Sample records for dynamics simulation application
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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.
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2015-09-01
Discontinuous Element-Based Galerkin Methods on Dynamically Adaptive Grids with Application to Atmospheric Simulations 5a. CONTRACT NUMBER 5b. GRANT NUMBER...Discontinuous Element-Based Galerkin Methods on Dynamically Adaptive Grids with Application to Atmospheric Simulations. Michal A. Koperaa,∗, Francis X...mass conservation, as it is an important feature for many atmospheric applications . We believe this is a good metric because, for smooth solutions
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DOT National Transportation Integrated Search
2017-07-04
The primary objective of this project is to develop multiple simulation testbeds/transportation models to evaluate the impacts of Dynamic Mobility Application (DMA) connected vehicle applications and Active Transportation and Dynamic management (ATDM...
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NASA Astrophysics Data System (ADS)
Othman, M. F.; Kurniawan, R.; Schramm, D.; Ariffin, A. K.
2018-05-01
Modeling a cable model in multibody dynamics simulation tool which dynamically varies in length, mass and stiffness is a challenging task. Simulation of cable-driven parallel robots (CDPR) for instance requires a cable model that can dynamically change in length for every desired pose of the platform. Thus, in this paper, a detailed procedure for modeling and simulation of a dynamic cable model in Dymola is proposed. The approach is also applicable for other types of Modelica simulation environments. The cable is modeled using standard mechanical elements like mass, spring, damper and joint. The parameters of the cable model are based on the factsheet of the manufacturer and experimental results. Its dynamic ability is tested by applying it on a complete planar CDPR model in which the parameters are based on a prototype named CABLAR, which is developed in Chair of Mechatronics, University of Duisburg-Essen. The prototype has been developed to demonstrate an application of CDPR as a goods storage and retrieval machine. The performance of the cable model during the simulation is analyzed and discussed.
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Quantum Fragment Based ab Initio Molecular Dynamics for Proteins.
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.
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Distributed dynamic simulations of networked control and building performance applications.
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.
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Distributed dynamic simulations of networked control and building performance applications
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
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DOE Office of Scientific and Technical Information (OSTI.GOV)
2015-10-20
Look-ahead dynamic simulation software system incorporates the high performance parallel computing technologies, significantly reduces the solution time for each transient simulation case, and brings the dynamic simulation analysis into on-line applications to enable more transparency for better reliability and asset utilization. It takes the snapshot of the current power grid status, functions in parallel computing the system dynamic simulation, and outputs the transient response of the power system in real time.
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Molecular dynamics simulations: advances and applications
Hospital, Adam; Goñi, Josep Ramon; Orozco, Modesto; Gelpí, Josep L
2015-01-01
Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed. PMID:26604800
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DOT National Transportation Integrated Search
2017-07-04
The primary objective of this project is to develop multiple simulation testbeds/transportation models to evaluate the impacts of Dynamic Mobility Application (DMA) connected vehicle applications and Active Transportation and Demand management (ATDM)...
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Chen, Zhiwei; Chen, Bo
2014-01-01
Many long-span bridges have been built throughout the world in recent years but they are often subject to multiple types of dynamic loads, especially those located in wind-prone regions and carrying both trains and road vehicles. To ensure the safety and functionality of these bridges, dynamic responses of long-span bridges are often required for bridge assessment. Given that there are several limitations for the assessment based on field measurement of dynamic responses, a promising approach is based on numerical simulation technologies. This paper provides a detailed review of key issues involved in dynamic response analysis of long-span multiload bridges based on numerical simulation technologies, including dynamic interactions between running trains and bridge, between running road vehicles and bridge, and between wind and bridge, and in the wind-vehicle-bridge coupled system. Then a comprehensive review is conducted for engineering applications of newly developed numerical simulation technologies to safety assessment of long-span bridges, such as assessment of fatigue damage and assessment under extreme events. Finally, the existing problems and promising research efforts for the numerical simulation technologies and their applications to assessment of long-span multiload bridges are explored.
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Chen, Zhiwei; Chen, Bo
2014-01-01
Many long-span bridges have been built throughout the world in recent years but they are often subject to multiple types of dynamic loads, especially those located in wind-prone regions and carrying both trains and road vehicles. To ensure the safety and functionality of these bridges, dynamic responses of long-span bridges are often required for bridge assessment. Given that there are several limitations for the assessment based on field measurement of dynamic responses, a promising approach is based on numerical simulation technologies. This paper provides a detailed review of key issues involved in dynamic response analysis of long-span multiload bridges based on numerical simulation technologies, including dynamic interactions between running trains and bridge, between running road vehicles and bridge, and between wind and bridge, and in the wind-vehicle-bridge coupled system. Then a comprehensive review is conducted for engineering applications of newly developed numerical simulation technologies to safety assessment of long-span bridges, such as assessment of fatigue damage and assessment under extreme events. Finally, the existing problems and promising research efforts for the numerical simulation technologies and their applications to assessment of long-span multiload bridges are explored. PMID:25006597
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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.
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NASA Astrophysics Data System (ADS)
Hai-yang, Zhao; Min-qiang, Xu; Jin-dong, Wang; Yong-bo, Li
2015-05-01
In order to improve the accuracy of dynamics response simulation for mechanism with joint clearance, a parameter optimization method for planar joint clearance contact force model was presented in this paper, and the optimized parameters were applied to the dynamics response simulation for mechanism with oversized joint clearance fault. By studying the effect of increased clearance on the parameters of joint clearance contact force model, the relation of model parameters between different clearances was concluded. Then the dynamic equation of a two-stage reciprocating compressor with four joint clearances was developed using Lagrange method, and a multi-body dynamic model built in ADAMS software was used to solve this equation. To obtain a simulated dynamic response much closer to that of experimental tests, the parameters of joint clearance model, instead of using the designed values, were optimized by genetic algorithms approach. Finally, the optimized parameters were applied to simulate the dynamics response of model with oversized joint clearance fault according to the concluded parameter relation. The dynamics response of experimental test verified the effectiveness of this application.
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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
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Wavelet-based surrogate time series for multiscale simulation of heterogeneous catalysis
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
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Comparative Implementation of High Performance Computing for Power System Dynamic Simulations
DOE Office of Scientific and Technical Information (OSTI.GOV)
Jin, Shuangshuang; Huang, Zhenyu; Diao, Ruisheng
Dynamic simulation for transient stability assessment is one of the most important, but intensive, computations for power system planning and operation. Present commercial software is mainly designed for sequential computation to run a single simulation, which is very time consuming with a single processer. The application of High Performance Computing (HPC) to dynamic simulations is very promising in accelerating the computing process by parallelizing its kernel algorithms while maintaining the same level of computation accuracy. This paper describes the comparative implementation of four parallel dynamic simulation schemes in two state-of-the-art HPC environments: Message Passing Interface (MPI) and Open Multi-Processing (OpenMP).more » These implementations serve to match the application with dedicated multi-processor computing hardware and maximize the utilization and benefits of HPC during the development process.« less
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Dynamic computer simulations of electrophoresis: three decades of active research.
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.
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DOT National Transportation Integrated Search
2016-04-20
The primary objective of this project is to develop multiple simulation Testbeds/transportation models to evaluate the impacts of DMA connected vehicle applications and the active and dynamic transportation management (ATDM) strategies. The outputs (...
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DOT National Transportation Integrated Search
2016-10-01
The primary objective of this project is to develop multiple simulation Testbeds/transportation models to evaluate the impacts of DMA connected vehicle applications and the active and dynamic transportation management (ATDM) strategies. The outputs (...
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DOT National Transportation Integrated Search
2016-07-13
The primary objective of this project is to develop multiple simulation Testbeds/transportation models to evaluate the impacts of DMA connected vehicle applications and the active and dynamic transportation management (ATDM) strategies. The outputs (...
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DOT National Transportation Integrated Search
2016-10-01
The primary objective of this project is to develop multiple simulation Testbeds/transportation models to evaluate the impacts of DMA connected vehicle applications and the active and dynamic transportation management (ATDM) strategies. The outputs (...
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DOT National Transportation Integrated Search
2017-04-01
The primary objective of this project is to develop multiple simulation testbeds and transportation models to evaluate the impacts of Connected Vehicle Dynamic Mobility Applications (DMA) and Active Transportation and Demand Management (ATDM) strateg...
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DOT National Transportation Integrated Search
2017-04-01
The primary objective of this project is to develop multiple simulation testbeds and transportation models to evaluate the impacts of Connected Vehicle Dynamic Mobility Applications (DMA) and Active Transportation and Demand Management (ATDM) strateg...
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DOT National Transportation Integrated Search
2016-10-01
The primary objective of this project is to develop multiple simulation Testbeds/transportation models to evaluate the impacts of DMA connected vehicle applications and the active and dynamic transportation management (ATDM) strategies. The outputs (...
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DOT National Transportation Integrated Search
2016-06-30
The primary objective of this project is to develop multiple simulation Testbeds/transportation models to evaluate the impacts of DMA connected vehicle applications and the active and dynamic transportation management (ATDM) strategies. The outputs (...
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DOT National Transportation Integrated Search
2017-07-16
The primary objective of this project is to develop multiple simulation testbeds/transportation models to evaluate the impacts of Dynamic Mobility Applications (DMA) and the Active Transportation and Demand Management (ATDM) strategies. Specifically,...
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DOT National Transportation Integrated Search
2016-10-01
The primary objective of this project is to develop multiple simulation Testbeds/transportation models to evaluate the impacts of DMA connected vehicle applications and the active and dynamic transportation management (ATDM) strategies. The outputs (...
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DOT National Transportation Integrated Search
2016-06-16
The primary objective of this project is to develop multiple simulation Testbeds/transportation models to evaluate the impacts of DMA connected vehicle applications and the active and dynamic transportation management (ATDM) strategies. The outputs (...
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DOT National Transportation Integrated Search
2016-06-16
The primary objective of this project is to develop multiple simulation Testbeds/transportation models to evaluate theimpacts of DMA connected vehicle applications and the active and dynamic transportation management (ATDM)strategies. The outputs (mo...
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DOT National Transportation Integrated Search
2017-02-02
The primary objective of this project is to develop multiple simulation testbeds/transportation models to evaluate the impacts of DMA connected vehicle applications and the active and dynamic transportation management (ATDM) strategies. The outputs (...
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NASA Technical Reports Server (NTRS)
Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)
1995-01-01
Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).
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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
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ls1 mardyn: The Massively Parallel Molecular Dynamics Code for Large Systems.
Niethammer, Christoph; Becker, Stefan; Bernreuther, Martin; Buchholz, Martin; Eckhardt, Wolfgang; Heinecke, Alexander; Werth, Stephan; Bungartz, Hans-Joachim; Glass, Colin W; Hasse, Hans; Vrabec, Jadran; Horsch, Martin
2014-10-14
The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures and currently holds the world record for the largest molecular simulation with over four trillion particles. It enables the application of pair potentials to length and time scales that were previously out of scope for molecular dynamics simulation. With an efficient dynamic load balancing scheme, it delivers high scalability even for challenging heterogeneous configurations. Presently, multicenter rigid potential models based on Lennard-Jones sites, point charges, and higher-order polarities are supported. Due to its modular design, ls1 mardyn can be extended to new physical models, methods, and algorithms, allowing future users to tailor it to suit their respective needs. Possible applications include scenarios with complex geometries, such as fluids at interfaces, as well as nonequilibrium molecular dynamics simulation of heat and mass transfer.
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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...
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Molecular dynamics simulations of large macromolecular complexes.
Perilla, Juan R; Goh, Boon Chong; Cassidy, C Keith; Liu, Bo; Bernardi, Rafael C; Rudack, Till; Yu, Hang; Wu, Zhe; Schulten, Klaus
2015-04-01
Connecting dynamics to structural data from diverse experimental sources, molecular dynamics simulations permit the exploration of biological phenomena in unparalleled detail. Advances in simulations are moving the atomic resolution descriptions of biological systems into the million-to-billion atom regime, in which numerous cell functions reside. In this opinion, we review the progress, driven by large-scale molecular dynamics simulations, in the study of viruses, ribosomes, bioenergetic systems, and other diverse applications. These examples highlight the utility of molecular dynamics simulations in the critical task of relating atomic detail to the function of supramolecular complexes, a task that cannot be achieved by smaller-scale simulations or existing experimental approaches alone. Copyright © 2015 Elsevier Ltd. All rights reserved.
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DOT National Transportation Integrated Search
2016-08-22
The primary objective of this project is to develop multiple simulation Testbeds/transportation models to evaluate the impacts of DMA connected vehicle applications and the active and dynamic transportation management (ATDM) strategies. The outputs (...
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DOT National Transportation Integrated Search
2016-10-01
The primary objective of this project is to develop multiple simulation testbeds/transportation models to evaluate the impacts of DMA connected vehicle applications and the active and dynamic transportation management (ATDM) strategies. The outputs (...
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DOT National Transportation Integrated Search
2017-05-01
The primary objective of AMS project is to develop multiple simulation Testbeds/transportation models to evaluate the impacts of DMA connected vehicle applications and the active and dynamic transportation management (ATDM) strategies. Through this p...
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DOT National Transportation Integrated Search
2017-07-01
The primary objective of this project is to develop multiple simulation testbeds and transportation models to evaluate the impacts of Connected Vehicle Dynamic Mobility Applications (DMA) and Active Transportation and Demand Management (ATDM) strateg...
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DOT National Transportation Integrated Search
2017-07-01
The primary objective of this project is to develop multiple simulation testbeds and transportation models to evaluate the impacts of Connected Vehicle Dynamic Mobility Applications (DMA) and Active Transportation and Demand Management (ATDM) strateg...
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DOT National Transportation Integrated Search
2016-10-01
The primary objective of this project is to develop multiple simulation Testbeds/transportation models to evaluate the impacts of DMA connected vehicle applications and the active and dynamic transportation management (ATDM) strategies. The outputs (...
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DOT National Transportation Integrated Search
2017-08-01
The primary objective of this project is to develop multiple simulation testbeds and transportation models to evaluate the impacts of Connected Vehicle Dynamic Mobility Applications (DMA) and Active Transportation and Demand Management (ATDM) strateg...
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DOT National Transportation Integrated Search
2017-08-01
The primary objective of AMS Testbed project is to develop multiple simulation Testbeds/transportation models to evaluate the impacts of DMA connected vehicle applications and the active and dynamic transportation management (ATDM) strategies. Throug...
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DOT National Transportation Integrated Search
2016-06-29
The primary objective of this project is to develop multiple simulation testbeds/transportation models to evaluate the impacts of DMA connected vehicle applications and the active and dynamic transportation management (ATDM) strategies. The outputs (...
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NASA Technical Reports Server (NTRS)
Fortenbaugh, R. L.
1980-01-01
A mathematical model of a high performance airplane capable of vertical attitude takeoff and landing (VATOL) was developed. An off line digital simulation program incorporating this model was developed to provide trim conditions and dynamic check runs for the piloted simulation studies and support dynamic analyses of proposed VATOL configuration and flight control concepts. Development details for the various simulation component models and the application of the off line simulation program, Vertical Attitude Take-Off and Landing Simulation (VATLAS), to develop a baseline control system for the Vought SF-121 VATOL airplane concept are described.
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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.
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Khruschev, S S; Abaturova, A M; Diakonova, A N; Fedorov, V A; Ustinin, D M; Kovalenko, I B; Riznichenko, G Yu; Rubin, A B
2015-01-01
The application of Brownian dynamics for simulation of transient protein-protein interactions is reviewed. The review focuses on theoretical basics of Brownian dynamics method, its particular implementations, advantages and drawbacks of the method. The outlook for future development of Brownian dynamics-based simulation techniques is discussed. Special attention is given to analysis of Brownian dynamics trajectories. The second part of the review is dedicated to the role of Brownian dynamics simulations in studying photosynthetic electron transport. Interactions of mobile electron carriers (plastocyanin, cytochrome c6, and ferredoxin) with their reaction partners (cytochrome b6f complex, photosystem I, ferredoxin:NADP-reductase, and hydrogenase) are considered.
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Modelling, simulation and applications of longitudinal train dynamics
NASA Astrophysics Data System (ADS)
Cole, Colin; Spiryagin, Maksym; Wu, Qing; Sun, Yan Quan
2017-10-01
Significant developments in longitudinal train simulation and an overview of the approaches to train models and modelling vehicle force inputs are firstly presented. The most important modelling task, that of the wagon connection, consisting of energy absorption devices such as draft gears and buffers, draw gear stiffness, coupler slack and structural stiffness is then presented. Detailed attention is given to the modelling approaches for friction wedge damped and polymer draft gears. A significant issue in longitudinal train dynamics is the modelling and calculation of the input forces - the co-dimensional problem. The need to push traction performances higher has led to research and improvement in the accuracy of traction modelling which is discussed. A co-simulation method that combines longitudinal train simulation, locomotive traction control and locomotive vehicle dynamics is presented. The modelling of other forces, braking propulsion resistance, curve drag and grade forces are also discussed. As extensions to conventional longitudinal train dynamics, lateral forces and coupler impacts are examined in regards to interaction with wagon lateral and vertical dynamics. Various applications of longitudinal train dynamics are then presented. As an alternative to the tradition single wagon mass approach to longitudinal train dynamics, an example incorporating fully detailed wagon dynamics is presented for a crash analysis problem. Further applications of starting traction, air braking, distributed power, energy analysis and tippler operation are also presented.
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Nonlinear absorption dynamics using field-induced surface hopping: zinc porphyrin in water.
Röhr, Merle I S; Petersen, Jens; Wohlgemuth, Matthias; Bonačić-Koutecký, Vlasta; Mitrić, Roland
2013-05-10
We wish to present the application of our field-induced surface-hopping (FISH) method to simulate nonlinear absorption dynamics induced by strong nonresonant laser fields. We provide a systematic comparison of the FISH approach with exact quantum dynamics simulations on a multistate model system and demonstrate that FISH allows for accurate simulations of nonlinear excitation processes including multiphoton electronic transitions. In particular, two different approaches for simulating two-photon transitions are compared. The first approach is essentially exact and involves the solution of the time-dependent Schrödinger equation in an extended manifold of excited states, while in the second one only transiently populated nonessential states are replaced by an effective quadratic coupling term, and dynamics is performed in a considerably smaller manifold of states. We illustrate the applicability of our method to complex molecular systems by simulating the linear and nonlinear laser-driven dynamics in zinc (Zn) porphyrin in the gas phase and in water. For this purpose, the FISH approach is connected with the quantum mechanical-molecular mechanical approach (QM/MM) which is generally applicable to large classes of complex systems. Our findings that multiphoton absorption and dynamics increase the population of higher excited states of Zn porphyrin in the nonlinear regime, in particular in solution, provides a means for manipulating excited-state properties, such as transient absorption dynamics and electronic relaxation. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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DOT National Transportation Integrated Search
2017-07-26
The datasets in this zip file are in support of FHWA-JPO-16-379, Analysis, Modeling, and Simulation (AMS) Testbed Development and Evaluation to Support Dynamic Mobility Applications (DMA) and Active Transportation and Demand Management (ATDM) Program...
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DOT National Transportation Integrated Search
2017-06-26
This zip file contains files of data to support FHWA-JPO-16-370, Analysis, Modeling, and Simulation (AMS) Testbed Development and Evaluation to Support Dynamic Mobility Applications (DMA) and Active Transportation and Demand Management (ATDM) Program...
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Testing the World with Simulations.
ERIC Educational Resources Information Center
Roberts, Nancy
1983-01-01
Explains the three main concepts of the system dynamics approach to model building (dynamics, feedback, and systems) and the basic steps to problem solving by simulation applicable to all educational levels. Some DYNAMO commands are briefly described. (EAO)
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Mori, Takaharu; Miyashita, Naoyuki; Im, Wonpil; Feig, Michael; Sugita, Yuji
2016-01-01
This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins. Guest Editors: J.C. Gumbart and Sergei Noskov. PMID:26766517
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Gamma ray observatory dynamics simulator in Ada (GRODY)
NASA Technical Reports Server (NTRS)
1990-01-01
This experiment involved the parallel development of dynamics simulators for the Gamma Ray Observatory in both FORTRAN and Ada for the purpose of evaluating the applicability of Ada to the NASA/Goddard Space Flight Center's flight dynamics environment. The experiment successfully demonstrated that Ada is a viable, valuable technology for use in this environment. In addition to building a simulator, the Ada team evaluated training approaches, developed an Ada methodology appropriate to the flight dynamics environment, and established a baseline for evaluating future Ada projects.
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NASA Astrophysics Data System (ADS)
Fitkov-Norris, Elena; Yeghiazarian, Ara
2016-11-01
The analytical tools available to social scientists have traditionally been adapted from tools originally designed for analysis of natural science phenomena. This article discusses the applicability of systems dynamics - a qualitative based modelling approach, as a possible analysis and simulation tool that bridges the gap between social and natural sciences. After a brief overview of the systems dynamics modelling methodology, the advantages as well as limiting factors of systems dynamics to the potential applications in the field of social sciences and human interactions are discussed. The issues arise with regards to operationalization and quantification of latent constructs at the simulation building stage of the systems dynamics methodology and measurement theory is proposed as a ready and waiting solution to the problem of dynamic model calibration, with a view of improving simulation model reliability and validity and encouraging the development of standardised, modular system dynamics models that can be used in social science research.
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NASA Astrophysics Data System (ADS)
Nemirsky, Kristofer Kevin
In this thesis, the history and evolution of rotor aircraft with simulated annealing-based PID application were reviewed and quadcopter dynamics are presented. The dynamics of a quadcopter were then modeled, analyzed, and linearized. A cascaded loop architecture with PID controllers was used to stabilize the plant dynamics, which was improved upon through the application of simulated annealing (SA). A Simulink model was developed to test the controllers and verify the functionality of the proposed control system design. In addition, the data that the Simulink model provided were compared with flight data to present the validity of derived dynamics as a proper mathematical model representing the true dynamics of the quadcopter system. Then, the SA-based global optimization procedure was applied to obtain optimized PID parameters. It was observed that the tuned gains through the SA algorithm produced a better performing PID controller than the original manually tuned one. Next, we investigated the uncertain dynamics of the quadcopter setup. After adding uncertainty to the gyroscopic effects associated with pitch-and-roll rate dynamics, the controllers were shown to be robust against the added uncertainty. A discussion follows to summarize SA-based algorithm PID controller design and performance outcomes. Lastly, future work on SA application on multi-input-multi-output (MIMO) systems is briefly discussed.
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Application of the GRC Stirling Convertor System Dynamic Model
NASA Technical Reports Server (NTRS)
Regan, Timothy F.; Lewandowski, Edward J.; Schreiber, Jeffrey G. (Technical Monitor)
2004-01-01
The GRC Stirling Convertor System Dynamic Model (SDM) has been developed to simulate dynamic performance of power systems incorporating free-piston Stirling convertors. This paper discusses its use in evaluating system dynamics and other systems concerns. Detailed examples are provided showing the use of the model in evaluation of off-nominal operating conditions. The many degrees of freedom in both the mechanical and electrical domains inherent in the Stirling convertor and the nonlinear dynamics make simulation an attractive analysis tool in conjunction with classical analysis. Application of SDM in studying the relationship of the size of the resonant circuit quality factor (commonly referred to as Q) in the various resonant mechanical and electrical sub-systems is discussed.
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NASA Astrophysics Data System (ADS)
Abisset-Chavanne, Emmanuelle; Duval, Jean Louis; Cueto, Elias; Chinesta, Francisco
2018-05-01
Traditionally, Simulation-Based Engineering Sciences (SBES) has relied on the use of static data inputs (model parameters, initial or boundary conditions, … obtained from adequate experiments) to perform simulations. A new paradigm in the field of Applied Sciences and Engineering has emerged in the last decade. Dynamic Data-Driven Application Systems [9, 10, 11, 12, 22] allow the linkage of simulation tools with measurement devices for real-time control of simulations and applications, entailing the ability to dynamically incorporate additional data into an executing application, and in reverse, the ability of an application to dynamically steer the measurement process. It is in that context that traditional "digital-twins" are giving raise to a new generation of goal-oriented data-driven application systems, also known as "hybrid-twins", embracing models based on physics and models exclusively based on data adequately collected and assimilated for filling the gap between usual model predictions and measurements. Within this framework new methodologies based on model learners, machine learning and kinetic goal-oriented design are defining a new paradigm in materials, processes and systems engineering.
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Hamiltonian quantum simulation with bounded-strength controls
NASA Astrophysics Data System (ADS)
Bookatz, Adam D.; Wocjan, Pawel; Viola, Lorenza
2014-04-01
We propose dynamical control schemes for Hamiltonian simulation in many-body quantum systems that avoid instantaneous control operations and rely solely on realistic bounded-strength control Hamiltonians. Each simulation protocol consists of periodic repetitions of a basic control block, constructed as a modification of an ‘Eulerian decoupling cycle,’ that would otherwise implement a trivial (zero) target Hamiltonian. For an open quantum system coupled to an uncontrollable environment, our approach may be employed to engineer an effective evolution that simulates a target Hamiltonian on the system while suppressing unwanted decoherence to the leading order, thereby allowing for dynamically corrected simulation. We present illustrative applications to both closed- and open-system simulation settings, with emphasis on simulation of non-local (two-body) Hamiltonians using only local (one-body) controls. In particular, we provide simulation schemes applicable to Heisenberg-coupled spin chains exposed to general linear decoherence, and show how to simulate Kitaev's honeycomb lattice Hamiltonian starting from Ising-coupled qubits, as potentially relevant to the dynamical generation of a topologically protected quantum memory. Additional implications for quantum information processing are discussed.
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A simulation system to hide dynamic objects selectively at visible wavelengths
NASA Astrophysics Data System (ADS)
Cheng, Qiluan; Zhang, Shu; Ding, Chizhu; Tan, Zuojun; Wang, Guo Ping
2018-04-01
Currently, invisibility devices are increasingly approaching practical application requirements, such as using easily obtained materials for construction and hiding dynamic objects. Here, using phase retrieval and computer-generated holography techniques, we design an invisibility system in simulation to produce a phase-conjugation signal that changes with the dynamic object to hide it. This system is highly selective for the hidden objects, i.e., it only hides the target object and has no effect on the others. Such function may provide our invisibility system with great potential in special fields, such as biology and military applications for living and dynamic target recognition, selective camouflaging, and others.
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Dynamic Clamp in Cardiac and Neuronal Systems Using RTXI
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
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Multibody dynamic simulation of knee contact mechanics
Bei, Yanhong; Fregly, Benjamin J.
2006-01-01
Multibody dynamic musculoskeletal models capable of predicting muscle forces and joint contact pressures simultaneously would be valuable for studying clinical issues related to knee joint degeneration and restoration. Current three-dimensional multi-body knee models are either quasi-static with deformable contact or dynamic with rigid contact. This study proposes a computationally efficient methodology for combining multibody dynamic simulation methods with a deformable contact knee model. The methodology requires preparation of the articular surface geometry, development of efficient methods to calculate distances between contact surfaces, implementation of an efficient contact solver that accounts for the unique characteristics of human joints, and specification of an application programming interface for integration with any multibody dynamic simulation environment. The current implementation accommodates natural or artificial tibiofemoral joint models, small or large strain contact models, and linear or nonlinear material models. Applications are presented for static analysis (via dynamic simulation) of a natural knee model created from MRI and CT data and dynamic simulation of an artificial knee model produced from manufacturer’s CAD data. Small and large strain natural knee static analyses required 1 min of CPU time and predicted similar contact conditions except for peak pressure, which was higher for the large strain model. Linear and nonlinear artificial knee dynamic simulations required 10 min of CPU time and predicted similar contact force and torque but different contact pressures, which were lower for the nonlinear model due to increased contact area. This methodology provides an important step toward the realization of dynamic musculoskeletal models that can predict in vivo knee joint motion and loading simultaneously. PMID:15564115
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Movement Characteristics Analysis and Dynamic Simulation of Collaborative Measuring Robot
NASA Astrophysics Data System (ADS)
guoqing, MA; li, LIU; zhenglin, YU; guohua, CAO; yanbin, ZHENG
2017-03-01
Human-machine collaboration is becoming increasingly more necessary, and so collaborative robot applications are also in high demand. We selected a UR10 robot as our research subject for this study. First, we applied D-H coordinate transformation of the robot to establish a link system, and we then used inverse transformation to solve the robot’s inverse kinematics and find all the joints. Use Lagrange method to analysis UR robot dynamics; use ADAMS multibody dynamics simulation software to dynamic simulation; verifying the correctness of the derived kinetic models.
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Du, Likai; Lan, Zhenggang
2015-04-14
Nonadiabatic dynamics simulations have rapidly become an indispensable tool for understanding ultrafast photochemical processes in complex systems. Here, we present our recently developed on-the-fly nonadiabatic dynamics package, JADE, which allows researchers to perform nonadiabatic excited-state dynamics simulations of polyatomic systems at an all-atomic level. The nonadiabatic dynamics is based on Tully's surface-hopping approach. Currently, several electronic structure methods (CIS, TDHF, TDDFT(RPA/TDA), and ADC(2)) are supported, especially TDDFT, aiming at performing nonadiabatic dynamics on medium- to large-sized molecules. The JADE package has been interfaced with several quantum chemistry codes, including Turbomole, Gaussian, and Gamess (US). To consider environmental effects, the Langevin dynamics was introduced as an easy-to-use scheme into the standard surface-hopping dynamics. The JADE package is mainly written in Fortran for greater numerical performance and Python for flexible interface construction, with the intent of providing open-source, easy-to-use, well-modularized, and intuitive software in the field of simulations of photochemical and photophysical processes. To illustrate the possible applications of the JADE package, we present a few applications of excited-state dynamics for various polyatomic systems, such as the methaniminium cation, fullerene (C20), p-dimethylaminobenzonitrile (DMABN) and its primary amino derivative aminobenzonitrile (ABN), and 10-hydroxybenzo[h]quinoline (10-HBQ).
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2013-09-01
hydrogen bonds in Tyrosine-containing peptides. Dalkas et al[7] used docking and molecular dynamics simulations to study a variety of MAPKK-based... simulated using NAMD molecular dynamics and the CHARMM[20] forcefield at 300K and employing the Generalized Born Implicit Solvent (GBIS[21]) with the...which were reported in Section 2. Specifically, after a ~10ns molecular dynamics simulation in TIP3 explicit water, significant motion of domains III
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Integrating open-source software applications to build molecular dynamics systems.
Allen, Bruce M; Predecki, Paul K; Kumosa, Maciej
2014-04-05
Three open-source applications, NanoEngineer-1, packmol, and mis2lmp are integrated using an open-source file format to quickly create molecular dynamics (MD) cells for simulation. The three software applications collectively make up the open-source software (OSS) suite known as MD Studio (MDS). The software is validated through software engineering practices and is verified through simulation of the diglycidyl ether of bisphenol-a and isophorone diamine (DGEBA/IPD) system. Multiple simulations are run using the MDS software to create MD cells, and the data generated are used to calculate density, bulk modulus, and glass transition temperature of the DGEBA/IPD system. Simulation results compare well with published experimental and numerical results. The MDS software prototype confirms that OSS applications can be analyzed against real-world research requirements and integrated to create a new capability. Copyright © 2014 Wiley Periodicals, Inc.
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NASA Astrophysics Data System (ADS)
Chaturvedi, K.; Willenborg, B.; Sindram, M.; Kolbe, T. H.
2017-10-01
Semantic 3D city models play an important role in solving complex real-world problems and are being adopted by many cities around the world. A wide range of application and simulation scenarios directly benefit from the adoption of international standards such as CityGML. However, most of the simulations involve properties, whose values vary with respect to time, and the current generation semantic 3D city models do not support time-dependent properties explicitly. In this paper, the details of solar potential simulations are provided operating on the CityGML standard, assessing and estimating solar energy production for the roofs and facades of the 3D building objects in different ways. Furthermore, the paper demonstrates how the time-dependent simulation results are better-represented inline within 3D city models utilizing the so-called Dynamizer concept. This concept not only allows representing the simulation results in standardized ways, but also delivers a method to enhance static city models by such dynamic property values making the city models truly dynamic. The dynamizer concept has been implemented as an Application Domain Extension of the CityGML standard within the OGC Future City Pilot Phase 1. The results are given in this paper.
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JGromacs: a Java package for analyzing protein simulations.
Münz, Márton; Biggin, Philip C
2012-01-23
In this paper, we introduce JGromacs, a Java API (Application Programming Interface) that facilitates the development of cross-platform data analysis applications for Molecular Dynamics (MD) simulations. The API supports parsing and writing file formats applied by GROMACS (GROningen MAchine for Chemical Simulations), one of the most widely used MD simulation packages. JGromacs builds on the strengths of object-oriented programming in Java by providing a multilevel object-oriented representation of simulation data to integrate and interconvert sequence, structure, and dynamics information. The easy-to-learn, easy-to-use, and easy-to-extend framework is intended to simplify and accelerate the implementation and development of complex data analysis algorithms. Furthermore, a basic analysis toolkit is included in the package. The programmer is also provided with simple tools (e.g., XML-based configuration) to create applications with a user interface resembling the command-line interface of GROMACS applications. JGromacs and detailed documentation is freely available from http://sbcb.bioch.ox.ac.uk/jgromacs under a GPLv3 license .
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JGromacs: A Java Package for Analyzing Protein Simulations
2011-01-01
In this paper, we introduce JGromacs, a Java API (Application Programming Interface) that facilitates the development of cross-platform data analysis applications for Molecular Dynamics (MD) simulations. The API supports parsing and writing file formats applied by GROMACS (GROningen MAchine for Chemical Simulations), one of the most widely used MD simulation packages. JGromacs builds on the strengths of object-oriented programming in Java by providing a multilevel object-oriented representation of simulation data to integrate and interconvert sequence, structure, and dynamics information. The easy-to-learn, easy-to-use, and easy-to-extend framework is intended to simplify and accelerate the implementation and development of complex data analysis algorithms. Furthermore, a basic analysis toolkit is included in the package. The programmer is also provided with simple tools (e.g., XML-based configuration) to create applications with a user interface resembling the command-line interface of GROMACS applications. Availability: JGromacs and detailed documentation is freely available from http://sbcb.bioch.ox.ac.uk/jgromacs under a GPLv3 license. PMID:22191855
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Genetic Algorithms and Their Application to the Protein Folding Problem
1993-12-01
and symbolic methods, random methods such as Monte Carlo simulation and simulated annealing, distance geometry, and molecular dynamics. Many of these...calculated energies with those obtained using the molecular simulation software package called CHARMm. 10 9) Test both the simple and parallel simpie genetic...homology-based, and simplification techniques. 3.21 Molecular Dynamics. Perhaps the most natural approach is to actually simulate the folding process. This
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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
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Mori, Takaharu; Miyashita, Naoyuki; Im, Wonpil; Feig, Michael; Sugita, Yuji
2016-07-01
This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.
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DOT National Transportation Integrated Search
2002-07-01
The purpose of the work is to validate the safety assessment methodology previously developed for passenger rail vehicle dynamics, which requires the application of simulation tools as well as testing of vehicles under different track scenarios. This...
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Parallel Multiscale Algorithms for Astrophysical Fluid Dynamics Simulations
NASA Technical Reports Server (NTRS)
Norman, Michael L.
1997-01-01
Our goal is to develop software libraries and applications for astrophysical fluid dynamics simulations in multidimensions that will enable us to resolve the large spatial and temporal variations that inevitably arise due to gravity, fronts and microphysical phenomena. The software must run efficiently on parallel computers and be general enough to allow the incorporation of a wide variety of physics. Cosmological structure formation with realistic gas physics is the primary application driver in this work. Accurate simulations of e.g. galaxy formation require a spatial dynamic range (i.e., ratio of system scale to smallest resolved feature) of 104 or more in three dimensions in arbitrary topologies. We take this as our technical requirement. We have achieved, and in fact, surpassed these goals.
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Booth, Jonathan; Vazquez, Saulo; Martinez-Nunez, Emilio; Marks, Alison; Rodgers, Jeff; Glowacki, David R; Shalashilin, Dmitrii V
2014-08-06
In this paper, we briefly review the boxed molecular dynamics (BXD) method which allows analysis of thermodynamics and kinetics in complicated molecular systems. BXD is a multiscale technique, in which thermodynamics and long-time dynamics are recovered from a set of short-time simulations. In this paper, we review previous applications of BXD to peptide cyclization, solution phase organic reaction dynamics and desorption of ions from self-assembled monolayers (SAMs). We also report preliminary results of simulations of diamond etching mechanisms and protein unfolding in atomic force microscopy experiments. The latter demonstrate a correlation between the protein's structural motifs and its potential of mean force. Simulations of these processes by standard molecular dynamics (MD) is typically not possible, because the experimental time scales are very long. However, BXD yields well-converged and physically meaningful results. Compared with other methods of accelerated MD, our BXD approach is very simple; it is easy to implement, and it provides an integrated approach for simultaneously obtaining both thermodynamics and kinetics. It also provides a strategy for obtaining statistically meaningful dynamical results in regions of configuration space that standard MD approaches would visit only very rarely.
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Molecular dynamics simulations and applications in computational toxicology and nanotoxicology.
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.
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Molecular Dynamics Simulations of Shear Induced Transformations in Nitromethane
NASA Astrophysics Data System (ADS)
Larentzos, James; Steele, Brad
2017-06-01
Recent experiments demonstrate that NM undergoes explosive chemical initiation under compressive shear stress. The atomistic dynamics of the shear response of single-crystalline and bi-crystalline nitromethane (NM) are simulated using molecular dynamics simulations under high pressure conditions to aid in interpreting these experiments. The atomic interactions are described using a recently re-optimized ReaxFF-lg potential trained specifically for NM under pressure. The simulations demonstrate that the NM crystal transforms into a disordered state upon sufficient application of shear stress; its maximum value, shear angle, and atomic-scale dynamics being highly dependent on crystallographic orientation of the applied shear. Shear simulations in bi-crystalline NM show more complex behavior resulting in the appearance of the disordered state at the grain boundary.
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Molecular Dynamics Simulations of Shear Induced Transformations in Nitromethane
NASA Astrophysics Data System (ADS)
Larentzos, James; Steele, Brad
Recent experiments demonstrate that NM undergoes explosive chemical initiation under compressive shear stress. The atomistic dynamics of the shear response of single-crystalline and bi-crystalline nitromethane (NM) are simulated using molecular dynamics simulations under high pressure conditions to aid in interpreting these experiments. The atomic interactions are described using a recently re-optimized ReaxFF-lg potential trained specifically for NM under pressure. The simulations demonstrate that the NM crystal transforms into a disordered state upon sufficient application of shear stress; its maximum value, shear angle, and atomic-scale dynamics being highly dependent on crystallographic orientation of the applied shear. Shear simulations in bi-crystalline NM show more complex behavior resulting in the appearance of the disordered state at the grain boundary.
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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.
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Integration of Dynamic Models in Range Operations
NASA Technical Reports Server (NTRS)
Bardina, Jorge; Thirumalainambi, Rajkumar
2004-01-01
This work addresses the various model interactions in real-time to make an efficient internet based decision making tool for Shuttle launch. The decision making tool depends on the launch commit criteria coupled with physical models. Dynamic interaction between a wide variety of simulation applications and techniques, embedded algorithms, and data visualizations are needed to exploit the full potential of modeling and simulation. This paper also discusses in depth details of web based 3-D graphics and applications to range safety. The advantages of this dynamic model integration are secure accessibility and distribution of real time information to other NASA centers.
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Review of Dynamic Modeling and Simulation of Large Scale Belt Conveyor System
NASA Astrophysics Data System (ADS)
He, Qing; Li, Hong
Belt conveyor is one of the most important devices to transport bulk-solid material for long distance. Dynamic analysis is the key to decide whether the design is rational in technique, safe and reliable in running, feasible in economy. It is very important to study dynamic properties, improve efficiency and productivity, guarantee conveyor safe, reliable and stable running. The dynamic researches and applications of large scale belt conveyor are discussed. The main research topics, the state-of-the-art of dynamic researches on belt conveyor are analyzed. The main future works focus on dynamic analysis, modeling and simulation of main components and whole system, nonlinear modeling, simulation and vibration analysis of large scale conveyor system.
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CFD-Based Design of Turbopump Inlet Duct for Reduced Dynamic Loads
NASA Technical Reports Server (NTRS)
Rothermel, Jeffry; Dorney, Suzanne M.; Dorney, Daniel J.
2003-01-01
Numerical simulations have been completed for a variety of designs for a 90 deg elbow duct. The objective is to identify a design that minimizes the dynamic load entering a LOX turbopump located at the elbow exit. Designs simulated to date indicate that simpler duct geometries result in lower losses. Benchmark simulations have verified that the compressible flow codes used in this study are applicable to these incompressible flow simulations.
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CFD-based Design of LOX Pump Inlet Duct for Reduced Dynamic Loads
NASA Technical Reports Server (NTRS)
Rothermel, Jeffry; Dorney, Daniel J.; Dorney, Suzanne M.
2003-01-01
Numerical simulations have been completed for a variety of designs for a 90 deg elbow duct. The objective is to identify a design that minimizes the dynamic load entering a LOX turbopump located at the elbow exit. Designs simulated to date indicate that simpler duct geometries result in lower losses. Benchmark simulations have verified that the compressible flow code used in this study is applicable to these incompressible flow simulations.
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NASA Astrophysics Data System (ADS)
Barnes, Brian C.; Leiter, Kenneth W.; Becker, Richard; Knap, Jaroslaw; Brennan, John K.
2017-07-01
We describe the development, accuracy, and efficiency of an automation package for molecular simulation, the large-scale atomic/molecular massively parallel simulator (LAMMPS) integrated materials engine (LIME). Heuristics and algorithms employed for equation of state (EOS) calculation using a particle-based model of a molecular crystal, hexahydro-1,3,5-trinitro-s-triazine (RDX), are described in detail. The simulation method for the particle-based model is energy-conserving dissipative particle dynamics, but the techniques used in LIME are generally applicable to molecular dynamics simulations with a variety of particle-based models. The newly created tool set is tested through use of its EOS data in plate impact and Taylor anvil impact continuum simulations of solid RDX. The coarse-grain model results from LIME provide an approach to bridge the scales from atomistic simulations to continuum simulations.
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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.
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Applying Parallel Processing Techniques to Tether Dynamics Simulation
NASA Technical Reports Server (NTRS)
Wells, B. Earl
1996-01-01
The focus of this research has been to determine the effectiveness of applying parallel processing techniques to a sizable real-world problem, the simulation of the dynamics associated with a tether which connects two objects in low earth orbit, and to explore the degree to which the parallelization process can be automated through the creation of new software tools. The goal has been to utilize this specific application problem as a base to develop more generally applicable techniques.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Zitney, S.E.
