid flow, heat transfer, mass transfer, etc. One of the challenges of Computational Fluid Dynamics is the extreme hardware demand. Nowadays super-computers (e.g. High Performance Computing, HPC) featuring multiple CPU cores are applied for solving-the simulation domain is split into partitions for each core. Some of the different methods for partitioning are investigated in this paper. As a practical example, a new open source based solver was utilized for simulating packed bed adsorption, a common separation method within the field of thermal process engineering. Adsorption can for example be applied for removal of trace gases from a gas stream or pure gases production like Hydrogen. For comparing the performance of the partitioning methods, a 60 million cell mesh for a packed bed of spherical adsorbents was created; one second of the adsorption process was simulated. Different partitioning methods available in OpenFOAM® (Scotch, Simple, and Hierarchical) have been used with different numbers of sub-domains. The effect of the different methods and number of processor cores on the simulation speedup and also energy consumption were investigated for two different hardware infrastructures (Vienna Scientific Clusters VSC 2 and VSC 3). As a general recommendation an optimum number of cells per processor core was calculated. Optimized simulation speed, lower energy consumption and consequently the cost effects are reported here.

Aeroelastic, CFD, and Dynamics Computation and Optimization for Buffet and Flutter Applications

NASA Technical Reports Server (NTRS)

Kandil, Osama A.

1997-01-01

Accomplishments achieved during the reporting period are listed. These accomplishments included 6 papers published in various journals or presented at various conferences; 1 abstract submitted to a technical conference; production of 2 animated movies; and a proposal for use of the National Aerodynamic Simulation Facility at NASA Ames Research Center for further research. The published and presented papers and animated movies addressed the following topics: aeroelasticity, computational fluid dynamics, structural dynamics, wing and tail buffet, vortical flow interactions, and delta wings.

Ultrafast spectroscopy reveals subnanosecond peptide conformational dynamics and validates molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Spörlein, Sebastian; Carstens, Heiko; Satzger, Helmut; Renner, Christian; Behrendt, Raymond; Moroder, Luis; Tavan, Paul; Zinth, Wolfgang; Wachtveitl, Josef

2002-06-01

Femtosecond time-resolved spectroscopy on model peptides with built-in light switches combined with computer simulation of light-triggered motions offers an attractive integrated approach toward the understanding of peptide conformational dynamics. It was applied to monitor the light-induced relaxation dynamics occurring on subnanosecond time scales in a peptide that was backbone-cyclized with an azobenzene derivative as optical switch and spectroscopic probe. The femtosecond spectra permit the clear distinguishing and characterization of the subpicosecond photoisomerization of the chromophore, the subsequent dissipation of vibrational energy, and the subnanosecond conformational relaxation of the peptide. The photochemical cis/trans-isomerization of the chromophore and the resulting peptide relaxations have been simulated with molecular dynamics calculations. The calculated reaction kinetics, as monitored by the energy content of the peptide, were found to match the spectroscopic data. Thus we verify that all-atom molecular dynamics simulations can quantitatively describe the subnanosecond conformational dynamics of peptides, strengthening confidence in corresponding predictions for longer time scales.

Segmentation of Unstructured Datasets

NASA Technical Reports Server (NTRS)

Bhat, Smitha

1996-01-01

Datasets generated by computer simulations and experiments in Computational Fluid Dynamics tend to be extremely large and complex. It is difficult to visualize these datasets using standard techniques like Volume Rendering and Ray Casting. Object Segmentation provides a technique to extract and quantify regions of interest within these massive datasets. This thesis explores basic algorithms to extract coherent amorphous regions from two-dimensional and three-dimensional scalar unstructured grids. The techniques are applied to datasets from Computational Fluid Dynamics and from Finite Element Analysis.

Trends in Programming Languages for Neuroscience Simulations

PubMed Central

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

2009-01-01

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

Trends in programming languages for neuroscience simulations.

PubMed

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

2009-01-01

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

Active learning of constitutive relation from mesoscopic dynamics for macroscopic modeling of non-Newtonian flows

NASA Astrophysics Data System (ADS)

Zhao, Lifei; Li, Zhen; Caswell, Bruce; Ouyang, Jie; Karniadakis, George Em

2018-06-01

We simulate complex fluids by means of an on-the-fly coupling of the bulk rheology to the underlying microstructure dynamics. In particular, a continuum model of polymeric fluids is constructed without a pre-specified constitutive relation, but instead it is actively learned from mesoscopic simulations where the dynamics of polymer chains is explicitly computed. To couple the bulk rheology of polymeric fluids and the microscale dynamics of polymer chains, the continuum approach (based on the finite volume method) provides the transient flow field as inputs for the (mesoscopic) dissipative particle dynamics (DPD), and in turn DPD returns an effective constitutive relation to close the continuum equations. In this multiscale modeling procedure, we employ an active learning strategy based on Gaussian process regression (GPR) to minimize the number of expensive DPD simulations, where adaptively selected DPD simulations are performed only as necessary. Numerical experiments are carried out for flow past a circular cylinder of a non-Newtonian fluid, modeled at the mesoscopic level by bead-spring chains. The results show that only five DPD simulations are required to achieve an effective closure of the continuum equations at Reynolds number Re = 10. Furthermore, when Re is increased to 100, only one additional DPD simulation is required for constructing an extended GPR-informed model closure. Compared to traditional message-passing multiscale approaches, applying an active learning scheme to multiscale modeling of non-Newtonian fluids can significantly increase the computational efficiency. Although the method demonstrated here obtains only a local viscosity from the polymer dynamics, it can be extended to other multiscale models of complex fluids whose macro-rheology is unknown.