This presentation will examine process systems engineering R&D needs for application to advanced fossil energy (FE) systems and highlight ongoing research activities at the National Energy Technology Laboratory (NETL) under the auspices of a recently launched Collaboratory for Process & Dynamic Systems Research. The three current technology focus areas include: 1) High-fidelity systems with NETL's award-winning Advanced Process Engineering Co-Simulator (APECS) technology for integrating process simulation with computational fluid dynamics (CFD) and virtual engineering concepts, 2) Dynamic systems with R&D on plant-wide IGCC dynamic simulation, control, and real-time training applications, and 3) Systems optimization including large-scale process optimization, stochastic simulationmore » for risk/uncertainty analysis, and cost estimation. Continued R&D aimed at these and other key process systems engineering models, methods, and tools will accelerate the development of advanced gasification-based FE systems and produce increasingly valuable outcomes for DOE and the Nation.« less
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Development of the ARISTOTLE webware for cloud-based rarefied gas flow modeling
NASA Astrophysics Data System (ADS)
Deschenes, Timothy R.; Grot, Jonathan; Cline, Jason A.
2016-11-01
Rarefied gas dynamics are important for a wide variety of applications. An improvement in the ability of general users to predict these gas flows will enable optimization of current, and discovery of future processes. Despite this potential, most rarefied simulation software is designed by and for experts in the community. This has resulted in low adoption of the methods outside of the immediate RGD community. This paper outlines an ongoing effort to create a rarefied gas dynamics simulation tool that can be used by a general audience. The tool leverages a direct simulation Monte Carlo (DSMC) library that is available to the entire community and a web-based simulation process that will enable all users to take advantage of high performance computing capabilities. First, the DSMC library and simulation architecture are described. Then the DSMC library is used to predict a number of representative transient gas flows that are applicable to the rarefied gas dynamics community. The paper closes with a summary and future direction.
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Inoue, Kentaro; Maeda, Kazuhiro; Miyabe, Takaaki; Matsuoka, Yu; Kurata, Hiroyuki
2014-09-01
Mathematical modeling has become a standard technique to understand the dynamics of complex biochemical systems. To promote the modeling, we had developed the CADLIVE dynamic simulator that automatically converted a biochemical map into its associated mathematical model, simulated its dynamic behaviors and analyzed its robustness. To enhance the feasibility by CADLIVE and extend its functions, we propose the CADLIVE toolbox available for MATLAB, which implements not only the existing functions of the CADLIVE dynamic simulator, but also the latest tools including global parameter search methods with robustness analysis. The seamless, bottom-up processes consisting of biochemical network construction, automatic construction of its dynamic model, simulation, optimization, and S-system analysis greatly facilitate dynamic modeling, contributing to the research of systems biology and synthetic biology. This application can be freely downloaded from http://www.cadlive.jp/CADLIVE_MATLAB/ together with an instruction.
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2000-12-01
Numerical Simulations ..... ................. .... 42 1.4.1. Impact of a rod on a rigid wall ..... ................. .... 42 1.4.2. Impact of two...dissipative properties of the proposed scheme . . . . 81 II.4. Representative Numerical Simulations ...... ................. ... 84 11.4.1. Forging of...Representative numerical simulations ...... ............. .. 123 111.3. Model Problem II: a Simplified Model of Thin Beams ... ......... ... 127 III
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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.
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Update: Advancement of Contact Dynamics Modeling for Human Spaceflight Simulation Applications
NASA Technical Reports Server (NTRS)
Brain, Thomas A.; Kovel, Erik B.; MacLean, John R.; Quiocho, Leslie J.
2017-01-01
Pong is a new software tool developed at the NASA Johnson Space Center that advances interference-based geometric contact dynamics based on 3D graphics models. The Pong software consists of three parts: a set of scripts to extract geometric data from 3D graphics models, a contact dynamics engine that provides collision detection and force calculations based on the extracted geometric data, and a set of scripts for visualizing the dynamics response with the 3D graphics models. The contact dynamics engine can be linked with an external multibody dynamics engine to provide an integrated multibody contact dynamics simulation. This paper provides a detailed overview of Pong including the overall approach and modeling capabilities, which encompasses force generation from contact primitives and friction to computational performance. Two specific Pong-based examples of International Space Station applications are discussed, and the related verification and validation using this new tool are also addressed.
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MDANSE: An Interactive Analysis Environment for Molecular Dynamics Simulations.
Goret, G; Aoun, B; Pellegrini, E
2017-01-23
The MDANSE software-Molecular Dynamics Analysis of Neutron Scattering Experiments-is presented. It is an interactive application for postprocessing molecular dynamics (MD) simulations. Given the widespread use of MD simulations in material and biomolecular sciences to get a better insight for experimental techniques such as thermal neutron scattering (TNS), the development of MDANSE has focused on providing a user-friendly, interactive, graphical user interface for analyzing many trajectories in the same session and running several analyses simultaneously independently of the interface. This first version of MDANSE already proposes a broad range of analyses, and the application has been designed to facilitate the introduction of new analyses in the framework. All this makes MDANSE a valuable tool for extracting useful information from trajectories resulting from a wide range of MD codes.
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Matthews, A P; Garenne, M L
2013-09-01
A dynamic, two-sex, age-structured marriage model is presented. Part 1 focused on first marriage only and described a marriage market matching algorithm. In Part 2 the model is extended to include divorce, widowing, and remarriage. The model produces a self-consistent set of marital states distributed by age and sex in a stable population by means of a gender-symmetric numerical method. The model is compared with empirical data for the case of Zambia. Furthermore, a dynamic marriage function for a changing population is demonstrated in simulations of three hypothetical scenarios of elevated mortality in young to middle adulthood. The marriage model has its primary application to simulation of HIV-AIDS epidemics in African countries. Copyright © 2013 Elsevier Inc. All rights reserved.
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Simulation gravity modeling to spacecraft-tracking data - Analysis and application
NASA Technical Reports Server (NTRS)
Phillips, R. J.; Sjogren, W. L.; Abbott, E. A.; Zisk, S. H.
1978-01-01
It is proposed that line-of-sight gravity measurements derived from spacecraft-tracking data can be used for quantitative subsurface density modeling by suitable orbit simulation procedures. Such an approach avoids complex dynamic reductions and is analogous to the modeling of conventional surface gravity data. This procedure utilizes the vector calculations of a given gravity model in a simplified trajectory integration program that simulates the line-of-sight gravity. Solutions from an orbit simulation inversion and a dynamic inversion on Doppler observables compare well (within 1% in mass and size), and the error sources in the simulation approximation are shown to be quite small. An application of this technique is made to lunar crater gravity anomalies by simulating the complete Bouguer correction to several large young lunar craters. It is shown that the craters all have negative Bouguer anomalies.
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Marshall, Deborah A; Burgos-Liz, Lina; IJzerman, Maarten J; Crown, William; Padula, William V; Wong, Peter K; Pasupathy, Kalyan S; Higashi, Mitchell K; Osgood, Nathaniel D
2015-03-01
In a previous report, the ISPOR Task Force on Dynamic Simulation Modeling Applications in Health Care Delivery Research Emerging Good Practices introduced the fundamentals of dynamic simulation modeling and identified the types of health care delivery problems for which dynamic simulation modeling can be used more effectively than other modeling methods. The hierarchical relationship between the health care delivery system, providers, patients, and other stakeholders exhibits a level of complexity that ought to be captured using dynamic simulation modeling methods. As a tool to help researchers decide whether dynamic simulation modeling is an appropriate method for modeling the effects of an intervention on a health care system, we presented the System, Interactions, Multilevel, Understanding, Loops, Agents, Time, Emergence (SIMULATE) checklist consisting of eight elements. This report builds on the previous work, systematically comparing each of the three most commonly used dynamic simulation modeling methods-system dynamics, discrete-event simulation, and agent-based modeling. We review criteria for selecting the most suitable method depending on 1) the purpose-type of problem and research questions being investigated, 2) the object-scope of the model, and 3) the method to model the object to achieve the purpose. Finally, we provide guidance for emerging good practices for dynamic simulation modeling in the health sector, covering all aspects, from the engagement of decision makers in the model design through model maintenance and upkeep. We conclude by providing some recommendations about the application of these methods to add value to informed decision making, with an emphasis on stakeholder engagement, starting with the problem definition. Finally, we identify areas in which further methodological development will likely occur given the growing "volume, velocity and variety" and availability of "big data" to provide empirical evidence and techniques such as machine learning for parameter estimation in dynamic simulation models. Upon reviewing this report in addition to using the SIMULATE checklist, the readers should be able to identify whether dynamic simulation modeling methods are appropriate to address the problem at hand and to recognize the differences of these methods from those of other, more traditional modeling approaches such as Markov models and decision trees. This report provides an overview of these modeling methods and examples of health care system problems in which such methods have been useful. The primary aim of the report was to aid decisions as to whether these simulation methods are appropriate to address specific health systems problems. The report directs readers to other resources for further education on these individual modeling methods for system interventions in the emerging field of health care delivery science and implementation. Copyright © 2015. Published by Elsevier Inc.
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NASA Astrophysics Data System (ADS)
Guan, Fada
Monte Carlo method has been successfully applied in simulating the particles transport problems. Most of the Monte Carlo simulation tools are static and they can only be used to perform the static simulations for the problems with fixed physics and geometry settings. Proton therapy is a dynamic treatment technique in the clinical application. In this research, we developed a method to perform the dynamic Monte Carlo simulation of proton therapy using Geant4 simulation toolkit. A passive-scattering treatment nozzle equipped with a rotating range modulation wheel was modeled in this research. One important application of the Monte Carlo simulation is to predict the spatial dose distribution in the target geometry. For simplification, a mathematical model of a human body is usually used as the target, but only the average dose over the whole organ or tissue can be obtained rather than the accurate spatial dose distribution. In this research, we developed a method using MATLAB to convert the medical images of a patient from CT scanning into the patient voxel geometry. Hence, if the patient voxel geometry is used as the target in the Monte Carlo simulation, the accurate spatial dose distribution in the target can be obtained. A data analysis tool---root was used to score the simulation results during a Geant4 simulation and to analyze the data and plot results after simulation. Finally, we successfully obtained the accurate spatial dose distribution in part of a human body after treating a patient with prostate cancer using proton therapy.
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Virtual acoustic environments for comprehensive evaluation of model-based hearing devices.
Grimm, Giso; Luberadzka, Joanna; Hohmann, Volker
2018-06-01
Create virtual acoustic environments (VAEs) with interactive dynamic rendering for applications in audiology. A toolbox for creation and rendering of dynamic virtual acoustic environments (TASCAR) that allows direct user interaction was developed for application in hearing aid research and audiology. The software architecture and the simulation methods used to produce VAEs are outlined. Example environments are described and analysed. With the proposed software, a tool for simulation of VAEs is available. A set of VAEs rendered with the proposed software was described.
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Quantum Molecular Dynamics Simulations of Nanotube Tip Assisted Reactions
NASA Technical Reports Server (NTRS)
Menon, Madhu
1998-01-01
In this report we detail the development and application of an efficient quantum molecular dynamics computational algorithm and its application to the nanotube-tip assisted reactions on silicon and diamond surfaces. The calculations shed interesting insights into the microscopic picture of tip surface interactions.
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Molecular dynamics simulations and novel drug discovery.
Liu, Xuewei; Shi, Danfeng; Zhou, Shuangyan; Liu, Hongli; Liu, Huanxiang; Yao, Xiaojun
2018-01-01
Molecular dynamics (MD) simulations can provide not only plentiful dynamical structural information on biomacromolecules but also a wealth of energetic information about protein and ligand interactions. Such information is very important to understanding the structure-function relationship of the target and the essence of protein-ligand interactions and to guiding the drug discovery and design process. Thus, MD simulations have been applied widely and successfully in each step of modern drug discovery. Areas covered: In this review, the authors review the applications of MD simulations in novel drug discovery, including the pathogenic mechanisms of amyloidosis diseases, virtual screening and the interaction mechanisms between drugs and targets. Expert opinion: MD simulations have been used widely in investigating the pathogenic mechanisms of diseases caused by protein misfolding, in virtual screening, and in investigating drug resistance mechanisms caused by mutations of the target. These issues are very difficult to solve by experimental methods alone. Thus, in the future, MD simulations will have wider application with the further improvement of computational capacity and the development of better sampling methods and more accurate force fields together with more efficient analysis methods.
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Das, Atanu; Mukhopadhyay, Chaitali
2007-10-28
We have performed molecular dynamics (MD) simulation of the thermal denaturation of one protein and one peptide-ubiquitin and melittin. To identify the correlation in dynamics among various secondary structural fragments and also the individual contribution of different residues towards thermal unfolding, principal component analysis method was applied in order to give a new insight to protein dynamics by analyzing the contribution of coefficients of principal components. The cross-correlation matrix obtained from MD simulation trajectory provided important information regarding the anisotropy of backbone dynamics that leads to unfolding. Unfolding of ubiquitin was found to be a three-state process, while that of melittin, though smaller and mostly helical, is more complicated.
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NASA Astrophysics Data System (ADS)
Das, Atanu; Mukhopadhyay, Chaitali
2007-10-01
We have performed molecular dynamics (MD) simulation of the thermal denaturation of one protein and one peptide—ubiquitin and melittin. To identify the correlation in dynamics among various secondary structural fragments and also the individual contribution of different residues towards thermal unfolding, principal component analysis method was applied in order to give a new insight to protein dynamics by analyzing the contribution of coefficients of principal components. The cross-correlation matrix obtained from MD simulation trajectory provided important information regarding the anisotropy of backbone dynamics that leads to unfolding. Unfolding of ubiquitin was found to be a three-state process, while that of melittin, though smaller and mostly helical, is more complicated.
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From laws of inference to protein folding dynamics.
Tseng, Chih-Yuan; Yu, Chun-Ping; Lee, H C
2010-08-01
Protein folding dynamics is one of major issues constantly investigated in the study of protein functions. The molecular dynamic (MD) simulation with the replica exchange method (REM) is a common theoretical approach considered. Yet a trade-off in applying the REM is that the dynamics toward the native configuration in the simulations seems lost. In this work, we show that given REM-MD simulation results, protein folding dynamics can be directly derived from laws of inference. The applicability of the resulting approach, the entropic folding dynamics, is illustrated by investigating a well-studied Trp-cage peptide. Our results are qualitatively comparable with those from other studies. The current studies suggest that the incorporation of laws of inference and physics brings in a comprehensive perspective on exploring the protein folding dynamics.
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Application of Adaptive Autopilot Designs for an Unmanned Aerial Vehicle
NASA Technical Reports Server (NTRS)
Shin, Yoonghyun; Calise, Anthony J.; Motter, Mark A.
2005-01-01
This paper summarizes the application of two adaptive approaches to autopilot design, and presents an evaluation and comparison of the two approaches in simulation for an unmanned aerial vehicle. One approach employs two-stage dynamic inversion and the other employs feedback dynamic inversions based on a command augmentation system. Both are augmented with neural network based adaptive elements. The approaches permit adaptation to both parametric uncertainty and unmodeled dynamics, and incorporate a method that permits adaptation during periods of control saturation. Simulation results for an FQM-117B radio controlled miniature aerial vehicle are presented to illustrate the performance of the neural network based adaptation.
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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.
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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
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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
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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
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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.
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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…
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DOT National Transportation Integrated Search
2010-12-01
A number of initiatives were undertaken to support education, training, and technology transfer objectives related to UAB UTC Domain 2 Project: Development of a Dynamic Traffic Assignment and Simulation Model for Incident and Emergency Management App...
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A Dynamic Compliance Cervix Phantom Robot for Latent Labor Simulation.
Luk, Michelle Jennifer; Lobb, Derek; Smith, James Andrew
2018-06-01
Physical simulation systems are commonly used in training of midwifery and obstetrics students, but none of these systems offers a dynamic compliance aspect that would make them more truly representative of cervix ripening. In this study, we introduce a unique soft robot phantom that simulates the cervix softening during the latent labor phase of birth. This proof-of-concept robotic phantom can be dilated by 1 cm and effaced by 35% through the application of a Foley catheter-like loading mechanism. Furthermore, psychophysics trials demonstrate how untrained subjects can identify hard and soft states of the phantom with specificities of 91% and 87%, respectively. Both results indicated the appropriateness for application of this soft robot technology to birth training simulators.
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Boldon, Lauren; Laliberte, Fallon; Liu, Li
2015-01-01
In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics' equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques.
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NASA Astrophysics Data System (ADS)
Zhang, Ruili; Wang, Yulei; He, Yang; Xiao, Jianyuan; Liu, Jian; Qin, Hong; Tang, Yifa
2018-02-01
Relativistic dynamics of a charged particle in time-dependent electromagnetic fields has theoretical significance and a wide range of applications. The numerical simulation of relativistic dynamics is often multi-scale and requires accurate long-term numerical simulations. Therefore, explicit symplectic algorithms are much more preferable than non-symplectic methods and implicit symplectic algorithms. In this paper, we employ the proper time and express the Hamiltonian as the sum of exactly solvable terms and product-separable terms in space-time coordinates. Then, we give the explicit symplectic algorithms based on the generating functions of orders 2 and 3 for relativistic dynamics of a charged particle. The methodology is not new, which has been applied to non-relativistic dynamics of charged particles, but the algorithm for relativistic dynamics has much significance in practical simulations, such as the secular simulation of runaway electrons in tokamaks.
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Land Cover Applications, Landscape Dynamics, and Global Change
Tieszen, Larry L.
2007-01-01
The Land Cover Applications, Landscape Dynamics, and Global Change project at U.S. Geological Survey (USGS) Center for Earth Resources Observation and Science (EROS) seeks to integrate remote sensing and simulation models to better understand and seek solutions to national and global issues. Modeling processes related to population impacts, natural resource management, climate change, invasive species, land use changes, energy development, and climate mitigation all pose significant scientific opportunities. The project activities use remotely sensed data to support spatial monitoring, provide sensitivity analyses across landscapes and large regions, and make the data and results available on the Internet with data access and distribution, decision support systems, and on-line modeling. Applications support sustainable natural resource use, carbon cycle science, biodiversity conservation, climate change mitigation, and robust simulation modeling approaches that evaluate ecosystem and landscape dynamics.
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Simulation of wetlands forest vegetation dynamics
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.
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Purpose and applications [Chapter 1
Nicholas L. Crookston
2003-01-01
The Fire and Fuels Extension (FFE) to the Forest Vegetation Simulator (FVS) simulates fuel dynamics and potential fire behavior over time, in the context of stand development and management. This chapter provides an introduction to the model by illustrating its purpose and chronicling some of the applications it has supported.
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Dynamic P-Technique for Modeling Patterns of Data: Applications to Pediatric Psychology Research
Aylward, Brandon S.; Rausch, Joseph R.
2011-01-01
Objective Dynamic p-technique (DPT) is a potentially useful statistical method for examining relationships among dynamic constructs in a single individual or small group of individuals over time. The purpose of this article is to offer a nontechnical introduction to DPT. Method An overview of DPT analysis, with an emphasis on potential applications to pediatric psychology research, is provided. To illustrate how DPT might be applied, an example using simulated data is presented for daily pain and negative mood ratings. Results The simulated example demonstrates the application of DPT to a relevant pediatric psychology research area. In addition, the potential application of DPT to the longitudinal study of adherence is presented. Conclusion Although it has not been utilized frequently within pediatric psychology, DPT could be particularly well-suited for research in this field because of its ability to powerfully model repeated observations from very small samples. PMID:21486938
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Dynamic p-technique for modeling patterns of data: applications to pediatric psychology research.
Nelson, Timothy D; Aylward, Brandon S; Rausch, Joseph R
2011-10-01
Dynamic p-technique (DPT) is a potentially useful statistical method for examining relationships among dynamic constructs in a single individual or small group of individuals over time. The purpose of this article is to offer a nontechnical introduction to DPT. An overview of DPT analysis, with an emphasis on potential applications to pediatric psychology research, is provided. To illustrate how DPT might be applied, an example using simulated data is presented for daily pain and negative mood ratings. The simulated example demonstrates the application of DPT to a relevant pediatric psychology research area. In addition, the potential application of DPT to the longitudinal study of adherence is presented. Although it has not been utilized frequently within pediatric psychology, DPT could be particularly well-suited for research in this field because of its ability to powerfully model repeated observations from very small samples.
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Computer modeling and simulation of human movement. Applications in sport and rehabilitation.
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.
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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.
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CFD Approaches for Simulation of Wing-Body Stage Separation
NASA Technical Reports Server (NTRS)
Buning, Pieter G.; Gomez, Reynaldo J.; Scallion, William I.
2004-01-01
A collection of computational fluid dynamics tools and techniques are being developed and tested for application to stage separation and abort simulation for next-generation launch vehicles. In this work, an overset grid Navier-Stokes flow solver has been enhanced and demonstrated on a matrix of proximity cases and on a dynamic separation simulation of a belly-to-belly wing-body configuration. Steady cases show excellent agreement between Navier-Stokes results, Cartesian grid Euler solutions, and wind tunnel data at Mach 3. Good agreement has been obtained between Navier-Stokes, Euler, and wind tunnel results at Mach 6. An analysis of a dynamic separation at Mach 3 demonstrates that unsteady aerodynamic effects are not important for this scenario. Results provide an illustration of the relative applicability of Euler and Navier-Stokes methods to these types of problems.
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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.
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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.
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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.
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Mapping Conformational Dynamics of Proteins Using Torsional Dynamics Simulations
Gangupomu, Vamshi K.; Wagner, Jeffrey R.; Park, In-Hee; Jain, Abhinandan; Vaidehi, Nagarajan
2013-01-01
All-atom molecular dynamics simulations are widely used to study the flexibility of protein conformations. However, enhanced sampling techniques are required for simulating protein dynamics that occur on the millisecond timescale. In this work, we show that torsional molecular dynamics simulations enhance protein conformational sampling by performing conformational search in the low-frequency torsional degrees of freedom. In this article, we use our recently developed torsional-dynamics method called Generalized Newton-Euler Inverse Mass Operator (GNEIMO) to study the conformational dynamics of four proteins. We investigate the use of the GNEIMO method in simulations of the conformationally flexible proteins fasciculin and calmodulin, as well as the less flexible crambin and bovine pancreatic trypsin inhibitor. For the latter two proteins, the GNEIMO simulations with an implicit-solvent model reproduced the average protein structural fluctuations and sample conformations similar to those from Cartesian simulations with explicit solvent. The application of GNEIMO with replica exchange to the study of fasciculin conformational dynamics produced sampling of two of this protein’s experimentally established conformational substates. Conformational transition of calmodulin from the Ca2+-bound to the Ca2+-free conformation occurred readily with GNEIMO simulations. Moreover, the GNEIMO method generated an ensemble of conformations that satisfy about half of both short- and long-range interresidue distances obtained from NMR structures of holo to apo transitions in calmodulin. Although unconstrained all-atom Cartesian simulations have failed to sample transitions between the substates of fasciculin and calmodulin, GNEIMO simulations show the transitions in both systems. The relatively short simulation times required to capture these long-timescale conformational dynamics indicate that GNEIMO is a promising molecular-dynamics technique for studying domain motion in proteins. PMID:23663843
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Mapping conformational dynamics of proteins using torsional dynamics simulations.
Gangupomu, Vamshi K; Wagner, Jeffrey R; Park, In-Hee; Jain, Abhinandan; Vaidehi, Nagarajan
2013-05-07
All-atom molecular dynamics simulations are widely used to study the flexibility of protein conformations. However, enhanced sampling techniques are required for simulating protein dynamics that occur on the millisecond timescale. In this work, we show that torsional molecular dynamics simulations enhance protein conformational sampling by performing conformational search in the low-frequency torsional degrees of freedom. In this article, we use our recently developed torsional-dynamics method called Generalized Newton-Euler Inverse Mass Operator (GNEIMO) to study the conformational dynamics of four proteins. We investigate the use of the GNEIMO method in simulations of the conformationally flexible proteins fasciculin and calmodulin, as well as the less flexible crambin and bovine pancreatic trypsin inhibitor. For the latter two proteins, the GNEIMO simulations with an implicit-solvent model reproduced the average protein structural fluctuations and sample conformations similar to those from Cartesian simulations with explicit solvent. The application of GNEIMO with replica exchange to the study of fasciculin conformational dynamics produced sampling of two of this protein's experimentally established conformational substates. Conformational transition of calmodulin from the Ca(2+)-bound to the Ca(2+)-free conformation occurred readily with GNEIMO simulations. Moreover, the GNEIMO method generated an ensemble of conformations that satisfy about half of both short- and long-range interresidue distances obtained from NMR structures of holo to apo transitions in calmodulin. Although unconstrained all-atom Cartesian simulations have failed to sample transitions between the substates of fasciculin and calmodulin, GNEIMO simulations show the transitions in both systems. The relatively short simulation times required to capture these long-timescale conformational dynamics indicate that GNEIMO is a promising molecular-dynamics technique for studying domain motion in proteins. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.
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Tian, Wei; Han, Xu; Zuo, Wangda; ...
2018-01-31
This paper presents a comprehensive review of the open literature on motivations, methods and applications of linking stratified airflow simulation to building energy simulation (BES). First, we reviewed the motivations for coupling prediction models for building energy and indoor environment. This review classified various exchanged data in different applications as interface data and state data, and found that choosing different data sets may lead to varying performance of stability, convergence, and speed for the co-simulation. Second, our review shows that an external coupling scheme is substantially more popular in implementations of co-simulation than an internal coupling scheme. The external couplingmore » is shown to be generally faster in computational speed, as well as easier to implement, maintain and expand than the internal coupling. Third, the external coupling can be carried out in different data synchronization schemes, including static coupling and dynamic coupling. In comparison, the static coupling that performs data exchange only once is computationally faster and more stable than the dynamic coupling. However, concerning accuracy, the dynamic coupling that requires multiple times of data exchange is more accurate than the static coupling. Furthermore, the review identified that the implementation of the external coupling can be achieved through customized interfaces, middleware, and standard interfaces. The customized interface is straightforward but may be limited to a specific coupling application. The middleware is versatile and user-friendly but usually limited in data synchronization schemes. The standard interface is versatile and promising, but may be difficult to implement. Current applications of the co-simulation are mainly energy performance evaluation and control studies. Finally, we discussed the limitations of the current research and provided an overview for future research.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Tian, Wei; Han, Xu; Zuo, Wangda
This paper presents a comprehensive review of the open literature on motivations, methods and applications of linking stratified airflow simulation to building energy simulation (BES). First, we reviewed the motivations for coupling prediction models for building energy and indoor environment. This review classified various exchanged data in different applications as interface data and state data, and found that choosing different data sets may lead to varying performance of stability, convergence, and speed for the co-simulation. Second, our review shows that an external coupling scheme is substantially more popular in implementations of co-simulation than an internal coupling scheme. The external couplingmore » is shown to be generally faster in computational speed, as well as easier to implement, maintain and expand than the internal coupling. Third, the external coupling can be carried out in different data synchronization schemes, including static coupling and dynamic coupling. In comparison, the static coupling that performs data exchange only once is computationally faster and more stable than the dynamic coupling. However, concerning accuracy, the dynamic coupling that requires multiple times of data exchange is more accurate than the static coupling. Furthermore, the review identified that the implementation of the external coupling can be achieved through customized interfaces, middleware, and standard interfaces. The customized interface is straightforward but may be limited to a specific coupling application. The middleware is versatile and user-friendly but usually limited in data synchronization schemes. The standard interface is versatile and promising, but may be difficult to implement. Current applications of the co-simulation are mainly energy performance evaluation and control studies. Finally, we discussed the limitations of the current research and provided an overview for future research.« less
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2009-08-12
Man-In- The-Loop Simulation Integration & Demonstrators FTTS JLTV Future Force MRAP Thermal / CFD Crew Safety Structures/Durability Blast Dynamics ...Scott Stilson – General Dynamics Land Systems Chief Engineer, Stryker Modernization (S-Mod) Program The Application of Modeling and Simulation to the S...Military Ground Vehicles Nammalwar Purushothaman, Paramsothy Jayakumar & James Critchley – BAE Systems Sandip Datta & Venkat Pisipati – TAC World Wide
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A Comparison of Three Random Number Generators for Aircraft Dynamic Modeling Applications
NASA Technical Reports Server (NTRS)
Grauer, Jared A.
2017-01-01
Three random number generators, which produce Gaussian white noise sequences, were compared to assess their suitability in aircraft dynamic modeling applications. The first generator considered was the MATLAB (registered) implementation of the Mersenne-Twister algorithm. The second generator was a website called Random.org, which processes atmospheric noise measured using radios to create the random numbers. The third generator was based on synthesis of the Fourier series, where the random number sequences are constructed from prescribed amplitude and phase spectra. A total of 200 sequences, each having 601 random numbers, for each generator were collected and analyzed in terms of the mean, variance, normality, autocorrelation, and power spectral density. These sequences were then applied to two problems in aircraft dynamic modeling, namely estimating stability and control derivatives from simulated onboard sensor data, and simulating flight in atmospheric turbulence. In general, each random number generator had good performance and is well-suited for aircraft dynamic modeling applications. Specific strengths and weaknesses of each generator are discussed. For Monte Carlo simulation, the Fourier synthesis method is recommended because it most accurately and consistently approximated Gaussian white noise and can be implemented with reasonable computational effort.
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Dynamic modeling of brushless dc motors for aerospace actuation
NASA Technical Reports Server (NTRS)
Demerdash, N. A.; Nehl, T. W.
1980-01-01
A discrete time model for simulation of the dynamics of samarium cobalt-type permanent magnet brushless dc machines is presented. The simulation model includes modeling of the interaction between these machines and their attached power conditioners. These are transistorized conditioner units. This model is part of an overall discrete-time analysis of the dynamic performance of electromechanical actuators, which was conducted as part of prototype development of such actuators studied and built for NASA-Johnson Space Center as a prospective alternative to hydraulic actuators presently used in shuttle orbiter applications. The resulting numerical simulations of the various machine and power conditioner current and voltage waveforms gave excellent correlation to the actual waveforms collected from actual hardware experimental testing. These results, numerical and experimental, are presented here for machine motoring, regeneration and dynamic braking modes. Application of the resulting model to the determination of machine current and torque profiles during closed-loop actuator operation were also analyzed and the results are given here. These results are given in light of an overall view of the actuator system components. The applicability of this method of analysis to design optimization and trouble-shooting in such prototype development is also discussed in light of the results at hand.
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Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations.
Hertig, Samuel; Latorraca, Naomi R; Dror, Ron O
2016-06-01
Molecular dynamics (MD) simulations have become a powerful and popular method for the study of protein allostery, the widespread phenomenon in which a stimulus at one site on a protein influences the properties of another site on the protein. By capturing the motions of a protein's constituent atoms, simulations can enable the discovery of allosteric binding sites and the determination of the mechanistic basis for allostery. These results can provide a foundation for applications including rational drug design and protein engineering. Here, we provide an introduction to the investigation of protein allostery using molecular dynamics simulation. We emphasize the importance of designing simulations that include appropriate perturbations to the molecular system, such as the addition or removal of ligands or the application of mechanical force. We also demonstrate how the bidirectional nature of allostery-the fact that the two sites involved influence one another in a symmetrical manner-can facilitate such investigations. Through a series of case studies, we illustrate how these concepts have been used to reveal the structural basis for allostery in several proteins and protein complexes of biological and pharmaceutical interest.
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Application of fire and evacuation models in evaluation of fire safety in railway tunnels
NASA Astrophysics Data System (ADS)
Cábová, Kamila; Apeltauer, Tomáš; Okřinová, Petra; Wald, František
2017-09-01
The paper describes an application of numerical simulation of fire dynamics and evacuation of people in a tunnel. The software tool Fire Dynamics Simulator is used to simulate temperature resolution and development of smoke in a railway tunnel. Comparing to temperature curves which are usually used in the design stage results of the model show that the numerical model gives lower temperature of hot smoke layer. Outputs of the numerical simulation of fire also enable to improve models of evacuation of people during fires in tunnels. In the presented study the calculated high of smoke layer in the tunnel is in 10 min after the fire ignition lower than the level of 2.2 m which is considered as the maximal limit for safe evacuation. Simulation of the evacuation process in bigger scale together with fire dynamics can provide very valuable information about important security conditions like Available Safe Evacuation Time (ASET) vs Required Safe Evacuation Time (RSET). On given example in software EXODUS the paper summarizes selected results of evacuation model which should be in mind of a designer when preparing an evacuation plan.
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Non-Linear System Identification for Aeroelastic Systems with Application to Experimental Data
NASA Technical Reports Server (NTRS)
Kukreja, Sunil L.
2008-01-01
Representation and identification of a non-linear aeroelastic pitch-plunge system as a model of the NARMAX class is considered. A non-linear difference equation describing this aircraft model is derived theoretically and shown to be of the NARMAX form. Identification methods for NARMAX models are applied to aeroelastic dynamics and its properties demonstrated via continuous-time simulations of experimental conditions. Simulation results show that (i) the outputs of the NARMAX model match closely those generated using continuous-time methods and (ii) NARMAX identification methods applied to aeroelastic dynamics provide accurate discrete-time parameter estimates. Application of NARMAX identification to experimental pitch-plunge dynamics data gives a high percent fit for cross-validated data.
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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.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Coleman, Justin Leigh; Veeraraghavan, Swetha; Bolisetti, Chandrakanth
MASTODON has the capability to model stochastic nonlinear soil-structure interaction (NLSSI) in a dynamic probabilistic risk assessment framework. The NLSSI simulations include structural dynamics, time integration, dynamic porous media flow, nonlinear hysteretic soil constitutive models, geometric nonlinearities (gapping, sliding, and uplift). MASTODON is also the MOOSE based master application for dynamic PRA of external hazards.
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CYBER 200 Applications Seminar
NASA Technical Reports Server (NTRS)
Gary, J. P. (Compiler)
1984-01-01
Applications suited for the CYBER 200 digital computer are discussed. Various areas of application including meteorology, algorithms, fluid dynamics, monte carlo methods, petroleum, electronic circuit simulation, biochemistry, lattice gauge theory, economics and ray tracing are discussed.
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NASA Technical Reports Server (NTRS)
Mukhopadhyay, A. K.
1978-01-01
A description is presented of six simulation cases investigating the effect of the variation of static-dynamic Coulomb friction on servo system stability/performance. The upper and lower levels of dynamic Coulomb friction which allowed operation within requirements were determined roughly to be three times and 50% respectively of nominal values considered in a table. A useful application for the nonlinear time response simulation is the sensitivity analysis of final hardware design with respect to such system parameters as cannot be varied realistically or easily in the actual hardware. Parameters of the static/dynamic Coulomb friction fall in this category.
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NASA Technical Reports Server (NTRS)
Demerdash, N. A.; Nehl, T. W.
1980-01-01
A comprehensive digital model for the analysis and possible optimization of the closed loop dynamic (instantaneous) performance of a power conditioner fed, brushless dc motor powered, electromechanical actuator system (EMA) is presented. This model was developed for the simulation of the dynamic performance of an actual prototype EMA built for NASA-JSC as a possible alternative to hydraulic actuators for consideration in Space Shuttle Orbiter applications. Excellent correlation was achieved between numerical model simulation and experimental test results obtained from the actual hardware. These results include: various current and voltage waveforms in the machine-power conditioner (MPC) unit, flap position as well as other control loop variables in response to step commands of change of flap position. These results with consequent conclusions are detailed in the paper.
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Conformation and dynamics of the ligand shell of a water-soluble Au102 nanoparticle.
Salorinne, Kirsi; Malola, Sami; Wong, O Andrea; Rithner, Christopher D; Chen, Xi; Ackerson, Christopher J; Häkkinen, Hannu
2016-01-21
Inorganic nanoparticles, stabilized by a passivating layer of organic molecules, form a versatile class of nanostructured materials with potential applications in material chemistry, nanoscale physics, nanomedicine and structural biology. While the structure of the nanoparticle core is often known to atomic precision, gaining precise structural and dynamical information on the organic layer poses a major challenge. Here we report a full assignment of (1)H and (13)C NMR shifts to all ligands of a water-soluble, atomically precise, 102-atom gold nanoparticle stabilized by 44 para-mercaptobenzoic acid ligands in solution, by using a combination of multidimensional NMR methods, density functional theory calculations and molecular dynamics simulations. Molecular dynamics simulations augment the data by giving information about the ligand disorder and visualization of possible distinct ligand conformations of the most dynamic ligands. The method demonstrated here opens a way to controllable strategies for functionalization of ligated nanoparticles for applications.
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Conformation and dynamics of the ligand shell of a water-soluble Au102 nanoparticle
Salorinne, Kirsi; Malola, Sami; Wong, O. Andrea; Rithner, Christopher D.; Chen, Xi; Ackerson, Christopher J.; Häkkinen, Hannu
2016-01-01
Inorganic nanoparticles, stabilized by a passivating layer of organic molecules, form a versatile class of nanostructured materials with potential applications in material chemistry, nanoscale physics, nanomedicine and structural biology. While the structure of the nanoparticle core is often known to atomic precision, gaining precise structural and dynamical information on the organic layer poses a major challenge. Here we report a full assignment of 1H and 13C NMR shifts to all ligands of a water-soluble, atomically precise, 102-atom gold nanoparticle stabilized by 44 para-mercaptobenzoic acid ligands in solution, by using a combination of multidimensional NMR methods, density functional theory calculations and molecular dynamics simulations. Molecular dynamics simulations augment the data by giving information about the ligand disorder and visualization of possible distinct ligand conformations of the most dynamic ligands. The method demonstrated here opens a way to controllable strategies for functionalization of ligated nanoparticles for applications. PMID:26791253
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A user's guide to the Flexible Spacecraft Dynamics and Control Program
NASA Technical Reports Server (NTRS)
Fedor, J. V.
1984-01-01
A guide to the use of the Flexible Spacecraft Dynamics Program (FSD) is presented covering input requirements, control words, orbit generation, spacecraft description and simulation options, and output definition. The program can be used in dynamics and control analysis as well as in orbit support of deployment and control of spacecraft. The program is applicable to inertially oriented spinning, Earth oriented or gravity gradient stabilized spacecraft. Internal and external environmental effects can be simulated.
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78 FR 70536 - Application(s) for Duty-Free Entry of Scientific Instruments
Federal Register 2010, 2011, 2012, 2013, 2014
2013-11-26
... instrument is the only confocal using a single micro lens disk, making it the only spinning disk system... modulus and damping versus strain, and evaluate the influence of soil-content on its dynamic properties. It is critical to have the capability to simulate realistic static and dynamic stress conditions to...
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Protocols for Molecular Dynamics Simulations of RNA Nanostructures.
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.
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Modeling structural change in spatial system dynamics: A Daisyworld example.
Neuwirth, C; Peck, A; Simonović, S P
2015-03-01
System dynamics (SD) is an effective approach for helping reveal the temporal behavior of complex systems. Although there have been recent developments in expanding SD to include systems' spatial dependencies, most applications have been restricted to the simulation of diffusion processes; this is especially true for models on structural change (e.g. LULC modeling). To address this shortcoming, a Python program is proposed to tightly couple SD software to a Geographic Information System (GIS). The approach provides the required capacities for handling bidirectional and synchronized interactions of operations between SD and GIS. In order to illustrate the concept and the techniques proposed for simulating structural changes, a fictitious environment called Daisyworld has been recreated in a spatial system dynamics (SSD) environment. The comparison of spatial and non-spatial simulations emphasizes the importance of considering spatio-temporal feedbacks. Finally, practical applications of structural change models in agriculture and disaster management are proposed.
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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.
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Boldon, Lauren; Laliberte, Fallon; Liu, Li
2015-01-01
In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics’ equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques. PMID:25721341
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DOT National Transportation Integrated Search
2017-03-01
The primary objective of this project is to develop multiple simulation testbeds/transportation models to evaluate the impacts of DMA connected vehicle applications and the active transportation and demand management (ATDM) strategies. The primary pu...
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DOT National Transportation Integrated Search
2017-04-01
The datasets in this zip file are in support of Intelligent Transportation Systems Joint Program Office (ITS JPO) report FHWA-JPO-16-385, "Analysis, Modeling, and Simulation (AMS) Testbed Development and Evaluation to Support Dynamic Mobility Applica...
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DOT National Transportation Integrated Search
2017-07-26
The datasets in this zip file are in support of Intelligent Transportation Systems Joint Program Office (ITS JPO) report FHWA-JPO-16-385, "Analysis, Modeling, and Simulation (AMS) Testbed Development and Evaluation to Support Dynamic Mobility Applica...
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TADSim: Discrete Event-based Performance Prediction for Temperature Accelerated Dynamics
Mniszewski, Susan M.; Junghans, Christoph; Voter, Arthur F.; ...
2015-04-16
Next-generation high-performance computing will require more scalable and flexible performance prediction tools to evaluate software--hardware co-design choices relevant to scientific applications and hardware architectures. Here, we present a new class of tools called application simulators—parameterized fast-running proxies of large-scale scientific applications using parallel discrete event simulation. Parameterized choices for the algorithmic method and hardware options provide a rich space for design exploration and allow us to quickly find well-performing software--hardware combinations. We demonstrate our approach with a TADSim simulator that models the temperature-accelerated dynamics (TAD) method, an algorithmically complex and parameter-rich member of the accelerated molecular dynamics (AMD) family ofmore » molecular dynamics methods. The essence of the TAD application is captured without the computational expense and resource usage of the full code. We accomplish this by identifying the time-intensive elements, quantifying algorithm steps in terms of those elements, abstracting them out, and replacing them by the passage of time. We use TADSim to quickly characterize the runtime performance and algorithmic behavior for the otherwise long-running simulation code. We extend TADSim to model algorithm extensions, such as speculative spawning of the compute-bound stages, and predict performance improvements without having to implement such a method. Validation against the actual TAD code shows close agreement for the evolution of an example physical system, a silver surface. Finally, focused parameter scans have allowed us to study algorithm parameter choices over far more scenarios than would be possible with the actual simulation. This has led to interesting performance-related insights and suggested extensions.« less
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NASA Astrophysics Data System (ADS)
Brodeck, M.; Alvarez, F.; Arbe, A.; Juranyi, F.; Unruh, T.; Holderer, O.; Colmenero, J.; Richter, D.
2009-03-01
We performed quasielastic neutron scattering experiments and atomistic molecular dynamics simulations on a poly(ethylene oxide) (PEO) homopolymer system above the melting point. The excellent agreement found between both sets of data, together with a successful comparison with literature diffraction results, validates the condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field used to produce our dynamic runs and gives support to their further analysis. This provided direct information on magnitudes which are not accessible from experiments such as the radial probability distribution functions of specific atoms at different times and their moments. The results of our simulations on the H-motions and different experiments indicate that in the high-temperature range investigated the dynamics is Rouse-like for Q-values below ≈0.6 Å-1. We then addressed the single chain dynamic structure factor with the simulations. A mode analysis, not possible directly experimentally, reveals the limits of applicability of the Rouse model to PEO. We discuss the possible origins for the observed deviations.
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Brodeck, M; Alvarez, F; Arbe, A; Juranyi, F; Unruh, T; Holderer, O; Colmenero, J; Richter, D
2009-03-07
We performed quasielastic neutron scattering experiments and atomistic molecular dynamics simulations on a poly(ethylene oxide) (PEO) homopolymer system above the melting point. The excellent agreement found between both sets of data, together with a successful comparison with literature diffraction results, validates the condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field used to produce our dynamic runs and gives support to their further analysis. This provided direct information on magnitudes which are not accessible from experiments such as the radial probability distribution functions of specific atoms at different times and their moments. The results of our simulations on the H-motions and different experiments indicate that in the high-temperature range investigated the dynamics is Rouse-like for Q-values below approximately 0.6 A(-1). We then addressed the single chain dynamic structure factor with the simulations. A mode analysis, not possible directly experimentally, reveals the limits of applicability of the Rouse model to PEO. We discuss the possible origins for the observed deviations.
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VEDA: a web-based virtual environment for dynamic atomic force microscopy.
Melcher, John; Hu, Shuiqing; Raman, Arvind
2008-06-01
We describe here the theory and applications of virtual environment dynamic atomic force microscopy (VEDA), a suite of state-of-the-art simulation tools deployed on nanoHUB (www.nanohub.org) for the accurate simulation of tip motion in dynamic atomic force microscopy (dAFM) over organic and inorganic samples. VEDA takes advantage of nanoHUB's cyberinfrastructure to run high-fidelity dAFM tip dynamics computations on local clusters and the teragrid. Consequently, these tools are freely accessible and the dAFM simulations are run using standard web-based browsers without requiring additional software. A wide range of issues in dAFM ranging from optimal probe choice, probe stability, and tip-sample interaction forces, power dissipation, to material property extraction and scanning dynamics over hetereogeneous samples can be addressed.
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Invited Article: VEDA: A web-based virtual environment for dynamic atomic force microscopy
NASA Astrophysics Data System (ADS)
Melcher, John; Hu, Shuiqing; Raman, Arvind
2008-06-01
We describe here the theory and applications of virtual environment dynamic atomic force microscopy (VEDA), a suite of state-of-the-art simulation tools deployed on nanoHUB (www.nanohub.org) for the accurate simulation of tip motion in dynamic atomic force microscopy (dAFM) over organic and inorganic samples. VEDA takes advantage of nanoHUB's cyberinfrastructure to run high-fidelity dAFM tip dynamics computations on local clusters and the teragrid. Consequently, these tools are freely accessible and the dAFM simulations are run using standard web-based browsers without requiring additional software. A wide range of issues in dAFM ranging from optimal probe choice, probe stability, and tip-sample interaction forces, power dissipation, to material property extraction and scanning dynamics over hetereogeneous samples can be addressed.
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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.
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Xu, Rosalind J; Blasiak, Bartosz; Cho, Minhaeng; Layfield, Joshua P; Londergan, Casey H
2018-05-17
A quantitative connection between molecular dynamics simulations and vibrational spectroscopy of probe-labeled systems would enable direct translation of experimental data into structural and dynamical information. To constitute this connection, all-atom molecular dynamics (MD) simulations were performed for two SCN probe sites (solvent-exposed and buried) in a calmodulin-target peptide complex. Two frequency calculation approaches with substantial nonelectrostatic components, a quantum mechanics/molecular mechanics (QM/MM)-based technique and a solvatochromic fragment potential (SolEFP) approach, were used to simulate the infrared probe line shapes. While QM/MM results disagreed with experiment, SolEFP results matched experimental frequencies and line shapes and revealed the physical and dynamic bases for the observed spectroscopic behavior. The main determinant of the CN probe frequency is the exchange repulsion between the probe and its local structural neighbors, and there is a clear dynamic explanation for the relatively broad probe line shape observed at the "buried" probe site. This methodology should be widely applicable to vibrational probes in many environments.
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Potential-based dynamical reweighting for Markov state models of protein dynamics.
Weber, Jeffrey K; Pande, Vijay S
2015-06-09
As simulators attempt to replicate the dynamics of large cellular components in silico, problems related to sampling slow, glassy degrees of freedom in molecular systems will be amplified manyfold. It is tempting to augment simulation techniques with external biases to overcome such barriers with ease; biased simulations, however, offer little utility unless equilibrium properties of interest (both kinetic and thermodynamic) can be recovered from the data generated. In this Article, we present a general scheme that harnesses the power of Markov state models (MSMs) to extract equilibrium kinetic properties from molecular dynamics trajectories collected on biased potential energy surfaces. We first validate our reweighting protocol on a simple two-well potential, and we proceed to test our method on potential-biased simulations of the Trp-cage miniprotein. In both cases, we find that equilibrium populations, time scales, and dynamical processes are reliably reproduced as compared to gold standard, unbiased data sets. We go on to discuss the limitations of our dynamical reweighting approach, and we suggest auspicious target systems for further application.
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NASA Astrophysics Data System (ADS)
Kanjilal, Oindrila; Manohar, C. S.
2017-07-01
The study considers the problem of simulation based time variant reliability analysis of nonlinear randomly excited dynamical systems. Attention is focused on importance sampling strategies based on the application of Girsanov's transformation method. Controls which minimize the distance function, as in the first order reliability method (FORM), are shown to minimize a bound on the sampling variance of the estimator for the probability of failure. Two schemes based on the application of calculus of variations for selecting control signals are proposed: the first obtains the control force as the solution of a two-point nonlinear boundary value problem, and, the second explores the application of the Volterra series in characterizing the controls. The relative merits of these schemes, vis-à-vis the method based on ideas from the FORM, are discussed. Illustrative examples, involving archetypal single degree of freedom (dof) nonlinear oscillators, and a multi-degree of freedom nonlinear dynamical system, are presented. The credentials of the proposed procedures are established by comparing the solutions with pertinent results from direct Monte Carlo simulations.
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A new airborne laser rangefinder dynamic target simulator for non-stationary environment
NASA Astrophysics Data System (ADS)
Ma, Pengge; Pang, Dongdong; Yi, Yang
2017-11-01
For the non-stationary environment simulation in laser range finder product testing, a new dynamic target simulation system is studied. First of all, the three-pulsed laser ranging principle, laser target signal composition and mathematical representation are introduced. Then, the actual nonstationary working environment of laser range finder is analyzed, and points out that the real sunshine background light clutter and target shielding effect in laser echo become the main influencing factors. After that, the dynamic laser target signal simulation method is given. Eventlly, the implementation of automatic test system based on arbitrary waveform generator is described. Practical application shows that the new echo signal automatic test system can simulate the real laser ranging environment of laser range finder, and is suitable for performance test of products.
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CABS-flex: Server for fast simulation of protein structure fluctuations.
Jamroz, Michal; Kolinski, Andrzej; Kmiecik, Sebastian
2013-07-01
The CABS-flex server (http://biocomp.chem.uw.edu.pl/CABSflex) implements CABS-model-based protocol for the fast simulations of near-native dynamics of globular proteins. In this application, the CABS model was shown to be a computationally efficient alternative to all-atom molecular dynamics--a classical simulation approach. The simulation method has been validated on a large set of molecular dynamics simulation data. Using a single input (user-provided file in PDB format), the CABS-flex server outputs an ensemble of protein models (in all-atom PDB format) reflecting the flexibility of the input structure, together with the accompanying analysis (residue mean-square-fluctuation profile and others). The ensemble of predicted models can be used in structure-based studies of protein functions and interactions.
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NASA Astrophysics Data System (ADS)
Kinsey, Adam M.; Diederich, Chris J.; Nau, William H.; Ross, Anthony B.; Butts Pauly, Kim; Rieke, Viola; Sommer, Graham
2006-05-01
Multi-sectored ultrasound heating applicators with dynamic angular and longitudinal control of heating profiles are being investigated for the thermal treatment of tumors in sites such as prostate, uterus, and brain. Multi-sectored tubular ultrasound transducers with independent sector power control were incorporated into interstitial and transurethral applicators and provided dynamic angular control of a heating pattern without requiring device manipulation during treatment. Acoustic beam measurements of each applicator type demonstrated a 35-40° acoustic dead zone between each independent sector, with negligible mechanical or electrical coupling. Despite the acoustic dead zone between sectors, simulations and experiments under MR temperature (MRT) monitoring showed that the variance from the maximum lesion radius (scalloping) with all elements activated on a transducer was minimal and did not affect conformal heating of a target area. A biothermal model with a multi-point controller was used to adjust the applied power and treatment time of individual transducer segments as the tissue temperature changed in simulations of thermal lesions with both interstitial and transurethral applicators. Transurethral ultrasound applicators for benign prostatic hyperplasia (BPH) treatment with either three or four sectors conformed a thermal dose to a simulated target area in the angular and radial dimensions. The simulated treatment was controlled to a maximum temperature of 85°C, and had a maximum duration of 5 min when power was turned off as the 52°C temperature contour reach a predetermined control point for each sector in the tissue. Experiments conducted with multi-sectored applicators under MRT monitoring showed thermal ablation and hyperthermia treatments had little or no border `scalloping', conformed to a pretreatment target area, and correlated very well with the simulated thermal lesions. The radial penetration of the heat treatments in tissue with interstitial (1.5-1.8 mm OD transducer) and transurethral (2.5-4.0 mm OD transducer) applicators was at least 1.5 cm and 2.0 cm, respectively, for a treatment duration of 10 min. Angular control of thermal ablation and hyperthermia therapy often relies upon non-adjustable angular power deposition patterns and/or mechanical manipulation of the heating device. The multi-sectored ultrasound applicators developed in this study provide dynamic control of the angular heating distribution during treatment without device manipulation and maintain previously reported heating penetration and spatial control characteristics of similar ultrasound devices.
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Internal Coordinate Molecular Dynamics: A Foundation for Multiscale Dynamics
2015-01-01
Internal coordinates such as bond lengths, bond angles, and torsion angles (BAT) are natural coordinates for describing a bonded molecular system. However, the molecular dynamics (MD) simulation methods that are widely used for proteins, DNA, and polymers are based on Cartesian coordinates owing to the mathematical simplicity of the equations of motion. However, constraints are often needed with Cartesian MD simulations to enhance the conformational sampling. This makes the equations of motion in the Cartesian coordinates differential-algebraic, which adversely impacts the complexity and the robustness of the simulations. On the other hand, constraints can be easily placed in BAT coordinates by removing the degrees of freedom that need to be constrained. Thus, the internal coordinate MD (ICMD) offers an attractive alternative to Cartesian coordinate MD for developing multiscale MD method. The torsional MD method is a special adaptation of the ICMD method, where all the bond lengths and bond angles are kept rigid. The advantages of ICMD simulation methods are the longer time step size afforded by freezing high frequency degrees of freedom and performing a conformational search in the more important low frequency torsional degrees of freedom. However, the advancements in the ICMD simulations have been slow and stifled by long-standing mathematical bottlenecks. In this review, we summarize the recent mathematical advancements we have made based on spatial operator algebra, in developing a robust long time scale ICMD simulation toolkit useful for various applications. We also present the applications of ICMD simulations to study conformational changes in proteins and protein structure refinement. We review the advantages of the ICMD simulations over the Cartesian simulations when used with enhanced sampling methods and project the future use of ICMD simulations in protein dynamics. PMID:25517406
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Gaussian Accelerated Molecular Dynamics: Theory, Implementation, and Applications
Miao, Yinglong; McCammon, J. Andrew
2018-01-01
A novel Gaussian Accelerated Molecular Dynamics (GaMD) method has been developed for simultaneous unconstrained enhanced sampling and free energy calculation of biomolecules. Without the need to set predefined reaction coordinates, GaMD enables unconstrained enhanced sampling of the biomolecules. Furthermore, by constructing a boost potential that follows a Gaussian distribution, accurate reweighting of GaMD simulations is achieved via cumulant expansion to the second order. The free energy profiles obtained from GaMD simulations allow us to identify distinct low energy states of the biomolecules and characterize biomolecular structural dynamics quantitatively. In this chapter, we present the theory of GaMD, its implementation in the widely used molecular dynamics software packages (AMBER and NAMD), and applications to the alanine dipeptide biomolecular model system, protein folding, biomolecular large-scale conformational transitions and biomolecular recognition. PMID:29720925
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High-frequency intrinsic dynamics of the electrocaloric effect from direct atomistic simulations
NASA Astrophysics Data System (ADS)
Lisenkov, S.; Ponomareva, I.
2018-05-01
We propose a computational methodology capable of harvesting isothermal heat and entropy change in molecular dynamics simulations. The methodology is applied to study high-frequency dynamics of the electrocaloric effect (ECE) in ferroelectric PbTiO3. ECE is associated with a reversible change in temperature under adiabatic application of electric field or with a reversible change in entropy under isothermal application of the electric field. Accurate assessment of electrocaloric performance requires the knowledge of three quantities: isothermal heat, isothermal entropy change, and adiabatic temperature change. Our methodology allows computations of all these quantities directly, that is, without restoring to the reversible thermodynamical models. Consequently, it captures both reversible and irreversible effects, which is critical for ECE simulations. The approach is well suited to address the dynamics of the ECE, which so far remains underexplored. We report the following basic features of the intrinsic dynamics of ECE: (i) the ECE is independent of the electric field frequency, rate of application, or field profile; (ii) the effect persists up to the frequencies associated with the onset of dielectric losses and deteriorates from there due to the creation of irreversible entropy; and (iii) in the vicinity of the phase transition and in the paraelectric phase the onset of irreversible dynamics occurs at lower frequency as compared to the ferroelectric phase. The latter is attributed to lower intrinsic soft-mode frequencies and and larger losses in the paraelectric phase.
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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)
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Local Dynamics of Acid- and Ion-containing Copolymer Melts
NASA Astrophysics Data System (ADS)
Winey, Karen; Middleton, Robert; Tarver, Jacob; Tyagi, Madhusudan; Soles, Christopher; Frischknecht, Amalie
Interest in acid- and ion-containing polymers arises in part from applications as single-ion conductors for selectively transporting a counter ion for battery applications. Structurally, the low dielectric constant of organic polymers and strong ionic interactions leads to ionic aggregation. Here the polymer backbone motion was investigated through quasi-elastic neutron scattering measurements (QENS) and compared with fully atomistic molecular dynamic simulations of precise poly(ethylene-acrylic acid) copolymers and their ionomers (pxAA-y%Li). The effect of carbon spacer length (x =9, 15, 21) between the acid groups and the degree of neutralization (y) with Li on PE backbone dynamics were considered. Systematic slowing in chain dynamics were observed with increasing neutralization where polymer dynamics appear constrained due to anchoring effects. Simulations provide complementary viewpoints indicating a gradient in chain dynamics as a distance away from acid groups. These results indicate that the addition of pendant acid groups inhibit typical PE backbone motion and the neutralized forms strongly suppress the fraction of mobile PE chain.
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Nonlinear System Identification for Aeroelastic Systems with Application to Experimental Data
NASA Technical Reports Server (NTRS)
Kukreja, Sunil L.
2008-01-01
Representation and identification of a nonlinear aeroelastic pitch-plunge system as a model of the Nonlinear AutoRegressive, Moving Average eXogenous (NARMAX) class is considered. A nonlinear difference equation describing this aircraft model is derived theoretically and shown to be of the NARMAX form. Identification methods for NARMAX models are applied to aeroelastic dynamics and its properties demonstrated via continuous-time simulations of experimental conditions. Simulation results show that (1) the outputs of the NARMAX model closely match those generated using continuous-time methods, and (2) NARMAX identification methods applied to aeroelastic dynamics provide accurate discrete-time parameter estimates. Application of NARMAX identification to experimental pitch-plunge dynamics data gives a high percent fit for cross-validated data.
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Analysis of a digital RF memory in a signal-delay application
DOE Office of Scientific and Technical Information (OSTI.GOV)
Jelinek, D.A.
1992-03-01
Laboratory simulation of the approach of a radar fuze towards a target is an important factor in our ability to accurately measure the radar's performance. This simulation is achieved, in part, by dynamically delaying and attenuating the radar's transmitted pulse and sending the result back to the radar's receiver. Historically, the device used to perform the dynamic delay has been a limiting factor in the evaluation of a radar's performance and characteristics. A new device has been proposed that appears to have more capability than previous dynamic delay devices. This device is the digital RF memory. This report presents themore » results of an analysis of a digital RF memory used in a signal-delay application. 2 refs.« less
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The dynamic two-fluid model OLGA; Theory and application
DOE Office of Scientific and Technical Information (OSTI.GOV)
Bendiksen, K.H.; Maines, D.; Moe, R.
1991-05-01
Dynamic two-fluid models have found a wide range of application in the simulation of two-phase-flow systems, particularly for the analysis of steam/water flow in the core of a nuclear reactor. Until quite recently, however, very few attempts have been made to use such models in the simulation of two-phase oil and gas flow in pipelines. This paper presents a dynamic two-fluid model, OLGA, in detail, stressing the basic equations and the two-fluid models applied. Predictions of steady-state pressure drop, liquid hold-up, and flow-regime transitions are compared with data from the SINTEF Two-Phase Flow Laboratory and from the literature. Comparisons withmore » evaluated field data are also presented.« less
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Transistor analogs of emergent iono-neuronal dynamics.
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.
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A Simple Simulator to Teach Enzyme Kinetics Dynamics. Application in a Problem-Solving Exercise
ERIC Educational Resources Information Center
Torres, Néstor; Santos, Guido
2017-01-01
Enzyme kinetics is an essential part of biochemistry programs, which have been gaining importance in recent years for their applications in biotechnology and biomedicine. The teaching and learning of these issues has been traditionally hampered by difficulties that stem mainly from the dynamic and mathematical nature of the topic and the…
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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.
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NASA Astrophysics Data System (ADS)
Kuznetsov, N. V.; Leonov, G. A.; Yuldashev, M. V.; Yuldashev, R. V.
2017-10-01
During recent years it has been shown that hidden oscillations, whose basin of attraction does not overlap with small neighborhoods of equilibria, may significantly complicate simulation of dynamical models, lead to unreliable results and wrong conclusions, and cause serious damage in drilling systems, aircrafts control systems, electromechanical systems, and other applications. This article provides a survey of various phase-locked loop based circuits (used in satellite navigation systems, optical, and digital communication), where such difficulties take place in MATLAB and SPICE. Considered examples can be used for testing other phase-locked loop based circuits and simulation tools, and motivate the development and application of rigorous analytical methods for the global analysis of phase-locked loop based circuits.
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Coarse-grained protein-protein stiffnesses and dynamics from all-atom simulations
NASA Astrophysics Data System (ADS)
Hicks, Stephen D.; Henley, C. L.
2010-03-01
Large protein assemblies, such as virus capsids, may be coarse-grained as a set of rigid units linked by generalized (rotational and stretching) harmonic springs. We present an ab initio method to obtain the elastic parameters and overdamped dynamics for these springs from all-atom molecular-dynamics simulations of one pair of units at a time. The computed relaxation times of this pair give a consistency check for the simulation, and we can also find the corrective force needed to null systematic drifts. As a first application we predict the stiffness of an HIV capsid layer and the relaxation time for its breathing mode.
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Li, Jingrui; Kondov, Ivan; Wang, Haobin; Thoss, Michael
2015-04-10
A recently developed methodology to simulate photoinduced electron transfer processes at dye-semiconductor interfaces is outlined. The methodology employs a first-principles-based model Hamiltonian and accurate quantum dynamics simulations using the multilayer multiconfiguration time-dependent Hartree approach. This method is applied to study electron injection in the dye-semiconductor system coumarin 343-TiO2. Specifically, the influence of electronic-vibrational coupling is analyzed. Extending previous work, we consider the influence of Dushinsky rotation of the normal modes as well as anharmonicities of the potential energy surfaces on the electron transfer dynamics.
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NASA Astrophysics Data System (ADS)
Regev, Shaked; Farago, Oded
2018-10-01
We use a one-dimensional two layer model with a semi-permeable membrane to study the diffusion of a therapeutic drug delivered from a drug-eluting stent (DES). The rate of drug transfer from the stent coating to the arterial wall is calculated by using underdamped Langevin dynamics simulations. Our results reveal that the membrane has virtually no delay effect on the rate of delivery from the DES. The work demonstrates the great potential of underdamped Langevin dynamics simulations as an easy to implement, efficient, method for solving complicated diffusion problems in systems with a spatially-dependent diffusion coefficient.
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Research on dynamic routing mechanisms in wireless sensor networks.
Zhao, A Q; Weng, Y N; Lu, Y; Liu, C Y
2014-01-01
WirelessHART is the most widely applied standard in wireless sensor networks nowadays. However, it does not provide any dynamic routing mechanism, which is important for the reliability and robustness of the wireless network applications. In this paper, a collection tree protocol based, dynamic routing mechanism was proposed for WirelessHART network. The dynamic routing mechanism was evaluated through several simulation experiments in three aspects: time for generating the topology, link quality, and stability of network. Besides, the data transmission efficiency of this routing mechanism was analyzed. The simulation and evaluation results show that this mechanism can act as a dynamic routing mechanism for the TDMA-based wireless sensor network.
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NASA Technical Reports Server (NTRS)
Demerdash, N. A. O.; Nehl, T. W.
1979-01-01
A mathematical model was developed and computerized simulations were obtained for a brushless dc motor. Experimentally obtained oscillograms of the machine phase currents are presented and the corresponding current and voltage waveforms for various modes of operation of the motor are presented and discussed.
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Qi, Shuanhu; Schmid, Friederike
2017-11-08
We present a multiscale hybrid particle-field scheme for the simulation of relaxation and diffusion behavior of soft condensed matter systems. It combines particle-based Brownian dynamics and field-based local dynamics in an adaptive sense such that particles can switch their level of resolution on the fly. The switching of resolution is controlled by a tuning function which can be chosen at will according to the geometry of the system. As an application, the hybrid scheme is used to study the kinetics of interfacial broadening of a polymer blend, and is validated by comparing the results to the predictions from pure Brownian dynamics and pure local dynamics calculations.
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DOT National Transportation Integrated Search
2016-06-26
The datasets in this zip file are in support of Intelligent Transportation Systems Joint Program Office (ITS JPO) report FHWA-JPO-16-385, "Analysis, Modeling, and Simulation (AMS) Testbed Development and Evaluation to Support Dynamic Mobility Applica...
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Ultrafast impact dynamics of reactive materials (Dlott)
2013-04-16
Kalia, A. Nakano, B. E. Hohman, and K. L. McNesby, Multimillion atom reactive simulations of nanostructured energetic materials, J. Propul. Power 23...34Materials for Energy Applications - Experiment, Modeling and Simulations ", Mar. 2011, Los Angeles, CA. 7. (invited) Studium Conference on in situ...intermetallics. 7,20-24 The dynamics of conventional reactive materials containing micron to millimeter particles are usually viewed within a
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ADDRESSING ENVIRONMENTAL ENGINEERING CHALLENGES WITH COMPUTATIONAL FLUID DYNAMICS
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 ...
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On the application of accelerated molecular dynamics to liquid water simulations.
de Oliveira, César Augusto F; Hamelberg, Donald; McCammon, J Andrew
2006-11-16
Our group recently proposed a robust bias potential function that can be used in an efficient all-atom accelerated molecular dynamics (MD) approach to simulate the transition of high energy barriers without any advance knowledge of the potential-energy landscape. The main idea is to modify the potential-energy surface by adding a bias, or boost, potential in regions close to the local minima, such that all transitions rates are increased. By applying the accelerated MD simulation method to liquid water, we observed that this new simulation technique accelerates the molecular motion without losing its microscopic structure and equilibrium properties. Our results showed that the application of a small boost energy on the potential-energy surface significantly reduces the statistical inefficiency of the simulation while keeping all the other calculated properties unchanged. On the other hand, although aggressive acceleration of the dynamics simulation increases the self-diffusion coefficient of water molecules greatly and dramatically reduces the correlation time of the simulation, configurations representative of the true structure of liquid water are poorly sampled. Our results also showed the strength and robustness of this simulation technique, which confirm this approach as a very useful and promising tool to extend the time scale of the all-atom simulations of biological system with explicit solvent models. However, we should keep in mind that there is a compromise between the strength of the boost applied in the simulation and the reproduction of the ensemble average properties.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Corbet Jr., Thomas F; Beyeler, Walter E; Vanwestrienen, Dirk
NetFlow Dynamics is a web-accessible analysis environment for simulating dynamic flows of materials on model networks. Performing a simulation requires both the NetFlow Dynamics application and a network model which is a description of the structure of the nodes and edges of a network including the flow capacity of each edge and the storage capacity of each node, and the sources and sinks of the material flowing on the network. NetFlow Dynamics consists of databases for storing network models, algorithms to calculate flows on networks, and a GIS-based graphical interface for performing simulations and viewing simulation results. Simulated flows aremore » dynamic in the sense that flows on each edge of the network and inventories at each node change with time and can be out of equilibrium with boundary conditions. Any number of network models could be simulated using Net Flow Dynamics. To date, the models simulated have been models of petroleum infrastructure. The main model has been the National Transportation Fuels Model (NTFM), a network of U.S. oil fields, transmission pipelines, rail lines, refineries, tank farms, and distribution terminals. NetFlow Dynamics supports two different flow algorithms, the Gradient Flow algorithm and the Inventory Control algorithm, that were developed specifically for the NetFlow Dynamics application. The intent is to add additional algorithms in the future as needed. The ability to select from multiple algorithms is desirable because a single algorithm never covers all analysis needs. The current algorithms use a demand-driven capacity-constrained formulation which means that the algorithms strive to use all available capacity and stored inventory to meet desired flows to sinks, subject to the capacity constraints of each network component. The current flow algorithms are best suited for problems in which a material flows on a capacity-constrained network representing a supply chain in which the material supplied can be stored at each node of the network. In the petroleum models, the flowing materials are crude oil and refined products that can be stored at tank farms, refineries, or terminals (i.e. the nodes of the network). Examples of other network models that could be simulated are currency flowing in a financial network, agricultural products moving to market, or natural gas flowing on a pipeline network.« less
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A Component-Based FPGA Design Framework for Neuronal Ion Channel Dynamics Simulations
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
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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.
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Formation and field-driven dynamics of nematic spheroids.
Fu, Fred; Abukhdeir, Nasser Mohieddin
2017-07-19
Unlike the canonical application of liquid crystals (LCs), LC displays, emerging technologies based on LC materials are increasingly leveraging the presence of nanoscale defects. The inherent nanoscale characteristics of LC defects present both significant opportunities as well as barriers for the application of this fascinating class of materials. Simulation-based approaches to the study of the effects of confinement and interface anchoring conditions on LC domains has resulted in significant progress over the past decade, where simulations are now able to access experimentally-relevant length scales while simultaneously capturing nanoscale defect structures. In this work, continuum simulations were performed in order to study the dynamics of micron-scale nematic LC spheroids of varying shape. Nematic spheroids are one of the simplest inherently defect-containing LC structures and are relevant to polymer-dispersed LC-based "smart" window technology. Simulation results include nematic phase formation and external field-switching dynamics of nematic spheroids ranging in shape from oblate to prolate. Results include both qualitative and quantitative insight into the complex coupling of nanoscale defect dynamics and structure transitions to micron-scale reorientation. Dynamic mechanisms are presented and related to structural transitions in LC defects present in the nematic domain. Domain-averaged metrics including order parameters and response times are determined for a range of experimentally-accessible electric field strengths. These results have both fundamental and technological relevance, in that increased understanding of LC dynamics in the presence of defects is a key barrier to continued advancement in the field.
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A flexible object-oriented software framework for developing complex multimedia simulations.
DOE Office of Scientific and Technical Information (OSTI.GOV)
Sydelko, P. J.; Dolph, J. E.; Christiansen, J. H.
Decision makers involved in brownfields redevelopment and long-term stewardship must consider environmental conditions, future-use potential, site ownership, area infrastructure, funding resources, cost recovery, regulations, risk and liability management, community relations, and expected return on investment in a comprehensive and integrated fashion to achieve desired results. Successful brownfields redevelopment requires the ability to assess the impacts of redevelopment options on multiple interrelated aspects of the ecosystem, both natural and societal. Computer-based tools, such as simulation models, databases, and geographical information systems (GISs) can be used to address brownfields planning and project execution. The transparent integration of these tools into a comprehensivemore » and dynamic decision support system would greatly enhance the brownfields assessment process. Such a system needs to be able to adapt to shifting and expanding analytical requirements and contexts. The Dynamic Information Architecture System (DIAS) is a flexible, extensible, object-oriented framework for developing and maintaining complex multidisciplinary simulations of a wide variety of application domains. The modeling domain of a specific DIAS-based simulation is determined by (1) software objects that represent the real-world entities that comprise the problem space (atmosphere, watershed, human), and (2) simulation models and other data processing applications that express the dynamic behaviors of the domain entities. Models and applications used to express dynamic behaviors can be either internal or external to DIAS, including existing legacy models written in various languages (FORTRAN, C, etc.). The flexible design framework of DIAS makes the objects adjustable to the context of the problem without a great deal of recoding. The DIAS Spatial Data Set facility allows parameters to vary spatially depending on the simulation context according to any of a number of 1-D, 2-D, or 3-D topologies. DIAS is also capable of interacting with other GIS packages and can import many standard spatial data formats. DIAS simulation capabilities can also be extended by including societal process models. Models that implement societal behaviors of individuals and organizations within larger DIAS-based natural systems simulations allow for interaction and feedback among natural and societal processes. The ability to simulate the complex interplay of multimedia processes makes DIAS a promising tool for constructing applications for comprehensive community planning, including the assessment of multiple development and redevelopment scenarios.« less
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2006-09-01
compression, including real-time cinematography of failure under dynamic compression, was evaluated. The results (figure 10) clearly show that the failure... art of simulations of dynamic failure and damage mechanisms. An explicit dynamic parallel code has been developed to track damage mechanisms in the
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Development of a Gas Dynamic and Thermodynamic Simulation Model of the Lontra Blade Compressor™
NASA Astrophysics Data System (ADS)
Karlovsky, Jerome
2015-08-01
The Lontra Blade Compressor™ is a patented double acting, internally compressing, positive displacement rotary compressor of innovative design. The Blade Compressor is in production for waste-water treatment, and will soon be launched for a range of applications at higher pressure ratios. In order to aid the design and development process, a thermodynamic and gas dynamic simulation program has been written in house. The software has been successfully used to optimise geometries and running conditions of current designs, and is also being used to evaluate future designs for different applications and markets. The simulation code has three main elements. A positive displacement chamber model, a leakage model and a gas dynamic model to simulate gas flow through ports and to track pressure waves in the inlet and outlet pipes. All three of these models are interlinked in order to track mass and energy flows within the system. A correlation study has been carried out to verify the software. The main correlation markers used were mass flow, chamber pressure, pressure wave tracking in the outlet pipe, and volumetric efficiency. It will be shown that excellent correlation has been achieved between measured and simulated data. Mass flow predictions were to within 2% of measured data, and the timings and magnitudes of all major gas dynamic effects were well replicated. The simulation will be further developed in the near future to help with the optimisation of exhaust and inlet silencers.
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Parallel Programming Strategies for Irregular Adaptive Applications
NASA Technical Reports Server (NTRS)
Biswas, Rupak; Biegel, Bryan (Technical Monitor)
2001-01-01
Achieving scalable performance for dynamic irregular applications is eminently challenging. Traditional message-passing approaches have been making steady progress towards this goal; however, they suffer from complex implementation requirements. The use of a global address space greatly simplifies the programming task, but can degrade the performance for such computations. In this work, we examine two typical irregular adaptive applications, Dynamic Remeshing and N-Body, under competing programming methodologies and across various parallel architectures. The Dynamic Remeshing application simulates flow over an airfoil, and refines localized regions of the underlying unstructured mesh. The N-Body experiment models two neighboring Plummer galaxies that are about to undergo a merger. Both problems demonstrate dramatic changes in processor workloads and interprocessor communication with time; thus, dynamic load balancing is a required component.
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Vortex Filaments in Grids for Scalable, Fine Smoke Simulation.
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.
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PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks
Craveur, Pierrick; Joseph, Agnel Praveen; Jallu, Vincent
2017-01-01
This paper describes the development and application of a suite of tools, called PBxplore, to analyze the dynamics and deformability of protein structures using Protein Blocks (PBs). Proteins are highly dynamic macromolecules, and a classical way to analyze their inherent flexibility is to perform molecular dynamics simulations. The advantage of using small structural prototypes such as PBs is to give a good approximation of the local structure of the protein backbone. More importantly, by reducing the conformational complexity of protein structures, PBs allow analysis of local protein deformability which cannot be done with other methods and had been used efficiently in different applications. PBxplore is able to process large amounts of data such as those produced by molecular dynamics simulations. It produces frequencies, entropy and information logo outputs as text and graphics. PBxplore is available at https://github.com/pierrepo/PBxplore and is released under the open-source MIT license. PMID:29177113
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Morales, Y.; Weber, L.J.; Mynett, A.E.; Newton, T.J.
2006-01-01
A model for simulating freshwater mussel population dynamics is presented. The model is a hydroinformatics tool that integrates principles from ecology, river hydraulics, fluid mechanics and sediment transport, and applies the individual-based modelling approach for simulating population dynamics. The general model layout, data requirements, and steps of the simulation process are discussed. As an illustration, simulation results from an application in a 10 km reach of the Upper Mississippi River are presented. The model was used to investigate the spatial distribution of mussels and the effects of food competition in native unionid mussel communities, and communities infested by Dreissena polymorpha, the zebra mussel. Simulation results were found to be realistic and coincided with data obtained from the literature. These results indicate that the model can be a useful tool for assessing the potential effects of different stressors on long-term population dynamics, and consequently, may improve the current understanding of cause and effect relationships in freshwater mussel communities. ?? 2006 Elsevier B.V. All rights reserved.
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The NEST Dry-Run Mode: Efficient Dynamic Analysis of Neuronal Network Simulation Code.
Kunkel, Susanne; Schenck, Wolfram
2017-01-01
NEST is a simulator for spiking neuronal networks that commits to a general purpose approach: It allows for high flexibility in the design of network models, and its applications range from small-scale simulations on laptops to brain-scale simulations on supercomputers. Hence, developers need to test their code for various use cases and ensure that changes to code do not impair scalability. However, running a full set of benchmarks on a supercomputer takes up precious compute-time resources and can entail long queuing times. Here, we present the NEST dry-run mode, which enables comprehensive dynamic code analysis without requiring access to high-performance computing facilities. A dry-run simulation is carried out by a single process, which performs all simulation steps except communication as if it was part of a parallel environment with many processes. We show that measurements of memory usage and runtime of neuronal network simulations closely match the corresponding dry-run data. Furthermore, we demonstrate the successful application of the dry-run mode in the areas of profiling and performance modeling.
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The NEST Dry-Run Mode: Efficient Dynamic Analysis of Neuronal Network Simulation Code
Kunkel, Susanne; Schenck, Wolfram
2017-01-01
NEST is a simulator for spiking neuronal networks that commits to a general purpose approach: It allows for high flexibility in the design of network models, and its applications range from small-scale simulations on laptops to brain-scale simulations on supercomputers. Hence, developers need to test their code for various use cases and ensure that changes to code do not impair scalability. However, running a full set of benchmarks on a supercomputer takes up precious compute-time resources and can entail long queuing times. Here, we present the NEST dry-run mode, which enables comprehensive dynamic code analysis without requiring access to high-performance computing facilities. A dry-run simulation is carried out by a single process, which performs all simulation steps except communication as if it was part of a parallel environment with many processes. We show that measurements of memory usage and runtime of neuronal network simulations closely match the corresponding dry-run data. Furthermore, we demonstrate the successful application of the dry-run mode in the areas of profiling and performance modeling. PMID:28701946
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Hirshberg, Barak; Sagiv, Lior; Gerber, R Benny
2017-03-14
Algorithms for quantum molecular dynamics simulations that directly use ab initio methods have many potential applications. In this article, the ab initio classical separable potentials (AICSP) method is proposed as the basis for approximate algorithms of this type. The AICSP method assumes separability of the total time-dependent wave function of the nuclei and employs mean-field potentials that govern the dynamics of each degree of freedom. In the proposed approach, the mean-field potentials are determined by classical ab initio molecular dynamics simulations. The nuclear wave function can thus be propagated in time using the effective potentials generated "on the fly". As a test of the method for realistic systems, calculations of the stationary anharmonic frequencies of hydrogen stretching modes were carried out for several polyatomic systems, including three amino acids and the guanine-cytosine pair of nucleobases. Good agreement with experiments was found. The method scales very favorably with the number of vibrational modes and should be applicable for very large molecules, e.g., peptides. The method should also be applicable for properties such as vibrational line widths and line shapes. Work in these directions is underway.
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Zhou, Yu-Ping; Jiang, Jin-Wu
2017-01-01
While most existing theoretical studies on the borophene are based on first-principles calculations, the present work presents molecular dynamics simulations for the lattice dynamical and mechanical properties in borophene. The obtained mechanical quantities are in good agreement with previous first-principles calculations. The key ingredients for these molecular dynamics simulations are the two efficient empirical potentials developed in the present work for the interaction of borophene with low-energy triangular structure. The first one is the valence force field model, which is developed with the assistance of the phonon dispersion of borophene. The valence force field model is a linear potential, so it is rather efficient for the calculation of linear quantities in borophene. The second one is the Stillinger-Weber potential, whose parameters are derived based on the valence force field model. The Stillinger-Weber potential is applicable in molecular dynamics simulations of nonlinear physical or mechanical quantities in borophene. PMID:28349983
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Analytical investigation of the dynamics of tethered constellations in Earth orbit, phase 2
NASA Technical Reports Server (NTRS)
Lorenzini, Enrico C.; Gullahorn, Gordon E.; Cosmo, Mario L.; Estes, Robert D.; Grossi, Mario D.
1994-01-01
This final report covers nine years of research on future tether applications and on the actual flights of the Small Expendable Deployment System (SEDS). Topics covered include: (1) a description of numerical codes used to simulate the orbital and attitude dynamics of tethered systems during station keeping and deployment maneuvers; (2) a comparison of various tethered system simulators; (3) dynamics analysis, conceptual design, potential applications and propagation of disturbances and isolation from noise of a variable gravity/microgravity laboratory tethered to the Space Station; (4) stability of a tethered space centrifuge; (5) various proposed two-dimensional tethered structures for low Earth orbit for use as planar array antennas; (6) tethered high gain antennas; (7) numerical calculation of the electromagnetic wave field on the Earth's surface on an electrodynamically tethered satellite; (8) reentry of tethered capsules; (9) deployment dynamics of SEDS-1; (10) analysis of SEDS-1 flight data; and (11) dynamics and control of SEDS-2.
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Smoothed-particle hydrodynamics and nonequilibrium molecular dynamics
DOE Office of Scientific and Technical Information (OSTI.GOV)
Hoover, W. G.; Hoover, C. G.
1993-08-01
Gingold, Lucy, and Monaghan invented a grid-free version of continuum mechanics ``smoothed-particle hydrodynamics,`` in 1977. It is a likely contributor to ``hybrid`` simulations combining atomistic and continuum simulations. We describe applications of this particle-based continuum technique from the closely-related standpoint of nonequilibrium molecular dynamics. We compare chaotic Lyapunov spectra for atomistic solids and fluids with those which characterize a two-dimensional smoothed-particle fluid system.
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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
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Moritsugu, Kei; Koike, Ryotaro; Yamada, Kouki; Kato, Hiroaki; Kidera, Akinori
2015-01-01
Molecular dynamics (MD) simulations of proteins provide important information to understand their functional mechanisms, which are, however, likely to be hidden behind their complicated motions with a wide range of spatial and temporal scales. A straightforward and intuitive analysis of protein dynamics observed in MD simulation trajectories is therefore of growing significance with the large increase in both the simulation time and system size. In this study, we propose a novel description of protein motions based on the hierarchical clustering of fluctuations in the inter-atomic distances calculated from an MD trajectory, which constructs a single tree diagram, named a “Motion Tree”, to determine a set of rigid-domain pairs hierarchically along with associated inter-domain fluctuations. The method was first applied to the MD trajectory of substrate-free adenylate kinase to clarify the usefulness of the Motion Tree, which illustrated a clear-cut dynamics picture of the inter-domain motions involving the ATP/AMP lid and the core domain together with the associated amplitudes and correlations. The comparison of two Motion Trees calculated from MD simulations of ligand-free and -bound glutamine binding proteins clarified changes in inherent dynamics upon ligand binding appeared in both large domains and a small loop that stabilized ligand molecule. Another application to a huge protein, a multidrug ATP binding cassette (ABC) transporter, captured significant increases of fluctuations upon binding a drug molecule observed in both large scale inter-subunit motions and a motion localized at a transmembrane helix, which may be a trigger to the subsequent structural change from inward-open to outward-open states to transport the drug molecule. These applications demonstrated the capabilities of Motion Trees to provide an at-a-glance view of various sizes of functional motions inherent in the complicated MD trajectory. PMID:26148295
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Analysis of a digital RF memory in a signal-delay application
DOE Office of Scientific and Technical Information (OSTI.GOV)
Jelinek, D.A.
1992-03-01
Laboratory simulation of the approach of a radar fuze towards a target is an important factor in our ability to accurately measure the radar`s performance. This simulation is achieved, in part, by dynamically delaying and attenuating the radar`s transmitted pulse and sending the result back to the radar`s receiver. Historically, the device used to perform the dynamic delay has been a limiting factor in the evaluation of a radar`s performance and characteristics. A new device has been proposed that appears to have more capability than previous dynamic delay devices. This device is the digital RF memory. This report presents themore » results of an analysis of a digital RF memory used in a signal-delay application. 2 refs.« less
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NASA Astrophysics Data System (ADS)
Lapusta, N.; Thomas, M.; Noda, H.; Avouac, J.