Simulations of SSLV Ascent and Debris Transport

NASA Technical Reports Server (NTRS)

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

2006-01-01

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

DEVELOPMENTS AND APPLICATIONS OF CFD SIMULATIONS OF MICROMETEOROLOGY AND POLLUTION TRANSPORT IN SUPPORT OF AIR QUALITY MODELING

EPA Science Inventory

Development and application of computational fluid dynamics (CFD) simulations are being advanced through case studies for simulating air pollutant concentrations from sources within open fields and within complex urban building environments. CFD applications have been under deve...

Probability Simulations by Non-Lipschitz Chaos

NASA Technical Reports Server (NTRS)

Zak, Michail

1996-01-01

It has been demonstrated that classical probabilities, and in particular, probabilistic Turing machine, can be simulated by combining chaos and non-Lipschitz dynamics, without utilization of any man-made devices. Self-organizing properties of systems coupling simulated and calculated probabilities and their link to quantum computations are discussed.

Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments

PubMed Central

De Paris, Renata; Quevedo, Christian V.; Ruiz, Duncan D.; Norberto de Souza, Osmar; Barros, Rodrigo C.

2015-01-01

Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR) model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand. PMID:25873944

Analytical investigation of the dynamics of tethered constellations in Earth orbit, phase 2

NASA Technical Reports Server (NTRS)

Lorenzini, E.

1985-01-01

This Quarterly Report deals with the deployment maneuver of a single-axis, vertical constellation with three masses. A new, easy to handle, computer code that simulates the two-dimensional dynamics of the constellation has been implemented. This computer code is used for designing control laws for the deployment maneuver that minimizes the acceleration level of the low-g platform during the maneuver.

Use of computer modeling to investigate a dynamic interaction problem in the Skylab TACS quad-valve package

NASA Technical Reports Server (NTRS)

Hesser, R. J.; Gershman, R.

1975-01-01

A valve opening-response problem encountered during development of a control valve for the Skylab thruster attitude control system (TACS) is described. The problem involved effects of dynamic interaction among valves in the quad-redundant valve package. Also described is a detailed computer simulation of the quad-valve package which was helpful in resolving the problem.

The fusion code XGC: Enabling kinetic study of multi-scale edge turbulent transport in ITER [Book Chapter

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

D'Azevedo, Eduardo; Abbott, Stephen; Koskela, Tuomas

The XGC fusion gyrokinetic code combines state-of-the-art, portable computational and algorithmic technologies to enable complicated multiscale simulations of turbulence and transport dynamics in ITER edge plasma on the largest US open-science computer, the CRAY XK7 Titan, at its maximal heterogeneous capability, which have not been possible before due to a factor of over 10 shortage in the time-to-solution for less than 5 days of wall-clock time for one physics case. Frontier techniques such as nested OpenMP parallelism, adaptive parallel I/O, staging I/O and data reduction using dynamic and asynchronous applications interactions, dynamic repartitioning for balancing computational work in pushing particlesmore » and in grid related work, scalable and accurate discretization algorithms for non-linear Coulomb collisions, and communication-avoiding subcycling technology for pushing particles on both CPUs and GPUs are also utilized to dramatically improve the scalability and time-to-solution, hence enabling the difficult kinetic ITER edge simulation on a present-day leadership class computer.« less

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

Koniges, A.E.; Craddock, G.G.; Schnack, D.D.

The purpose of the workshop was to assemble workers, both within and outside of the fusion-related computations areas, for discussion regarding the issues of dynamically adaptive gridding. There were three invited talks related to adaptive gridding application experiences in various related fields of computational fluid dynamics (CFD), and nine short talks reporting on the progress of adaptive techniques in the specific areas of scrape-off-layer (SOL) modeling and magnetohydrodynamic (MHD) stability. Adaptive mesh methods have been successful in a number of diverse fields of CFD for over a decade. The method involves dynamic refinement of computed field profiles in a waymore » that disperses uniformly the numerical errors associated with discrete approximations. Because the process optimizes computational effort, adaptive mesh methods can be used to study otherwise the intractable physical problems that involve complex boundary shapes or multiple spatial/temporal scales. Recent results indicate that these adaptive techniques will be required for tokamak fluid-based simulations involving the diverted tokamak SOL modeling and MHD simulations problems related to the highest priority ITER relevant issues.Individual papers are indexed separately on the energy data bases.« less

Intrinsic map dynamics exploration for uncharted effective free-energy landscapes

PubMed Central

Covino, Roberto; Coifman, Ronald R.; Gear, C. William; Georgiou, Anastasia S.; Kevrekidis, Ioannis G.

2017-01-01

We describe and implement a computer-assisted approach for accelerating the exploration of uncharted effective free-energy surfaces (FESs). More generally, the aim is the extraction of coarse-grained, macroscopic information from stochastic or atomistic simulations, such as molecular dynamics (MD). The approach functionally links the MD simulator with nonlinear manifold learning techniques. The added value comes from biasing the simulator toward unexplored phase-space regions by exploiting the smoothness of the gradually revealed intrinsic low-dimensional geometry of the FES. PMID:28634293

A Component-Based FPGA Design Framework for Neuronal Ion Channel Dynamics Simulations

PubMed Central

Mak, Terrence S. T.; Rachmuth, Guy; Lam, Kai-Pui; Poon, Chi-Sang

2008-01-01

Neuron-machine interfaces such as dynamic clamp and brain-implantable neuroprosthetic devices require real-time simulations of neuronal ion channel dynamics. Field Programmable Gate Array (FPGA) has emerged as a high-speed digital platform ideal for such application-specific computations. We propose an efficient and flexible component-based FPGA design framework for neuronal ion channel dynamics simulations, which overcomes certain limitations of the recently proposed memory-based approach. A parallel processing strategy is used to minimize computational delay, and a hardware-efficient factoring approach for calculating exponential and division functions in neuronal ion channel models is used to conserve resource consumption. Performances of the various FPGA design approaches are compared theoretically and experimentally in corresponding implementations of the AMPA and NMDA synaptic ion channel models. Our results suggest that the component-based design framework provides a more memory economic solution as well as more efficient logic utilization for large word lengths, whereas the memory-based approach may be suitable for time-critical applications where a higher throughput rate is desired. PMID:17190033

A generalized computer code for developing dynamic gas turbine engine models (DIGTEM)

NASA Technical Reports Server (NTRS)

Daniele, C. J.