2012-12-01
Long-term simulations that incorporate both seismic events and aseismic slip are quite important for studies of earthquake physics but challenging computationally. To study long deformation histories, most simulation methods do not incorporate full inertial effects (wave propagation) during simulated earthquakes, using quasi-dynamic approximations instead. Here we compare the results of quasi-dynamic simulations to the fully dynamic ones for a range of problems to determine the applicability of the quasi-dynamic approach. Intuitively, the quasi-dynamic approach should do relatively well in problems where wave-mediated effects are relatively simple but should have substantially different (and hence wrong) response when the wave-mediated stress transfers dominate the character of the seismic events. This is exactly what we observe in our simulations. We consider a 2D model of a rate-and-state fault with a seismogenic (steady-state velocity-weakening) zone surrounded by creeping (steady-state velocity-strengthening) areas. If the seismogenic zone is described by the standard Dieterich-Ruina rate-and-state friction, the resulting earthquake sequences consist of relatively simple crack-like ruptures, and the inclusion of true wave-propagation effects mostly serves to concentrate stress more efficiently at the rupture front. Hence, in such models, rupture speeds and slip rates are significantly (several times) lower in the quasi-dynamic simulations compared to the fully dynamic ones, but the total slip, the crack-like nature of seismic events, and the overall pattern of earthquake sequences is comparable, consistently with prior studies. Such behavior can be classified as qualitatively similar but quantitatively different, and it motivates the popularity of the quasi-dynamic methods in simulations. However, the comparison changes dramatically once we consider a model with enhanced dynamic weakening in the seismogenic zone in the form of flash heating. In this case, the fully dynamic simulations produce seismic ruptures in the form of short-duration slip pulses, where the pulses form due to a combination of enhanced weakening and wave effects. The quasi-dynamic simulations in the same model produce completely different results, with large crack-like ruptures, different total slips, different rupture patterns, and different prestress state before large, model-spanning events. Such qualitative differences between the quasi-dynamic and fully-dynamic simulation should result in any model where inertial effects lead to qualitative differences, such as cases with supershear transition or fault with different materials on the two sides. We will present results on our current work on how the quasi-dynamic and fully dynamic simulations compare for the cases with heterogeneous fault properties.
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Coarse-grained molecular dynamics simulations for giant protein-DNA complexes
NASA Astrophysics Data System (ADS)
Takada, Shoji
Biomolecules are highly hierarchic and intrinsically flexible. Thus, computational modeling calls for multi-scale methodologies. We have been developing a coarse-grained biomolecular model where on-average 10-20 atoms are grouped into one coarse-grained (CG) particle. Interactions among CG particles are tuned based on atomistic interactions and the fluctuation matching algorithm. CG molecular dynamics methods enable us to simulate much longer time scale motions of much larger molecular systems than fully atomistic models. After broad sampling of structures with CG models, we can easily reconstruct atomistic models, from which one can continue conventional molecular dynamics simulations if desired. Here, we describe our CG modeling methodology for protein-DNA complexes, together with various biological applications, such as the DNA duplication initiation complex, model chromatins, and transcription factor dynamics on chromatin-like environment.
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Pastor, Nina; Amero, Carlos
2015-01-01
Proteins participate in information pathways in cells, both as links in the chain of signals, and as the ultimate effectors. Upon ligand binding, proteins undergo conformation and motion changes, which can be sensed by the following link in the chain of information. Nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations represent powerful tools for examining the time-dependent function of biological molecules. The recent advances in NMR and the availability of faster computers have opened the door to more detailed analyses of structure, dynamics, and interactions. Here we briefly describe the recent applications that allow NMR spectroscopy and MD simulations to offer unique insight into the basic motions that underlie information transfer within and between cells. PMID:25999971
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Moving Contact Lines: Linking Molecular Dynamics and Continuum-Scale Modeling.
Smith, Edward R; Theodorakis, Panagiotis E; Craster, Richard V; Matar, Omar K
2018-05-17
Despite decades of research, the modeling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily life applications. On the one hand, molecular dynamics (MD) simulation has the ability to provide unique insight into the microscopic details that determine the dynamic behavior of the contact line, which is not possible with either continuum-scale simulations or experiments. On the other hand, continuum-based models provide a link to the macroscopic description of the system. In this Feature Article, we explore the complex range of physical factors, including the presence of surfactants, which governs the contact line motion through MD simulations. We also discuss links between continuum- and molecular-scale modeling and highlight the opportunities for future developments in this area.
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Computational design and multiscale modeling of a nanoactuator using DNA actuation.
Hamdi, Mustapha
2009-12-02
Developments in the field of nanobiodevices coupling nanostructures and biological components are of great interest in medical nanorobotics. As the fundamentals of bio/non-bio interaction processes are still poorly understood in the design of these devices, design tools and multiscale dynamics modeling approaches are necessary at the fabrication pre-project stage. This paper proposes a new concept of optimized carbon nanotube based servomotor design for drug delivery and biomolecular transport applications. The design of an encapsulated DNA-multi-walled carbon nanotube actuator is prototyped using multiscale modeling. The system is parametrized by using a quantum level approach and characterized by using a molecular dynamics simulation. Based on the analysis of the simulation results, a servo nanoactuator using ionic current feedback is simulated and analyzed for application as a drug delivery carrier.
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Quantum Dynamics in Biological Systems
NASA Astrophysics Data System (ADS)
Shim, Sangwoo
In the first part of this dissertation, recent efforts to understand quantum mechanical effects in biological systems are discussed. Especially, long-lived quantum coherences observed during the electronic energy transfer process in the Fenna-Matthews-Olson complex at physiological condition are studied extensively using theories of open quantum systems. In addition to the usual master equation based approaches, the effect of the protein structure is investigated in atomistic detail through the combined application of quantum chemistry and molecular dynamics simulations. To evaluate the thermalized reduced density matrix, a path-integral Monte Carlo method with a novel importance sampling approach is developed for excitons coupled to an arbitrary phonon bath at a finite temperature. In the second part of the thesis, simulations of molecular systems and applications to vibrational spectra are discussed. First, the quantum dynamics of a molecule is simulated by combining semiclassical initial value representation and density funcitonal theory with analytic derivatives. A computationally-tractable approximation to the sum-of-states formalism of Raman spectra is subsequently discussed.
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Molecular Dynamics Simulations of Adhesion at Epoxy Interfaces
NASA Technical Reports Server (NTRS)
Frankland, Sarah-Jane V.; Clancy, Thomas C.; Hinkley, J. A.; Gates. T. S.
2008-01-01
The effect of moisture on adhesives used in aerospace applications can be modeled with chemically specific techniques such as molecular dynamics simulation. In the present study, the surface energy and work of adhesion are calculated for epoxy surfaces and interfaces, respectively, by using molecular dynamics simulation. Modifications are made to current theory to calculate the work of adhesion at the epoxy-epoxy interface with and without water. Quantitative agreement with experimental values is obtained for the surface energy and work of adhesion at the interface without water. The work of adhesion agrees qualitatively with the experimental values for the interface with water: the magnitude is reduced 15% with respect to the value for the interface without water. A variation of 26% in the magnitude is observed depending on the water configuration at a concentration of 1.6 wt%. The methods and modifications to the method that are employed to obtain these values are expected to be applicable for other epoxy adhesives to determine the effects of moisture uptake on their work of adhesion.
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NASA Astrophysics Data System (ADS)
Schruff, T.; Liang, R.; Rüde, U.; Schüttrumpf, H.; Frings, R. M.
2018-01-01
The knowledge of structural properties of granular materials such as porosity is highly important in many application-oriented and scientific fields. In this paper we present new results of computer-based packing simulations where we use the non-smooth granular dynamics (NSGD) method to simulate gravitational random dense packing of spherical particles with various particle size distributions and two types of depositional conditions. A bin packing scenario was used to compare simulation results to laboratory porosity measurements and to quantify the sensitivity of the NSGD regarding critical simulation parameters such as time step size. The results of the bin packing simulations agree well with laboratory measurements across all particle size distributions with all absolute errors below 1%. A large-scale packing scenario with periodic side walls was used to simulate the packing of up to 855,600 spherical particles with various particle size distributions (PSD). Simulation outcomes are used to quantify the effect of particle-domain-size ratio on the packing compaction. A simple correction model, based on the coordination number, is employed to compensate for this effect on the porosity and to determine the relationship between PSD and porosity. Promising accuracy and stability results paired with excellent computational performance recommend the application of NSGD for large-scale packing simulations, e.g. to further enhance the generation of representative granular deposits.
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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.
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Development and application of dynamic simulations of a subsonic wind tunnel
NASA Technical Reports Server (NTRS)
Szuch, J. R.; Cole, G. L.; Seidel, R. C.; Arpasi, D. J.
1986-01-01
Efforts are currently underway at NASA Lewis to improve and expand ground test facilities and to develop supporting technologies to meet anticipated aeropropulsion research needs. Many of these efforts have been focused on a proposed rehabilitation of the Altitude Wind Tunnel (AWT). In order to insure a technically sound design, an AWT modeling program (both analytical and physical) was initiated to provide input to the AWT final design process. This paper describes the approach taken to develop analytical, dynamic computer simulations of the AWT, and the use of these simulations as test-beds for: (1) predicting the dynamic response characteristics of the AWT, and (2) evaluating proposed AWT control concepts. Plans for developing a portable, real-time simulator for the AWT facility are also described.
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Weighted Ensemble Simulation: Review of Methodology, Applications, and Software
Zuckerman, Daniel M.; Chong, Lillian T.
2018-01-01
The weighted ensemble (WE) methodology orchestrates quasi-independent parallel simulations run with intermittent communication that can enhance sampling of rare events such as protein conformational changes, folding, and binding. The WE strategy can achieve superlinear scaling—the unbiased estimation of key observables such as rate constants and equilibrium state populations to greater precision than would be possible with ordinary parallel simulation. WE software can be used to control any dynamics engine, such as standard molecular dynamics and cell-modeling packages. This article reviews the theoretical basis of WE and goes on to describe successful applications to a number of complex biological processes—protein conformational transitions, (un)binding, and assembly processes, as well as cell-scale processes in systems biology. We furthermore discuss the challenges that need to be overcome in the next phase of WE methodological development. Overall, the combined advances in WE methodology and software have enabled the simulation of long-timescale processes that would otherwise not be practical on typical computing resources using standard simulation. PMID:28301772
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Weighted Ensemble Simulation: Review of Methodology, Applications, and Software.
Zuckerman, Daniel M; Chong, Lillian T
2017-05-22
The weighted ensemble (WE) methodology orchestrates quasi-independent parallel simulations run with intermittent communication that can enhance sampling of rare events such as protein conformational changes, folding, and binding. The WE strategy can achieve superlinear scaling-the unbiased estimation of key observables such as rate constants and equilibrium state populations to greater precision than would be possible with ordinary parallel simulation. WE software can be used to control any dynamics engine, such as standard molecular dynamics and cell-modeling packages. This article reviews the theoretical basis of WE and goes on to describe successful applications to a number of complex biological processes-protein conformational transitions, (un)binding, and assembly processes, as well as cell-scale processes in systems biology. We furthermore discuss the challenges that need to be overcome in the next phase of WE methodological development. Overall, the combined advances in WE methodology and software have enabled the simulation of long-timescale processes that would otherwise not be practical on typical computing resources using standard simulation.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Bialasiewicz, J.T.; Muljadi, E.; Nix, G.R.
This version of the RPM-SIM User's Guide supersedes the October 1999 edition. Using the VisSimTM visual environment, researchers developed a modular simulation system to facilitate an application-specific, low-cost study of the system dynamics for wind-diesel hybrid power systems. This manual presents the principal modules of the simulator and, using case studies of a hybrid system, demonstrates some of the benefits that can be gained from understanding the effects of the designer's modifications to these complex dynamic systems.
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Quantum simulation of dissipative processes without reservoir engineering
Di Candia, R.; Pedernales, J. S.; del Campo, A.; ...
2015-05-29
We present a quantum algorithm to simulate general finite dimensional Lindblad master equations without the requirement of engineering the system-environment interactions. The proposed method is able to simulate both Markovian and non-Markovian quantum dynamics. It consists in the quantum computation of the dissipative corrections to the unitary evolution of the system of interest, via the reconstruction of the response functions associated with the Lindblad operators. Our approach is equally applicable to dynamics generated by effectively non-Hermitian Hamiltonians. We confirm the quality of our method providing specific error bounds that quantify its accuracy.
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Brownian dynamics simulation of rigid particles of arbitrary shape in external fields.
Fernandes, Miguel X; de la Torre, José García
2002-12-01
We have developed a Brownian dynamics simulation algorithm to generate Brownian trajectories of an isolated, rigid particle of arbitrary shape in the presence of electric fields or any other external agents. Starting from the generalized diffusion tensor, which can be calculated with the existing HYDRO software, the new program BROWNRIG (including a case-specific subprogram for the external agent) carries out a simulation that is analyzed later to extract the observable dynamic properties. We provide a variety of examples of utilization of this method, which serve as tests of its performance, and also illustrate its applicability. Examples include free diffusion, transport in an electric field, and diffusion in a restricting environment.
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Dynamic Inversion based Control of a Docking Mechanism
NASA Technical Reports Server (NTRS)
Kulkarni, Nilesh V.; Ippolito, Corey; Krishnakumar, Kalmanje
2006-01-01
The problem of position and attitude control of the Stewart platform based docking mechanism is considered motivated by its future application in space missions requiring the autonomous docking capability. The control design is initiated based on the framework of the intelligent flight control architecture being developed at NASA Ames Research Center. In this paper, the baseline position and attitude control system is designed using dynamic inversion with proportional-integral augmentation. The inverse dynamics uses a Newton-Euler formulation that includes the platform dynamics, the dynamics of the individual legs along with viscous friction in the joints. Simulation results are presented using forward dynamics simulated by a commercial physics engine that builds the system as individual elements with appropriate joints and uses constrained numerical integration,
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Application of linear logic to simulation
NASA Astrophysics Data System (ADS)
Clarke, Thomas L.
1998-08-01
Linear logic, since its introduction by Girard in 1987 has proven expressive and powerful. Linear logic has provided natural encodings of Turing machines, Petri nets and other computational models. Linear logic is also capable of naturally modeling resource dependent aspects of reasoning. The distinguishing characteristic of linear logic is that it accounts for resources; two instances of the same variable are considered differently from a single instance. Linear logic thus must obey a form of the linear superposition principle. A proportion can be reasoned with only once, unless a special operator is applied. Informally, linear logic distinguishes two kinds of conjunction, two kinds of disjunction, and also introduces a modal storage operator that explicitly indicates propositions that can be reused. This paper discuses the application of linear logic to simulation. A wide variety of logics have been developed; in addition to classical logic, there are fuzzy logics, affine logics, quantum logics, etc. All of these have found application in simulations of one sort or another. The special characteristics of linear logic and its benefits for simulation will be discussed. Of particular interest is a connection that can be made between linear logic and simulated dynamics by using the concept of Lie algebras and Lie groups. Lie groups provide the connection between the exponential modal storage operators of linear logic and the eigen functions of dynamic differential operators. Particularly suggestive are possible relations between complexity result for linear logic and non-computability results for dynamical systems.
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NASA Astrophysics Data System (ADS)
Cao, Huijun; Cao, Yong; Chu, Yuchuan; He, Xiaoming; Lin, Tao
2018-06-01
Surface evolution is an unavoidable issue in engineering plasma applications. In this article an iterative method for modeling plasma-surface interactions with moving interface is proposed and validated. In this method, the plasma dynamics is simulated by an immersed finite element particle-in-cell (IFE-PIC) method, and the surface evolution is modeled by the Huygens wavelet method which is coupled with the iteration of the IFE-PIC method. Numerical experiments, including prototypical engineering applications, such as the erosion of Hall thruster channel wall, are presented to demonstrate features of this Huygens IFE-PIC method for simulating the dynamic plasma-surface interactions.
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Application of physics engines in virtual worlds
NASA Astrophysics Data System (ADS)
Norman, Mark; Taylor, Tim
2002-03-01
Dynamic virtual worlds potentially can provide a much richer and more enjoyable experience than static ones. To realize such worlds, three approaches are commonly used. The first of these, and still widely applied, involves importing traditional animations from a modeling system such as 3D Studio Max. This approach is therefore limited to predefined animation scripts or combinations/blends thereof. The second approach involves the integration of some specific-purpose simulation code, such as car dynamics, and is thus generally limited to one (class of) application(s). The third approach involves the use of general-purpose physics engines, which promise to enable a range of compelling dynamic virtual worlds and to considerably speed up development. By far the largest market today for real-time simulation is computer games, revenues exceeding those of the movie industry. Traditionally, the simulation is produced by game developers in-house for specific titles. However, off-the-shelf middleware physics engines are now available for use in games and related domains. In this paper, we report on our experiences of using middleware physics engines to create a virtual world as an interactive experience, and an advanced scenario where artificial life techniques generate controllers for physically modeled characters.
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NASA Astrophysics Data System (ADS)
DiPietro, Kelsey L.; Lindsay, Alan E.
2017-11-01
We present an efficient moving mesh method for the simulation of fourth order nonlinear partial differential equations (PDEs) in two dimensions using the Parabolic Monge-Ampére (PMA) equation. PMA methods have been successfully applied to the simulation of second order problems, but not on systems with higher order equations which arise in many topical applications. Our main application is the resolution of fine scale behavior in PDEs describing elastic-electrostatic interactions. The PDE system considered has multiple parameter dependent singular solution modalities, including finite time singularities and sharp interface dynamics. We describe how to construct a dynamic mesh algorithm for such problems which incorporates known self similar or boundary layer scalings of the underlying equation to locate and dynamically resolve fine scale solution features in these singular regimes. We find a key step in using the PMA equation for mesh generation in fourth order problems is the adoption of a high order representation of the transformation from the computational to physical mesh. We demonstrate the efficacy of the new method on a variety of examples and establish several new results and conjectures on the nature of self-similar singularity formation in higher order PDEs.
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Entangled trajectories Hamiltonian dynamics for treating quantum nuclear effects
NASA Astrophysics Data System (ADS)
Smith, Brendan; Akimov, Alexey V.
2018-04-01
A simple and robust methodology, dubbed Entangled Trajectories Hamiltonian Dynamics (ETHD), is developed to capture quantum nuclear effects such as tunneling and zero-point energy through the coupling of multiple classical trajectories. The approach reformulates the classically mapped second-order Quantized Hamiltonian Dynamics (QHD-2) in terms of coupled classical trajectories. The method partially enforces the uncertainty principle and facilitates tunneling. The applicability of the method is demonstrated by studying the dynamics in symmetric double well and cubic metastable state potentials. The methodology is validated using exact quantum simulations and is compared to QHD-2. We illustrate its relationship to the rigorous Bohmian quantum potential approach, from which ETHD can be derived. Our simulations show a remarkable agreement of the ETHD calculation with the quantum results, suggesting that ETHD may be a simple and inexpensive way of including quantum nuclear effects in molecular dynamics simulations.
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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.
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Molecular Dynamics, Monte Carlo Simulations, and Langevin Dynamics: A Computational Review
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
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i3Drive, a 3D interactive driving simulator.
Ambroz, Miha; Prebil, Ivan
2010-01-01
i3Drive, a wheeled-vehicle simulator, can accurately simulate vehicles of various configurations with up to eight wheels in real time on a desktop PC. It presents the vehicle dynamics as an interactive animation in a virtual 3D environment. The application is fully GUI-controlled, giving users an easy overview of the simulation parameters and letting them adjust those parameters interactively. It models all relevant vehicle systems, including the mechanical models of the suspension, power train, and braking and steering systems. The simulation results generally correspond well with actual measurements, making the system useful for studying vehicle performance in various driving scenarios. i3Drive is thus a worthy complement to other, more complex tools for vehicle-dynamics simulation and analysis.
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Generalized simulation technique for turbojet engine system analysis
NASA Technical Reports Server (NTRS)
Seldner, K.; Mihaloew, J. R.; Blaha, R. J.
1972-01-01
A nonlinear analog simulation of a turbojet engine was developed. The purpose of the study was to establish simulation techniques applicable to propulsion system dynamics and controls research. A schematic model was derived from a physical description of a J85-13 turbojet engine. Basic conservation equations were applied to each component along with their individual performance characteristics to derive a mathematical representation. The simulation was mechanized on an analog computer. The simulation was verified in both steady-state and dynamic modes by comparing analytical results with experimental data obtained from tests performed at the Lewis Research Center with a J85-13 engine. In addition, comparison was also made with performance data obtained from the engine manufacturer. The comparisons established the validity of the simulation technique.
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Time-Dependent Density Functional Theory for Open Systems and Its Applications.
Chen, Shuguang; Kwok, YanHo; Chen, GuanHua
2018-02-20
Photovoltaic devices, electrochemical cells, catalysis processes, light emitting diodes, scanning tunneling microscopes, molecular electronics, and related devices have one thing in common: open quantum systems where energy and matter are not conserved. Traditionally quantum chemistry is confined to isolated and closed systems, while quantum dissipation theory studies open quantum systems. The key quantity in quantum dissipation theory is the reduced system density matrix. As the reduced system density matrix is an O(M! × M!) matrix, where M is the number of the particles of the system of interest, quantum dissipation theory can only be employed to simulate systems of a few particles or degrees of freedom. It is thus important to combine quantum chemistry and quantum dissipation theory so that realistic open quantum systems can be simulated from first-principles. We have developed a first-principles method to simulate the dynamics of open electronic systems, the time-dependent density functional theory for open systems (TDDFT-OS). Instead of the reduced system density matrix, the key quantity is the reduced single-electron density matrix, which is an N × N matrix where N is the number of the atomic bases of the system of interest. As the dimension of the key quantity is drastically reduced, the TDDFT-OS can thus be used to simulate the dynamics of realistic open electronic systems and efficient numerical algorithms have been developed. As an application, we apply the method to study how quantum interference develops in a molecular transistor in time domain. We include electron-phonon interaction in our simulation and show that quantum interference in the given system is robust against nuclear vibration not only in the steady state but also in the transient dynamics. As another application, by combining TDDFT-OS with Ehrenfest dynamics, we study current-induced dissociation of water molecules under scanning tunneling microscopy and follow its time dependent dynamics. Given the rapid development in ultrafast experiments with atomic resolution in recent years, time dependent simulation of open electronic systems will be useful to gain insight and understanding of such experiments. This Account will mainly focus on the practical aspects of the TDDFT-OS method, describing the numerical implementation and demonstrating the method with applications.
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Fluid Dynamics Lagrangian Simulation Model
NASA Astrophysics Data System (ADS)
Hyman, Ellis
1994-02-01
The work performed by Science Applications International Corporation (SAIC) on this contract, Fluid Dynamics Lagrangian Simulation Model, Contract Number N00014-89-C-2106, SAIC Project Number 01-0157-03-0768, focused on a number of research topics in fluid dynamics. The work was in support of the programs of NRL's Laboratory for Computational Physics and Fluid Dynamics and covered the period from 10 September 1989 to 9 December 1993. In the following sections, we describe each of the efforts and the results obtained. Much of the research work has resulted in journal publications. These are included in Appendices of this report for which the reader is referred for complete details.
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NASA Technical Reports Server (NTRS)
Vrnak, Daniel R.; Stueber, Thomas J.; Le, Dzu K.
2012-01-01
This report presents a method for running a dynamic legacy inlet simulation in concert with another dynamic simulation that uses a graphical interface. The legacy code, NASA's LArge Perturbation INlet (LAPIN) model, was coded using the FORTRAN 77 (The Portland Group, Lake Oswego, OR) programming language to run in a command shell similar to other applications that used the Microsoft Disk Operating System (MS-DOS) (Microsoft Corporation, Redmond, WA). Simulink (MathWorks, Natick, MA) is a dynamic simulation that runs on a modern graphical operating system. The product of this work has both simulations, LAPIN and Simulink, running synchronously on the same computer with periodic data exchanges. Implementing the method described in this paper avoided extensive changes to the legacy code and preserved its basic operating procedure. This paper presents a novel method that promotes inter-task data communication between the synchronously running processes.
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Non-spatial dynamics are core to landscape simulations. Unit models simulate system interactions aggregated within one space unit of resolution used within a spatial model. For unit models to be applicable to spatial simulations they have to be formulated in a general enough w...
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Lu, Yuhua; Liu, Qian
2018-01-01
We propose a novel method to simulate soft tissue deformation for virtual surgery applications. The method considers the mechanical properties of soft tissue, such as its viscoelasticity, nonlinearity and incompressibility; its speed, stability and accuracy also meet the requirements for a surgery simulator. Modifying the traditional equation for mass spring dampers (MSD) introduces nonlinearity and viscoelasticity into the calculation of elastic force. Then, the elastic force is used in the constraint projection step for naturally reducing constraint potential. The node position is enforced by the combined spring force and constraint conservative force through Newton's second law. We conduct a comparison study of conventional MSD and position-based dynamics for our new integrating method. Our approach enables stable, fast and large step simulation by freely controlling visual effects based on nonlinearity, viscoelasticity and incompressibility. We implement a laparoscopic cholecystectomy simulator to demonstrate the practicality of our method, in which liver and gallbladder deformation can be simulated in real time. Our method is an appropriate choice for the development of real-time virtual surgery applications. PMID:29515870
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Xu, Lang; Lu, Yuhua; Liu, Qian
2018-02-01
We propose a novel method to simulate soft tissue deformation for virtual surgery applications. The method considers the mechanical properties of soft tissue, such as its viscoelasticity, nonlinearity and incompressibility; its speed, stability and accuracy also meet the requirements for a surgery simulator. Modifying the traditional equation for mass spring dampers (MSD) introduces nonlinearity and viscoelasticity into the calculation of elastic force. Then, the elastic force is used in the constraint projection step for naturally reducing constraint potential. The node position is enforced by the combined spring force and constraint conservative force through Newton's second law. We conduct a comparison study of conventional MSD and position-based dynamics for our new integrating method. Our approach enables stable, fast and large step simulation by freely controlling visual effects based on nonlinearity, viscoelasticity and incompressibility. We implement a laparoscopic cholecystectomy simulator to demonstrate the practicality of our method, in which liver and gallbladder deformation can be simulated in real time. Our method is an appropriate choice for the development of real-time virtual surgery applications.
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Soler, C M Tojo; Bado, V B; Traore, K; Bostick, W McNair; Jones, J W; Hoogenboom, G
2011-10-01
In recent years, simulation models have been used as a complementary tool for research and for quantifying soil carbon sequestration under widely varying conditions. This has improved the understanding and prediction of soil organic carbon (SOC) dynamics and crop yield responses to soil and climate conditions and crop management scenarios. The goal of the present study was to estimate the changes in SOC for different cropping systems in West Africa using a simulation model. A crop rotation experiment conducted in Farakô-Ba, Burkina Faso was used to evaluate the performance of the cropping system model (CSM) of the Decision Support System for Agrotechnology Transfer (DSSAT) for simulating yield of different crops. Eight crop rotations that included cotton, sorghum, peanut, maize and fallow, and three different management scenarios, one without N (control), one with chemical fertilizer (N) and one with manure applications, were studied. The CSM was able to simulate the yield trends of various crops, with inconsistencies for a few years. The simulated SOC increased slightly across the years for the sorghum-fallow rotation with manure application. However, SOC decreased for all other rotations except for the continuous fallow (native grassland), in which the SOC remained stable. The model simulated SOC for the continuous fallow system with a high degree of accuracy normalized root mean square error (RMSE)=0·001, while for the other crop rotations the simulated SOC values were generally within the standard deviation (s.d.) range of the observed data. The crop rotations that included a supplemental N-fertilizer or manure application showed an increase in the average simulated aboveground biomass for all crops. The incorporation of this biomass into the soil after harvest reduced the loss of SOC. In the present study, the observed SOC data were used for characterization of production systems with different SOC dynamics. Following careful evaluation of the CSM with observed soil organic matter (SOM) data similar to the study presented here, there are many opportunities for the application of the CSM for carbon sequestration and resource management in Sub-Saharan Africa.
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New method for qualitative simulations of water resources systems. 2. Applications
DOE Office of Scientific and Technical Information (OSTI.GOV)
Antunes, M.P.; Seixas, M.J.; Camara, A.S.
1987-11-01
SLIN (Simulacao Linguistica) is a new method for qualitative dynamic simulation. As was presented previously, SLIN relies upon a categorical representation of variables which are manipulated by logical rules. Two applications to water resources systems are included to illustrate SLIN's potential usefulness: the environmental impact evaluation of a hydropower plant and the assessment of oil dispersion in the sea after a tanker wreck.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Ji, Pengfei; Zhang, Yuwen, E-mail: zhangyu@missouri.edu; Yang, Mo
The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heatmore » transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.« less
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NASA Astrophysics Data System (ADS)
Ji, Pengfei; Zhang, Yuwen; Yang, Mo
2013-12-01
The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.
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Forest dynamics in Oregon landscapes: Evaluation and application of an individual-based model
Busing, R.T.; Solomon, A.M.; McKane, R.B.; Burdick, C.A.
2007-01-01
The FORCLIM model of forest dynamics was tested against field survey data for its ability to simulate basal area and composition of old forests across broad climatic gradients in western Oregon, USA. The model was also tested for its ability to capture successional trends in ecoregions of the west Cascade Range. It was then applied to simulate present and future (1990-2050) forest landscape dynamics of a watershed in the west Cascades. Various regimes of climate change and harvesting in the watershed were considered in the landscape application. The model was able to capture much of the variation in forest basal area and composition in western Oregon even though temperature and precipitation were the only inputs that were varied among simulated sites. The measured decline in total basal area from tall coastal forests eastward to interior steppe was matched by simulations. Changes in simulated forest dominants also approximated those in the actual data. Simulated abundances of a few minor species did not match actual abundances, however. Subsequent projections of climate change and harvest effects in a west Cascades landscape indicated no change in forest dominance as of 2050. Yet, climate-driven shifts in the distributions of some species were projected. The simulation of both stand-replacing and partial-stand disturbances across western Oregon improved agreement between simulated and actual data. Simulations with fire as an agent of partial disturbance suggested that frequent fires of low severity can alter forest composition and structure as much or more than severe fires at historic frequencies. ?? 2007 by the Ecological Society of America.
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Frequency-response identification of XV-15 tilt-rotor aircraft dynamics
NASA Technical Reports Server (NTRS)
Tischler, Mark B.
1987-01-01
The timely design and development of the next generation of tilt-rotor aircraft (JVX) depend heavily on the in-depth understanding of existing XV-15 dynamics and the availability of fully validated simulation models. Previous studies have considered aircraft and simulation trim characteristics, but analyses of basic flight vehicle dynamics were limited to qualitative pilot evaluation. The present study has the following objectives: documentation and evaluation of XV-15 bare-airframe dynamics; comparison of aircraft and simulation responses; and development of a validated transfer-function description of the XV-15 needed for future studies. A nonparametric frequency-response approach is used which does not depend on assumed model order or structure. Transfer-function representations are subsequently derived which fit the frequency responses in the bandwidth of greatest concern for piloted handling-qualities and control-system applications.
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Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics.
Martínez, Enrique; Cawkwell, Marc J; Voter, Arthur F; Niklasson, Anders M N
2015-04-21
Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached at each time step. The thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.
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A review on vegetation models and applicability to climate simulations at regional scale
NASA Astrophysics Data System (ADS)
Myoung, Boksoon; Choi, Yong-Sang; Park, Seon Ki
2011-11-01
The lack of accurate representations of biospheric components and their biophysical and biogeochemical processes is a great source of uncertainty in current climate models. The interactions between terrestrial ecosystems and the climate include exchanges not only of energy, water and momentum, but also of carbon and nitrogen. Reliable simulations of these interactions are crucial for predicting the potential impacts of future climate change and anthropogenic intervention on terrestrial ecosystems. In this paper, two biogeographical (Neilson's rule-based model and BIOME), two biogeochemical (BIOME-BGC and PnET-BGC), and three dynamic global vegetation models (Hybrid, LPJ, and MC1) were reviewed and compared in terms of their biophysical and physiological processes. The advantages and limitations of the models were also addressed. Lastly, the applications of the dynamic global vegetation models to regional climate simulations have been discussed.
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Relaxation dynamics of internal segments of DNA chains in nanochannels
NASA Astrophysics Data System (ADS)
Jain, Aashish; Muralidhar, Abhiram; Dorfman, Kevin; Dorfman Group Team
We will present relaxation dynamics of internal segments of a DNA chain confined in nanochannel. The results have direct application in genome mapping technology, where long DNA molecules containing sequence-specific fluorescent probes are passed through an array of nanochannels to linearize them, and then the distances between these probes (the so-called ``DNA barcode'') are measured. The relaxation dynamics of internal segments set the experimental error due to dynamic fluctuations. We developed a multi-scale simulation algorithm, combining a Pruned-Enriched Rosenbluth Method (PERM) simulation of a discrete wormlike chain model with hard spheres with Brownian dynamics (BD) simulations of a bead-spring chain. Realistic parameters such as the bead friction coefficient and spring force law parameters are obtained from PERM simulations and then mapped onto the bead-spring model. The BD simulations are carried out to obtain the extension autocorrelation functions of various segments, which furnish their relaxation times. Interestingly, we find that (i) corner segments relax faster than the center segments and (ii) relaxation times of corner segments do not depend on the contour length of DNA chain, whereas the relaxation times of center segments increase linearly with DNA chain size.
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Dynamic Decision Making under Uncertainty and Partial Information
2017-01-30
order to address these problems, we investigated efficient computational methodologies for dynamic decision making under uncertainty and partial...information. In the course of this research, we developed and studied efficient simulation-based methodologies for dynamic decision making under...uncertainty and partial information; (ii) studied the application of these decision making models and methodologies to practical problems, such as those
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Tan, Yaw Sing; Spring, David R; Abell, Chris; Verma, Chandra S
2015-07-14
A computational ligand-mapping approach to detect protein surface pockets that interact with hydrophobic moieties is presented. In this method, we incorporated benzene molecules into explicit solvent molecular dynamics simulations of various protein targets. The benzene molecules successfully identified the binding locations of hydrophobic hot-spot residues and all-hydrocarbon cross-links from known peptidic ligands. They also unveiled cryptic binding sites that are occluded by side chains and the protein backbone. Our results demonstrate that ligand-mapping molecular dynamics simulations hold immense promise to guide the rational design of peptidic modulators of protein-protein interactions, including that of stapled peptides, which show promise as an exciting new class of cell-penetrating therapeutic molecules.
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Nonholonomic Hamiltonian Method for Molecular Dynamics Simulations of Reacting Shocks
NASA Astrophysics Data System (ADS)
Fahrenthold, Eric; Bass, Joseph
2015-06-01
Conventional molecular dynamics simulations of reacting shocks employ a holonomic Hamiltonian formulation: the breaking and forming of covalent bonds is described by potential functions. In general these potential functions: (a) are algebraically complex, (b) must satisfy strict smoothness requirements, and (c) contain many fitted parameters. In recent research the authors have developed a new noholonomic formulation of reacting molecular dynamics. In this formulation bond orders are determined by rate equations and the bonding-debonding process need not be described by differentiable functions. This simplifies the representation of complex chemistry and reduces the number of fitted model parameters. Example applications of the method show molecular level shock to detonation simulations in nitromethane and RDX. Research supported by the Defense Threat Reduction Agency.
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Stability analysis and application of a mathematical cholera model.
Liao, Shu; Wang, Jin
2011-07-01
In this paper, we conduct a dynamical analysis of the deterministic cholera model proposed in [9]. We study the stability of both the disease-free and endemic equilibria so as to explore the complex epidemic and endemic dynamics of the disease. We demonstrate a real-world application of this model by investigating the recent cholera outbreak in Zimbabwe. Meanwhile, we present numerical simulation results to verify the analytical predictions.
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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.
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The use of the articulated total body model as a robot dynamics simulation tool
NASA Technical Reports Server (NTRS)
Obergfell, Louise A.; Avula, Xavier J. R.; Kalegs, Ints
1988-01-01
The Articulated Total Body (ATB) model is a computer sumulation program which was originally developed for the study of aircrew member dynamics during ejection from high-speed aircraft. This model is totally three-dimensional and is based on the rigid body dynamics of coupled systems which use Euler's equations of motion with constraint relations of the type employed in the Lagrange method. In this paper the use of the ATB model as a robot dynamics simulation tool is discussed and various simulations are demonstrated. For this purpose the ATB model has been modified to allow for the application of torques at the joints as functions of state variables of the system. Specifically, the motion of a robotic arm with six revolute articulations with joint torques prescribed as functions of angular displacement and angular velocity are demonstrated. The simulation procedures developed in this work may serve as valuable tools for analyzing robotic mechanisms, dynamic effects, joint load transmissions, feed-back control algorithms employed in the actuator control and end-effector trajectories.
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NASA Astrophysics Data System (ADS)
Darema, F.
2016-12-01
InfoSymbiotics/DDDAS embodies the power of Dynamic Data Driven Applications Systems (DDDAS), a concept whereby an executing application model is dynamically integrated, in a feed-back loop, with the real-time data-acquisition and control components, as well as other data sources of the application system. Advanced capabilities can be created through such new computational approaches in modeling and simulations, and in instrumentation methods, and include: enhancing the accuracy of the application model; speeding-up the computation to allow faster and more comprehensive models of a system, and create decision support systems with the accuracy of full-scale simulations; in addition, the notion of controlling instrumentation processes by the executing application results in more efficient management of application-data and addresses challenges of how to architect and dynamically manage large sets of heterogeneous sensors and controllers, an advance over the static and ad-hoc ways of today - with DDDAS these sets of resources can be managed adaptively and in optimized ways. Large-Scale-Dynamic-Data encompasses the next wave of Big Data, and namely dynamic data arising from ubiquitous sensing and control in engineered, natural, and societal systems, through multitudes of heterogeneous sensors and controllers instrumenting these systems, and where opportunities and challenges at these "large-scales" relate not only to data size but the heterogeneity in data, data collection modalities, fidelities, and timescales, ranging from real-time data to archival data. In tandem with this important dimension of dynamic data, there is an extended view of Big Computing, which includes the collective computing by networked assemblies of multitudes of sensors and controllers, this range from the high-end to the real-time seamlessly integrated and unified, and comprising the Large-Scale-Big-Computing. InfoSymbiotics/DDDAS engenders transformative impact in many application domains, ranging from the nano-scale to the terra-scale and to the extra-terra-scale. The talk will address opportunities for new capabilities together with corresponding research challenges, with illustrative examples from several application areas including environmental sciences, geosciences, and space sciences.
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A heuristic re-mapping algorithm reducing inter-level communication in SAMR applications.
DOE Office of Scientific and Technical Information (OSTI.GOV)
Steensland, Johan; Ray, Jaideep
2003-07-01
This paper aims at decreasing execution time for large-scale structured adaptive mesh refinement (SAMR) applications by proposing a new heuristic re-mapping algorithm and experimentally showing its effectiveness in reducing inter-level communication. Tests were done for five different SAMR applications. The overall goal is to engineer a dynamically adaptive meta-partitioner capable of selecting and configuring the most appropriate partitioning strategy at run-time based on current system and application state. Such a metapartitioner can significantly reduce execution times for general SAMR applications. Computer simulations of physical phenomena are becoming increasingly popular as they constitute an important complement to real-life testing. In manymore » cases, such simulations are based on solving partial differential equations by numerical methods. Adaptive methods are crucial to efficiently utilize computer resources such as memory and CPU. But even with adaption, the simulations are computationally demanding and yield huge data sets. Thus parallelization and the efficient partitioning of data become issues of utmost importance. Adaption causes the workload to change dynamically, calling for dynamic (re-) partitioning to maintain efficient resource utilization. The proposed heuristic algorithm reduced inter-level communication substantially. Since the complexity of the proposed algorithm is low, this decrease comes at a relatively low cost. As a consequence, we draw the conclusion that the proposed re-mapping algorithm would be useful to lower overall execution times for many large SAMR applications. Due to its usefulness and its parameterization, the proposed algorithm would constitute a natural and important component of the meta-partitioner.« less
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Ab-Initio Molecular Dynamics Simulation of Graphene Sheet
NASA Astrophysics Data System (ADS)
Kolev, S.; Balchev, I.; Cvetkov, K.; Tinchev, S.; Milenov, T.
2017-01-01
The study of graphene is important because it is a promising material for a variety of applications in the electronic industry. In the present work, the properties of а 2D periodic graphene sheet are studied with the use of ab initio molecular dynamics. DFT in the generalized gradient approximation is used in order to carry out the dynamical simulations. The PBE functional and DZVP-MOLOPT basis set are implemented in the CP2K/Quickstep package. A periodic box, consisting of 288 carbon atoms is chosen for the simulations. After geometry optimization it has dimensions 2964 x 2964 x 1500 pm and form angles of 90, 90, 60 degrees. The dynamical simulation is run for 1 ps in the NPT ensemble, at temperature T = 298.15 K. The radial distribution function shows a first peak at 142 pm, marking the bond length between carbon atoms. The density of states for the periodic systems is simulated as occupied orbitals represent the valence band and unoccupied ones the conduction band. The calculated bandgap, as expected is close to 0 eV.
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NASA Astrophysics Data System (ADS)
Kreis, Karsten; Kremer, Kurt; Potestio, Raffaello; Tuckerman, Mark E.
2017-12-01
Path integral-based methodologies play a crucial role for the investigation of nuclear quantum effects by means of computer simulations. However, these techniques are significantly more demanding than corresponding classical simulations. To reduce this numerical effort, we recently proposed a method, based on a rigorous Hamiltonian formulation, which restricts the quantum modeling to a small but relevant spatial region within a larger reservoir where particles are treated classically. In this work, we extend this idea and show how it can be implemented along with state-of-the-art path integral simulation techniques, including path-integral molecular dynamics, which allows for the calculation of quantum statistical properties, and ring-polymer and centroid molecular dynamics, which allow the calculation of approximate quantum dynamical properties. To this end, we derive a new integration algorithm that also makes use of multiple time-stepping. The scheme is validated via adaptive classical-path-integral simulations of liquid water. Potential applications of the proposed multiresolution method are diverse and include efficient quantum simulations of interfaces as well as complex biomolecular systems such as membranes and proteins.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Du, Jincheng; Rimsza, Jessica
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
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Molecular dynamics simulations of oxide memory resistors (memristors).
Savel'ev, S E; Alexandrov, A S; Bratkovsky, A M; Williams, R Stanley
2011-06-24
Reversible bipolar nanoswitches that can be set and read electronically in a solid-state two-terminal device are very promising for applications. We have performed molecular dynamics simulations that mimic systems with oxygen vacancies interacting via realistic potentials and driven by an external bias voltage. The competing short- and long-range interactions among charged mobile vacancies lead to density fluctuations and short-range ordering, while illustrating some aspects of observed experimental behavior, such as memristor polarity inversion. The simulations show that the 'localized conductive filaments' and 'uniform push/pull' models for memristive switching are actually two extremes of the one stochastic mechanism.
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Using collective variables to drive molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Fiorin, Giacomo; Klein, Michael L.; Hénin, Jérôme
2013-12-01
A software framework is introduced that facilitates the application of biasing algorithms to collective variables of the type commonly employed to drive massively parallel molecular dynamics (MD) simulations. The modular framework that is presented enables one to combine existing collective variables into new ones, and combine any chosen collective variable with available biasing methods. The latter include the classic time-dependent biases referred to as steered MD and targeted MD, the temperature-accelerated MD algorithm, as well as the adaptive free-energy biases called metadynamics and adaptive biasing force. The present modular software is extensible, and portable between commonly used MD simulation engines.