1984-01-01

This paper describes DIGTEM (digital turbofan engine model), a computer program that simulates two spool, two stream (turbofan) engines. DIGTEM was developed to support the development of a real time multiprocessor based engine simulator being designed at the Lewis Research Center. The turbofan engine model in DIGTEM contains steady state performance maps for all the components and has control volumes where continuity and energy balances are maintained. Rotor dynamics and duct momentum dynamics are also included. DIGTEM features an implicit integration scheme for integrating stiff systems and trims the model equations to match a prescribed design point by calculating correction coefficients that balance out the dynamic equations. It uses the same coefficients at off design points and iterates to a balanced engine condition. Transients are generated by defining the engine inputs as functions of time in a user written subroutine (TMRSP). Closed loop controls can also be simulated. DIGTEM is generalized in the aerothermodynamic treatment of components. This feature, along with DIGTEM's trimming at a design point, make it a very useful tool for developing a model of a specific turbofan engine.

A generalized computer code for developing dynamic gas turbine engine models (DIGTEM)

NASA Technical Reports Server (NTRS)

Daniele, C. J.

1983-01-01

This paper describes DIGTEM (digital turbofan engine model), a computer program that simulates two spool, two stream (turbofan) engines. DIGTEM was developed to support the development of a real time multiprocessor based engine simulator being designed at the Lewis Research Center. The turbofan engine model in DIGTEM contains steady state performance maps for all the components and has control volumes where continuity and energy balances are maintained. Rotor dynamics and duct momentum dynamics are also included. DIGTEM features an implicit integration scheme for integrating stiff systems and trims the model equations to match a prescribed design point by calculating correction coefficients that balance out the dynamic equations. It uses the same coefficients at off design points and iterates to a balanced engine condition. Transients are generated by defining the engine inputs as functions of time in a user written subroutine (TMRSP). Closed loop controls can also be simulated. DIGTEM is generalized in the aerothermodynamic treatment of components. This feature, along with DIGTEM's trimming at a design point, make it a very useful tool for developing a model of a specific turbofan engine.

| NREL

Science.gov Websites

of NREL's Computational Science Center, where he uses electronic structure calculations and other introductory chemistry and physical chemistry. Research Interests Electronic structure and dynamics in the quantum/classical molecular dynamics simulation|Coupling of molecular electronic structure to

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.

Exploring Biomolecular Recognition by Modeling and Simulation

NASA Astrophysics Data System (ADS)

Wade, Rebecca

2007-12-01

Biomolecular recognition is complex. The balance between the different molecular properties that contribute to molecular recognition, such as shape, electrostatics, dynamics and entropy, varies from case to case. This, along with the extent of experimental characterization, influences the choice of appropriate computational approaches to study biomolecular interactions. I will present computational studies in which we aim to make concerted use of bioinformatics, biochemical network modeling and molecular simulation techniques to study protein-protein and protein-small molecule interactions and to facilitate computer-aided drug design.

[Computer simulation by passenger wound analysis of vehicle collision].

PubMed

Zou, Dong-Hua; Liu, Nning-Guo; Shen, Jie; Zhang, Xiao-Yun; Jin, Xian-Long; Chen, Yi-Jiu

2006-08-15

To reconstruct the course of vehicle collision, so that to provide the reference for forensic identification and disposal of traffic accidents. Through analyzing evidences left both on passengers and vehicles, technique of momentum impulse combined with multi-dynamics was applied to simulate the motion and injury of passengers as well as the track of vehicles. Model of computer stimulation perfectly reconstructed phases of the traffic collision, which coincide with details found by forensic investigation. Computer stimulation is helpful and feasible for forensic identification in traffic accidents.

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

Wake characteristics of wind turbines in utility-scale wind farms

NASA Astrophysics Data System (ADS)

Yang, Xiaolei; Foti, Daniel; Sotiropoulos, Fotis

2017-11-01

The dynamics of turbine wakes is affected by turbine operating conditions, ambient atmospheric turbulent flows, and wakes from upwind turbines. Investigations of the wake from a single turbine have been extensively carried out in the literature. Studies on the wake dynamics in utility-scale wind farms are relatively limited. In this work, we employ large-eddy simulation with an actuator surface or actuator line model for turbine blades to investigate the wake dynamics in utility-scale wind farms. Simulations of three wind farms, i.e., the Horns Rev wind farm in Denmark, Pleasant Valley wind farm in Minnesota, and the Vantage wind farm in Washington are carried out. The computed power shows a good agreement with measurements. Analysis of the wake dynamics in the three wind farms is underway and will be presented in the conference. This work was support by Xcel Energy (RD4-13). The computational resources were provided by National Renewable Energy Laboratory.

Molecular dynamics simulations of the dielectric properties of fructose aqueous solutions

NASA Astrophysics Data System (ADS)

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

2016-10-01

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

Space robot simulator vehicle

NASA Technical Reports Server (NTRS)

Cannon, R. H., Jr.; Alexander, H.

1985-01-01

A Space Robot Simulator Vehicle (SRSV) was constructed to model a free-flying robot capable of doing construction, manipulation and repair work in space. The SRSV is intended as a test bed for development of dynamic and static control methods for space robots. The vehicle is built around a two-foot-diameter air-cushion vehicle that carries batteries, power supplies, gas tanks, computer, reaction jets and radio equipment. It is fitted with one or two two-link manipulators, which may be of many possible designs, including flexible-link versions. Both the vehicle body and its first arm are nearly complete. Inverse dynamic control of the robot's manipulator has been successfully simulated using equations generated by the dynamic simulation package SDEXACT. In this mode, the position of the manipulator tip is controlled not by fixing the vehicle base through thruster operation, but by controlling the manipulator joint torques to achieve the desired tip motion, while allowing for the free motion of the vehicle base. One of the primary goals is to minimize use of the thrusters in favor of intelligent control of the manipulator. Ways to reduce the computational burden of control are described.

Experimental and Computational Study of Sonic and Supersonic Jet Plumes

NASA Technical Reports Server (NTRS)

Venkatapathy, E.; Naughton, J. W.; Fletcher, D. G.; Edwards, Thomas A. (Technical Monitor)

1994-01-01

Study of sonic and supersonic jet plumes are relevant to understanding such phenomenon as jet-noise, plume signatures, and rocket base-heating and radiation. Jet plumes are simple to simulate and yet, have complex flow structures such as Mach disks, triple points, shear-layers, barrel shocks, shock-shear-layer interaction, etc. Experimental and computational simulation of sonic and supersonic jet plumes have been performed for under- and over-expanded, axisymmetric plume conditions. The computational simulation compare very well with the experimental observations of schlieren pictures. Experimental data such as temperature measurements with hot-wire probes are yet to be measured and will be compared with computed values. Extensive analysis of the computational simulations presents a clear picture of how the complex flow structure develops and the conditions under which self-similar flow structures evolve. From the computations, the plume structure can be further classified into many sub-groups. In the proposed paper, detail results from the experimental and computational simulations for single, axisymmetric, under- and over-expanded, sonic and supersonic plumes will be compared and the fluid dynamic aspects of flow structures will be discussed.

Dynamic simulation of concentrated macromolecular solutions with screened long-range hydrodynamic interactions: Algorithm and limitations

PubMed Central

Ando, Tadashi; Chow, Edmond; Skolnick, Jeffrey

2013-01-01

Hydrodynamic interactions exert a critical effect on the dynamics of macromolecules. As the concentration of macromolecules increases, by analogy to the behavior of semidilute polymer solutions or the flow in porous media, one might expect hydrodynamic screening to occur. Hydrodynamic screening would have implications both for the understanding of macromolecular dynamics as well as practical implications for the simulation of concentrated macromolecular solutions, e.g., in cells. Stokesian dynamics (SD) is one of the most accurate methods for simulating the motions of N particles suspended in a viscous fluid at low Reynolds number, in that it considers both far-field and near-field hydrodynamic interactions. This algorithm traditionally involves an O(N3) operation to compute Brownian forces at each time step, although asymptotically faster but more complex SD methods are now available. Motivated by the idea of hydrodynamic screening, the far-field part of the hydrodynamic matrix in SD may be approximated by a diagonal matrix, which is equivalent to assuming that long range hydrodynamic interactions are completely screened. This approximation allows sparse matrix methods to be used, which can reduce the apparent computational scaling to O(N). Previously there were several simulation studies using this approximation for monodisperse suspensions. Here, we employ newly designed preconditioned iterative methods for both the computation of Brownian forces and the solution of linear systems, and consider the validity of this approximation in polydisperse suspensions. We evaluate the accuracy of the diagonal approximation method using an intracellular-like suspension. The diffusivities of particles obtained with this approximation are close to those with the original method. However, this approximation underestimates intermolecular correlated motions, which is a trade-off between accuracy and computing efficiency. The new method makes it possible to perform large-scale and long-time simulation with an approximate accounting of hydrodynamic interactions. PMID:24089734

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

Computational Models of Protein Kinematics and Dynamics: Beyond Simulation

PubMed Central

Gipson, Bryant; Hsu, David; Kavraki, Lydia E.; Latombe, Jean-Claude

2016-01-01

Physics-based simulation represents a powerful method for investigating the time-varying behavior of dynamic protein systems at high spatial and temporal resolution. Such simulations, however, can be prohibitively difficult or lengthy for large proteins or when probing the lower-resolution, long-timescale behaviors of proteins generally. Importantly, not all questions about a protein system require full space and time resolution to produce an informative answer. For instance, by avoiding the simulation of uncorrelated, high-frequency atomic movements, a larger, domain-level picture of protein dynamics can be revealed. The purpose of this review is to highlight the growing body of complementary work that goes beyond simulation. In particular, this review focuses on methods that address kinematics and dynamics, as well as those that address larger organizational questions and can quickly yield useful information about the long-timescale behavior of a protein. PMID:22524225

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.

Hybrid Method for Power Control Simulation of a Single Fluid Plasma Thruster

NASA Astrophysics Data System (ADS)

Jaisankar, S.; Sheshadri, T. S.