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Whitley, Heather D.; Scullard, Christian R.; Benedict, Lorin X.; ...
2014-12-04
Here, we present a discussion of kinetic theory treatments of linear electrical and thermal transport in hydrogen plasmas, for a regime of interest to inertial confinement fusion applications. In order to assess the accuracy of one of the more involved of these approaches, classical Lenard-Balescu theory, we perform classical molecular dynamics simulations of hydrogen plasmas using 2-body quantum statistical potentials and compute both electrical and thermal conductivity from out particle trajectories using the Kubo approach. Our classical Lenard-Balescu results employing the identical statistical potentials agree well with the simulations.
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Prior, C; Danilāne, L; Oganesyan, V S
2018-05-16
We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of electron paramagnetic resonance (EPR) spectra of spin labelled DNA. Models for two structurally different DNA spin probes with either the rigid or flexible position of the nitroxide group in the base pair, employed in experimental studies previously, have been developed. By the application of the combined MD-EPR simulation methodology we aimed at the following. Firstly, to provide a test bed against a sensitive spectroscopic technique for the recently developed improved version of the parmbsc1 force field for MD modelling of DNA. The predicted EPR spectra show good agreement with the experimental ones available from the literature, thus confirming the accuracy of the currently employed DNA force fields. Secondly, to provide a quantitative interpretation of the motional contributions into the dynamics of spin probes in both duplex and single-strand DNA fragments and to analyse their perturbing effects on the local DNA structure. Finally, a combination of MD and EPR allowed us to test the validity of the application of the Model-Free (M-F) approach coupled with the partial averaging of magnetic tensors to the simulation of EPR spectra of DNA systems by comparing the resultant EPR spectra with those simulated directly from MD trajectories. The advantage of the M-F based EPR simulation approach over the direct propagation techniques is that it requires motional and order parameters that can be calculated from shorter MD trajectories. The reported MD-EPR methodology is transferable to the prediction and interpretation of EPR spectra of higher order DNA structures with novel types of spin labels.
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Temporal Gillespie Algorithm: Fast Simulation of Contagion Processes on Time-Varying Networks
Vestergaard, Christian L.; Génois, Mathieu
2015-01-01
Stochastic simulations are one of the cornerstones of the analysis of dynamical processes on complex networks, and are often the only accessible way to explore their behavior. The development of fast algorithms is paramount to allow large-scale simulations. The Gillespie algorithm can be used for fast simulation of stochastic processes, and variants of it have been applied to simulate dynamical processes on static networks. However, its adaptation to temporal networks remains non-trivial. We here present a temporal Gillespie algorithm that solves this problem. Our method is applicable to general Poisson (constant-rate) processes on temporal networks, stochastically exact, and up to multiple orders of magnitude faster than traditional simulation schemes based on rejection sampling. We also show how it can be extended to simulate non-Markovian processes. The algorithm is easily applicable in practice, and as an illustration we detail how to simulate both Poissonian and non-Markovian models of epidemic spreading. Namely, we provide pseudocode and its implementation in C++ for simulating the paradigmatic Susceptible-Infected-Susceptible and Susceptible-Infected-Recovered models and a Susceptible-Infected-Recovered model with non-constant recovery rates. For empirical networks, the temporal Gillespie algorithm is here typically from 10 to 100 times faster than rejection sampling. PMID:26517860
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Temporal Gillespie Algorithm: Fast Simulation of Contagion Processes on Time-Varying Networks.
Vestergaard, Christian L; Génois, Mathieu
2015-10-01
Stochastic simulations are one of the cornerstones of the analysis of dynamical processes on complex networks, and are often the only accessible way to explore their behavior. The development of fast algorithms is paramount to allow large-scale simulations. The Gillespie algorithm can be used for fast simulation of stochastic processes, and variants of it have been applied to simulate dynamical processes on static networks. However, its adaptation to temporal networks remains non-trivial. We here present a temporal Gillespie algorithm that solves this problem. Our method is applicable to general Poisson (constant-rate) processes on temporal networks, stochastically exact, and up to multiple orders of magnitude faster than traditional simulation schemes based on rejection sampling. We also show how it can be extended to simulate non-Markovian processes. The algorithm is easily applicable in practice, and as an illustration we detail how to simulate both Poissonian and non-Markovian models of epidemic spreading. Namely, we provide pseudocode and its implementation in C++ for simulating the paradigmatic Susceptible-Infected-Susceptible and Susceptible-Infected-Recovered models and a Susceptible-Infected-Recovered model with non-constant recovery rates. For empirical networks, the temporal Gillespie algorithm is here typically from 10 to 100 times faster than rejection sampling.
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CFD applications: The Lockheed perspective
NASA Technical Reports Server (NTRS)
Miranda, Luis R.
1987-01-01
The Numerical Aerodynamic Simulator (NAS) epitomizes the coming of age of supercomputing and opens exciting horizons in the world of numerical simulation. An overview of supercomputing at Lockheed Corporation in the area of Computational Fluid Dynamics (CFD) is presented. This overview will focus on developments and applications of CFD as an aircraft design tool and will attempt to present an assessment, withing this context, of the state-of-the-art in CFD methodology.
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NASA Technical Reports Server (NTRS)
Young, L. R.
1976-01-01
Investigations for the improvement of flight simulators are reported. Topics include: visual cues in landing, comparison of linear and nonlinear washout filters using a model of the vestibular system, and visual vestibular interactions (yaw axis). An abstract is given for a thesis on the applications of human dynamic orientation models to motion simulation.
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On coarse projective integration for atomic deposition in amorphous systems
DOE Office of Scientific and Technical Information (OSTI.GOV)
Chuang, Claire Y., E-mail: yungc@seas.upenn.edu, E-mail: meister@unm.edu, E-mail: zepedaruiz1@llnl.gov; Sinno, Talid, E-mail: talid@seas.upenn.edu; Han, Sang M., E-mail: yungc@seas.upenn.edu, E-mail: meister@unm.edu, E-mail: zepedaruiz1@llnl.gov
2015-10-07
Direct molecular dynamics simulation of atomic deposition under realistic conditions is notoriously challenging because of the wide range of time scales that must be captured. Numerous simulation approaches have been proposed to address the problem, often requiring a compromise between model fidelity, algorithmic complexity, and computational efficiency. Coarse projective integration, an example application of the “equation-free” framework, offers an attractive balance between these constraints. Here, periodically applied, short atomistic simulations are employed to compute time derivatives of slowly evolving coarse variables that are then used to numerically integrate differential equations over relatively large time intervals. A key obstacle to themore » application of this technique in realistic settings is the “lifting” operation in which a valid atomistic configuration is recreated from knowledge of the coarse variables. Using Ge deposition on amorphous SiO{sub 2} substrates as an example application, we present a scheme for lifting realistic atomistic configurations comprised of collections of Ge islands on amorphous SiO{sub 2} using only a few measures of the island size distribution. The approach is shown to provide accurate initial configurations to restart molecular dynamics simulations at arbitrary points in time, enabling the application of coarse projective integration for this morphologically complex system.« less
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On Coarse Projective Integration for Atomic Deposition in Amorphous Systems
Chuang, Claire Y.; Han, Sang M.; Zepeda-Ruiz, Luis A.; ...
2015-10-02
Direct molecular dynamics simulation of atomic deposition under realistic conditions is notoriously challenging because of the wide range of timescales that must be captured. Numerous simulation approaches have been proposed to address the problem, often requiring a compromise between model fidelity, algorithmic complexity and computational efficiency. Coarse projective integration, an example application of the ‘equation-free’ framework, offers an attractive balance between these constraints. Here, periodically applied, short atomistic simulations are employed to compute gradients of slowly-evolving coarse variables that are then used to numerically integrate differential equations over relatively large time intervals. A key obstacle to the application of thismore » technique in realistic settings is the ‘lifting’ operation in which a valid atomistic configuration is recreated from knowledge of the coarse variables. Using Ge deposition on amorphous SiO 2 substrates as an example application, we present a scheme for lifting realistic atomistic configurations comprised of collections of Ge islands on amorphous SiO 2 using only a few measures of the island size distribution. In conclusion, the approach is shown to provide accurate initial configurations to restart molecular dynamics simulations at arbitrary points in time, enabling the application of coarse projective integration for this morphologically complex system.« less
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NASA Astrophysics Data System (ADS)
Wollherr, Stephanie; Gabriel, Alice-Agnes; Uphoff, Carsten
2018-05-01
The dynamics and potential size of earthquakes depend crucially on rupture transfers between adjacent fault segments. To accurately describe earthquake source dynamics, numerical models can account for realistic fault geometries and rheologies such as nonlinear inelastic processes off the slip interface. We present implementation, verification, and application of off-fault Drucker-Prager plasticity in the open source software SeisSol (www.seissol.org). SeisSol is based on an arbitrary high-order derivative modal Discontinuous Galerkin (ADER-DG) method using unstructured, tetrahedral meshes specifically suited for complex geometries. Two implementation approaches are detailed, modelling plastic failure either employing sub-elemental quadrature points or switching to nodal basis coefficients. At fine fault discretizations the nodal basis approach is up to 6 times more efficient in terms of computational costs while yielding comparable accuracy. Both methods are verified in community benchmark problems and by three dimensional numerical h- and p-refinement studies with heterogeneous initial stresses. We observe no spectral convergence for on-fault quantities with respect to a given reference solution, but rather discuss a limitation to low-order convergence for heterogeneous 3D dynamic rupture problems. For simulations including plasticity, a high fault resolution may be less crucial than commonly assumed, due to the regularization of peak slip rate and an increase of the minimum cohesive zone width. In large-scale dynamic rupture simulations based on the 1992 Landers earthquake, we observe high rupture complexity including reverse slip, direct branching, and dynamic triggering. The spatio-temporal distribution of rupture transfers are altered distinctively by plastic energy absorption, correlated with locations of geometrical fault complexity. Computational cost increases by 7% when accounting for off-fault plasticity in the demonstrating application. Our results imply that the combination of fully 3D dynamic modelling, complex fault geometries, and off-fault plastic yielding is important to realistically capture dynamic rupture transfers in natural fault systems.
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Molecular dynamics force-field refinement against quasi-elastic neutron scattering data
Borreguero Calvo, Jose M.; Lynch, Vickie E.
2015-11-23
Quasi-elastic neutron scattering (QENS) is one of the experimental techniques of choice for probing the dynamics at length and time scales that are also in the realm of full-atom molecular dynamics (MD) simulations. This overlap enables extension of current fitting methods that use time-independent equilibrium measurements to new methods fitting against dynamics data. We present an algorithm that fits simulation-derived incoherent dynamical structure factors against QENS data probing the diffusive dynamics of the system. We showcase the difficulties inherent to this type of fitting problem, namely, the disparity between simulation and experiment environment, as well as limitations in the simulationmore » due to incomplete sampling of phase space. We discuss a methodology to overcome these difficulties and apply it to a set of full-atom MD simulations for the purpose of refining the force-field parameter governing the activation energy of methyl rotation in the octa-methyl polyhedral oligomeric silsesquioxane molecule. Our optimal simulated activation energy agrees with the experimentally derived value up to a 5% difference, well within experimental error. We believe the method will find applicability to other types of diffusive motions and other representation of the systems such as coarse-grain models where empirical fitting is essential. In addition, the refinement method can be extended to the coherent dynamic structure factor with no additional effort.« less
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Insights from molecular dynamics simulations for computational protein design.
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.
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Insights from molecular dynamics simulations for computational protein design
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
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Ahlstrom, Logan S.; Vorontsov, Ivan I.; Shi, Jun; Miyashita, Osamu
2017-01-01
Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure. This agreement is most striking for crystal-contacting residues during crystal simulation. Given the high level of correspondence between our simulations and the X-ray data, we compare side-chain ensembles in solution and crystal simulations. We observe large decreases in conformational entropy in the crystal for several long, polar and contacting residues on the protein surface. Such cases agree well with the average loss in conformational entropy per residue upon protein folding and are accompanied by a change in side-chain conformation. This finding supports the application of surface engineering to facilitate crystallization. Our simulation-based approach demonstrated here with Cyanovirin-N establishes a framework for quantitatively comparing side-chain ensembles in solution and in the crystal across a larger set of proteins to elucidate the effect of the crystal environment on protein conformations. PMID:28107510
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Ahlstrom, Logan S; Vorontsov, Ivan I; Shi, Jun; Miyashita, Osamu
2017-01-01
Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure. This agreement is most striking for crystal-contacting residues during crystal simulation. Given the high level of correspondence between our simulations and the X-ray data, we compare side-chain ensembles in solution and crystal simulations. We observe large decreases in conformational entropy in the crystal for several long, polar and contacting residues on the protein surface. Such cases agree well with the average loss in conformational entropy per residue upon protein folding and are accompanied by a change in side-chain conformation. This finding supports the application of surface engineering to facilitate crystallization. Our simulation-based approach demonstrated here with Cyanovirin-N establishes a framework for quantitatively comparing side-chain ensembles in solution and in the crystal across a larger set of proteins to elucidate the effect of the crystal environment on protein conformations.
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NASA Astrophysics Data System (ADS)
Benedetto, Antonio; Ballone, Pietro
2018-05-01
Increasing attention is being devoted to the interaction of a new class of organic ionic liquids known as room-temperature ionic liquids (RTILs) with biomolecules, partly because of health and environment concerns, and, even more, for the prospect of exciting new applications in biomedicine, sensing and energy technologies. Here we focus on the interaction between RTILs and phospholipid bilayers that are well-accepted models for bio-membranes. We discuss how neutron scattering has been used to probe both the structure and the dynamics of these systems, and how its integration with molecular dynamics simulation has allowed the determination of the microscopic details of their interaction.
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NASA Technical Reports Server (NTRS)
Lan, C. Edward; Ge, Fuying
1989-01-01
Control system design for general nonlinear flight dynamic models is considered through numerical simulation. The design is accomplished through a numerical optimizer coupled with analysis of flight dynamic equations. The general flight dynamic equations are numerically integrated and dynamic characteristics are then identified from the dynamic response. The design variables are determined iteratively by the optimizer to optimize a prescribed objective function which is related to desired dynamic characteristics. Generality of the method allows nonlinear effects to aerodynamics and dynamic coupling to be considered in the design process. To demonstrate the method, nonlinear simulation models for an F-5A and an F-16 configurations are used to design dampers to satisfy specifications on flying qualities and control systems to prevent departure. The results indicate that the present method is simple in formulation and effective in satisfying the design objectives.
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A Dynamic Health Assessment Approach for Shearer Based on Artificial Immune Algorithm
Wang, Zhongbin; Xu, Xihua; Si, Lei; Ji, Rui; Liu, Xinhua; Tan, Chao
2016-01-01
In order to accurately identify the dynamic health of shearer, reducing operating trouble and production accident of shearer and improving coal production efficiency further, a dynamic health assessment approach for shearer based on artificial immune algorithm was proposed. The key technologies such as system framework, selecting the indicators for shearer dynamic health assessment, and health assessment model were provided, and the flowchart of the proposed approach was designed. A simulation example, with an accuracy of 96%, based on the collected data from industrial production scene was provided. Furthermore, the comparison demonstrated that the proposed method exhibited higher classification accuracy than the classifiers based on back propagation-neural network (BP-NN) and support vector machine (SVM) methods. Finally, the proposed approach was applied in an engineering problem of shearer dynamic health assessment. The industrial application results showed that the paper research achievements could be used combining with shearer automation control system in fully mechanized coal face. The simulation and the application results indicated that the proposed method was feasible and outperforming others. PMID:27123002
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Mathematics in medicine: tumor detection, radiation dosimetry, and simulation in psychotherapy
DOE Office of Scientific and Technical Information (OSTI.GOV)
Bellman, R.; Kashef, B.; Smith, C.P.
1975-05-01
Work done in the application of mathematics to medicine over the last 20 years is briefly reviewed. Scan-rescan processes, radiation dosimetry, and medical interviewing are discussed. The first uses dynamic programming, the second invariant imbedding, and the third simulation. (ACR)
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NASA Technical Reports Server (NTRS)
Whelan, Todd Michael
1996-01-01
In a real-time or batch mode simulation that is designed to model aircraft dynamics over a wide range of flight conditions, a table look- up scheme is implemented to determine the forces and moments on the vehicle based upon the values of parameters such as angle of attack, altitude, Mach number, and control surface deflections. Simulation Aerodynamic Variable Interface (SAVI) is a graphical user interface to the flight simulation input data, designed to operate on workstations that support X Windows. The purpose of the application is to provide two and three dimensional visualization of the data, to allow an intuitive sense of the data set. SAVI also allows the user to manipulate the data, either to conduct an interactive study of the influence of changes on the vehicle dynamics, or to make revisions to data set based on new information such as flight test. This paper discusses the reasons for developing the application, provides an overview of its capabilities, and outlines the software architecture and operating environment.
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Parameters Identification for Motorcycle Simulator's Platform Characterization
NASA Astrophysics Data System (ADS)
Nehaoua, L.; Arioui, H.
2008-06-01
This paper presents the dynamics modeling and parameters identification of a motorcycle simulator's platform. This model begins with some suppositions which consider that the leg dynamics can be neglected with respect to the mobile platform one. The objectif is to synthesis a simplified control scheme, adapted to driving simulation application, minimising dealys and without loss of tracking performance. Electronic system of platform actuation is described. It's based on a CAN BUS communication which offers a large transmission robustness and error handling. Despite some disadvanteges, we adapted a control solution which overcome these inconvenients and preserve the quality of tracking trajectory. A bref description of the simulator's platform is given and results are shown and justified according to our specifications.
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Discrete event performance prediction of speculatively parallel temperature-accelerated dynamics
DOE Office of Scientific and Technical Information (OSTI.GOV)
Zamora, Richard James; Voter, Arthur F.; Perez, Danny
Due to its unrivaled ability to predict the dynamical evolution of interacting atoms, molecular dynamics (MD) is a widely used computational method in theoretical chemistry, physics, biology, and engineering. Despite its success, MD is only capable of modeling time scales within several orders of magnitude of thermal vibrations, leaving out many important phenomena that occur at slower rates. The Temperature Accelerated Dynamics (TAD) method overcomes this limitation by thermally accelerating the state-to-state evolution captured by MD. Due to the algorithmically complex nature of the serial TAD procedure, implementations have yet to improve performance by parallelizing the concurrent exploration of multiplemore » states. Here we utilize a discrete event-based application simulator to introduce and explore a new Speculatively Parallel TAD (SpecTAD) method. We investigate the SpecTAD algorithm, without a full-scale implementation, by constructing an application simulator proxy (SpecTADSim). Finally, following this method, we discover that a nontrivial relationship exists between the optimal SpecTAD parameter set and the number of CPU cores available at run-time. Furthermore, we find that a majority of the available SpecTAD boost can be achieved within an existing TAD application using relatively simple algorithm modifications.« less
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Discrete event performance prediction of speculatively parallel temperature-accelerated dynamics
Zamora, Richard James; Voter, Arthur F.; Perez, Danny; ...
2016-12-01
Due to its unrivaled ability to predict the dynamical evolution of interacting atoms, molecular dynamics (MD) is a widely used computational method in theoretical chemistry, physics, biology, and engineering. Despite its success, MD is only capable of modeling time scales within several orders of magnitude of thermal vibrations, leaving out many important phenomena that occur at slower rates. The Temperature Accelerated Dynamics (TAD) method overcomes this limitation by thermally accelerating the state-to-state evolution captured by MD. Due to the algorithmically complex nature of the serial TAD procedure, implementations have yet to improve performance by parallelizing the concurrent exploration of multiplemore » states. Here we utilize a discrete event-based application simulator to introduce and explore a new Speculatively Parallel TAD (SpecTAD) method. We investigate the SpecTAD algorithm, without a full-scale implementation, by constructing an application simulator proxy (SpecTADSim). Finally, following this method, we discover that a nontrivial relationship exists between the optimal SpecTAD parameter set and the number of CPU cores available at run-time. Furthermore, we find that a majority of the available SpecTAD boost can be achieved within an existing TAD application using relatively simple algorithm modifications.« less
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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.
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Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems
Radak, Brian K.; Chipot, Christophe; Suh, Donghyuk; ...
2017-11-07
We report that an increasingly important endeavor is to develop computational strategies that enable molecular dynamics (MD) simulations of biomolecular systems with spontaneous changes in protonation states under conditions of constant pH. The present work describes our efforts to implement the powerful constant-pH MD simulation method, based on a hybrid nonequilibrium MD/Monte Carlo (neMD/MC) technique within the highly scalable program NAMD. The constant-pH hybrid neMD/MC method has several appealing features; it samples the correct semigrand canonical ensemble rigorously, the computational cost increases linearly with the number of titratable sites, and it is applicable to explicit solvent simulations. The present implementationmore » of the constant-pH hybrid neMD/MC in NAMD is designed to handle a wide range of biomolecular systems with no constraints on the choice of force field. Furthermore, the sampling efficiency can be adaptively improved on-the-fly by adjusting algorithmic parameters during the simulation. Finally, illustrative examples emphasizing medium- and large-scale applications on next-generation supercomputing architectures are provided.« less
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Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems
DOE Office of Scientific and Technical Information (OSTI.GOV)
Radak, Brian K.; Chipot, Christophe; Suh, Donghyuk
We report that an increasingly important endeavor is to develop computational strategies that enable molecular dynamics (MD) simulations of biomolecular systems with spontaneous changes in protonation states under conditions of constant pH. The present work describes our efforts to implement the powerful constant-pH MD simulation method, based on a hybrid nonequilibrium MD/Monte Carlo (neMD/MC) technique within the highly scalable program NAMD. The constant-pH hybrid neMD/MC method has several appealing features; it samples the correct semigrand canonical ensemble rigorously, the computational cost increases linearly with the number of titratable sites, and it is applicable to explicit solvent simulations. The present implementationmore » of the constant-pH hybrid neMD/MC in NAMD is designed to handle a wide range of biomolecular systems with no constraints on the choice of force field. Furthermore, the sampling efficiency can be adaptively improved on-the-fly by adjusting algorithmic parameters during the simulation. Finally, illustrative examples emphasizing medium- and large-scale applications on next-generation supercomputing architectures are provided.« less
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Least Squares Shadowing Sensitivity Analysis of Chaotic Flow Around a Two-Dimensional Airfoil
NASA Technical Reports Server (NTRS)
Blonigan, Patrick J.; Wang, Qiqi; Nielsen, Eric J.; Diskin, Boris
2016-01-01
Gradient-based sensitivity analysis has proven to be an enabling technology for many applications, including design of aerospace vehicles. However, conventional sensitivity analysis methods break down when applied to long-time averages of chaotic systems. This breakdown is a serious limitation because many aerospace applications involve physical phenomena that exhibit chaotic dynamics, most notably high-resolution large-eddy and direct numerical simulations of turbulent aerodynamic flows. A recently proposed methodology, Least Squares Shadowing (LSS), avoids this breakdown and advances the state of the art in sensitivity analysis for chaotic flows. The first application of LSS to a chaotic flow simulated with a large-scale computational fluid dynamics solver is presented. The LSS sensitivity computed for this chaotic flow is verified and shown to be accurate, but the computational cost of the current LSS implementation is high.
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Pseudo-dynamic source characterization accounting for rough-fault effects
NASA Astrophysics Data System (ADS)
Galis, Martin; Thingbaijam, Kiran K. S.; Mai, P. Martin
2016-04-01
Broadband ground-motion simulations, ideally for frequencies up to ~10Hz or higher, are important for earthquake engineering; for example, seismic hazard analysis for critical facilities. An issue with such simulations is realistic generation of radiated wave-field in the desired frequency range. Numerical simulations of dynamic ruptures propagating on rough faults suggest that fault roughness is necessary for realistic high-frequency radiation. However, simulations of dynamic ruptures are too expensive for routine applications. Therefore, simplified synthetic kinematic models are often used. They are usually based on rigorous statistical analysis of rupture models inferred by inversions of seismic and/or geodetic data. However, due to limited resolution of the inversions, these models are valid only for low-frequency range. In addition to the slip, parameters such as rupture-onset time, rise time and source time functions are needed for complete spatiotemporal characterization of the earthquake rupture. But these parameters are poorly resolved in the source inversions. To obtain a physically consistent quantification of these parameters, we simulate and analyze spontaneous dynamic ruptures on rough faults. First, by analyzing the impact of fault roughness on the rupture and seismic radiation, we develop equivalent planar-fault kinematic analogues of the dynamic ruptures. Next, we investigate the spatial interdependencies between the source parameters to allow consistent modeling that emulates the observed behavior of dynamic ruptures capturing the rough-fault effects. Based on these analyses, we formulate a framework for pseudo-dynamic source model, physically consistent with the dynamic ruptures on rough faults.
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Efficient Parallel Engineering Computing on Linux Workstations
NASA Technical Reports Server (NTRS)
Lou, John Z.
2010-01-01
A C software module has been developed that creates lightweight processes (LWPs) dynamically to achieve parallel computing performance in a variety of engineering simulation and analysis applications to support NASA and DoD project tasks. The required interface between the module and the application it supports is simple, minimal and almost completely transparent to the user applications, and it can achieve nearly ideal computing speed-up on multi-CPU engineering workstations of all operating system platforms. The module can be integrated into an existing application (C, C++, Fortran and others) either as part of a compiled module or as a dynamically linked library (DLL).
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NASA Astrophysics Data System (ADS)
Nelson, Hunter Barton
A simplified second-order transfer function actuator model used in most flight dynamics applications cannot easily capture the effects of different actuator parameters. The present work integrates a nonlinear actuator model into a nonlinear state space rotorcraft model to determine the effect of actuator parameters on key flight dynamics. The completed actuator model was integrated with a swashplate kinematics where step responses were generated over a range of key hydraulic parameters. The actuator-swashplate system was then introduced into a nonlinear state space rotorcraft simulation where flight dynamics quantities such as bandwidth and phase delay analyzed. Frequency sweeps were simulated for unique actuator configurations using the coupled nonlinear actuator-rotorcraft system. The software package CIFER was used for system identification and compared directly to the linearized models. As the actuator became rate saturated, the effects on bandwidth and phase delay were apparent on the predicted handling qualities specifications.
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A novel energy conversion based method for velocity correction in molecular dynamics simulations
DOE Office of Scientific and Technical Information (OSTI.GOV)
Jin, Hanhui; Collaborative Innovation Center of Advanced Aero-Engine, Hangzhou 310027; Liu, Ningning
2017-05-01
Molecular dynamics (MD) simulation has become an important tool for studying micro- or nano-scale dynamics and the statistical properties of fluids and solids. In MD simulations, there are mainly two approaches: equilibrium and non-equilibrium molecular dynamics (EMD and NEMD). In this paper, a new energy conversion based correction (ECBC) method for MD is developed. Unlike the traditional systematic correction based on macroscopic parameters, the ECBC method is developed strictly based on the physical interaction processes between the pair of molecules or atoms. The developed ECBC method can apply to EMD and NEMD directly. While using MD with this method, themore » difference between the EMD and NEMD is eliminated, and no macroscopic parameters such as external imposed potentials or coefficients are needed. With this method, many limits of using MD are lifted. The application scope of MD is greatly extended.« less
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Structure and dynamics of acetate anion-based ionic liquids from molecular dynamics study
NASA Astrophysics Data System (ADS)
Chandran, Aneesh; Prakash, Karthigeyan; Senapati, Sanjib
2010-08-01
Acetate anion-based ionic liquids (ILs) have found wide range of applications. The microstructure and dynamics of this IL family have not been clearly understood yet. We report molecular dynamics simulation results of three acetate anion-based ionic liquids that encompass the most common IL cations. Simulations are performed based on a set of proposed force field parameters for IL acetate anion which can be combined with existing parameters for IL cations to simulate large variety of ILs. The computed liquid density and IR spectral data for [BMIM][Ac] are found to match very well with available experimental results. The strong amino-group-associated interactions in [TMG][Ac] are seen to bring about higher cohesive energy density, stronger ion packing, and more restricted translational and rotational mobilities of the constituent ions. The IL anions are found to track the cation movements in all systems, implying that ions in ILs travel in pairs or clusters.
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Exploring RNA structure and dynamics through enhanced sampling simulations.
Mlýnský, Vojtěch; Bussi, Giovanni
2018-04-01
RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this timescale to be effectively extended in order to probe biologically relevant conformational changes and chemical reactions. Here, we review the role of enhanced sampling techniques in the study of RNA systems. We discuss the challenges and promises associated with the application of these methods to force-field validation, exploration of conformational landscapes and ion/ligand-RNA interactions, as well as catalytic pathways. Important technical aspects of these methods, such as the choice of the biased collective variables and the analysis of multi-replica simulations, are examined in detail. Finally, a perspective on the role of these methods in the characterization of RNA dynamics is provided. Copyright © 2018 Elsevier Ltd. All rights reserved.
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Kinetics from Replica Exchange Molecular Dynamics Simulations.
Stelzl, Lukas S; Hummer, Gerhard
2017-08-08
Transitions between metastable states govern many fundamental processes in physics, chemistry and biology, from nucleation events in phase transitions to the folding of proteins. The free energy surfaces underlying these processes can be obtained from simulations using enhanced sampling methods. However, their altered dynamics makes kinetic and mechanistic information difficult or impossible to extract. Here, we show that, with replica exchange molecular dynamics (REMD), one can not only sample equilibrium properties but also extract kinetic information. For systems that strictly obey first-order kinetics, the procedure to extract rates is rigorous. For actual molecular systems whose long-time dynamics are captured by kinetic rate models, accurate rate coefficients can be determined from the statistics of the transitions between the metastable states at each replica temperature. We demonstrate the practical applicability of the procedure by constructing master equation (Markov state) models of peptide and RNA folding from REMD simulations.
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Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics
DOE Office of Scientific and Technical Information (OSTI.GOV)
Martínez, Enrique; Cawkwell, Marc J.; Voter, Arthur F.
Here, Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached atmore » each time step. Lastly, the thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.« less
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Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics
Martínez, Enrique; Cawkwell, Marc J.; Voter, Arthur F.; ...
2015-04-21
Here, Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached atmore » each time step. Lastly, the thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.« less
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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...
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Simulating the Transport and Fate of Trifluralin in Soil
Ying Ouyang; Jia-En Zhang; Li Hua Cui; Peter Nkedi-Kizza
2012-01-01
Understanding herbicide dynamics in agricultural soils is crucial to evaluate herbicide application efficiency and its environmental consequences. A model for herbicide trifluralin (α,α,α-reifluoro-2,6-dinitro-N,N-dipropyl-ρtoluidine) dynamics namely runoff, erosion, leaching, volatilization, and degradation losses in agricultural...
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Pham, Tuan Anh; Kweon, Kyoung E.; Samanta, Amit; ...
2017-09-18
The development of sodium and potassium batteries offers a promising way to meet the scaling and cost challenges of energy storage. However, compared to Li +, several intrinsic properties of Na + and K +, including their solvation and dynamics in typical organic electrolytes utilized in battery applications, are less well-understood. Here in this paper, we report a systematic investigation of Na + and K + in ethylene carbonate (EC) using first-principles molecular dynamics simulations. Our simulations reveal significant differences in the solvation structure and dynamical properties of Na + and K + compared to Li +. We find that,more » in contrast to Li + which exhibits a well-defined first solvation shell, the larger Na+ and K+ ions show more disordered and flexible solvation structures. These differences in solvation were found to significantly influence the ion dynamics, leading to larger diffusion coefficients of Na + and K + compared to Li +. Our simulations also reveal a clear and interesting analog in the behavior of the ions in EC and aqueous environments, particularly in the specific ion effects on the solvent dynamics. Lastly, this work provides fundamental understanding of the intrinsic properties of Na + and K + in organic electrolytes, which may ultimately influence the intercalation mechanism at the electrode–electrolyte interface and therefore battery performance, lifetime, and safety.« less
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A digital strategy for manometer dynamic enhancement. [for wind tunnel monitoring
NASA Technical Reports Server (NTRS)
Stoughton, J. W.
1978-01-01
Application of digital signal processing techniques to improve the non-linear dynamic characteristics of a sonar-type mercury manometer is described. The dynamic enhancement strategy quasi-linearizes the manometer characteristics and improves the effective bandwidth in the context of a wind-tunnel pressure regulation system. Model identification data and real-time hybrid simulation data demonstrate feasibility of approach.
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Nam, Kanghyun; Cho, Kwanghyun; Park, Sang-Shin; Choi, Seibum B.
2017-01-01
This paper details the new design and dynamic simulation of an electro-hydraulic camless engine valve actuator (EH-CEVA) and experimental verification with lift position sensors. In general, camless engine technologies have been known for improving fuel efficiency, enhancing power output, and reducing emissions of internal combustion engines. Electro-hydraulic valve actuators are used to eliminate the camshaft of an existing internal combustion engines and used to control the valve timing and valve duration independently. This paper presents novel electro-hydraulic actuator design, dynamic simulations, and analysis based on design specifications required to satisfy the operation performances. An EH-CEVA has initially been designed and modeled by means of a powerful hydraulic simulation software, AMESim, which is useful for the dynamic simulations and analysis of hydraulic systems. Fundamental functions and performances of the EH-CEVA have been validated through comparisons with experimental results obtained in a prototype test bench. PMID:29258270
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Nam, Kanghyun; Cho, Kwanghyun; Park, Sang-Shin; Choi, Seibum B
2017-12-18
This paper details the new design and dynamic simulation of an electro-hydraulic camless engine valve actuator (EH-CEVA) and experimental verification with lift position sensors. In general, camless engine technologies have been known for improving fuel efficiency, enhancing power output, and reducing emissions of internal combustion engines. Electro-hydraulic valve actuators are used to eliminate the camshaft of an existing internal combustion engines and used to control the valve timing and valve duration independently. This paper presents novel electro-hydraulic actuator design, dynamic simulations, and analysis based on design specifications required to satisfy the operation performances. An EH-CEVA has initially been designed and modeled by means of a powerful hydraulic simulation software, AMESim, which is useful for the dynamic simulations and analysis of hydraulic systems. Fundamental functions and performances of the EH-CEVA have been validated through comparisons with experimental results obtained in a prototype test bench.
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Infrastructure dynamics: A selected bibliography
NASA Technical Reports Server (NTRS)
Dajani, J. S.; Bencosme, A. J.
1978-01-01
The term infrastructure is used to denote the set of life support and public service systems which is necessary for the development of growth of human settlements. Included are some basic references in the field of dynamic simulation, as well as a number of relevant applications in the area of infrastructure planning. The intent is to enable the student or researcher to quickly identify such applications to the extent necessary for initiating further work in the field.
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Protonation States in molecular dynamics simulations of peptide folding and binding.
Ben-Shimon, Avraham; Shalev, Deborah E; Niv, Masha Y
2013-01-01
Peptides are important signaling modules, acting both as individual hormones and as parts of larger molecules, mediating their protein-protein interactions. Many peptidic and peptidomimetic drugs have reached the marketplace and opportunities for peptide-based drug discovery are on the rise. pH-dependent behavior of peptides is well documented in the context of misfolding diseases and peptide translocation. Changes in the protonation states of peptide residues often have a crucial effect on a peptide's structure, dynamics and function, which may be exploited for biotechnological applications. The current review surveys the increasing levels of sophistication in the treatment of protonation states in computational studies involving peptides. Specifically we describe I) the common practice of assigning a single protonation state and using it throughout the dynamic simulation, II) approaches that consider multiple protonation states and compare computed observables to experimental ones, III) constant pH molecular dynamics methods that couple changes in protonation states with conformational dynamics "on the fly". Applications of conformational dynamics treatment of peptides in the context of binding, folding and interactions with the membrane are presented, illustrating the growing body of work in this field and highlighting the importance of careful handling of protonation states of peptidic residues.
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Simulation of generation and dynamics of polarization singularities with circular Airy beams.
Ye, Dong; Peng, Xinyu; Zhou, Muchun; Xin, Yu; Song, Minmin
2017-11-01
The generation and dynamics of polarization singularities have been underresearched for years, while the focusing property of the topological configuration has not been explored much. In this paper, we simulated the generation of low-order polarization singularities with a circular Airy beam and explored the focusing property of the synthetic light field during propagation due to the autofocusing of the component. Our work researched the focusing properties of the polarization singularity configuration, which may help to develop its application prospect.
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Interaction Dynamics Between a Flexible Rotor and an Auxiliary Clearance Bearing
NASA Technical Reports Server (NTRS)
Lawen, James L., Jr.; Flowers, George T.
1996-01-01
This study investigates the application of synchronous interaction dynamics methodology to the design of auxiliary bearing systems. The technique is applied to a flexible rotor system and comparisons are made between the behavior predicted by this analysis method and the observed simulation response characteristics. Of particular interest is the influence of coupled shaft/bearing vibration modes on rotordynamical behavior. Experimental studies are also perFormed to validate the simulation results and provide insight into the expected behavior of such a system.
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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.
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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.
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Structure and dynamics of solvated polyethylenimine chains
NASA Astrophysics Data System (ADS)
Beu, Titus A.; Farcaş, Alexandra
2017-12-01
Polimeric gene-delivery carriers have attracted great interest in recent years, owing to their applicability in gene therapy. In particular, cationic polymers represent the most promising delivery vectors for nucleic acids into the cells. This study presents extensive atomistic molecular dynamics simulations of linear polyethylenimine chains. The simulations show that the variation of the chain size and protonation fraction causes a substantial change of the diffusion coefficient. Examination of the solvated chains suggests the possibility of controlling the polymer diffusion mobility in solution.
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Park, Hyun June; Park, Kyungmoon; Kim, Yong Hwan; Yoo, Young Je
2014-12-20
Candida antarctica lipase B (CalB) is one of the most useful enzyme for various reactions and bioconversions. Enhancing thermostability of CalB is required for industrial applications. In this study, we propose a computational design strategy to improve the thermostability of CalB. Molecular dynamics simulations at various temperatures were used to investigate the common fluctuation sites in CalB, which are considered to be thermally weak points. The RosettaDesign algorithm was used to design the selected residues. The redesigned CalB was simulated to verify both the enhancement of intramolecular interactions and the lowering of the overall root-mean-square deviation (RMSD) values. The A251E mutant designed using this strategy showed a 2.5-fold higher thermostability than the wild-type CalB. This strategy could apply to other industry applicable enzymes. Copyright © 2014 Elsevier B.V. All rights reserved.
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Instrument For Simulation Of Piezoelectric Transducers
NASA Technical Reports Server (NTRS)
Mcnichol, Randal S.
1996-01-01
Electronic instrument designed to simulate dynamic output of integrated-circuit piezoelectric acceleration or pressure transducer. Operates in conjunction with external signal-conditioning circuit, generating square-wave signal of known amplitude for use in calibrating signal-conditioning circuit. Instrument also useful as special-purpose square-wave generator in other applications.
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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...
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Intelligent robot control using an adaptive critic with a task control center and dynamic database
NASA Astrophysics Data System (ADS)
Hall, E. L.; Ghaffari, M.; Liao, X.; Alhaj Ali, S. M.
2006-10-01
The purpose of this paper is to describe the design, development and simulation of a real time controller for an intelligent, vision guided robot. The use of a creative controller that can select its own tasks is demonstrated. This creative controller uses a task control center and dynamic database. The dynamic database stores both global environmental information and local information including the kinematic and dynamic models of the intelligent robot. The kinematic model is very useful for position control and simulations. However, models of the dynamics of the manipulators are needed for tracking control of the robot's motions. Such models are also necessary for sizing the actuators, tuning the controller, and achieving superior performance. Simulations of various control designs are shown. Also, much of the model has also been used for the actual prototype Bearcat Cub mobile robot. This vision guided robot was designed for the Intelligent Ground Vehicle Contest. A novel feature of the proposed approach is that the method is applicable to both robot arm manipulators and robot bases such as wheeled mobile robots. This generality should encourage the development of more mobile robots with manipulator capability since both models can be easily stored in the dynamic database. The multi task controller also permits wide applications. The use of manipulators and mobile bases with a high-level control are potentially useful for space exploration, certain rescue robots, defense robots, and medical robotics aids.
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NASA Astrophysics Data System (ADS)
Drukker, Karen; Hammes-Schiffer, Sharon
1997-07-01
This paper presents an analytical derivation of a multiconfigurational self-consistent-field (MC-SCF) solution of the time-independent Schrödinger equation for nuclear motion (i.e. vibrational modes). This variational MC-SCF method is designed for the mixed quantum/classical molecular dynamics simulation of multiple proton transfer reactions, where the transferring protons are treated quantum mechanically while the remaining degrees of freedom are treated classically. This paper presents a proof that the Hellmann-Feynman forces on the classical degrees of freedom are identical to the exact forces (i.e. the Pulay corrections vanish) when this MC-SCF method is used with an appropriate choice of basis functions. This new MC-SCF method is applied to multiple proton transfer in a protonated chain of three hydrogen-bonded water molecules. The ground state and the first three excited state energies and the ground state forces agree well with full configuration interaction calculations. Sample trajectories are obtained using adiabatic molecular dynamics methods, and nonadiabatic effects are found to be insignificant for these sample trajectories. The accuracy of the excited states will enable this MC-SCF method to be used in conjunction with nonadiabatic molecular dynamics methods. This application differs from previous work in that it is a real-time quantum dynamical nonequilibrium simulation of multiple proton transfer in a chain of water molecules.
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Modeling of bubble dynamics in relation to medical applications
DOE Office of Scientific and Technical Information (OSTI.GOV)
Amendt, P.A.; London, R.A.; Strauss, M.
1997-03-12
In various pulsed-laser medical applications, strong stress transients can be generated in advance of vapor bubble formation. To better understand the evolution of stress transients and subsequent formation of vapor bubbles, two-dimensional simulations are presented in channel or cylindrical geometry with the LATIS (LAser TISsue) computer code. Differences with one-dimensional modeling are explored, and simulated experimental conditions for vapor bubble generation are presented and compared with data. 22 refs., 8 figs.
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A new method for qualitative simulation of water resources systems: 2. Applications
NASA Astrophysics Data System (ADS)
Antunes, M. P.; Seixas, M. J.; Camara, A. S.; Pinheiro, M.
1987-11-01
SLIN (Simulação Linguistica) is a new method for qualitative dynamic simulation. As was presented previously (Camara et al., this issue), SLIN relies upon a categorical representation of variables which are manipulated by logical rules. Two applications to water resources systems are included to illustrate SLIN's potential usefulness: the environmental impact evaluation of a hydropower plant and the assessment of oil dispersion in the sea after a tanker wreck.