2018-05-01

Propulsive plasma flow through a cylindrical-conical diverging thruster is simulated by a power controlled hybrid method to obtain the basic flow, thermodynamic and electromagnetic variables. Simulation is based on a single fluid model with electromagnetics being described by the equations of potential Poisson, Maxwell and the Ohm's law while the compressible fluid dynamics by the Navier Stokes in cylindrical form. The proposed method solved the electromagnetics and fluid dynamics separately, both to segregate the two prominent scales for an efficient computation and for the delivery of voltage controlled rated power. The magnetic transport is solved for steady state while fluid dynamics is allowed to evolve in time along with an electromagnetic source using schemes based on generalized finite difference discretization. The multistep methodology with power control is employed for simulating fully ionized propulsive flow of argon plasma through the thruster. Numerical solution shows convergence of every part of the solver including grid stability causing the multistep hybrid method to converge for a rated power delivery. Simulation results are reasonably in agreement with the reported physics of plasma flow in the thruster thus indicating the potential utility of this hybrid computational framework, especially when single fluid approximation of plasma is relevant.

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

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

Multispan Elevated Guideway Design for Passenger Transport Vehicles : Volume 2. Appendixes.

DOT National Transportation Integrated Search

1975-04-01

Contents: Appendix A - derivation of vehicle-guideway interaction equations; Appendix B - evaluation of pier support dynamics; Appendix C - computer simulation program of two-dimensional vehicle over a multi-span guideway; Appendix D - computer progr...

Teaching Ionic Solvation Structure with a Monte Carlo Liquid Simulation Program

ERIC Educational Resources Information Center

Serrano, Agostinho; Santos, Flavia M. T.; Greca, Ileana M.

2004-01-01

The use of molecular dynamics and Monte Carlo methods has provided efficient means to stimulate the behavior of molecular liquids and solutions. A Monte Carlo simulation program is used to compute the structure of liquid water and of water as a solvent to Na(super +), Cl(super -), and Ar on a personal computer to show that it is easily feasible to…

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.

Advanced Dynamically Adaptive Algorithms for Stochastic Simulations on Extreme Scales

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

Xiu, Dongbin

2017-03-03

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

A membrane computing simulator of trans-hierarchical antibiotic resistance evolution dynamics in nested ecological compartments (ARES).

PubMed

Campos, Marcelino; Llorens, Carlos; Sempere, José M; Futami, Ricardo; Rodriguez, Irene; Carrasco, Purificación; Capilla, Rafael; Latorre, Amparo; Coque, Teresa M; Moya, Andres; Baquero, Fernando

2015-08-05

Antibiotic resistance is a major biomedical problem upon which public health systems demand solutions to construe the dynamics and epidemiological risk of resistant bacteria in anthropogenically-altered environments. The implementation of computable models with reciprocity within and between levels of biological organization (i.e. essential nesting) is central for studying antibiotic resistances. Antibiotic resistance is not just the result of antibiotic-driven selection but more properly the consequence of a complex hierarchy of processes shaping the ecology and evolution of the distinct subcellular, cellular and supra-cellular vehicles involved in the dissemination of resistance genes. Such a complex background motivated us to explore the P-system standards of membrane computing an innovative natural computing formalism that abstracts the notion of movement across membranes to simulate antibiotic resistance evolution processes across nested levels of micro- and macro-environmental organization in a given ecosystem. In this article, we introduce ARES (Antibiotic Resistance Evolution Simulator) a software device that simulates P-system model scenarios with five types of nested computing membranes oriented to emulate a hierarchy of eco-biological compartments, i.e. a) peripheral ecosystem; b) local environment; c) reservoir of supplies; d) animal host; and e) host's associated bacterial organisms (microbiome). Computational objects emulating molecular entities such as plasmids, antibiotic resistance genes, antimicrobials, and/or other substances can be introduced into this framework and may interact and evolve together with the membranes, according to a set of pre-established rules and specifications. ARES has been implemented as an online server and offers additional tools for storage and model editing and downstream analysis. The stochastic nature of the P-system model implemented in ARES explicitly links within and between host dynamics into a simulation, with feedback reciprocity among the different units of selection influenced by antibiotic exposure at various ecological levels. ARES offers the possibility of modeling predictive multilevel scenarios of antibiotic resistance evolution that can be interrogated, edited and re-simulated if necessary, with different parameters, until a correct model description of the process in the real world is convincingly approached. ARES can be accessed at http://gydb.org/ares.

Systematic Computation of Nonlinear Cellular and Molecular Dynamics with Low-Power CytoMimetic Circuits: A Simulation Study

PubMed Central

Papadimitriou, Konstantinos I.; Stan, Guy-Bart V.; Drakakis, Emmanuel M.

2013-01-01

This paper presents a novel method for the systematic implementation of low-power microelectronic circuits aimed at computing nonlinear cellular and molecular dynamics. The method proposed is based on the Nonlinear Bernoulli Cell Formalism (NBCF), an advanced mathematical framework stemming from the Bernoulli Cell Formalism (BCF) originally exploited for the modular synthesis and analysis of linear, time-invariant, high dynamic range, logarithmic filters. Our approach identifies and exploits the striking similarities existing between the NBCF and coupled nonlinear ordinary differential equations (ODEs) typically appearing in models of naturally encountered biochemical systems. The resulting continuous-time, continuous-value, low-power CytoMimetic electronic circuits succeed in simulating fast and with good accuracy cellular and molecular dynamics. The application of the method is illustrated by synthesising for the first time microelectronic CytoMimetic topologies which simulate successfully: 1) a nonlinear intracellular calcium oscillations model for several Hill coefficient values and 2) a gene-protein regulatory system model. The dynamic behaviours generated by the proposed CytoMimetic circuits are compared and found to be in very good agreement with their biological counterparts. The circuits exploit the exponential law codifying the low-power subthreshold operation regime and have been simulated with realistic parameters from a commercially available CMOS process. They occupy an area of a fraction of a square-millimetre, while consuming between 1 and 12 microwatts of power. Simulations of fabrication-related variability results are also presented. PMID:23393550

Indonesia’s Electricity Demand Dynamic Modelling

NASA Astrophysics Data System (ADS)

Sulistio, J.; Wirabhuana, A.; Wiratama, M. G.