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Applicability of mode-coupling theory to polyisobutylene: a molecular dynamics simulation study.
Khairy, Y; Alvarez, F; Arbe, A; Colmenero, J
2013-10-01
The applicability of Mode Coupling Theory (MCT) to the glass-forming polymer polyisobutylene (PIB) has been explored by using fully atomistic molecular dynamics simulations. MCT predictions for the so-called asymptotic regime have been successfully tested on the dynamic structure factor and the self-correlation function of PIB main-chain carbons calculated from the simulated cell. The factorization theorem and the time-temperature superposition principle are satisfied. A consistent fitting procedure of the simulation data to the MCT asymptotic power-laws predicted for the α-relaxation regime has delivered the dynamic exponents of the theory-in particular, the exponent parameter λ-the critical non-ergodicity parameters, and the critical temperature T(c). The obtained values of λ and T(c) agree, within the uncertainties involved in both studies, with those deduced from depolarized light scattering experiments [A. Kisliuk et al., J. Polym. Sci. Part B: Polym. Phys. 38, 2785 (2000)]. Both, λ and T(c)/T(g) values found for PIB are unusually large with respect to those commonly obtained in low molecular weight systems. Moreover, the high T(c)/T(g) value is compatible with a certain correlation of this parameter with the fragility in Angell's classification. Conversely, the value of λ is close to that reported for real polymers, simulated "realistic" polymers and simple polymer models with intramolecular barriers. In the framework of the MCT, such finding should be the signature of two different mechanisms for the glass-transition in real polymers: intermolecular packing and intramolecular barriers combined with chain connectivity.
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NASA Technical Reports Server (NTRS)
Demerdash, N. A. O.; Nehl, T. W.
1979-01-01
The development, fabrication and evaluation of a prototype electromechanical actuator (EMA) is discussed. Application of the EMA as a motor for control surfaces in aerospace flight is examined. A mathematical model of the EMA is developed for design optimization. Nonlinearities which complicate the mathematical model are discussed. The dynamics of the EMA from the underlying physical principles are determined and a discussion of similating the control logic by means of equivalent boolean expressions is presented.
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Spatio-Temporal Process Simulation of Dam-Break Flood Based on SPH
NASA Astrophysics Data System (ADS)
Wang, H.; Ye, F.; Ouyang, S.; Li, Z.
2018-04-01
On the basis of introducing the SPH (Smooth Particle Hydrodynamics) simulation method, the key research problems were given solutions in this paper, which ere the spatial scale and temporal scale adapting to the GIS(Geographical Information System) application, the boundary condition equations combined with the underlying surface, and the kernel function and parameters applicable to dam-break flood simulation. In this regards, a calculation method of spatio-temporal process emulation with elaborate particles for dam-break flood was proposed. Moreover the spatio-temporal process was dynamic simulated by using GIS modelling and visualization. The results show that the method gets more information, objectiveness and real situations.
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Liu, Shuguang; Tan, Zhengxi; Chen, Mingshi; Liu, Jinxun; Wein, Anne; Li, Zhengpeng; Huang, Shengli; Oeding, Jennifer; Young, Claudia; Verma, Shashi B.; Suyker, Andrew E.; Faulkner, Stephen P.
2012-01-01
The General Ensemble Biogeochemical Modeling System (GEMS) was es in individual models, it uses multiple site-scale biogeochemical models to perform model simulations. Second, it adopts Monte Carlo ensemble simulations of each simulation unit (one site/pixel or group of sites/pixels with similar biophysical conditions) to incorporate uncertainties and variability (as measured by variances and covariance) of input variables into model simulations. In this chapter, we illustrate the applications of GEMS at the site and regional scales with an emphasis on incorporating agricultural practices. Challenges in modeling soil carbon dynamics and greenhouse emissions are also discussed.
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NASA Astrophysics Data System (ADS)
Petsev, Nikolai D.; Leal, L. Gary; Shell, M. Scott
2017-12-01
Hybrid molecular-continuum simulation techniques afford a number of advantages for problems in the rapidly burgeoning area of nanoscale engineering and technology, though they are typically quite complex to implement and limited to single-component fluid systems. We describe an approach for modeling multicomponent hydrodynamic problems spanning multiple length scales when using particle-based descriptions for both the finely resolved (e.g., molecular dynamics) and coarse-grained (e.g., continuum) subregions within an overall simulation domain. This technique is based on the multiscale methodology previously developed for mesoscale binary fluids [N. D. Petsev, L. G. Leal, and M. S. Shell, J. Chem. Phys. 144, 084115 (2016)], simulated using a particle-based continuum method known as smoothed dissipative particle dynamics. An important application of this approach is the ability to perform coupled molecular dynamics (MD) and continuum modeling of molecularly miscible binary mixtures. In order to validate this technique, we investigate multicomponent hybrid MD-continuum simulations at equilibrium, as well as non-equilibrium cases featuring concentration gradients.
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Linkage of mike she to wetland-dndc for carbon budgeting and anaerobic biogeochemistry simulation
Jianbo Cui; Changsheng Li; Ge Sun; Carl Trettin
2005-01-01
This study reports the linkage between MIKE SHE and Wetland-DNDC for carbon dynamics and greenhouse gases (GHGs) emissions simulation in forested wetland.Wet1and-DNDC was modified by parameterizing management measures, refining anaerobic biogeochemical processes, and was linked to the hydrological model - MIKE SHE. As a preliminary application, we simulated the effect...
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NASA Astrophysics Data System (ADS)
Xu, X.; Song, C.; Wang, Y.; Ricciuto, D. M.; Lipson, D.; Shi, X.; Zona, D.; Song, X.; Yuan, F.; Oechel, W. C.; Thornton, P. E.
2017-12-01
A microbial model is introduced for simulating microbial mechanisms controlling soil carbon and nitrogen biogeochemical cycling and methane fluxes. The model is built within the CN (carbon-nitrogen) framework of Community Land Model 4.5, named as CLM-Microbe to emphasize its explicit representation of microbial mechanisms to biogeochemistry. Based on the CLM4.5, three new pools were added: bacteria, fungi, and dissolved organic matter. It has 11 pools and 34 transitional processes, compared with 8 pools and 9 transitional flow in the CLM4.5. The dissolve organic carbon was linked with a new microbial functional group based methane module to explicitly simulate methane production, oxidation, transport and their microbial controls. Comparing with CLM4.5-CN, the CLM-Microbe model has a number of new features, (1) microbial control on carbon and nitrogen flows between soil carbon/nitrogen pools; (2) an implicit representation of microbial community structure as bacteria and fungi; (3) a microbial functional-group based methane module. The model sensitivity analysis suggests the importance of microbial carbon allocation parameters on soil biogeochemistry and microbial controls on methane dynamics. Preliminary simulations validate the model's capability for simulating carbon and nitrogen dynamics and methane at a number of sites across the globe. The regional application to Asia has verified the model in simulating microbial mechanisms in controlling methane dynamics at multiple scales.
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Learning by stimulation avoidance: A principle to control spiking neural networks dynamics
Sinapayen, Lana; Ikegami, Takashi
2017-01-01
Learning based on networks of real neurons, and learning based on biologically inspired models of neural networks, have yet to find general learning rules leading to widespread applications. In this paper, we argue for the existence of a principle allowing to steer the dynamics of a biologically inspired neural network. Using carefully timed external stimulation, the network can be driven towards a desired dynamical state. We term this principle “Learning by Stimulation Avoidance” (LSA). We demonstrate through simulation that the minimal sufficient conditions leading to LSA in artificial networks are also sufficient to reproduce learning results similar to those obtained in biological neurons by Shahaf and Marom, and in addition explains synaptic pruning. We examined the underlying mechanism by simulating a small network of 3 neurons, then scaled it up to a hundred neurons. We show that LSA has a higher explanatory power than existing hypotheses about the response of biological neural networks to external simulation, and can be used as a learning rule for an embodied application: learning of wall avoidance by a simulated robot. In other works, reinforcement learning with spiking networks can be obtained through global reward signals akin simulating the dopamine system; we believe that this is the first project demonstrating sensory-motor learning with random spiking networks through Hebbian learning relying on environmental conditions without a separate reward system. PMID:28158309
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Learning by stimulation avoidance: A principle to control spiking neural networks dynamics.
Sinapayen, Lana; Masumori, Atsushi; Ikegami, Takashi
2017-01-01
Learning based on networks of real neurons, and learning based on biologically inspired models of neural networks, have yet to find general learning rules leading to widespread applications. In this paper, we argue for the existence of a principle allowing to steer the dynamics of a biologically inspired neural network. Using carefully timed external stimulation, the network can be driven towards a desired dynamical state. We term this principle "Learning by Stimulation Avoidance" (LSA). We demonstrate through simulation that the minimal sufficient conditions leading to LSA in artificial networks are also sufficient to reproduce learning results similar to those obtained in biological neurons by Shahaf and Marom, and in addition explains synaptic pruning. We examined the underlying mechanism by simulating a small network of 3 neurons, then scaled it up to a hundred neurons. We show that LSA has a higher explanatory power than existing hypotheses about the response of biological neural networks to external simulation, and can be used as a learning rule for an embodied application: learning of wall avoidance by a simulated robot. In other works, reinforcement learning with spiking networks can be obtained through global reward signals akin simulating the dopamine system; we believe that this is the first project demonstrating sensory-motor learning with random spiking networks through Hebbian learning relying on environmental conditions without a separate reward system.
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Simulator technology as a tool for education in cardiac care.
Hravnak, Marilyn; Beach, Michael; Tuite, Patricia
2007-01-01
Assisting nurses in gaining the cognitive and psychomotor skills necessary to safely and effectively care for patients with cardiovascular disease can be challenging for educators. Ideally, nurses would have the opportunity to synthesize and practice these skills in a protected training environment before application in the dynamic clinical setting. Recently, a technology known as high fidelity human simulation was introduced, which permits learners to interact with a simulated patient. The dynamic physiologic parameters and physical assessment capabilities of the simulated patient provide for a realistic learning environment. This article describes the High Fidelity Human Simulation Laboratory at the University of Pittsburgh School of Nursing and presents strategies for using this technology as a tool in teaching complex cardiac nursing care at the basic and advanced practice nursing levels. The advantages and disadvantages of high fidelity human simulation in learning are discussed.
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Atomistic Computer Simulations of Water Interactions and Dissolution of Inorganic Glasses
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
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Validated simulator for space debris removal with nets and other flexible tethers applications
NASA Astrophysics Data System (ADS)
Gołębiowski, Wojciech; Michalczyk, Rafał; Dyrek, Michał; Battista, Umberto; Wormnes, Kjetil
2016-12-01
In the context of active debris removal technologies and preparation activities for the e.Deorbit mission, a simulator for net-shaped elastic bodies dynamics and their interactions with rigid bodies, has been developed. Its main application is to aid net design and test scenarios for space debris deorbitation. The simulator can model all the phases of the debris capturing process: net launch, flight and wrapping around the target. It handles coupled simulation of rigid and flexible bodies dynamics. Flexible bodies were implemented using Cosserat rods model. It allows to simulate flexible threads or wires with elasticity and damping for stretching, bending and torsion. Threads may be combined into structures of any topology, so the software is able to simulate nets, pure tethers, tether bundles, cages, trusses, etc. Full contact dynamics was implemented. Programmatic interaction with simulation is possible - i.e. for control implementation. The underlying model has been experimentally validated and due to significant gravity influence, experiment had to be performed in microgravity conditions. Validation experiment for parabolic flight was a downscaled process of Envisat capturing. The prepacked net was launched towards the satellite model, it expanded, hit the model and wrapped around it. The whole process was recorded with 2 fast stereographic camera sets for full 3D trajectory reconstruction. The trajectories were used to compare net dynamics to respective simulations and then to validate the simulation tool. The experiments were performed on board of a Falcon-20 aircraft, operated by National Research Council in Ottawa, Canada. Validation results show that model reflects phenomenon physics accurately enough, so it may be used for scenario evaluation and mission design purposes. The functionalities of the simulator are described in detail in the paper, as well as its underlying model, sample cases and methodology behind validation. Results are presented and typical use cases are discussed showing that the software may be used to design throw nets for space debris capturing, but also to simulate deorbitation process, chaser control system or general interactions between rigid and elastic bodies - all in convenient and efficient way. The presented work was led by SKA Polska under the ESA contract, within the CleanSpace initiative.
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CABS-flex: server for fast simulation of protein structure fluctuations
Jamroz, Michal; Kolinski, Andrzej; Kmiecik, Sebastian
2013-01-01
The CABS-flex server (http://biocomp.chem.uw.edu.pl/CABSflex) implements CABS-model–based protocol for the fast simulations of near-native dynamics of globular proteins. In this application, the CABS model was shown to be a computationally efficient alternative to all-atom molecular dynamics—a classical simulation approach. The simulation method has been validated on a large set of molecular dynamics simulation data. Using a single input (user-provided file in PDB format), the CABS-flex server outputs an ensemble of protein models (in all-atom PDB format) reflecting the flexibility of the input structure, together with the accompanying analysis (residue mean-square-fluctuation profile and others). The ensemble of predicted models can be used in structure-based studies of protein functions and interactions. PMID:23658222
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Fuzzy Constraint Based Model for Efficient Management of Dynamic Purchasing Environments
NASA Astrophysics Data System (ADS)
Sakas, D. P.; Vlachos, D. S.; Simos, T. E.
2007-12-01
This paper considers the application of a fuzzy constraint based model for handling dynamic environments where only one of possibly many bundles of items must be purchased and quotes for items open and close over time. Simulation results are presented and compared with the optimal solution.
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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.
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NASA Astrophysics Data System (ADS)
Espinosa Duran, John Michael
The study of nanosystems and their emergent properties requires the development of multiscale computational models, theories and methods that preserve atomic and femtosecond resolution, to reveal details that cannot be resolved experimentally today. Considering this, three long time scale phenomena were studied using molecular dynamics and multiscale methods: self-assembly of organic molecules on graphite, energy transfer in nanosystems, and structural transition in vault nanoparticles. Molecular dynamics simulations of the self-assembly of alkoxybenzonitriles with different tail lengths on graphite were performed to learn about intermolecular interactions and phases exhibited by self-organized materials. This is important for the design of ordered self-assembled organic photovoltaic materials with greater efficiency than the disordered blends. Simulations revealed surface dynamical behaviors that cannot be resolved experimentally today due to the lack of spatiotemporal resolution. Atom-resolved structures predicted by simulations agreed with scanning tunneling microscopy images and unit cell measurements. Then, a multiscale theory based on the energy density as a field variable is developed to study energy transfer in nanoscale systems. For applications like photothermal microscopy or cancer phototherapy is required to understand how the energy is transferred to/from nanosystems. This multiscale theory could be applied in this context and here is tested for cubic nanoparticles immersed in water for energy being transferred to/from the nanoparticle. The theory predicts the energy transfer dynamics and reveals phenomena that cannot be described by current phenomenological theories. Finally, temperature-triggered structural transitions were revealed for vault nanoparticles using molecular dynamics and multiscale simulations. Vault is a football-shaped supramolecular assembly very distinct from the commonly observed icosahedral viruses. It has very promising applications in drug delivery and has been extensively studied experimentally. Sub-microsecond multiscale simulations at 310 K on the vault revealed the opening and closing of fractures near the shoulder while preserving the overall structure. This fracture mechanism could explain the uptake and release of small drugs while maintaining the overall structure. Higher temperature simulations show the generation of large fractures near the waist, which enables interaction of the external medium with the inner vault residues. Simulation results agreed with microscopy and spectroscopy measurements, and revealed new structures and mechanisms.
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Storm Water Management Model Applications Manual
The EPA Storm Water Management Model (SWMM) is a dynamic rainfall-runoff simulation model that computes runoff quantity and quality from primarily urban areas. This manual is a practical application guide for new SWMM users who have already had some previous training in hydrolog...
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Venkataraman, Pranav; Browd, Samuel R; Lutz, Barry R
2016-09-01
OBJECTIVE The surgical placement of a shunt designed to resolve the brain's impaired ability to drain excess CSF is one of the most common treatments for hydrocephalus. The use of a dynamic testing platform is an important part of shunt testing that can faithfully reproduce the physiological environment of the implanted shunts. METHODS A simulation-based framework that serves as a proof of concept for enabling the application of virtual intracranial pressure (ICP) and CSF models to a physical shunt-testing system was engineered. This was achieved by designing hardware and software that enabled the application of dynamic model-driven inlet and outlet pressures to a shunt and the subsequent measurement of the resulting drainage rate. RESULTS A set of common physiological scenarios was simulated, including oscillations in ICP due to respiratory and cardiac cycles, changes in baseline ICP due to changes in patient posture, and transient ICP spikes caused by activities such as exercise, coughing, sneezing, and the Valsalva maneuver. The behavior of the Strata valve under a few of these physiological conditions is also demonstrated. CONCLUSIONS Testing shunts with dynamic ICP and CSF simulations can facilitate the optimization of shunts to be more failure resistant and better suited to patient physiology.
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NASA Astrophysics Data System (ADS)
Marcolongo, Juan P.; Zeida, Ari; Semelak, Jonathan A.; Foglia, Nicolás O.; Morzan, Uriel N.; Estrin, Dario A.; González Lebrero, Mariano C.; Scherlis, Damián A.
2018-03-01
In this work we present the current advances in the development and the applications of LIO, a lab-made code designed for density functional theory calculations in graphical processing units (GPU), that can be coupled with different classical molecular dynamics engines. This code has been thoroughly optimized to perform efficient molecular dynamics simulations at the QM/MM DFT level, allowing for an exhaustive sampling of the configurational space. Selected examples are presented for the description of chemical reactivity in terms of free energy profiles, and also for the computation of optical properties, such as vibrational and electronic spectra in solvent and protein environments.
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Parameter estimating state reconstruction
NASA Technical Reports Server (NTRS)
George, E. B.
1976-01-01
Parameter estimation is considered for systems whose entire state cannot be measured. Linear observers are designed to recover the unmeasured states to a sufficient accuracy to permit the estimation process. There are three distinct dynamics that must be accommodated in the system design: the dynamics of the plant, the dynamics of the observer, and the system updating of the parameter estimation. The latter two are designed to minimize interaction of the involved systems. These techniques are extended to weakly nonlinear systems. The application to a simulation of a space shuttle POGO system test is of particular interest. A nonlinear simulation of the system is developed, observers designed, and the parameters estimated.
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NASA Technical Reports Server (NTRS)
Pamadi, Bandu N.; Toniolo, Matthew D.; Tartabini, Paul V.; Roithmayr, Carlos M.; Albertson, Cindy W.; Karlgaard, Christopher D.
2016-01-01
The objective of this report is to develop and implement a physics based method for analysis and simulation of multi-body dynamics including launch vehicle stage separation. The constraint force equation (CFE) methodology discussed in this report provides such a framework for modeling constraint forces and moments acting at joints when the vehicles are still connected. Several stand-alone test cases involving various types of joints were developed to validate the CFE methodology. The results were compared with ADAMS(Registered Trademark) and Autolev, two different industry standard benchmark codes for multi-body dynamic analysis and simulations. However, these two codes are not designed for aerospace flight trajectory simulations. After this validation exercise, the CFE algorithm was implemented in Program to Optimize Simulated Trajectories II (POST2) to provide a capability to simulate end-to-end trajectories of launch vehicles including stage separation. The POST2/CFE methodology was applied to the STS-1 Space Shuttle solid rocket booster (SRB) separation and Hyper-X Research Vehicle (HXRV) separation from the Pegasus booster as a further test and validation for its application to launch vehicle stage separation problems. Finally, to demonstrate end-to-end simulation capability, POST2/CFE was applied to the ascent, orbit insertion, and booster return of a reusable two-stage-to-orbit (TSTO) vehicle concept. With these validation exercises, POST2/CFE software can be used for performing conceptual level end-to-end simulations, including launch vehicle stage separation, for problems similar to those discussed in this report.
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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).
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NASA Astrophysics Data System (ADS)
Ali, Azhar Tareq; Warip, Mohd Nazri Mohd; Yaakob, Naimah; Abduljabbar, Waleed Khalid; Atta, Abdu Mohammed Ali
2017-11-01
Vehicular Ad-hoc Networks (VANETs) is an area of wireless technologies that is attracting a great deal of interest. There are still several areas of VANETS, such as security and routing protocols, medium access control, that lack large amounts of research. There is also a lack of freely available simulators that can quickly and accurately simulate VANETs. The main goal of this paper is to develop a freely available VANETS simulator and to evaluate popular mobile ad-hoc network routing protocols in several VANETS scenarios. The VANETS simulator consisted of a network simulator, traffic (mobility simulator) and used a client-server application to keep the two simulators in sync. The VANETS simulator also models buildings to create a more realistic wireless network environment. Ad-Hoc Distance Vector routing (AODV), Dynamic Source Routing (DSR) and Dynamic MANET On-demand (DYMO) were initially simulated in a city, country, and highway environment to provide an overall evaluation.
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MUSE--Model for University Strategic Evaluation. AIR 2002 Forum Paper.
ERIC Educational Resources Information Center
Kutina, Kenneth L.; Zullig, Craig M.; Starkman, Glenn D.; Tanski, Laura E.
A model for simulating college and university operations, finances, program investments, and market response in terms of applicants, acceptances, and retention has been developed and implemented using the system dynamics approach. The Model for University Strategic Evaluation (MUSE) is a simulation of the total operations of the university,…
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Engine dynamic analysis with general nonlinear finite element codes
NASA Technical Reports Server (NTRS)
Adams, M. L.; Padovan, J.; Fertis, D. G.
1991-01-01
A general engine dynamic analysis as a standard design study computational tool is described for the prediction and understanding of complex engine dynamic behavior. Improved definition of engine dynamic response provides valuable information and insights leading to reduced maintenance and overhaul costs on existing engine configurations. Application of advanced engine dynamic simulation methods provides a considerable cost reduction in the development of new engine designs by eliminating some of the trial and error process done with engine hardware development.
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Beam dynamics simulations of the injector for a compact THz source
NASA Astrophysics Data System (ADS)
Li, Ji; Pei, Yuan-Ji; Shang, Lei; Feng, Guang-Yao; Hu, Tong-Ning; Chen, Qu-Shan; Li, Cheng-Long
2014-08-01
Terahertz radiation has broad application prospects due to its ability to penetrate deep into many organic materials without the damage caused by ionizing radiations. A free electron laser (FEL)-based THz source is the best choice to produce high-power radiation. In this paper, a 14 MeV injector is introduced for generating high-quality beam for FEL, is composed of an EC-ITC RF gun, compensating coils and a travelling-wave structure. Beam dynamics simulations have been done with ASTRA code to verify the design and to optimize parameters. Simulations of the operating mode at 6 MeV have also been executed.
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Application of Probabilistic Analysis to Aircraft Impact Dynamics
NASA Technical Reports Server (NTRS)
Lyle, Karen H.; Padula, Sharon L.; Stockwell, Alan E.
2003-01-01
Full-scale aircraft crash simulations performed with nonlinear, transient dynamic, finite element codes can incorporate structural complexities such as: geometrically accurate models; human occupant models; and advanced material models to include nonlinear stressstrain behaviors, laminated composites, and material failure. Validation of these crash simulations is difficult due to a lack of sufficient information to adequately determine the uncertainty in the experimental data and the appropriateness of modeling assumptions. This paper evaluates probabilistic approaches to quantify the uncertainty in the simulated responses. Several criteria are used to determine that a response surface method is the most appropriate probabilistic approach. The work is extended to compare optimization results with and without probabilistic constraints.
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NASA Technical Reports Server (NTRS)
Bune, Andris V.; Kaukler, William F.; Whitaker, Ann F. (Technical Monitor)
2001-01-01
Modeling approach to simulate both mesoscale and microscopic forces acting in a typical AFM experiment is presented. At mesoscale level interaction between the cantilever tip and the sample surface is primarily described by the balance of attractive Van der Waals and repulsive forces. The model of cantilever oscillations is applicable to both non-contact and "tapping" AFM. This model can be farther enhanced to describe nanoparticle manipulation by cantilever. At microscopic level tip contamination and details of tip-surface interaction can be simulated using molecular dynamics approach. Integration of mesoscale model with molecular dynamic model is discussed.
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Frank, Martin
2015-01-01
Complex carbohydrates usually have a large number of rotatable bonds and consequently a large number of theoretically possible conformations can be generated (combinatorial explosion). The application of systematic search methods for conformational analysis of carbohydrates is therefore limited to disaccharides and trisaccharides in a routine analysis. An alternative approach is to use Monte-Carlo methods or (high-temperature) molecular dynamics (MD) simulations to explore the conformational space of complex carbohydrates. This chapter describes how to use MD simulation data to perform a conformational analysis (conformational maps, hydrogen bonds) of oligosaccharides and how to build realistic 3D structures of large polysaccharides using Conformational Analysis Tools (CAT).
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A model for simulating adaptive, dynamic flows on networks: Application to petroleum infrastructure
Corbet, Thomas F.; Beyeler, Walt; Wilson, Michael L.; ...
2017-10-03
Simulation models can greatly improve decisions meant to control the consequences of disruptions to critical infrastructures. We describe a dynamic flow model on networks purposed to inform analyses by those concerned about consequences of disruptions to infrastructures and to help policy makers design robust mitigations. We conceptualize the adaptive responses of infrastructure networks to perturbations as market transactions and business decisions of operators. We approximate commodity flows in these networks by a diffusion equation, with nonlinearities introduced to model capacity limits. To illustrate the behavior and scalability of the model, we show its application first on two simple networks, thenmore » on petroleum infrastructure in the United States, where we analyze the effects of a hypothesized earthquake.« less
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A model for simulating adaptive, dynamic flows on networks: Application to petroleum infrastructure
DOE Office of Scientific and Technical Information (OSTI.GOV)
Corbet, Thomas F.; Beyeler, Walt; Wilson, Michael L.
Simulation models can greatly improve decisions meant to control the consequences of disruptions to critical infrastructures. We describe a dynamic flow model on networks purposed to inform analyses by those concerned about consequences of disruptions to infrastructures and to help policy makers design robust mitigations. We conceptualize the adaptive responses of infrastructure networks to perturbations as market transactions and business decisions of operators. We approximate commodity flows in these networks by a diffusion equation, with nonlinearities introduced to model capacity limits. To illustrate the behavior and scalability of the model, we show its application first on two simple networks, thenmore » on petroleum infrastructure in the United States, where we analyze the effects of a hypothesized earthquake.« less
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Zhou, Xiangmin; Zhang, Nan; Sha, Desong; Shen, Yunhe; Tamma, Kumar K; Sweet, Robert
2009-01-01
The inability to render realistic soft-tissue behavior in real time has remained a barrier to face and content aspects of validity for many virtual reality surgical training systems. Biophysically based models are not only suitable for training purposes but also for patient-specific clinical applications, physiological modeling and surgical planning. When considering the existing approaches for modeling soft tissue for virtual reality surgical simulation, the computer graphics-based approach lacks predictive capability; the mass-spring model (MSM) based approach lacks biophysically realistic soft-tissue dynamic behavior; and the finite element method (FEM) approaches fail to meet the real-time requirement. The present development stems from physics fundamental thermodynamic first law; for a space discrete dynamic system directly formulates the space discrete but time continuous governing equation with embedded material constitutive relation and results in a discrete mechanics framework which possesses a unique balance between the computational efforts and the physically realistic soft-tissue dynamic behavior. We describe the development of the discrete mechanics framework with focused attention towards a virtual laparoscopic nephrectomy application.
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NASA Astrophysics Data System (ADS)
Xu, Lei; Zhai, Wanming; Gao, Jianmin
2017-11-01
Track irregularities are inevitably in a process of stochastic evolution due to the uncertainty and continuity of wheel-rail interactions. For depicting the dynamic behaviours of vehicle-track coupling system caused by track random irregularities thoroughly, it is a necessity to develop a track irregularity probabilistic model to simulate rail surface irregularities with ergodic properties on amplitudes, wavelengths and probabilities, and to build a three-dimensional vehicle-track coupled model by properly considering the wheel-rail nonlinear contact mechanisms. In the present study, the vehicle-track coupled model is programmed by combining finite element method with wheel-rail coupling model firstly. Then, in light of the capability of power spectral density (PSD) in characterising amplitudes and wavelengths of stationary random signals, a track irregularity probabilistic model is presented to reveal and simulate the whole characteristics of track irregularity PSD. Finally, extended applications from three aspects, that is, extreme analysis, reliability analysis and response relationships between dynamic indices, are conducted to the evaluation and application of the proposed models.
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Sampling of Protein Folding Transitions: Multicanonical Versus Replica Exchange Molecular Dynamics.
Jiang, Ping; Yaşar, Fatih; Hansmann, Ulrich H E
2013-08-13
We compare the efficiency of multicanonical and replica exchange molecular dynamics for the sampling of folding/unfolding events in simulations of proteins with end-to-end β -sheet. In Go-model simulations of the 75-residue MNK6, we observe improvement factors of 30 in the number of folding/unfolding events of multicanonical molecular dynamics over replica exchange molecular dynamics. As an application, we use this enhanced sampling to study the folding landscape of the 36-residue DS119 with an all-atom physical force field and implicit solvent. Here, we find that the rate-limiting step is the formation of the central helix that then provides a scaffold for the parallel β -sheet formed by the two chain ends.
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Enhanced sampling techniques in molecular dynamics simulations of biological systems.
Bernardi, Rafael C; Melo, Marcelo C R; Schulten, Klaus
2015-05-01
Molecular dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.
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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.
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Norton, Tomás; Sun, Da-Wen; Grant, Jim; Fallon, Richard; Dodd, Vincent
2007-09-01
The application of computational fluid dynamics (CFD) in the agricultural industry is becoming ever more important. Over the years, the versatility, accuracy and user-friendliness offered by CFD has led to its increased take-up by the agricultural engineering community. Now CFD is regularly employed to solve environmental problems of greenhouses and animal production facilities. However, due to a combination of increased computer efficacy and advanced numerical techniques, the realism of these simulations has only been enhanced in recent years. This study provides a state-of-the-art review of CFD, its current applications in the design of ventilation systems for agricultural production systems, and the outstanding challenging issues that confront CFD modellers. The current status of greenhouse CFD modelling was found to be at a higher standard than that of animal housing, owing to the incorporation of user-defined routines that simulate crop biological responses as a function of local environmental conditions. Nevertheless, the most recent animal housing simulations have addressed this issue and in turn have become more physically realistic.
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Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems
Yazdani, Alireza; Tartakovsky, Alexandre; Karniadakis, George Em
2015-01-01
We present a transport dissipative particle dynamics (tDPD) model for simulating mesoscopic problems involving advection-diffusion-reaction (ADR) processes, along with a methodology for implementation of the correct Dirichlet and Neumann boundary conditions in tDPD simulations. tDPD is an extension of the classic dissipative particle dynamics (DPD) framework with extra variables for describing the evolution of concentration fields. The transport of concentration is modeled by a Fickian flux and a random flux between tDPD particles, and the advection is implicitly considered by the movements of these Lagrangian particles. An analytical formula is proposed to relate the tDPD parameters to the effective diffusion coefficient. To validate the present tDPD model and the boundary conditions, we perform three tDPD simulations of one-dimensional diffusion with different boundary conditions, and the results show excellent agreement with the theoretical solutions. We also performed two-dimensional simulations of ADR systems and the tDPD simulations agree well with the results obtained by the spectral element method. Finally, we present an application of the tDPD model to the dynamic process of blood coagulation involving 25 reacting species in order to demonstrate the potential of tDPD in simulating biological dynamics at the mesoscale. We find that the tDPD solution of this comprehensive 25-species coagulation model is only twice as computationally expensive as the conventional DPD simulation of the hydrodynamics only, which is a significant advantage over available continuum solvers. PMID:26156459
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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
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Koutsoumaris, C. Chr.; Tsamasphyros, G. J.; Vogiatzis, G. G.
2015-12-31
The nonlocal theory of elasticity is employed for the study of the free vibrations of carbon nanotubes (CNT). For the first time, a bi-Helmholtz operator has been used instead of the standard Helmholtz operator in a nonlocal beam model. Alongside the continuum formulation and its numerical solution, atomistic Molecular Dynamics (MD) simulations have been conducted in order to directly evaluate the eigenfrequencies of vibrating CNTs with a minimum of adjustable parameters. Our results show that the bi-Helmholtz operator is the most appropriate one to fit MD simulation results. However, the estimation of vibration eigenfrequencies from molecular simulations still remains anmore » open (albeit well-posed) problem.« less
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Model-data integration to improve the LPJmL dynamic global vegetation model
NASA Astrophysics Data System (ADS)
Forkel, Matthias; Thonicke, Kirsten; Schaphoff, Sibyll; Thurner, Martin; von Bloh, Werner; Dorigo, Wouter; Carvalhais, Nuno
2017-04-01
Dynamic global vegetation models show large uncertainties regarding the development of the land carbon balance under future climate change conditions. This uncertainty is partly caused by differences in how vegetation carbon turnover is represented in global vegetation models. Model-data integration approaches might help to systematically assess and improve model performances and thus to potentially reduce the uncertainty in terrestrial vegetation responses under future climate change. Here we present several applications of model-data integration with the LPJmL (Lund-Potsdam-Jena managed Lands) dynamic global vegetation model to systematically improve the representation of processes or to estimate model parameters. In a first application, we used global satellite-derived datasets of FAPAR (fraction of absorbed photosynthetic activity), albedo and gross primary production to estimate phenology- and productivity-related model parameters using a genetic optimization algorithm. Thereby we identified major limitations of the phenology module and implemented an alternative empirical phenology model. The new phenology module and optimized model parameters resulted in a better performance of LPJmL in representing global spatial patterns of biomass, tree cover, and the temporal dynamic of atmospheric CO2. Therefore, we used in a second application additionally global datasets of biomass and land cover to estimate model parameters that control vegetation establishment and mortality. The results demonstrate the ability to improve simulations of vegetation dynamics but also highlight the need to improve the representation of mortality processes in dynamic global vegetation models. In a third application, we used multiple site-level observations of ecosystem carbon and water exchange, biomass and soil organic carbon to jointly estimate various model parameters that control ecosystem dynamics. This exercise demonstrates the strong role of individual data streams on the simulated ecosystem dynamics which consequently changed the development of ecosystem carbon stocks and fluxes under future climate and CO2 change. In summary, our results demonstrate challenges and the potential of using model-data integration approaches to improve a dynamic global vegetation model.
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NASA Technical Reports Server (NTRS)
Bragg-Sitton, S. M.; Webster, K. L.
2007-01-01
Nonnuclear testing can be a valuable tool in the development of an in-space nuclear power or propulsion system. In a nonnuclear test facility, electric heaters are used to simulate heat from nuclear fuel. Standard testing allows one to fully assess thermal, heat transfer, and stress related attributes of a given system but fails to demonstrate the dynamic response that would be present in an integrated, fueled reactor system. The integration of thermal hydraulic hardware tests with simulated neutronic response provides a bridge between electrically heated testing and full nuclear testing. By implementing a neutronic response model to simulate the dynamic response that would be expected in a fueled reactor system, one can better understand system integration issues, characterize integrated system response times and response and response characteristics, and assess potential design improvements with a relatively small fiscal investment. Initial system dynamic response testing was demonstrated on the integrated SAFE 100a heat pipe cooled, electrically heated reactor and heat exchanger hardware. This Technical Memorandum discusses the status of the planned dynamic test methodology for implementation in the direct-drive gas-cooled reactor testing and assesses the additional instrumentation needed to implement high-fidelity dynamic testing.
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Applicability of land use models for the Houston area test site
NASA Technical Reports Server (NTRS)
Petersburg, R. K.; Bradford, L. H.
1973-01-01
Descriptions of land use models are presented which were considered for their applicability to the Houston Area Test Site. These models are representative both of the prevailing theories of land use dynamics and of basic approaches to simulation. The models considered are: a model of metropolis, land use simulation model, emperic land use forecasting model, a probabilistic model for residential growth, and the regional environmental management allocation process. Sources of environmental/resource information are listed.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Provost, G.; Zitney, S.; Turton, R.
2009-01-01
To meet increasing demand for education and experience with commercial-scale, coal-fired, integrated gasification combined cycle (IGCC) plants with CO2 capture, the Department of Energy’s (DOE) National Energy Technology Laboratory (NETL) is leading a project to deploy a generic, full-scope, real-time IGCC dynamic plant simulator for use in establishing a world-class research and training center, and to promote and demonstrate IGCC technology to power industry personnel. The simulator, being built by Invensys Process Systems (IPS), will be installed at two separate sites, at NETL and West Virginia University (WVU), and will combine a process/gasification simulator with a power/combined-cycle simulator together inmore » a single dynamic simulation framework for use in engineering research studies and training applications. The simulator, scheduled to be launched in mid-year 2010, will have the following capabilities: High-fidelity, dynamic model of process-side (gasification and gas cleaning with CO2 capture) and power-block-side (combined cycle) for a generic IGCC plant fueled by coal and/or petroleum coke. Highly flexible configuration that allows concurrent training on separate gasification and combined cycle simulators, or up to two IGCC simulators. Ability to enhance and modify the plant model to facilitate studies of changes in plant configuration, equipment, and control strategies to support future R&D efforts. Training capabilities including startup, shutdown, load following and shedding, response to fuel and ambient condition variations, control strategy analysis (turbine vs. gasifier lead, etc.), representative malfunctions/trips, alarms, scenarios, trending, snapshots, data historian, etc. To support this effort, process descriptions and control strategies were developed for key sections of the plant as part of the detailed functional specification, which is serving as the basis of the simulator development. In this paper, we highlight the contents of the detailed functional specification for the simulator. We also describe the engineering, design, and expert testing process that the simulator will undergo in order to ensure that maximum fidelity is built into the generic simulator. Future applications and training programs associated with gasification, combined cycle, and IGCC simulations are discussed, including plant operation and control demonstrations, as well as education and training services.« less
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Graphical user interface for wireless sensor networks simulator
NASA Astrophysics Data System (ADS)
Paczesny, Tomasz; Paczesny, Daniel; Weremczuk, Jerzy
2008-01-01
Wireless Sensor Networks (WSN) are currently very popular area of development. It can be suited in many applications form military through environment monitoring, healthcare, home automation and others. Those networks, when working in dynamic, ad-hoc model, need effective protocols which must differ from common computer networks algorithms. Research on those protocols would be difficult without simulation tool, because real applications often use many nodes and tests on such a big networks take much effort and costs. The paper presents Graphical User Interface (GUI) for simulator which is dedicated for WSN studies, especially in routing and data link protocols evaluation.
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Janice L. Coen; Philip J Riggan
2014-01-01
The 2006 Esperanza Fire in Riverside County, California, was simulated with the Coupled Atmosphere-Wildland Fire Environment (CAWFE) model to examine how dynamic interactions of the atmosphere with large-scale fire spread and energy release may affect observed patterns of fire behavior as mapped using the FireMapper thermal imaging radiometer. CAWFE simulated the...
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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.
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Presti, Davide; Pedone, Alfonso; Mancini, Giordano; Duce, Celia; Tiné, Maria Rosaria; Barone, Vincenzo
2016-01-21
Density functional theory calculations and classical molecular dynamics simulations have been used to investigate the structure and dynamics of water molecules on kaolinite surfaces and confined in the interlayer of a halloysite model of nanometric dimension. The first technique allowed us to accurately describe the structure of the tetrahedral-octahedral slab of kaolinite in vacuum and in interaction with water molecules and to assess the performance of two widely employed empirical force fields to model water/clay interfaces. Classical molecular dynamics simulations were used to study the hydrogen bond network structure and dynamics of water adsorbed on kaolinite surfaces and confined in the halloysite interlayer. The results are in nice agreement with the few experimental data available in the literature, showing a pronounced ordering and reduced mobility of water molecules at the hydrophilic octahedral surfaces of kaolinite and confined in the halloysite interlayer, with respect to water interacting with the hydrophobic tetrahedral surfaces and in the bulk. Finally, this investigation provides new atomistic insights into the structural and dynamical properties of water-clay interfaces, which are of fundamental importance for both natural processes and industrial applications.
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Recent Advances and Perspectives on Nonadiabatic Mixed Quantum-Classical Dynamics.
Crespo-Otero, Rachel; Barbatti, Mario
2018-05-16
Nonadiabatic mixed quantum-classical (NA-MQC) dynamics methods form a class of computational theoretical approaches in quantum chemistry tailored to investigate the time evolution of nonadiabatic phenomena in molecules and supramolecular assemblies. NA-MQC is characterized by a partition of the molecular system into two subsystems: one to be treated quantum mechanically (usually but not restricted to electrons) and another to be dealt with classically (nuclei). The two subsystems are connected through nonadiabatic couplings terms to enforce self-consistency. A local approximation underlies the classical subsystem, implying that direct dynamics can be simulated, without needing precomputed potential energy surfaces. The NA-MQC split allows reducing computational costs, enabling the treatment of realistic molecular systems in diverse fields. Starting from the three most well-established methods-mean-field Ehrenfest, trajectory surface hopping, and multiple spawning-this review focuses on the NA-MQC dynamics methods and programs developed in the last 10 years. It stresses the relations between approaches and their domains of application. The electronic structure methods most commonly used together with NA-MQC dynamics are reviewed as well. The accuracy and precision of NA-MQC simulations are critically discussed, and general guidelines to choose an adequate method for each application are delivered.
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Reversal time of jump-noise magnetization dynamics in nanomagnets via Monte Carlo simulations
NASA Astrophysics Data System (ADS)
Parthasarathy, Arun; Rakheja, Shaloo
2018-06-01
The jump-noise is a nonhomogeneous Poisson process which models thermal effects in magnetization dynamics, with special applications in low temperature escape rate phenomena. In this work, we develop improved numerical methods for Monte Carlo simulation of the jump-noise dynamics and validate the method by comparing the stationary distribution obtained empirically against the Boltzmann distribution. In accordance with the Néel-Brown theory, the jump-noise dynamics display an exponential relaxation toward equilibrium with a characteristic reversal time, which we extract for nanomagnets with uniaxial and cubic anisotropy. We relate the jump-noise dynamics to the equivalent Landau-Lifshitz dynamics up to second order correction for a general energy landscape and obtain the analogous Néel-Brown theory's solution of the reversal time. We find that the reversal time of jump-noise dynamics is characterized by Néel-Brown theory's solution at the energy saddle point for small noise. For large noise, the magnetization reversal due to jump-noise dynamics phenomenologically represents macroscopic tunneling of magnetization.
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NASA Astrophysics Data System (ADS)
Zobnina, V. G.; Kosevich, M. V.; Chagovets, V. V.; Boryak, O. A.
A problem of elucidation of structure of nanomaterials based on combination of proteins and polyether polymers is addressed on the monomeric level of single amino acids and oligomers of PEG-400 and OEG-5 polyethers. Efficiency of application of combined approach involving experimental electrospray mass spectrometry and computer modeling by molecular dynamics simulation is demonstrated. It is shown that oligomers of polyethers form stable complexes with amino acids valine, proline, histidine, glutamic, and aspartic acids. Molecular dynamics simulation has shown that stabilization of amino acid-polyether complexes is achieved due to winding of the polymeric chain around charged groups of amino acids. Structural motives revealed for complexes of single amino acids with polyethers can be realized in structures of protein-polyether nanoparticles currently designed for drug delivery.
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Dynamic Simulation on the Installation Process of HGIS in Transformer Substation
NASA Astrophysics Data System (ADS)
Lin, Tao; Li, Shaohua; Wang, Hu; Che, Deyong; Qi, Guangcai; Yao, Jianfeng; Zhang, Qingzhe
The technological requirements of Hypid Gas Insulated Switchgear (HGIS) installation in transformer substation is high and the control points of quality is excessive. Most of the engineers and technicians in the construction enterprises are not familiar with equipments of HGIS. In order to solve these problem, equipments of HGIS is modeled on the computer by SolidWorks software. Installation process of civil foundation and closed-type equipments is optimized dynamically with virtual assemble technology. Announcements and application work are composited into animation file. Skills of modeling and simulation is tidied classify as well. The result of the visual dynamic simulation can instruct the actual construction process of HGIS to a certain degree and can promote reasonable construction planning and management. It can also improve the method and quality of staff training for electric power construction enterprises.
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Kim, Minkyoung; Choi, Seung-Hoon; Kim, Junhyoung; Choi, Kihang; Shin, Jae-Min; Kang, Sang-Kee; Choi, Yun-Jaie; Jung, Dong Hyun
2009-11-01
This study describes the application of a density-based algorithm to clustering small peptide conformations after a molecular dynamics simulation. We propose a clustering method for small peptide conformations that enables adjacent clusters to be separated more clearly on the basis of neighbor density. Neighbor density means the number of neighboring conformations, so if a conformation has too few neighboring conformations, then it is considered as noise or an outlier and is excluded from the list of cluster members. With this approach, we can easily identify clusters in which the members are densely crowded in the conformational space, and we can safely avoid misclustering individual clusters linked by noise or outliers. Consideration of neighbor density significantly improves the efficiency of clustering of small peptide conformations sampled from molecular dynamics simulations and can be used for predicting peptide structures.
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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
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Scalable Cloning on Large-Scale GPU Platforms with Application to Time-Stepped Simulations on Grids
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
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REMOVAL OF TANK AND SEWER SEDIMENT BY GATE FLUSHING: COMPUTATIONAL FLUID DYNAMICS MODEL STUDIES
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...
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Data Intensive Systems (DIS) Benchmark Performance Summary
2003-08-01
models assumed by today’s conventional architectures. Such applications include model- based Automatic Target Recognition (ATR), synthetic aperture...radar (SAR) codes, large scale dynamic databases/battlefield integration, dynamic sensor- based processing, high-speed cryptanalysis, high speed...distributed interactive and data intensive simulations, data-oriented problems characterized by pointer- based and other highly irregular data structures
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Confidence in the application of models for forecasting and regulatory assessments is furthered by conducting four types of model evaluation: operational, dynamic, diagnostic, and probabilistic. Operational model evaluation alone does not reveal the confidence limits that can be ...
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Govind Rajan, Ananth; Strano, Michael S; Blankschtein, Daniel
2018-04-05
Hexagonal boron nitride (hBN) is an up-and-coming two-dimensional material, with applications in electronic devices, tribology, and separation membranes. Herein, we utilize density-functional-theory-based ab initio molecular dynamics (MD) simulations and lattice dynamics calculations to develop a classical force field (FF) for modeling hBN. The FF predicts the crystal structure, elastic constants, and phonon dispersion relation of hBN with good accuracy and exhibits remarkable agreement with the interlayer binding energy predicted by random phase approximation calculations. We demonstrate the importance of including Coulombic interactions but excluding 1-4 intrasheet interactions to obtain the correct phonon dispersion relation. We find that improper dihedrals do not modify the bulk mechanical properties and the extent of thermal vibrations in hBN, although they impact its flexural rigidity. Combining the FF with the accurate TIP4P/Ice water model yields excellent agreement with interaction energies predicted by quantum Monte Carlo calculations. Our FF should enable an accurate description of hBN interfaces in classical MD simulations.
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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
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Kanjilal, Oindrila, E-mail: oindrila@civil.iisc.ernet.in; Manohar, C.S., E-mail: manohar@civil.iisc.ernet.in
The study considers the problem of simulation based time variant reliability analysis of nonlinear randomly excited dynamical systems. Attention is focused on importance sampling strategies based on the application of Girsanov's transformation method. Controls which minimize the distance function, as in the first order reliability method (FORM), are shown to minimize a bound on the sampling variance of the estimator for the probability of failure. Two schemes based on the application of calculus of variations for selecting control signals are proposed: the first obtains the control force as the solution of a two-point nonlinear boundary value problem, and, the secondmore » explores the application of the Volterra series in characterizing the controls. The relative merits of these schemes, vis-à-vis the method based on ideas from the FORM, are discussed. Illustrative examples, involving archetypal single degree of freedom (dof) nonlinear oscillators, and a multi-degree of freedom nonlinear dynamical system, are presented. The credentials of the proposed procedures are established by comparing the solutions with pertinent results from direct Monte Carlo simulations. - Highlights: • The distance minimizing control forces minimize a bound on the sampling variance. • Establishing Girsanov controls via solution of a two-point boundary value problem. • Girsanov controls via Volterra's series representation for the transfer functions.« less
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Computational Fluid Dynamics (CFD) techniques are increasingly being applied to air quality modeling of short-range dispersion, especially the flow and dispersion around buildings and other geometrically complex structures. The proper application and accuracy of such CFD techniqu...
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Transport dissipative particle dynamics model for mesoscopic advection- diffusion-reaction problems
DOE Office of Scientific and Technical Information (OSTI.GOV)
Zhen, Li; Yazdani, Alireza; Tartakovsky, Alexandre M.
2015-07-07
We present a transport dissipative particle dynamics (tDPD) model for simulating mesoscopic problems involving advection-diffusion-reaction (ADR) processes, along with a methodology for implementation of the correct Dirichlet and Neumann boundary conditions in tDPD simulations. tDPD is an extension of the classic DPD framework with extra variables for describing the evolution of concentration fields. The transport of concentration is modeled by a Fickian flux and a random flux between particles, and an analytical formula is proposed to relate the mesoscopic concentration friction to the effective diffusion coefficient. To validate the present tDPD model and the boundary conditions, we perform three tDPDmore » simulations of one-dimensional diffusion with different boundary conditions, and the results show excellent agreement with the theoretical solutions. We also performed two-dimensional simulations of ADR systems and the tDPD simulations agree well with the results obtained by the spectral element method. Finally, we present an application of the tDPD model to the dynamic process of blood coagulation involving 25 reacting species in order to demonstrate the potential of tDPD in simulating biological dynamics at the mesoscale. We find that the tDPD solution of this comprehensive 25-species coagulation model is only twice as computationally expensive as the DPD simulation of the hydrodynamics only, which is a significant advantage over available continuum solvers.« less
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Babailov, S. P., E-mail: babajlov@niic.nsc.ru; National Research Tomsk Polytechnic University, Lenin Avenue 30, Tomsk 634050; Purtov, P. A.
An expression has been derived for the time dependence of the NMR line shape for systems with multi-site chemical exchange in the absence of spin-spin coupling, in a zero saturation limit. The dynamics of variation of the NMR line shape with time is considered in detail for the case of two-site chemical exchange. Mathematical programs have been designed for numerical simulation of the NMR spectra of chemical exchange systems. The analytical expressions obtained are useful for NMR line shape simulations for systems with photoinduced chemical exchange.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Picard, Richard Roy; Bhat, Kabekode Ghanasham
2017-07-18
We examine sensitivity analysis and uncertainty quantification for molecular dynamics simulation. Extreme (large or small) output values for the LAMMPS code often occur at the boundaries of input regions, and uncertainties in those boundary values are overlooked by common SA methods. Similarly, input values for which code outputs are consistent with calibration data can also occur near boundaries. Upon applying approaches in the literature for imprecise probabilities (IPs), much more realistic results are obtained than for the complacent application of standard SA and code calibration.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Mohsen, O.; Gonin, I.; Kephart, R.
High-power electron beams are sought-after tools in support to a wide array of societal applications. This paper investigates the production of high-power electron beams by combining a high-current field-emission electron source to a superconducting radio-frequency (SRF) cavity. We especially carry out beam-dynamics simulations that demonstrate the viability of the scheme to formmore » $$\\sim$$ 300 kW average-power electron beam using a 1+1/2-cell SRF gun.« less
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Simulation of economic agents interaction in a trade chain
NASA Astrophysics Data System (ADS)
Gimanova, I. A.; Dulesov, A. S.; Litvin, N. V.
2017-01-01
The mathematical model of economic agents interaction is offered in the work. It allowsconsidering the change of price and sales volumesin dynamics according to the process of purchase and sale in the single-product market of the trade and intermediary network. The description of data-flow processes is based on the use of the continuous dynamic market model. The application of ordinary differential equations during the simulation allows one to define areas of coefficients - characteristics of agents - and to investigate their interaction in a chain on stability.
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Application of Ensemble Kalman Filter in Power System State Tracking and Sensitivity
DOE Office of Scientific and Technical Information (OSTI.GOV)
Li, Yulan; Huang, Zhenyu; Zhou, Ning
2012-05-01
Ensemble Kalman Filter (EnKF) is proposed to track dynamic states of generators. The algorithm of EnKF and its application to generator state tracking are presented in detail. The accuracy and sensitivity of the method are analyzed with respect to initial state errors, measurement noise, unknown fault locations, time steps and parameter errors. It is demonstrated through simulation studies that even with some errors in the parameters, the developed EnKF can effectively track generator dynamic states using disturbance data.
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NASA Astrophysics Data System (ADS)
Barros, Ana; Ager, Alan; Preisler, Haiganoush; Day, Michelle; Spies, Tom; Bolte, John
2015-04-01
Agent-based models (ABM) allow users to examine the long-term effects of agent decisions in complex systems where multiple agents and processes interact. This framework has potential application to study the dynamics of coupled natural and human systems where multiple stimuli determine trajectories over both space and time. We used Envision, a landscape based ABM, to analyze long-term wildfire dynamics in a heterogeneous, multi-owner landscape in Oregon, USA. Landscape dynamics are affected by land management policies, actors decisions, and autonomous processes such as vegetation succession, wildfire, or at a broader scale, climate change. Key questions include: 1) How are landscape dynamics influenced by policies and institutions, and 2) How do land management policies and actor decisions interact to produce intended and unintended consequences with respect to wildfire on fire-prone landscapes. Applying Envision to address these questions required the development of a wildfire module that could accurately simulate wildfires on the heterogeneous landscapes within the study area in terms of replicating historical fire size distribution, spatial distribution and fire intensity. In this paper we describe the development and testing of a mechanistic fire simulation system within Envision and application of the model on a 3.2 million fire prone landscape in central Oregon USA. The core fire spread equations use the Minimum Travel Time algorithm developed by M Finney. The model operates on a daily time step and uses a fire prediction system based on the relationship between energy release component and historical fires. Specifically, daily wildfire probabilities and sizes are generated from statistical analyses of historical fires in relation to daily ERC values. The MTT was coupled with the vegetation dynamics module in Envision to allow communication between the respective subsystem and effectively model fire effects and vegetation dynamics after a wildfire. Canopy and surface fuels are modeled in a state and transition framework that accounts for succession, fire effects, and fuels management. Fire effects are modeled using simulated fire intensity (flame length) to calculate expected vegetation impacts for each vegetation state. This talk will describe the mechanics of the simulation system along with initial results of Envision simulations for the Central Oregon study area that explore the dynamics of wildfire, fuel management, and succession over time.
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Passler, Peter P; Hofer, Thomas S
2017-02-15
Stochastic dynamics is a widely employed strategy to achieve local thermostatization in molecular dynamics simulation studies; however, it suffers from an inherent violation of momentum conservation. Although this short-coming has little impact on structural and short-time dynamic properties, it can be shown that dynamics in the long-time limit such as diffusion is strongly dependent on the respective thermostat setting. Application of the methodically similar dissipative particle dynamics (DPD) provides a simple, effective strategy to ensure the advantages of local, stochastic thermostatization while at the same time the linear momentum of the system remains conserved. In this work, the key parameters to employ the DPD thermostats in the framework of periodic boundary conditions are investigated, in particular the dependence of the system properties on the size of the DPD-region as well as the treatment of forces near the cutoff. Structural and dynamical data for light and heavy water as well as a Lennard-Jones fluid have been compared to simulations executed via stochastic dynamics as well as via use of the widely employed Nose-Hoover chain and Berendsen thermostats. It is demonstrated that a small size of the DPD region is sufficient to achieve local thermalization, while at the same time artifacts in the self-diffusion characteristic for stochastic dynamics are eliminated. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
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SiC-VJFETs power switching devices: an improved model and parameter optimization technique
NASA Astrophysics Data System (ADS)
Ben Salah, T.; Lahbib, Y.; Morel, H.
2009-12-01
Silicon carbide junction field effect transistor (SiC-JFETs) is a mature power switch newly applied in several industrial applications. SiC-JFETs are often simulated by Spice model in order to predict their electrical behaviour. Although such a model provides sufficient accuracy for some applications, this paper shows that it presents serious shortcomings in terms of the neglect of the body diode model, among many others in circuit model topology. Simulation correction is then mandatory and a new model should be proposed. Moreover, this paper gives an enhanced model based on experimental dc and ac data. New devices are added to the conventional circuit model giving accurate static and dynamic behaviour, an effect not accounted in the Spice model. The improved model is implemented into VHDL-AMS language and steady-state dynamic and transient responses are simulated for many SiC-VJFETs samples. Very simple and reliable optimization algorithm based on the optimization of a cost function is proposed to extract the JFET model parameters. The obtained parameters are verified by comparing errors between simulations results and experimental data.
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Song, Chen; Corry, Ben
2011-01-01
The macroscopic Nernst-Planck (NP) theory has often been used for predicting ion channel currents in recent years, but the validity of this theory at the microscopic scale has not been tested. In this study we systematically tested the ability of the NP theory to accurately predict channel currents by combining and comparing the results with those of Brownian dynamics (BD) simulations. To thoroughly test the theory in a range of situations, calculations were made in a series of simplified cylindrical channels with radii ranging from 3 to 15 Å, in a more complex ‘catenary’ channel, and in a realistic model of the mechanosensitive channel MscS. The extensive tests indicate that the NP equation is applicable in narrow ion channels provided that accurate concentrations and potentials can be input as the currents obtained from the combination of BD and NP match well with those obtained directly from BD simulations, although some discrepancies are seen when the ion concentrations are not radially uniform. This finding opens a door to utilising the results of microscopic simulations in continuum theory, something that is likely to be useful in the investigation of a range of biophysical and nano-scale applications and should stimulate further studies in this direction. PMID:21731672
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Song, Chen; Corry, Ben
2011-01-01
The macroscopic Nernst-Planck (NP) theory has often been used for predicting ion channel currents in recent years, but the validity of this theory at the microscopic scale has not been tested. In this study we systematically tested the ability of the NP theory to accurately predict channel currents by combining and comparing the results with those of Brownian dynamics (BD) simulations. To thoroughly test the theory in a range of situations, calculations were made in a series of simplified cylindrical channels with radii ranging from 3 to 15 Å, in a more complex 'catenary' channel, and in a realistic model of the mechanosensitive channel MscS. The extensive tests indicate that the NP equation is applicable in narrow ion channels provided that accurate concentrations and potentials can be input as the currents obtained from the combination of BD and NP match well with those obtained directly from BD simulations, although some discrepancies are seen when the ion concentrations are not radially uniform. This finding opens a door to utilising the results of microscopic simulations in continuum theory, something that is likely to be useful in the investigation of a range of biophysical and nano-scale applications and should stimulate further studies in this direction.
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NASA Astrophysics Data System (ADS)
Amengonu, Yawo H.; Kakad, Yogendra P.
2014-07-01
Quasivelocity techniques were applied to derive the dynamics of a Differential Wheeled Mobile Robot (DWMR) in the companion paper. The present paper formulates a control system design for trajectory tracking of this class of robots. The method develops a feedback linearization technique for the nonlinear system using dynamic extension algorithm. The effectiveness of the nonlinear controller is illustrated with simulation example.
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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
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NASA Technical Reports Server (NTRS)
Manouchehri, Davoud; Lindsay, Thomas; Ghosh, David
1994-01-01
NASA's Langley Research Center (LaRC) is addressing the problem of isolating the vibrations of the Shuttle remote manipulator system (RMS) from its end-effector and/or payload by modeling an RMS flat-floor simulator with a dynamic payload. Analysis of the model can lead to control techniques that will improve the speed, accuracy, and safety of the RMS in capturing satellites and eventually facilitate berthing with the space station. Rockwell International Corporation, also involved in vibration isolation, has developed a hardware interface unit to isolate the end-effector from the vibrations of an arm on a Shuttle robotic tile processing system (RTPS). To apply the RTPS isolation techniques to long-reach arms like the RMS, engineers have modeled the dynamics of the hardware interface unit with simulation software. By integrating the Rockwell interface model with the NASA LaRC RMS simulator model, investigators can study the use of a hardware interface to isolate dynamic payloads from the RMS. The interface unit uses both active and passive compliance and damping for vibration isolation. Thus equipped, the RMS could be used as a telemanipulator with control characteristics for capture and berthing operations. The hardware interface also has applications in industry.
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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.
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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
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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
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Validating clustering of molecular dynamics simulations using polymer models.
Phillips, Joshua L; Colvin, Michael E; Newsam, Shawn
2011-11-14
Molecular dynamics (MD) simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our knowledge, our framework is the first to utilize model polymers to rigorously test the utility of clustering algorithms for studying biopolymers.
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Validating clustering of molecular dynamics simulations using polymer models
2011-01-01
Background Molecular dynamics (MD) simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. Results We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. Conclusions We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our knowledge, our framework is the first to utilize model polymers to rigorously test the utility of clustering algorithms for studying biopolymers. PMID:22082218
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Halloran, Jason P; Ackermann, Marko; Erdemir, Ahmet; van den Bogert, Antonie J
2010-10-19
Current computational methods for simulating locomotion have primarily used muscle-driven multibody dynamics, in which neuromuscular control is optimized. Such simulations generally represent joints and soft tissue as simple kinematic or elastic elements for computational efficiency. These assumptions limit application in studies such as ligament injury or osteoarthritis, where local tissue loading must be predicted. Conversely, tissue can be simulated using the finite element method with assumed or measured boundary conditions, but this does not represent the effects of whole body dynamics and neuromuscular control. Coupling the two domains would overcome these limitations and allow prediction of movement strategies guided by tissue stresses. Here we demonstrate this concept in a gait simulation where a musculoskeletal model is coupled to a finite element representation of the foot. Predictive simulations incorporated peak plantar tissue deformation into the objective of the movement optimization, as well as terms to track normative gait data and minimize fatigue. Two optimizations were performed, first without the strain minimization term and second with the term. Convergence to realistic gait patterns was achieved with the second optimization realizing a 44% reduction in peak tissue strain energy density. The study demonstrated that it is possible to alter computationally predicted neuromuscular control to minimize tissue strain while including desired kinematic and muscular behavior. Future work should include experimental validation before application of the methodology to patient care. Copyright © 2010 Elsevier Ltd. All rights reserved.
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Influence of changes in initial conditions for the simulation of dynamic systems
DOE Office of Scientific and Technical Information (OSTI.GOV)
Kotyrba, Martin
2015-03-10
Chaos theory is a field of study in mathematics, with applications in several disciplines including meteorology, sociology, physics, engineering, economics, biology, and philosophy. Chaos theory studies the behavior of dynamical systems that are highly sensitive to initial conditions—a paradigm popularly referred to as the butterfly effect. Small differences in initial conditions field widely diverging outcomes for such dynamical systems, rendering long-term prediction impossible in general. This happens even though these systems are deterministic, meaning that their future behavior is fully determined by their initial conditions, with no random elements involved. In this paperinfluence of changes in initial conditions will bemore » presented for the simulation of Lorenz system.« less
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Fast generating Greenberger-Horne-Zeilinger state via iterative interaction pictures
NASA Astrophysics Data System (ADS)
Huang, Bi-Hua; Chen, Ye-Hong; Wu, Qi-Cheng; Song, Jie; Xia, Yan
2016-10-01
We delve a little deeper into the construction of shortcuts to adiabatic passage for three-level systems by iterative interaction picture (multiple Schrödinger dynamics). As an application example, we use the deduced iterative based shortcuts to rapidly generate the Greenberger-Horne-Zeilinger (GHZ) state in a three-atom system with the help of quantum Zeno dynamics. Numerical simulation shows the dynamics designed by the iterative picture method is physically feasible and the shortcut scheme performs much better than that using the conventional adiabatic passage techniques. Also, the influences of various decoherence processes are discussed by numerical simulation and the results prove that the scheme is fast and robust against decoherence and operational imperfection.
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DECISION MAKING , * GROUP DYNAMICS, NAVAL TRAINING, TRANSFER OF TRAINING, SCIENTIFIC RESEARCH, CLASSIFICATION, PROBLEM SOLVING, MATHEMATICAL MODELS, SUBMARINES, SIMULATORS, PERFORMANCE(HUMAN), UNDERSEA WARFARE.
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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
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All-atom molecular dynamics of virus capsids as drug targets
Perilla, Juan R.; Hadden, Jodi A.; Goh, Boon Chong; ...
2016-04-29
Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid–protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways.more » When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Finally, the current challenges of performing all-atom capsid–drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets.« less
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NASA Astrophysics Data System (ADS)
Heimann, F. U. M.; Rickenmann, D.; Turowski, J. M.; Kirchner, J. W.
2014-07-01
Especially in mountainuous environments, the prediction of sediment dynamics is important for managing natural hazards, assessing in-stream habitats, and understanding geomorphic evolution. We present the new modelling tool sedFlow for simulating fractional bedload transport dynamics in mountain streams. The model can deal with the effects of adverse slopes and uses state of the art approaches for quantifying macro-roughness effects in steep channels. Local grain size distributions are dynamically adjusted according to the transport dynamics of each grain size fraction. The tool sedFlow features fast calculations and straightforward pre- and postprocessing of simulation data. The model is provided together with its complete source code free of charge under the terms of the GNU General Public License (www.wsl.ch/sedFlow). Examples of the application of sedFlow are given in a companion article by Heimann et al. (2014).
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All-atom molecular dynamics of virus capsids as drug targets
DOE Office of Scientific and Technical Information (OSTI.GOV)
Perilla, Juan R.; Hadden, Jodi A.; Goh, Boon Chong
Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid–protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways.more » When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Finally, the current challenges of performing all-atom capsid–drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets.« less
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Extended Phase-Space Methods for Enhanced Sampling in Molecular Simulations: A Review.
Fujisaki, Hiroshi; Moritsugu, Kei; Matsunaga, Yasuhiro; Morishita, Tetsuya; Maragliano, Luca
2015-01-01
Molecular Dynamics simulations are a powerful approach to study biomolecular conformational changes or protein-ligand, protein-protein, and protein-DNA/RNA interactions. Straightforward applications, however, are often hampered by incomplete sampling, since in a typical simulated trajectory the system will spend most of its time trapped by high energy barriers in restricted regions of the configuration space. Over the years, several techniques have been designed to overcome this problem and enhance space sampling. Here, we review a class of methods that rely on the idea of extending the set of dynamical variables of the system by adding extra ones associated to functions describing the process under study. In particular, we illustrate the Temperature Accelerated Molecular Dynamics (TAMD), Logarithmic Mean Force Dynamics (LogMFD), and Multiscale Enhanced Sampling (MSES) algorithms. We also discuss combinations with techniques for searching reaction paths. We show the advantages presented by this approach and how it allows to quickly sample important regions of the free-energy landscape via automatic exploration.
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NASA Astrophysics Data System (ADS)
Hill, James C.; Liu, Zhenping; Fox, Rodney O.; Passalacqua, Alberto; Olsen, Michael G.
2015-11-01
The multi-inlet vortex reactor (MIVR) has been developed to provide a platform for rapid mixing in the application of flash nanoprecipitation (FNP) for manufacturing functional nanoparticles. Unfortunately, commonly used RANS methods are unable to accurately model this complex swirling flow. Large eddy simulations have also been problematic, as expensive fine grids to accurately model the flow are required. These dilemmas led to the strategy of applying a Delayed Detached Eddy Simulation (DDES) method to the vortex reactor. In the current work, the turbulent swirling flow inside a scaled-up MIVR has been investigated by using a dynamic DDES model. In the DDES model, the eddy viscosity has a form similar to the Smagorinsky sub-grid viscosity in LES and allows the implementation of a dynamic procedure to determine its coefficient. The complex recirculating back flow near the reactor center has been successfully captured by using this dynamic DDES model. Moreover, the simulation results are found to agree with experimental data for mean velocity and Reynolds stresses.
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NASA Astrophysics Data System (ADS)
Zhu, W. C.; Niu, L. L.; Li, S. H.; Xu, Z. H.
2015-09-01
The tensile strength of rock subjected to dynamic loading constitutes many engineering applications such as rock drilling and blasting. The dynamic Brazilian test of rock specimens was conducted with the split Hopkinson pressure bar (SHPB) driven by pendulum hammer, in order to determine the indirect tensile strength of rock under an intermediate strain rate ranging from 5.2 to 12.9 s-1, which is achieved when the incident bar is impacted by pendulum hammer with different velocities. The incident wave excited by pendulum hammer is triangular in shape, featuring a long rising time, and it is considered to be helpful for achieving a constant strain rate in the rock specimen. The dynamic indirect tensile strength of rock increases with strain rate. Then, the numerical simulator RFPA-Dynamics, a well-recognized software for simulating the rock failure under dynamic loading, is validated by reproducing the Brazilian test of rock when the incident stress wave retrieved at the incident bar is input as the boundary condition, and then it is employed to study the Brazilian test of rock under the higher strain rate. Based on the numerical simulation, the strain-rate dependency of tensile strength and failure pattern of the Brazilian disc specimen under the intermediate strain rate are numerically simulated, and the associated failure mechanism is clarified. It is deemed that the material heterogeneity should be a reason for the strain-rate dependency of rock.
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Bandwidth and SIMDUCE as simulator fidelity criteria
NASA Technical Reports Server (NTRS)
Key, David
1992-01-01
The potential application of two concepts from the new Handling Qualities Specification for Military Rotorcraft was discussed. The first concept is bandwidth, a measure of the dynamic response to control. The second is a qualitative technique developed for assessing the visual cue environment the pilot has in bad weather and at night. Simulated Day Usable Cue Environment (SIMDUCE) applies this concept to assessing the day cuing fidelity in the simulator.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Soules, T F; Gilmer, G H; Matthews, M J
2010-10-21
We compare force fields (FF's) that have been used in molecular dynamic (MD) simulations of silica in order to assess their applicability for use in simulating IR-laser damage mitigation. Although pairwise FF?s obtained by fitting quantum mechanical calculations such as the BKS and CHIK potentials have been shown to reproduce many of the properties of silica including the stability of silica polymorphs and the densification of the liquid, we show that melting temperatures and fictive temperatures are much too high. Softer empirical force fields give liquid and glass properties at experimental temperatures but may not predict all properties important tomore » laser mitigation experiments.« less
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A novel Kinetic Monte Carlo algorithm for Non-Equilibrium Simulations
NASA Astrophysics Data System (ADS)
Jha, Prateek; Kuzovkov, Vladimir; Grzybowski, Bartosz; Olvera de La Cruz, Monica
2012-02-01
We have developed an off-lattice kinetic Monte Carlo simulation scheme for reaction-diffusion problems in soft matter systems. The definition of transition probabilities in the Monte Carlo scheme are taken identical to the transition rates in a renormalized master equation of the diffusion process and match that of the Glauber dynamics of Ising model. Our scheme provides several advantages over the Brownian dynamics technique for non-equilibrium simulations. Since particle displacements are accepted/rejected in a Monte Carlo fashion as opposed to moving particles following a stochastic equation of motion, nonphysical movements (e.g., violation of a hard core assumption) are not possible (these moves have zero acceptance). Further, the absence of a stochastic ``noise'' term resolves the computational difficulties associated with generating statistically independent trajectories with definitive mean properties. Finally, since the timestep is independent of the magnitude of the interaction forces, much longer time-steps can be employed than Brownian dynamics. We discuss the applications of this scheme for dynamic self-assembly of photo-switchable nanoparticles and dynamical problems in polymeric systems.
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Laszlo, Sarah; Armstrong, Blair C
2014-05-01
The Parallel Distributed Processing (PDP) framework is built on neural-style computation, and is thus well-suited for simulating the neural implementation of cognition. However, relatively little cognitive modeling work has concerned neural measures, instead focusing on behavior. Here, we extend a PDP model of reading-related components in the Event-Related Potential (ERP) to simulation of the N400 repetition effect. We accomplish this by incorporating the dynamics of cortical post-synaptic potentials--the source of the ERP signal--into the model. Simulations demonstrate that application of these dynamics is critical for model elicitation of repetition effects in the time and frequency domains. We conclude that by advancing a neurocomputational understanding of repetition effects, we are able to posit an interpretation of their source that is both explicitly specified and mechanistically different from the well-accepted cognitive one. Copyright © 2014 Elsevier Inc. All rights reserved.
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Contact dynamics recording and analysis system using an optical fiber sensor approach
NASA Astrophysics Data System (ADS)
Anghel, F.; Pavelescu, D.; Grattan, K. T. V.; Palmer, A. W.
1997-09-01
A contact dynamics recording and analysis system configured using an optical fiber sensor has been developed having been designed with a particular application to the accurate and time-varying description of moving contact operating during electrical arc breaking, in an experimental platform simulating the operation of a vacuum circuit breaker. The system utilizes dynamic displacement measurement and data recording and a post-process data analysis to reveal the dynamic speed and acceleration data of the equipment.
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Perspective: Markov models for long-timescale biomolecular dynamics.
Schwantes, C R; McGibbon, R T; Pande, V S
2014-09-07
Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is insufficient, as researchers must be able to transform the data in a simulation trajectory into specific scientific insights. Although this analysis step has often been taken for granted, it deserves further attention as large-scale simulations become increasingly routine. In this perspective, we discuss the application of Markov models to the analysis of large-scale biomolecular simulations. We draw attention to recent improvements in the construction of these models as well as several important open issues. In addition, we highlight recent theoretical advances that pave the way for a new generation of models of molecular kinetics.
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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.
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Analysis on the dynamic error for optoelectronic scanning coordinate measurement network
NASA Astrophysics Data System (ADS)
Shi, Shendong; Yang, Linghui; Lin, Jiarui; Guo, Siyang; Ren, Yongjie
2018-01-01
Large-scale dynamic three-dimension coordinate measurement technique is eagerly demanded in equipment manufacturing. Noted for advantages of high accuracy, scale expandability and multitask parallel measurement, optoelectronic scanning measurement network has got close attention. It is widely used in large components jointing, spacecraft rendezvous and docking simulation, digital shipbuilding and automated guided vehicle navigation. At present, most research about optoelectronic scanning measurement network is focused on static measurement capacity and research about dynamic accuracy is insufficient. Limited by the measurement principle, the dynamic error is non-negligible and restricts the application. The workshop measurement and positioning system is a representative which can realize dynamic measurement function in theory. In this paper we conduct deep research on dynamic error resources and divide them two parts: phase error and synchronization error. Dynamic error model is constructed. Based on the theory above, simulation about dynamic error is carried out. Dynamic error is quantized and the rule of volatility and periodicity has been found. Dynamic error characteristics are shown in detail. The research result lays foundation for further accuracy improvement.
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DEVELOPMENT AND APPLICATIONS OF CFD SIMULATIONS SUPPORTING URBAN AIR QUALITY AND HOMELAND SECURITY
Prior to September 11, 2001 developments of Computational Fluid Dynamics (CFD) were begun to support air quality applications. CFD models are emerging as a promising technology for such assessments, in part due to the advancing power of computational hardware and software. CFD si...
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Automated design of spacecraft systems power subsystems
NASA Technical Reports Server (NTRS)
Terrile, Richard J.; Kordon, Mark; Mandutianu, Dan; Salcedo, Jose; Wood, Eric; Hashemi, Mona
2006-01-01
This paper discusses the application of evolutionary computing to a dynamic space vehicle power subsystem resource and performance simulation in a parallel processing environment. Our objective is to demonstrate the feasibility, application and advantage of using evolutionary computation techniques for the early design search and optimization of space systems.
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There is a need to properly develop the application of Computational Fluid Dynamics (CFD) methods in support of air quality studies involving pollution sources near buildings at industrial sites. CFD models are emerging as a promising technology for such assessments, in part due ...
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Computational Fluid Dynamics (CFD) techniques are increasingly being applied to air quality modeling of short-range dispersion, especially the flow and dispersion around buildings and other geometrically complex structures. The proper application and accuracy of such CFD techniqu...
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NASA Technical Reports Server (NTRS)
Teles, Jerome (Editor); Samii, Mina V. (Editor)
1993-01-01
A conference on spaceflight dynamics produced papers in the areas of orbit determination, spacecraft tracking, autonomous navigation, the Deep Space Program Science Experiment Mission (DSPSE), the Global Positioning System, attitude control, geostationary satellites, interplanetary missions and trajectories, applications of estimation theory, flight dynamics systems, low-Earth orbit missions, orbital mechanics, mission experience in attitude dynamics, mission experience in sensor studies, attitude dynamics theory and simulations, and orbit-related experience. These papaers covered NASA, European, Russian, Japanese, Chinese, and Brazilian space programs and hardware.
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NASA Astrophysics Data System (ADS)
Byun, Hye Suk; El-Naggar, Mohamed Y.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya
2017-10-01
Kinetic Monte Carlo (KMC) simulations are used to study long-time dynamics of a wide variety of systems. Unfortunately, the conventional KMC algorithm is not scalable to larger systems, since its time scale is inversely proportional to the simulated system size. A promising approach to resolving this issue is the synchronous parallel KMC (SPKMC) algorithm, which makes the time scale size-independent. This paper introduces a formal derivation of the SPKMC algorithm based on local transition-state and time-dependent Hartree approximations, as well as its scalable parallel implementation based on a dual linked-list cell method. The resulting algorithm has achieved a weak-scaling parallel efficiency of 0.935 on 1024 Intel Xeon processors for simulating biological electron transfer dynamics in a 4.2 billion-heme system, as well as decent strong-scaling parallel efficiency. The parallel code has been used to simulate a lattice of cytochrome complexes on a bacterial-membrane nanowire, and it is broadly applicable to other problems such as computational synthesis of new materials.
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NASA Astrophysics Data System (ADS)
Esposti Ongaro, T.; Barsotti, S.; de'Michieli Vitturi, M.; Favalli, M.; Longo, A.; Nannipieri, L.; Neri, A.; Papale, P.; Saccorotti, G.
2009-12-01
Physical and numerical modelling is becoming of increasing importance in volcanology and volcanic hazard assessment. However, new interdisciplinary problems arise when dealing with complex mathematical formulations, numerical algorithms and their implementations on modern computer architectures. Therefore new frameworks are needed for sharing knowledge, software codes, and datasets among scientists. Here we present the Volcano Modelling and Simulation gateway (VMSg, accessible at http://vmsg.pi.ingv.it), a new electronic infrastructure for promoting knowledge growth and transfer in the field of volcanological modelling and numerical simulation. The new web portal, developed in the framework of former and ongoing national and European projects, is based on a dynamic Content Manager System (CMS) and was developed to host and present numerical models of the main volcanic processes and relationships including magma properties, magma chamber dynamics, conduit flow, plume dynamics, pyroclastic flows, lava flows, etc. Model applications, numerical code documentation, simulation datasets as well as model validation and calibration test-cases are also part of the gateway material.
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Process simulation and dynamic control for marine oily wastewater treatment using UV irradiation.
Jing, Liang; Chen, Bing; Zhang, Baiyu; Li, Pu
2015-09-15
UV irradiation and advanced oxidation processes have been recently regarded as promising solutions in removing polycyclic aromatic hydrocarbons (PAHs) from marine oily wastewater. However, such treatment methods are generally not sufficiently understood in terms of reaction mechanisms, process simulation and process control. These deficiencies can drastically hinder their application in shipping and offshore petroleum industries which produce bilge/ballast water and produced water as the main streams of marine oily wastewater. In this study, the factorial design of experiment was carried out to investigate the degradation mechanism of a typical PAH, namely naphthalene, under UV irradiation in seawater. Based on the experimental results, a three-layer feed-forward artificial neural network simulation model was developed to simulate the treatment process and to forecast the removal performance. A simulation-based dynamic mixed integer nonlinear programming (SDMINP) approach was then proposed to intelligently control the treatment process by integrating the developed simulation model, genetic algorithm and multi-stage programming. The applicability and effectiveness of the developed approach were further tested though a case study. The experimental results showed that the influences of fluence rate and temperature on the removal of naphthalene were greater than those of salinity and initial concentration. The developed simulation model could well predict the UV-induced removal process under varying conditions. The case study suggested that the SDMINP approach, with the aid of the multi-stage control strategy, was able to significantly reduce treatment cost when comparing to the traditional single-stage process optimization. The developed approach and its concept/framework have high potential of applicability in other environmental fields where a treatment process is involved and experimentation and modeling are used for process simulation and control. Copyright © 2015 Elsevier Ltd. All rights reserved.
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Demodulation System for Fiber Optic Bragg Grating Dynamic Pressure Sensing
NASA Technical Reports Server (NTRS)
Lekki, John D.; Adamovsky, Grigory; Floyd, Bertram
2001-01-01
Fiber optic Bragg gratings have been used for years to measure quasi-static phenomena. In aircraft engine applications there is a need to measure dynamic signals such as variable pressures. In order to monitor these pressures a detection system with broad dynamic range is needed. This paper describes an interferometric demodulator that was developed and optimized for this particular application. The signal to noise ratio was maximized through temporal coherence analysis. The demodulator was incorporated in a laboratory system that simulates conditions to be measured. Several pressure sensor configurations incorporating a fiber optic Bragg grating were also explored. The results of the experiments are reported in this paper.
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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.
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Foroutan, Masumeh; Fatemi, S Mahmood; Esmaeilian, Farshad
2017-02-01
During the past decade, the research on fluids in nanoconfined geometries has received considerable attention as a consequence of their wide applications in different fields. Several nanoconfined systems such as water and ionic liquids, together with an equally impressive array of nanoconfining media such as carbon nanotube, graphene and graphene oxide have received increasingly growing interest in the past years. Water is the first system that has been reviewed in this article, due to its important role in transport phenomena in environmental sciences. Water is often considered as a highly nanoconfined system, due to its reduction to a few layers of water molecules between the extended surface of large macromolecules. The second system discussed here is ionic liquids, which have been widely studied in the modern green chemistry movement. Considering the great importance of ionic liquids in industry, and also their oil/water counterpart, nanoconfined ionic liquid system has become an important area of research with many fascinating applications. Furthermore, the method of molecular dynamics simulation is one of the major tools in the theoretical study of water and ionic liquids in nanoconfinement, which increasingly has been joined with experimental procedures. In this way, the choice of water and ionic liquids in nanoconfinement is justified by applying molecular dynamics simulation approaches in this review article.
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MHSS: a material handling system simulator
DOE Office of Scientific and Technical Information (OSTI.GOV)
Pomernacki, L.; Hollstien, R.B.
1976-04-07
A Material Handling System Simulator (MHSS) program is described that provides specialized functional blocks for modeling and simulation of nuclear material handling systems. Models of nuclear fuel fabrication plants may be built using functional blocks that simulate material receiving, storage, transport, inventory, processing, and shipping operations as well as the control and reporting tasks of operators or on-line computers. Blocks are also provided that allow the user to observe and gather statistical information on the dynamic behavior of simulated plants over single or replicated runs. Although it is currently being developed for the nuclear materials handling application, MHSS can bemore » adapted to other industries in which material accountability is important. In this paper, emphasis is on the simulation methodology of the MHSS program with application to the nuclear material safeguards problem. (auth)« less
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Signature modelling and radiometric rendering equations in infrared scene simulation systems
NASA Astrophysics Data System (ADS)
Willers, Cornelius J.; Willers, Maria S.; Lapierre, Fabian
2011-11-01
The development and optimisation of modern infrared systems necessitates the use of simulation systems to create radiometrically realistic representations (e.g. images) of infrared scenes. Such simulation systems are used in signature prediction, the development of surveillance and missile sensors, signal/image processing algorithm development and aircraft self-protection countermeasure system development and evaluation. Even the most cursory investigation reveals a multitude of factors affecting the infrared signatures of realworld objects. Factors such as spectral emissivity, spatial/volumetric radiance distribution, specular reflection, reflected direct sunlight, reflected ambient light, atmospheric degradation and more, all affect the presentation of an object's instantaneous signature. The signature is furthermore dynamically varying as a result of internal and external influences on the object, resulting from the heat balance comprising insolation, internal heat sources, aerodynamic heating (airborne objects), conduction, convection and radiation. In order to accurately render the object's signature in a computer simulation, the rendering equations must therefore account for all the elements of the signature. In this overview paper, the signature models, rendering equations and application frameworks of three infrared simulation systems are reviewed and compared. The paper first considers the problem of infrared scene simulation in a framework for simulation validation. This approach provides concise definitions and a convenient context for considering signature models and subsequent computer implementation. The primary radiometric requirements for an infrared scene simulator are presented next. The signature models and rendering equations implemented in OSMOSIS (Belgian Royal Military Academy), DIRSIG (Rochester Institute of Technology) and OSSIM (CSIR & Denel Dynamics) are reviewed. In spite of these three simulation systems' different application focus areas, their underlying physics-based approach is similar. The commonalities and differences between the different systems are investigated, in the context of their somewhat different application areas. The application of an infrared scene simulation system towards the development of imaging missiles and missile countermeasures are briefly described. Flowing from the review of the available models and equations, recommendations are made to further enhance and improve the signature models and rendering equations in infrared scene simulators.
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The ReaxFF reactive force-field: Development, applications, and future directions
Senftle, Thomas; Hong, Sungwook; Islam, Md Mahbubul; ...