2017-06-01

Electricity Systems modelling is one of the emerging area in the Global Energy policy studies recently. System Dynamics approach and Computer Simulation has become one the common methods used in energy systems planning and evaluation in many conditions. On the other hand, Indonesia experiencing several major issues in Electricity system such as fossil fuel domination, demand - supply imbalances, distribution inefficiency, and bio-devastation. This paper aims to explain the development of System Dynamics modelling approaches and computer simulation techniques in representing and predicting electricity demand in Indonesia. In addition, this paper also described the typical characteristics and relationship of commercial business sector, industrial sector, and family / domestic sector as electricity subsystems in Indonesia. Moreover, it will be also present direct structure, behavioural, and statistical test as model validation approach and ended by conclusions.

Recent developments in structural proteomics for protein structure determination.

PubMed

Liu, Hsuan-Liang; Hsu, Jyh-Ping

2005-05-01

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

The Technique for CFD-Simulation of Fuel Valve from Pneumatic-Hydraulic System of Liquid-Propellant Rocket Engine

NASA Astrophysics Data System (ADS)

Shabliy, L. S.; Malov, D. V.; Bratchinin, D. S.

2018-01-01

In the article the description of technique for simulation of valves for pneumatic-hydraulic system of liquid-propellant rocket engine (LPRE) is given. Technique is based on approach of computational hydrodynamics (Computational Fluid Dynamics - CFD). The simulation of a differential valve used in closed circuit LPRE supply pipes of fuel components is performed to show technique abilities. A schematic and operation algorithm of this valve type is described in detail. Also assumptions made in the construction of the geometric model of the hydraulic path of the valve are described in detail. The calculation procedure for determining valve hydraulic characteristics is given. Based on these calculations certain hydraulic characteristics of the valve are given. Some ways of usage of the described simulation technique for research the static and dynamic characteristics of the elements of the pneumatic-hydraulic system of LPRE are proposed.

Importance of inlet boundary conditions for numerical simulation of combustor flows

NASA Technical Reports Server (NTRS)

Sturgess, G. J.; Syed, S. A.; Mcmanus, K. R.

1983-01-01

Fluid dynamic computer codes for the mathematical simulation of problems in gas turbine engine combustion systems are required as design and diagnostic tools. To eventually achieve a performance standard with these codes of more than qualitative accuracy it is desirable to use benchmark experiments for validation studies. Typical of the fluid dynamic computer codes being developed for combustor simulations is the TEACH (Teaching Elliptic Axisymmetric Characteristics Heuristically) solution procedure. It is difficult to find suitable experiments which satisfy the present definition of benchmark quality. For the majority of the available experiments there is a lack of information concerning the boundary conditions. A standard TEACH-type numerical technique is applied to a number of test-case experiments. It is found that numerical simulations of gas turbine combustor-relevant flows can be sensitive to the plane at which the calculations start and the spatial distributions of inlet quantities for swirling flows.

A High-Performance Cellular Automaton Model of Tumor Growth with Dynamically Growing Domains

PubMed Central

Poleszczuk, Jan; Enderling, Heiko

2014-01-01

Tumor growth from a single transformed cancer cell up to a clinically apparent mass spans many spatial and temporal orders of magnitude. Implementation of cellular automata simulations of such tumor growth can be straightforward but computing performance often counterbalances simplicity. Computationally convenient simulation times can be achieved by choosing appropriate data structures, memory and cell handling as well as domain setup. We propose a cellular automaton model of tumor growth with a domain that expands dynamically as the tumor population increases. We discuss memory access, data structures and implementation techniques that yield high-performance multi-scale Monte Carlo simulations of tumor growth. We discuss tumor properties that favor the proposed high-performance design and present simulation results of the tumor growth model. We estimate to which parameters the model is the most sensitive, and show that tumor volume depends on a number of parameters in a non-monotonic manner. PMID:25346862

Computer simulation of the processes of inactivation of bacterial cells by dynamic low-coherent speckles

NASA Astrophysics Data System (ADS)

Ulianova, Onega V.; Ulyanov, Sergey S.; Sazanova, Elena V.; Zhihong, Zhang; Sibo, Zhou; Luo, Qingming; Zudina, Irina; Bednov, Andrey

2006-05-01

Biochemical, biophysical and optical aspects of interaction of low-coherent light with bacterial cells have been discussed. Influence of low-coherent speckles on the colonies grows is investigated. It has been demonstrated that effects of light on the inhibition of cells (Francisella Tularensis) are connected with speckle dynamics. The regimes of illumination of cell suspension with purpose of devitalization of hazard bacteria, caused very dangerous infections, such as tularemia, are found. Mathematical model of interaction of low-coherent laser radiation with bacteria suspension has been proposed. Computer simulations of the processes of laser-cells interaction have been carried out.

Dynamic Deployment Simulations of Inflatable Space Structures

NASA Technical Reports Server (NTRS)

Wang, John T.

2005-01-01

The feasibility of using Control Volume (CV) method and the Arbitrary Lagrangian Eulerian (ALE) method in LSDYNA to simulate the dynamic deployment of inflatable space structures is investigated. The CV and ALE methods were used to predict the inflation deployments of three folded tube configurations. The CV method was found to be a simple and computationally efficient method that may be adequate for modeling slow inflation deployment sine the inertia of the inflation gas can be neglected. The ALE method was found to be very computationally intensive since it involves the solving of three conservative equations of fluid as well as dealing with complex fluid structure interactions.

Neuromechanic: a computational platform for simulation and analysis of the neural control of movement

PubMed Central

Bunderson, Nathan E.; Bingham, Jeffrey T.; Sohn, M. Hongchul; Ting, Lena H.; Burkholder, Thomas J.

2015-01-01

Neuromusculoskeletal models solve the basic problem of determining how the body moves under the influence of external and internal forces. Existing biomechanical modeling programs often emphasize dynamics with the goal of finding a feed-forward neural program to replicate experimental data or of estimating force contributions or individual muscles. The computation of rigid-body dynamics, muscle forces, and activation of the muscles are often performed separately. We have developed an intrinsically forward computational platform (Neuromechanic, www.neuromechanic.com) that explicitly represents the interdependencies among rigid body dynamics, frictional contact, muscle mechanics, and neural control modules. This formulation has significant advantages for optimization and forward simulation, particularly with application to neural controllers with feedback or regulatory features. Explicit inclusion of all state dependencies allows calculation of system derivatives with respect to kinematic states as well as muscle and neural control states, thus affording a wealth of analytical tools, including linearization, stability analyses and calculation of initial conditions for forward simulations. In this review, we describe our algorithm for generating state equations and explain how they may be used in integration, linearization and stability analysis tools to provide structural insights into the neural control of movement. PMID:23027632

Neuromechanic: a computational platform for simulation and analysis of the neural control of movement.

PubMed

Bunderson, Nathan E; Bingham, Jeffrey T; Sohn, M Hongchul; Ting, Lena H; Burkholder, Thomas J

2012-10-01

Neuromusculoskeletal models solve the basic problem of determining how the body moves under the influence of external and internal forces. Existing biomechanical modeling programs often emphasize dynamics with the goal of finding a feed-forward neural program to replicate experimental data or of estimating force contributions or individual muscles. The computation of rigid-body dynamics, muscle forces, and activation of the muscles are often performed separately. We have developed an intrinsically forward computational platform (Neuromechanic, www.neuromechanic.com) that explicitly represents the interdependencies among rigid body dynamics, frictional contact, muscle mechanics, and neural control modules. This formulation has significant advantages for optimization and forward simulation, particularly with application to neural controllers with feedback or regulatory features. Explicit inclusion of all state dependencies allows calculation of system derivatives with respect to kinematic states and muscle and neural control states, thus affording a wealth of analytical tools, including linearization, stability analyses and calculation of initial conditions for forward simulations. In this review, we describe our algorithm for generating state equations and explain how they may be used in integration, linearization, and stability analysis tools to provide structural insights into the neural control of movement. Copyright © 2012 John Wiley & Sons, Ltd.

Fast Particle Methods for Multiscale Phenomena Simulations

NASA Technical Reports Server (NTRS)

Koumoutsakos, P.; Wray, A.; Shariff, K.; Pohorille, Andrew

2000-01-01

We are developing particle methods oriented at improving computational modeling capabilities of multiscale physical phenomena in : (i) high Reynolds number unsteady vortical flows, (ii) particle laden and interfacial flows, (iii)molecular dynamics studies of nanoscale droplets and studies of the structure, functions, and evolution of the earliest living cell. The unifying computational approach involves particle methods implemented in parallel computer architectures. The inherent adaptivity, robustness and efficiency of particle methods makes them a multidisciplinary computational tool capable of bridging the gap of micro-scale and continuum flow simulations. Using efficient tree data structures, multipole expansion algorithms, and improved particle-grid interpolation, particle methods allow for simulations using millions of computational elements, making possible the resolution of a wide range of length and time scales of these important physical phenomena.The current challenges in these simulations are in : [i] the proper formulation of particle methods in the molecular and continuous level for the discretization of the governing equations [ii] the resolution of the wide range of time and length scales governing the phenomena under investigation. [iii] the minimization of numerical artifacts that may interfere with the physics of the systems under consideration. [iv] the parallelization of processes such as tree traversal and grid-particle interpolations We are conducting simulations using vortex methods, molecular dynamics and smooth particle hydrodynamics, exploiting their unifying concepts such as : the solution of the N-body problem in parallel computers, highly accurate particle-particle and grid-particle interpolations, parallel FFT's and the formulation of processes such as diffusion in the context of particle methods. This approach enables us to transcend among seemingly unrelated areas of research.

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

NASA Astrophysics Data System (ADS)

Chen, Jim Xiong

1995-01-01

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

Dynamic modeling method for infrared smoke based on enhanced discrete phase model

NASA Astrophysics Data System (ADS)

Zhang, Zhendong; Yang, Chunling; Zhang, Yan; Zhu, Hongbo

2018-03-01

The dynamic modeling of infrared (IR) smoke plays an important role in IR scene simulation systems and its accuracy directly influences the system veracity. However, current IR smoke models cannot provide high veracity, because certain physical characteristics are frequently ignored in fluid simulation; simplifying the discrete phase as a continuous phase and ignoring the IR decoy missile-body spinning. To address this defect, this paper proposes a dynamic modeling method for IR smoke, based on an enhanced discrete phase model (DPM). A mathematical simulation model based on an enhanced DPM is built and a dynamic computing fluid mesh is generated. The dynamic model of IR smoke is then established using an extended equivalent-blackbody-molecule model. Experiments demonstrate that this model realizes a dynamic method for modeling IR smoke with higher veracity.

The theory of reasoned action as parallel constraint satisfaction: towards a dynamic computational model of health behavior.

PubMed

Orr, Mark G; Thrush, Roxanne; Plaut, David C

2013-01-01

The reasoned action approach, although ubiquitous in health behavior theory (e.g., Theory of Reasoned Action/Planned Behavior), does not adequately address two key dynamical aspects of health behavior: learning and the effect of immediate social context (i.e., social influence). To remedy this, we put forth a computational implementation of the Theory of Reasoned Action (TRA) using artificial-neural networks. Our model re-conceptualized behavioral intention as arising from a dynamic constraint satisfaction mechanism among a set of beliefs. In two simulations, we show that constraint satisfaction can simultaneously incorporate the effects of past experience (via learning) with the effects of immediate social context to yield behavioral intention, i.e., intention is dynamically constructed from both an individual's pre-existing belief structure and the beliefs of others in the individual's social context. In a third simulation, we illustrate the predictive ability of the model with respect to empirically derived behavioral intention. As the first known computational model of health behavior, it represents a significant advance in theory towards understanding the dynamics of health behavior. Furthermore, our approach may inform the development of population-level agent-based models of health behavior that aim to incorporate psychological theory into models of population dynamics.

The Theory of Reasoned Action as Parallel Constraint Satisfaction: Towards a Dynamic Computational Model of Health Behavior

PubMed Central

Orr, Mark G.; Thrush, Roxanne; Plaut, David C.

2013-01-01

The reasoned action approach, although ubiquitous in health behavior theory (e.g., Theory of Reasoned Action/Planned Behavior), does not adequately address two key dynamical aspects of health behavior: learning and the effect of immediate social context (i.e., social influence). To remedy this, we put forth a computational implementation of the Theory of Reasoned Action (TRA) using artificial-neural networks. Our model re-conceptualized behavioral intention as arising from a dynamic constraint satisfaction mechanism among a set of beliefs. In two simulations, we show that constraint satisfaction can simultaneously incorporate the effects of past experience (via learning) with the effects of immediate social context to yield behavioral intention, i.e., intention is dynamically constructed from both an individual’s pre-existing belief structure and the beliefs of others in the individual’s social context. In a third simulation, we illustrate the predictive ability of the model with respect to empirically derived behavioral intention. As the first known computational model of health behavior, it represents a significant advance in theory towards understanding the dynamics of health behavior. Furthermore, our approach may inform the development of population-level agent-based models of health behavior that aim to incorporate psychological theory into models of population dynamics. PMID:23671603

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

PubMed

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

2010-04-15

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

ChainMail based neural dynamics modeling of soft tissue deformation for surgical simulation.

PubMed

Zhang, Jinao; Zhong, Yongmin; Smith, Julian; Gu, Chengfan

2017-07-20

Realistic and real-time modeling and simulation of soft tissue deformation is a fundamental research issue in the field of surgical simulation. In this paper, a novel cellular neural network approach is presented for modeling and simulation of soft tissue deformation by combining neural dynamics of cellular neural network with ChainMail mechanism. The proposed method formulates the problem of elastic deformation into cellular neural network activities to avoid the complex computation of elasticity. The local position adjustments of ChainMail are incorporated into the cellular neural network as the local connectivity of cells, through which the dynamic behaviors of soft tissue deformation are transformed into the neural dynamics of cellular neural network. Experiments demonstrate that the proposed neural network approach is capable of modeling the soft tissues' nonlinear deformation and typical mechanical behaviors. The proposed method not only improves ChainMail's linear deformation with the nonlinear characteristics of neural dynamics but also enables the cellular neural network to follow the principle of continuum mechanics to simulate soft tissue deformation.

Is an intuitive convergence definition of molecular dynamics simulations solely based on the root mean square deviation possible?

PubMed

Knapp, B; Frantal, S; Cibena, M; Schreiner, W; Bauer, P

2011-08-01

Molecular dynamics is a commonly used technique in computational biology. One key issue of each molecular dynamics simulation is: When does this simulation reach equilibrium state? A widely used way to determine this is the visual and intuitive inspection of root mean square deviation (RMSD) plots of the simulation. Although this technique has been criticized several times, it is still often used. Therefore, we present a study proving that this method is not reliable at all. We conducted a survey with participants from the field in which we illustrated different RMSD plots to scientists in the field of molecular dynamics. These plots were randomized and repeated, using a statistical model and different variants of the plots. We show that there is no mutual consent about the point of equilibrium. The decisions are severely biased by different parameters. Therefore, we conclude that scientists should not discuss the equilibration of a molecular dynamics simulation on the basis of a RMSD plot.

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

NASA Astrophysics Data System (ADS)

Yang, Zhengjun; Wang, Fujun; Zhou, Peijian

2012-09-01

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

Ground-motion signature of dynamic ruptures on rough faults

NASA Astrophysics Data System (ADS)

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

2016-04-01

Natural earthquakes occur on faults characterized by large-scale segmentation and small-scale roughness. This multi-scale geometrical complexity controls the dynamic rupture process, and hence strongly affects the radiated seismic waves and near-field shaking. For a fault system with given segmentation, the question arises what are the conditions for producing large-magnitude multi-segment ruptures, as opposed to smaller single-segment events. Similarly, for variable degrees of roughness, ruptures may be arrested prematurely or may break the entire fault. In addition, fault roughness induces rupture incoherence that determines the level of high-frequency radiation. Using HPC-enabled dynamic-rupture simulations, we generate physically self-consistent rough-fault earthquake scenarios (M~6.8) and their associated near-source seismic radiation. Because these computations are too expensive to be conducted routinely for simulation-based seismic hazard assessment, we thrive to develop an effective pseudo-dynamic source characterization that produces (almost) the same ground-motion characteristics. Therefore, we examine how variable degrees of fault roughness affect rupture properties and the seismic wavefield, and develop a planar-fault kinematic source representation that emulates the observed dynamic behaviour. We propose an effective workflow for improved pseudo-dynamic source modelling that incorporates rough-fault effects and its associated high-frequency radiation in broadband ground-motion computation for simulation-based seismic hazard assessment.