2016-03-04
The reactive force-field (ReaxFF) interatomic potential is a powerful computational tool for exploring, developing and optimizing material properties. Methods based on the principles of quantum mechanics (QM), while offering valuable theoretical guidance at the electronic level, are often too computationally intense for simulations that consider the full dynamic evolution of a system. Alternatively, empirical interatomic potentials that are based on classical principles require significantly fewer computational resources, which enables simulations to better describe dynamic processes over longer timeframes and on larger scales. Such methods, however, typically require a predefined connectivity between atoms, precluding simulations that involve reactive events. The ReaxFFmore » method was developed to help bridge this gap. Approaching the gap from the classical side, ReaxFF casts the empirical interatomic potential within a bond-order formalism, thus implicitly describing chemical bonding without expensive QM calculations. As a result, this article provides an overview of the development, application, and future directions of the ReaxFF method.« less
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Force fields and scoring functions for carbohydrate simulation.
Xiong, Xiuming; Chen, Zhaoqiang; Cossins, Benjamin P; Xu, Zhijian; Shao, Qiang; Ding, Kai; Zhu, Weiliang; Shi, Jiye
2015-01-12
Carbohydrate dynamics plays a vital role in many biological processes, but we are not currently able to probe this with experimental approaches. The highly flexible nature of carbohydrate structures differs in many aspects from other biomolecules, posing significant challenges for studies employing computational simulation. Over past decades, computational study of carbohydrates has been focused on the development of structure prediction methods, force field optimization, molecular dynamics simulation, and scoring functions for carbohydrate-protein interactions. Advances in carbohydrate force fields and scoring functions can be largely attributed to enhanced computational algorithms, application of quantum mechanics, and the increasing number of experimental structures determined by X-ray and NMR techniques. The conformational analysis of carbohydrates is challengeable and has gone into intensive study in elucidating the anomeric, the exo-anomeric, and the gauche effects. Here, we review the issues associated with carbohydrate force fields and scoring functions, which will have a broad application in the field of carbohydrate-based drug design. Copyright © 2014 Elsevier Ltd. All rights reserved.
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Computer-aided applications of nanoscale smart materials for biomedical applications.
Rakesh, L; Howell, B A; Chai, M; Mueller, A; Kujawski, M; Fan, D; Ravi, S; Slominski, C
2008-10-01
Nanotechnology has the potential to impact the treatment of many diseases that currently plague society: cancer, AIDS, dementia of various kinds and so on. Nanoscale smart materials, such as carbon nanotubes, C(60), dendrimers and cyclodextrins, hold great promise for use in the development of better diagnostics, drug delivery and the alteration of biological function. Although experimentation is being used to explore the potential offered by these materials, it is by its very nature expensive in terms of time, resources and expertise. Insight with respect to the behavior of these materials in the presence of biological entities can be obtained much more rapidly by molecular dynamics simulation. Furthermore, the results of simulation may be used to guide experimentation so that it is much more productive than it might be in the absence of such information. The interactions of several nanoscale structures with biological macromolecules can already be probed effectively using molecular dynamics simulation. The results obtained should form the basis for significant new developments in the treatment of disease.
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NASA Astrophysics Data System (ADS)
Bruschetta, M.; Maran, F.; Beghi, A.
2017-06-01
The use of dynamic driving simulators is constantly increasing in the automotive community, with applications ranging from vehicle development to rehab and driver training. The effectiveness of such devices is related to their capabilities of well reproducing the driving sensations, hence it is crucial that the motion control strategies generate both realistic and feasible inputs to the platform. Such strategies are called motion cueing algorithms (MCAs). In recent years several MCAs based on model predictive control (MPC) techniques have been proposed. The main drawback associated with the use of MPC is its computational burden, that may limit their application to high performance dynamic simulators. In the paper, a fast, real-time implementation of an MPC-based MCA for 9 DOF, high performance platform is proposed. Effectiveness of the approach in managing the available working area is illustrated by presenting experimental results from an implementation on a real device with a 200 Hz control frequency.
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Overview of ICE Project: Integration of Computational Fluid Dynamics and Experiments
NASA Technical Reports Server (NTRS)
Stegeman, James D.; Blech, Richard A.; Babrauckas, Theresa L.; Jones, William H.
2001-01-01
Researchers at the NASA Glenn Research Center have developed a prototype integrated environment for interactively exploring, analyzing, and validating information from computational fluid dynamics (CFD) computations and experiments. The Integrated CFD and Experiments (ICE) project is a first attempt at providing a researcher with a common user interface for control, manipulation, analysis, and data storage for both experiments and simulation. ICE can be used as a live, on-tine system that displays and archives data as they are gathered; as a postprocessing system for dataset manipulation and analysis; and as a control interface or "steering mechanism" for simulation codes while visualizing the results. Although the full capabilities of ICE have not been completely demonstrated, this report documents the current system. Various applications of ICE are discussed: a low-speed compressor, a supersonic inlet, real-time data visualization, and a parallel-processing simulation code interface. A detailed data model for the compressor application is included in the appendix.
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Molecular dynamics simulations through GPU video games technologies
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
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Machine learning from computer simulations with applications in rail vehicle dynamics
NASA Astrophysics Data System (ADS)
Taheri, Mehdi; Ahmadian, Mehdi
2016-05-01
The application of stochastic modelling for learning the behaviour of a multibody dynamics (MBD) models is investigated. Post-processing data from a simulation run are used to train the stochastic model that estimates the relationship between model inputs (suspension relative displacement and velocity) and the output (sum of suspension forces). The stochastic model can be used to reduce the computational burden of the MBD model by replacing a computationally expensive subsystem in the model (suspension subsystem). With minor changes, the stochastic modelling technique is able to learn the behaviour of a physical system and integrate its behaviour within MBD models. The technique is highly advantageous for MBD models where real-time simulations are necessary, or with models that have a large number of repeated substructures, e.g. modelling a train with a large number of railcars. The fact that the training data are acquired prior to the development of the stochastic model discards the conventional sampling plan strategies like Latin Hypercube sampling plans where simulations are performed using the inputs dictated by the sampling plan. Since the sampling plan greatly influences the overall accuracy and efficiency of the stochastic predictions, a sampling plan suitable for the process is developed where the most space-filling subset of the acquired data with ? number of sample points that best describes the dynamic behaviour of the system under study is selected as the training data.
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Salis, Howard; Kaznessis, Yiannis N
2005-12-01
Stochastic chemical kinetics more accurately describes the dynamics of "small" chemical systems, such as biological cells. Many real systems contain dynamical stiffness, which causes the exact stochastic simulation algorithm or other kinetic Monte Carlo methods to spend the majority of their time executing frequently occurring reaction events. Previous methods have successfully applied a type of probabilistic steady-state approximation by deriving an evolution equation, such as the chemical master equation, for the relaxed fast dynamics and using the solution of that equation to determine the slow dynamics. However, because the solution of the chemical master equation is limited to small, carefully selected, or linear reaction networks, an alternate equation-free method would be highly useful. We present a probabilistic steady-state approximation that separates the time scales of an arbitrary reaction network, detects the convergence of a marginal distribution to a quasi-steady-state, directly samples the underlying distribution, and uses those samples to accurately predict the state of the system, including the effects of the slow dynamics, at future times. The numerical method produces an accurate solution of both the fast and slow reaction dynamics while, for stiff systems, reducing the computational time by orders of magnitude. The developed theory makes no approximations on the shape or form of the underlying steady-state distribution and only assumes that it is ergodic. We demonstrate the accuracy and efficiency of the method using multiple interesting examples, including a highly nonlinear protein-protein interaction network. The developed theory may be applied to any type of kinetic Monte Carlo simulation to more efficiently simulate dynamically stiff systems, including existing exact, approximate, or hybrid stochastic simulation techniques.
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In-process, non-destructive, dynamic testing of high-speed polymer composite rotors
NASA Astrophysics Data System (ADS)
Kuschmierz, Robert; Filippatos, Angelos; Günther, Philipp; Langkamp, Albert; Hufenbach, Werner; Czarske, Jürgen; Fischer, Andreas
2015-03-01
Polymer composite rotors are lightweight and offer great perspectives in high-speed applications such as turbo machinery. Currently, novel rotor structures and materials are investigated for the purpose of increasing machine efficiency and lifetime, as well as allowing for higher dynamic loads. However, due to the complexity of the composite materials an in-process measurement system is required. This allows for monitoring the evolution of damages under dynamic loads, for testing and predicting the structural integrity of composite rotors in process. In rotor design, it can be used for calibrating and improving models, simulating the dynamic behaviour of polymer composite rotors. The measurement system is to work non-invasive, offer micron uncertainty, as well as a high measurement rate of several tens of kHz. Furthermore, it must be applicable at high surface speeds and under technical vacuum. In order to fulfil these demands a novel laser distance measurement system was developed. It provides the angle resolved measurement of the biaxial deformation of a fibre-reinforced polymer composite rotor with micron uncertainty at surface speeds of more than 300 m/s. Furthermore, a simulation procedure combining a finite element model and a damage mechanics model is applied. A comparison of the measured data and the numerically calculated data is performed to validate the simulation towards rotor expansion. This validating procedure can be used for a model calibration in the future. The simulation procedure could be used to investigate different damage-test cases of the rotor, in order to define its structural behaviour without further experiments.
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An Analysis of the Loads on and Dynamic Response of a Floating Flexible Tube in Waves and Currents
2014-05-09
the tube about 4.57 meters. The CFD code associated with the SolidWorks Flow Simulation tool was applied for this application. Flow Simulation uses...Liquid-Filled Membrane Structure in Waves," Journal of Fluids and Structures, no. 9, pp. 937-956, 1995. [16] SolidWorks , " Flow Simulation 2012...influence of Reynolds number on the drag coefficient. Simulations were performed with the 100% full (solid) model with flow velocities that yielded
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Dhindsa, Gurpreet K; Bhowmik, Debsindhu; Goswami, Monojoy; O'Neill, Hugh; Mamontov, Eugene; Sumpter, Bobby G; Hong, Liang; Ganesh, Panchapakesan; Chu, Xiang-Qiang
2016-09-14
Nontoxic, biocompatible nanodiamonds (ND) have recently been implemented in rational, systematic design of optimal therapeutic use in nanomedicines. However, hydrophilicity of the ND surface strongly influences structure and dynamics of biomolecules that restrict in situ applications of ND. Therefore, fundamental understanding of the impact of hydrophilic ND surface on biomolecules at the molecular level is essential. For tRNA, we observe an enhancement of dynamical behavior in the presence of ND contrary to generally observed slow motion at strongly interacting interfaces. We took advantage of neutron scattering experiments and computer simulations to demonstrate this atypical faster dynamics of tRNA on ND surface. The strong attractive interactions between ND, tRNA, and water give rise to unlike dynamical behavior and structural changes of tRNA in front of ND compared to without ND. Our new findings may provide new design principles for safer, improved drug delivery platforms.
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Elastically driven intermittent microscopic dynamics in soft solids
NASA Astrophysics Data System (ADS)
Bouzid, Mehdi; Colombo, Jader; Barbosa, Lucas Vieira; Del Gado, Emanuela
2017-06-01
Soft solids with tunable mechanical response are at the core of new material technologies, but a crucial limit for applications is their progressive aging over time, which dramatically affects their functionalities. The generally accepted paradigm is that such aging is gradual and its origin is in slower than exponential microscopic dynamics, akin to the ones in supercooled liquids or glasses. Nevertheless, time- and space-resolved measurements have provided contrasting evidence: dynamics faster than exponential, intermittency and abrupt structural changes. Here we use 3D computer simulations of a microscopic model to reveal that the timescales governing stress relaxation, respectively, through thermal fluctuations and elastic recovery are key for the aging dynamics. When thermal fluctuations are too weak, stress heterogeneities frozen-in upon solidification can still partially relax through elastically driven fluctuations. Such fluctuations are intermittent, because of strong correlations that persist over the timescale of experiments or simulations, leading to faster than exponential dynamics.
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Modelling of creep hysteresis in ferroelectrics
NASA Astrophysics Data System (ADS)
He, Xuan; Wang, Dan; Wang, Linxiang; Melnik, Roderick
2018-05-01
In the current paper, a macroscopic model is proposed to simulate the hysteretic dynamics of ferroelectric ceramics with creep phenomenon incorporated. The creep phenomenon in the hysteretic dynamics is attributed to the rate-dependent characteristic of the polarisation switching processes induced in the materials. A non-convex Helmholtz free energy based on Landau theory is proposed to model the switching dynamics. The governing equation of single-crystal model is formulated by applying the Euler-Lagrange equation. The polycrystalline model is obtained by combining the single crystal dynamics with a density function which is constructed to model the weighted contributions of different grains with different principle axis orientations. In addition, numerical simulations of hysteretic dynamics with creep phenomenon are presented. Comparison of the numerical results and their experimental counterparts is also presented. It is shown that the creep phenomenon is captured precisely, validating the capability of the proposed model in a range of its potential applications.
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Regional air quality models are frequently used for regulatory applications to predict changes in air quality due to changes in emissions or changes in meteorology. Dynamic model evaluation is thus an important step in establishing credibility in the model predicted pollutant re...
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Bennett, Charles R; Kelly, Brian P
2013-08-09
Standard in-vitro spine testing methods have focused on application of isolated and/or constant load components while the in-vivo spine is subject to multiple components that can be resolved into resultant dynamic load vectors. To advance towards more in-vivo like simulations the objective of the current study was to develop a methodology to apply robotically-controlled, non-zero, real-time dynamic resultant forces during flexion-extension on human lumbar motion segment units (MSU) with initial application towards simulation of an ideal follower load (FL) force vector. A proportional-integral-derivative (PID) controller with custom algorithms coordinated the motion of a Cartesian serial manipulator comprised of six axes each capable of position- or load-control. Six lumbar MSUs (L4-L5) were tested with continuously increasing sagittal plane bending to 8 Nm while force components were dynamically programmed to deliver a resultant 400 N FL that remained normal to the moving midline of the intervertebral disc. Mean absolute load-control tracking errors between commanded and experimental loads were computed. Global spinal ranges of motion and sagittal plane inter-body translations were compared to previously published values for non-robotic applications. Mean TEs for zero-commanded force and moment axes were 0.7 ± 0.4N and 0.03 ± 0.02 Nm, respectively. For non-zero force axes mean TEs were 0.8 ± 0.8 N, 1.3 ± 1.6 Nm, and 1.3 ± 1.6N for Fx, Fz, and the resolved ideal follower load vector FL(R), respectively. Mean extension and flexion ranges of motion were 2.6° ± 1.2° and 5.0° ± 1.7°, respectively. Relative vertebral body translations and rotations were very comparable to data collected with non-robotic systems in the literature. The robotically coordinated Cartesian load controlled testing system demonstrated robust real-time load-control that permitted application of a real-time dynamic non-zero load vector during flexion-extension. For single MSU investigations the methodology has potential to overcome conventional follower load limitations, most notably via application outside the sagittal plane. This methodology holds promise for future work aimed at reducing the gap between current in-vitro testing and in-vivo circumstances. Copyright © 2013 Elsevier Ltd. All rights reserved.
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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
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NASA Astrophysics Data System (ADS)
Dhindsa, Gurpreet K.
Neutron scattering has been proved to be a powerful tool to study the dynamics of biological systems under various conditions. This thesis intends to utilize neutron scattering techniques, combining with MD simulations, to develop fundamental understanding of several biologically interesting systems. Our systems include a drug delivery system containing Nanodiamonds with nucleic acid (RNA), and two specific model proteins, beta-Casein and Inorganic Pyrophosphatase (IPPase). RNA and nanodiamond (ND) both are suitable for drug-delivery applications in nano-biotechnology. The architecturally flexible RNA with catalytic functionality forms nanocomposites that can treat life-threatening diseases. The non-toxic ND has excellent mechanical and optical properties and functionalizable high surface area, and thus actively considered for biomedical applications. In this thesis, we utilized two tools, quasielastic neutron scattering (QENS) and Molecular Dynamics Simulations to probe the effect of ND on RNA dynamics. Our work provides fundamental understanding of how hydrated RNA motions are affected in the RNA-ND nanocomposites. From the experimental and Molecular Dynamics Simulation (MD), we found that hydrated RNA motion is faster on ND surface than a freestanding one. MD Simulation results showed that the failure of Stokes Einstein relation results the presence of dynamic heterogeneities in the biomacromolecules. Radial pair distribution function from MD Simulation confirmed that the hydrophilic nature of ND attracts more water than RNA results the de-confinement of RNA on ND. Therefore, RNA exhibits faster motion in the presence of ND than freestanding RNA. In the second project, we studied the dynamics of a natively disordered protein beta-Casein which lacks secondary structures. In this study, the temperature and hydration effects on the dynamics of beta-Casein are explored by Quasielastic Neutron Scattering (QENS). We investigated the mean square displacement (MSD) of hydrated and dry beta-Casein as a function of temperature, to study the effect of hydration on their flexibility. The Elastic Incoherent Structure Factor (EISF) in the energy domain reveals the fraction of hydrogen atoms participating in motion in a sphere of diffusion. In the time domain analysis, a logarithmic-like decay is observed in the range of picosecond to nanosecond (beta-relaxation time) in the dynamics of hydrated beta-Casein. Our temperature dependent QENS experiments provide evidence that lack of secondary structure in beta-Casein results in higher flexibility in its dynamics and easier reversible thermal unfolding compared to other rigid biomolecules. Lastly, we studied the domain motion of IPPase protein by Neutron Spin Echo Spectroscopy (NSE). We found that decrease in diffusion coefficient belongs to domain motion of IPPase. Moreover, Rg is varied by temperature and concentration.
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Quasielastic neutron scattering in biology: Theory and applications
DOE Office of Scientific and Technical Information (OSTI.GOV)
Vural, Derya; Univ. of Tennessee, Knoxville, TN; Hu, Xiaohu
Neutrons scatter quasielastically from stochastic, diffusive processes, such as overdamped vibrations, localized diffusion and transitions between energy minima. In biological systems, such as proteins and membranes, these relaxation processes are of considerable physical interest. We review here recent methodological advances and applications of quasielastic neutron scattering (QENS) in biology, concentrating on the role of molecular dynamics simulation in generating data with which neutron profiles can be unambiguously interpreted. We examine the use of massively-parallel computers in calculating scattering functions, and the application of Markov state modeling. The decomposition of MD-derived neutron dynamic susceptibilities is described, and the use of thismore » in combination with NMR spectroscopy. We discuss dynamics at very long times, including approximations to the infinite time mean-square displacement and nonequilibrium aspects of single-protein dynamics. Lastly, we examine how neutron scattering and MD can be combined to provide information on lipid nanodomains.« less
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Quasielastic neutron scattering in biology: Theory and applications
Vural, Derya; Univ. of Tennessee, Knoxville, TN; Hu, Xiaohu; ...
2016-06-15
Neutrons scatter quasielastically from stochastic, diffusive processes, such as overdamped vibrations, localized diffusion and transitions between energy minima. In biological systems, such as proteins and membranes, these relaxation processes are of considerable physical interest. We review here recent methodological advances and applications of quasielastic neutron scattering (QENS) in biology, concentrating on the role of molecular dynamics simulation in generating data with which neutron profiles can be unambiguously interpreted. We examine the use of massively-parallel computers in calculating scattering functions, and the application of Markov state modeling. The decomposition of MD-derived neutron dynamic susceptibilities is described, and the use of thismore » in combination with NMR spectroscopy. We discuss dynamics at very long times, including approximations to the infinite time mean-square displacement and nonequilibrium aspects of single-protein dynamics. Lastly, we examine how neutron scattering and MD can be combined to provide information on lipid nanodomains.« less
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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.
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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.
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de Souza, Isaac D T; Silva, Sergio N; Teles, Rafael M; Fernandes, Marcelo A C
2014-10-15
The development of new embedded algorithms for automation and control of industrial equipment usually requires the use of real-time testing. However, the equipment required is often expensive, which means that such tests are often not viable. The objective of this work was therefore to develop an embedded platform for the distributed real-time simulation of dynamic systems. This platform, called the Real-Time Simulator for Dynamic Systems (RTSDS), could be applied in both industrial and academic environments. In industrial applications, the RTSDS could be used to optimize embedded control algorithms. In the academic sphere, it could be used to support research into new embedded solutions for automation and control and could also be used as a tool to assist in undergraduate and postgraduate teaching related to the development of projects concerning on-board control systems.
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Platform for Real-Time Simulation of Dynamic Systems and Hardware-in-the-Loop for Control Algorithms
de Souza, Isaac D. T.; Silva, Sergio N.; Teles, Rafael M.; Fernandes, Marcelo A. C.
2014-01-01
The development of new embedded algorithms for automation and control of industrial equipment usually requires the use of real-time testing. However, the equipment required is often expensive, which means that such tests are often not viable. The objective of this work was therefore to develop an embedded platform for the distributed real-time simulation of dynamic systems. This platform, called the Real-Time Simulator for Dynamic Systems (RTSDS), could be applied in both industrial and academic environments. In industrial applications, the RTSDS could be used to optimize embedded control algorithms. In the academic sphere, it could be used to support research into new embedded solutions for automation and control and could also be used as a tool to assist in undergraduate and postgraduate teaching related to the development of projects concerning on-board control systems. PMID:25320906
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Fattebert, Jean-Luc; Lau, Edmond Y.; Bennion, Brian J.; ...
2015-10-22
Enzymes are complicated solvated systems that typically require many atoms to simulate their function with any degree of accuracy. We have recently developed numerical techniques for large scale First-Principles molecular dynamics simulations and applied them to study the enzymatic reaction catalyzed by acetylcholinesterase. We carried out Density functional theory calculations for a quantum mechanical (QM) sub- system consisting of 612 atoms with an O(N) complexity finite-difference approach. The QM sub-system is embedded inside an external potential field representing the electrostatic effect due to the environment. We obtained finite temperature sampling by First-Principles molecular dynamics for the acylation reaction of acetylcholinemore » catalyzed by acetylcholinesterase. Our calculations shows two energies barriers along the reaction coordinate for the enzyme catalyzed acylation of acetylcholine. In conclusion, the second barrier (8.5 kcal/mole) is rate-limiting for the acylation reaction and in good agreement with experiment.« less
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NASA Astrophysics Data System (ADS)
Sinha, T.; Gangodagamage, C.; Ale, S.; Frazier, A. G.; Giambelluca, T. W.; Kumagai, T.; Nakai, T.; Sato, H.
2017-12-01
Drought-related tree mortality at a regional scale causes drastic shifts in carbon and water cycling in Southeast Asian tropical rainforests, where severe droughts are projected to occur more frequently, especially under El Niño conditions. To provide a useful tool for projecting the tropical rainforest dynamics under climate change conditions, we developed the Spatially Explicit Individual-Based (SEIB) Dynamic Global Vegetation Model (DGVM) applicable to simulating mechanistic tree mortality induced by the climatic impacts via individual-tree-scale ecophysiology such as hydraulic failure and carbon starvation. In this study, we present the new model, SEIB-originated Terrestrial Ecosystem Dynamics (S-TEDy) model, and the computation results were compared with observations collected at a field site in a Bornean tropical rainforest. Furthermore, after validating the model's performance, numerical experiments addressing a future of the tropical rainforest were conducted using some global climate model (GCM) simulation outputs.
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NASA Astrophysics Data System (ADS)
Scheibe, T. D.; Yang, X.; Song, X.; Chen, X.; Hammond, G. E.; Song, H. S.; Hou, Z.; Murray, C. J.; Tartakovsky, A. M.; Tartakovsky, G.; Yang, X.; Zachara, J. M.
2016-12-01
Drought-related tree mortality at a regional scale causes drastic shifts in carbon and water cycling in Southeast Asian tropical rainforests, where severe droughts are projected to occur more frequently, especially under El Niño conditions. To provide a useful tool for projecting the tropical rainforest dynamics under climate change conditions, we developed the Spatially Explicit Individual-Based (SEIB) Dynamic Global Vegetation Model (DGVM) applicable to simulating mechanistic tree mortality induced by the climatic impacts via individual-tree-scale ecophysiology such as hydraulic failure and carbon starvation. In this study, we present the new model, SEIB-originated Terrestrial Ecosystem Dynamics (S-TEDy) model, and the computation results were compared with observations collected at a field site in a Bornean tropical rainforest. Furthermore, after validating the model's performance, numerical experiments addressing a future of the tropical rainforest were conducted using some global climate model (GCM) simulation outputs.
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Blöchliger, Nicolas; Caflisch, Amedeo; Vitalis, Andreas
2015-11-10
Data mining techniques depend strongly on how the data are represented and how distance between samples is measured. High-dimensional data often contain a large number of irrelevant dimensions (features) for a given query. These features act as noise and obfuscate relevant information. Unsupervised approaches to mine such data require distance measures that can account for feature relevance. Molecular dynamics simulations produce high-dimensional data sets describing molecules observed in time. Here, we propose to globally or locally weight simulation features based on effective rates. This emphasizes, in a data-driven manner, slow degrees of freedom that often report on the metastable states sampled by the molecular system. We couple this idea to several unsupervised learning protocols. Our approach unmasks slow side chain dynamics within the native state of a miniprotein and reveals additional metastable conformations of a protein. The approach can be combined with most algorithms for clustering or dimensionality reduction.
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Continuum Damage Modeling for Dynamic Fracture Toughness of Metal Matrix Composites
NASA Astrophysics Data System (ADS)
Lee, Intaek; Ochi, Yasuo; Bae, Sungin; Song, Jungil
Short fiber reinforced metal-matrix composites (MMCs) have widely adopted as structural materials and many experimental researches have been performed to study fracture toughness of it. Fracture toughness is often referred as the plane strain(maximum constraint) fracture toughness KIc determined by the well-established standard test method, such as ASTM E399. But the application for dynamic fracture toughness KId has not been popular yet, because of reliance in capturing the crack propagating time. This paper deals with dynamic fracture toughness testing and simulation using finite element method to evaluate fracture behaviors of MMCs manufactured by squeeze casting process when material combination is varied with the type of reinforcement (appearance, size), volume fraction and combination of reinforcements, and the matrix alloy. The instrumented Charphy impact test was used for KId determination and continuum damage model embedded in commercial FE program is used to investigate the dynamic fracture toughness with the influence of elasto-visco-plastic constitutive relation of quasi-brittle fracture that is typical examples of ceramics and some fibre reinforced composites. With Compared results between experimental method and FE simulation, the determination process for KId is presented. FE simulation coupled with continuum damage model is emphasized single shot simulation can predict the dynamic fracture toughness, KId and real time evolution of that directly.
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Neural nets with terminal chaos for simulation of non-deterministic patterns
NASA Technical Reports Server (NTRS)
Zak, Michail
1993-01-01
Models for simulating some aspects of neural intelligence are presented and discussed. Special attention is given to terminal neurodynamics as a particular architecture of terminal dynamics suitable for modeling information flows. Applications of terminal chaos to information fusion as well as to planning and modeling coordination among neurons in biological systems are disussed.
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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…
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International Symposium on Military Applications of Blast Simulation (5th)
1977-06-22
Centre d’Etudes de Grainat, Gramat , France, de- scribed their work in designing a blast simulator with a test section of 12—rn width and 7—rn height...de Gramat , Gramat , France) on the dynamic behavior of limestone. Through a series of high—pressure experiments of the type developed in the recent
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Fixed Equipment in the Energy Systems Integration Facility | Energy Systems
dynamic simulation of future energy systems. Photo of a robot used to test hydrogen coupling hardware. At test chambers (rated up to 60°C) for testing HVAC systems under simulated loading conditions Two bench performance Test stand for measuring performance of receiver tubes for concentrating solar power applications
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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…
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Feng, Sha; Vogelmann, Andrew M.; Li, Zhijin; ...
2015-01-20
Fine-resolution three-dimensional fields have been produced using the Community Gridpoint Statistical Interpolation (GSI) data assimilation system for the U.S. Department of Energy’s Atmospheric Radiation Measurement Program (ARM) Southern Great Plains region. The GSI system is implemented in a multi-scale data assimilation framework using the Weather Research and Forecasting model at a cloud-resolving resolution of 2 km. From the fine-resolution three-dimensional fields, large-scale forcing is derived explicitly at grid-scale resolution; a subgrid-scale dynamic component is derived separately, representing subgrid-scale horizontal dynamic processes. Analyses show that the subgrid-scale dynamic component is often a major component over the large-scale forcing for grid scalesmore » larger than 200 km. The single-column model (SCM) of the Community Atmospheric Model version 5 (CAM5) is used to examine the impact of the grid-scale and subgrid-scale dynamic components on simulated precipitation and cloud fields associated with a mesoscale convective system. It is found that grid-scale size impacts simulated precipitation, resulting in an overestimation for grid scales of about 200 km but an underestimation for smaller grids. The subgrid-scale dynamic component has an appreciable impact on the simulations, suggesting that grid-scale and subgrid-scale dynamic components should be considered in the interpretation of SCM simulations.« less
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Ablation dynamics - from absorption to heat accumulation/ultra-fast laser matter interaction
NASA Astrophysics Data System (ADS)
Kramer, Thorsten; Remund, Stefan; Jäggi, Beat; Schmid, Marc; Neuenschwander, Beat
2018-05-01
Ultra-short laser radiation is used in manifold industrial applications today. Although state-of-the-art laser sources are providing an average power of 10-100 W with repetition rates of up to several megahertz, most applications do not benefit from it. On the one hand, the processing speed is limited to some hundred millimeters per second by the dynamics of mechanical axes or galvanometric scanners. On the other hand, high repetition rates require consideration of new physical effects such as heat accumulation and shielding that might reduce the process efficiency. For ablation processes, process efficiency can be expressed by the specific removal rate, ablated volume per time, and average power. The analysis of the specific removal rate for different laser parameters, like average power, repetition rate or pulse duration, and process parameters, like scanning speed or material, can be used to find the best operation point for microprocessing applications. Analytical models and molecular dynamics simulations based on the so-called two-temperature model reveal the causes for the appearance of limiting physical effects. The findings of models and simulations can be used to take advantage and optimize processing strategies.
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Finite Element Modeling of Non-linear Coupled Interacting Fault System
NASA Astrophysics Data System (ADS)
Xing, H. L.; Zhang, J.; Wyborn, D.
2009-04-01
PANDAS - Parallel Adaptive static/dynamic Nonlinear Deformation Analysis System - a novel supercomputer simulation tool is developed for simulating the highly non-linear coupled geomechanical-fluid flow-thermal systems involving heterogeneously fractured geomaterials. PANDAS includes the following key components: Pandas/Pre, ESyS_Crustal, Pandas/Thermo, Pandas/Fluid and Pandas/Post as detailed in the following: • Pandas/Pre is developed to visualise the microseismicity events recorded during the hydraulic stimulation process to further evaluate the fracture location and evolution and geological setting of a certain reservoir, and then generate the mesh by it and/or other commercial graphics software (such as Patran) for the further finite element analysis of various cases; The Delaunay algorithm is applied as a suitable method for mesh generation using such a point set; • ESyS_Crustal is a finite element code developed for the interacting fault system simulation, which employs the adaptive static/dynamic algorithm to simulate the dynamics and evolution of interacting fault systems and processes that are relevant on short to mediate time scales in which several dynamic phenomena related with stick-slip instability along the faults need to be taken into account, i.e. (a). slow quasi-static stress accumulation, (b) rapid dynamic rupture, (c) wave propagation and (d) corresponding stress redistribution due to the energy release along the multiple fault boundaries; those are needed to better describe ruputure/microseimicity/earthquake related phenomena with applications in earthquake forecasting, hazard quantification, exploration, and environmental problems. It has been verified with various available experimental results[1-3]; • Pandas/Thermo is a finite element method based module for the thermal analysis of the fractured porous media; the temperature distribution is calculated from the heat transfer induced by the thermal boundary conditions without/with the coupled fluid effects and the geomechanical energy conversion for the pure/coupled thermal analysis. • Pandas/Fluid is a finite element method based module for simulating the fluid flow in the fractured porous media; the fluid flow velocity and pressure are calculated from energy equilibrium equations without/together with the coupling effects of the thermal and solid rock deformation for an independent/coupled fluid flow analysis; • Pandas/Post is to visualise the simulation results through the integration of VTK and/or Patran. All the above modules can be used independently/together to simulate individual/coupled phenomena (such as interacting fault system dynamics, heat flow and fluid flow) without/with coupling effects. PANDAS has been applied to the following issues: • visualisation of the microseismic events to monitor and determine where/how the underground rupture proceeds during a hydraulic stimulation, to generate the mesh using the recorded data for determining the domain of the ruptured zone and to evaluate the material parameters (i.e. the permeability) for the further numerical analysis; • interacting fault system simulation to determine the relevant complicated dynamic rupture process. • geomechanical-fluid flow coupling analysis to investigate the interactions between fluid flow and deformation in the fractured porous media under different loading conditions. • thermo-fluid flow coupling analysis of a fractured geothermal reservoir system. PANDAS will be further developed for a multiscale simulation of multiphase dynamic behaviour for a certain fractured geothermal reservoir. More details and additional application examples will be given during the presentation. References [1] Xing, H. L., Makinouchi, A. and Mora, P. (2007). Finite element modeling of interacting fault system, Physics of the Earth and Planetary Interiors, 163, 106-121.doi:10.1016/j.pepi.2007.05.006 [2] Xing, H. L., Mora, P., Makinouchi, A. (2006). An unified friction description and its application to simulation of frictional instability using finite element method. Philosophy Magazine, 86, 3453-3475 [3] Xing, H. L., Mora, P.(2006). Construction of an intraplate fault system model of South Australia, and simulation tool for the iSERVO institute seed project.. Pure and Applied Geophysics. 163, 2297-2316. DOI 10.1007/s00024-006-0127-x
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Flight Simulator Visual-Display Delay Compensation
NASA Technical Reports Server (NTRS)
Crane, D. Francis
1981-01-01
A piloted aircraft can be viewed as a closed-loop man-machine control system. When a simulator pilot is performing a precision maneuver, a delay in the visual display of aircraft response to pilot-control input decreases the stability of the pilot-aircraft system. The less stable system is more difficult to control precisely. Pilot dynamic response and performance change as the pilot attempts to compensate for the decrease in system stability. The changes in pilot dynamic response and performance bias the simulation results by influencing the pilot's rating of the handling qualities of the simulated aircraft. The study reported here evaluated an approach to visual-display delay compensation. The objective of the compensation was to minimize delay-induced change in pilot performance and workload, The compensation was effective. Because the compensation design approach is based on well-established control-system design principles, prospects are favorable for successful application of the approach in other simulations.
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Direct model reference adaptive control of robotic arms
NASA Technical Reports Server (NTRS)
Kaufman, Howard; Swift, David C.; Cummings, Steven T.; Shankey, Jeffrey R.
1993-01-01
The results of controlling A PUMA 560 Robotic Manipulator and the NASA shuttle Remote Manipulator System (RMS) using a Command Generator Tracker (CGT) based Model Reference Adaptive Controller (DMRAC) are presented. Initially, the DMRAC algorithm was run in simulation using a detailed dynamic model of the PUMA 560. The algorithm was tuned on the simulation and then used to control the manipulator using minimum jerk trajectories as the desired reference inputs. The ability to track a trajectory in the presence of load changes was also investigated in the simulation. Satisfactory performance was achieved in both simulation and on the actual robot. The obtained responses showed that the algorithm was robust in the presence of sudden load changes. Because these results indicate that the DMRAC algorithm can indeed be successfully applied to the control of robotic manipulators, additional testing was performed to validate the applicability of DMRAC to simulated dynamics of the shuttle RMS.
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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
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Automated sampling assessment for molecular simulations using the effective sample size
Zhang, Xin; Bhatt, Divesh; Zuckerman, Daniel M.
2010-01-01
To quantify the progress in the development of algorithms and forcefields used in molecular simulations, a general method for the assessment of the sampling quality is needed. Statistical mechanics principles suggest the populations of physical states characterize equilibrium sampling in a fundamental way. We therefore develop an approach for analyzing the variances in state populations, which quantifies the degree of sampling in terms of the effective sample size (ESS). The ESS estimates the number of statistically independent configurations contained in a simulated ensemble. The method is applicable to both traditional dynamics simulations as well as more modern (e.g., multi–canonical) approaches. Our procedure is tested in a variety of systems from toy models to atomistic protein simulations. We also introduce a simple automated procedure to obtain approximate physical states from dynamic trajectories: this allows sample–size estimation in systems for which physical states are not known in advance. PMID:21221418
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NASA Astrophysics Data System (ADS)
Heimann, F. U. M.; Rickenmann, D.; Turowski, J. M.; Kirchner, J. W.
2015-01-01
Especially in mountainous environments, the prediction of sediment dynamics is important for managing natural hazards, assessing in-stream habitats and understanding geomorphic evolution. We present the new modelling tool {sedFlow} for simulating fractional bedload transport dynamics in mountain streams. sedFlow is a one-dimensional model that aims to realistically reproduce the total transport volumes and overall morphodynamic changes resulting from sediment transport events such as major floods. The model is intended for temporal scales from the individual event (several hours to few days) up to longer-term evolution of stream channels (several years). The envisaged spatial scale covers complete catchments at a spatial discretisation of several tens of metres to a few hundreds of metres. sedFlow can deal with the effects of streambeds that slope uphill in a downstream direction and uses recently proposed and tested approaches for quantifying macro-roughness effects in steep channels. sedFlow offers different options for bedload transport equations, flow-resistance relationships and other elements which can be selected to fit the current application in a particular catchment. Local grain-size distributions are dynamically adjusted according to the transport dynamics of each grain-size fraction. sedFlow features fast calculations and straightforward pre- and postprocessing of simulation data. The high simulation speed allows for simulations of several years, which can be used, e.g., to assess the long-term impact of river engineering works or climate change effects. In combination with the straightforward pre- and postprocessing, the fast calculations facilitate efficient workflows for the simulation of individual flood events, because the modeller gets the immediate results as direct feedback to the selected parameter inputs. The model is provided together with its complete source code free of charge under the terms of the GNU General Public License (GPL) (www.wsl.ch/sedFlow). Examples of the application of sedFlow are given in a companion article by Heimann et al. (2015).
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Neural network based adaptive output feedback control: Applications and improvements
NASA Astrophysics Data System (ADS)
Kutay, Ali Turker
Application of recently developed neural network based adaptive output feedback controllers to a diverse range of problems both in simulations and experiments is investigated in this thesis. The purpose is to evaluate the theory behind the development of these controllers numerically and experimentally, identify the needs for further development in practical applications, and to conduct further research in directions that are identified to ultimately enhance applicability of adaptive controllers to real world problems. We mainly focus our attention on adaptive controllers that augment existing fixed gain controllers. A recently developed approach holds great potential for successful implementations on real world applications due to its applicability to systems with minimal information concerning the plant model and the existing controller. In this thesis the formulation is extended to the multi-input multi-output case for distributed control of interconnected systems and successfully tested on a formation flight wind tunnel experiment. The command hedging method is formulated for the approach to further broaden the class of systems it can address by including systems with input nonlinearities. Also a formulation is adopted that allows the approach to be applied to non-minimum phase systems for which non-minimum phase characteristics are modeled with sufficient accuracy and treated properly in the design of the existing controller. It is shown that the approach can also be applied to augment nonlinear controllers under certain conditions and an example is presented where the nonlinear guidance law of a spinning projectile is augmented. Simulation results on a high fidelity 6 degrees-of-freedom nonlinear simulation code are presented. The thesis also presents a preliminary adaptive controller design for closed loop flight control with active flow actuators. Behavior of such actuators in dynamic flight conditions is not known. To test the adaptive controller design in simulation, a fictitious actuator model is developed that fits experimentally observed characteristics of flow control actuators in static flight conditions as well as possible coupling effects between actuation, the dynamics of flow field, and the rigid body dynamics of the vehicle.
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NASA Astrophysics Data System (ADS)
Yue, Yingchao; Fan, Wenhui; Xiao, Tianyuan; Ma, Cheng
2013-07-01
High level architecture(HLA) is the open standard in the collaborative simulation field. Scholars have been paying close attention to theoretical research on and engineering applications of collaborative simulation based on HLA/RTI, which extends HLA in various aspects like functionality and efficiency. However, related study on the load balancing problem of HLA collaborative simulation is insufficient. Without load balancing, collaborative simulation under HLA/RTI may encounter performance reduction or even fatal errors. In this paper, load balancing is further divided into static problems and dynamic problems. A multi-objective model is established and the randomness of model parameters is taken into consideration for static load balancing, which makes the model more credible. The Monte Carlo based optimization algorithm(MCOA) is excogitated to gain static load balance. For dynamic load balancing, a new type of dynamic load balancing problem is put forward with regards to the variable-structured collaborative simulation under HLA/RTI. In order to minimize the influence against the running collaborative simulation, the ordinal optimization based algorithm(OOA) is devised to shorten the optimization time. Furthermore, the two algorithms are adopted in simulation experiments of different scenarios, which demonstrate their effectiveness and efficiency. An engineering experiment about collaborative simulation under HLA/RTI of high speed electricity multiple units(EMU) is also conducted to indentify credibility of the proposed models and supportive utility of MCOA and OOA to practical engineering systems. The proposed research ensures compatibility of traditional HLA, enhances the ability for assigning simulation loads onto computing units both statically and dynamically, improves the performance of collaborative simulation system and makes full use of the hardware resources.
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Dynamic Simulation of VEGA SRM Bench Firing By Using Propellant Complex Characterization
NASA Astrophysics Data System (ADS)
Di Trapani, C. D.; Mastrella, E.; Bartoccini, D.; Squeo, E. A.; Mastroddi, F.; Coppotelli, G.; Linari, M.
2012-07-01
During the VEGA launcher development, from the 2004 up to now, 8 firing tests have been performed at Salto di Quirra (Sardinia, Italy) and Kourou (Guyana, Fr) with the objective to characterize and qualify of the Zefiros and P80 Solid Rocket Motors (SRM). In fact the VEGA launcher configuration foreseen 3 solid stages based on P80, Z23 and Z9 Solid Rocket Motors respectively. One of the primary objectives of the firing test is to correctly characterize the dynamic response of the SRM in order to apply such a characterization to the predictions and simulations of the VEGA launch dynamic environment. Considering that the solid propellant is around 90% of the SRM mass, it is very important to dynamically characterize it, and to increase the confidence in the simulation of the dynamic levels transmitted to the LV upper part from the SRMs. The activity is articulated in three parts: • consolidation of an experimental method for the dynamic characterization of the complex dynamic elasticity modulus of elasticity of visco-elastic materials applicable to the SRM propellant operative conditions • introduction of the complex dynamic elasticity modulus in a numerical FEM benchmark based on MSC NASTRAN solver • analysis of the effect of the introduction of the complex dynamic elasticity modulus in the Zefiros FEM focusing on experimental firing test data reproduction with numerical approach.
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Active magnetic damper in a power transmission system
NASA Astrophysics Data System (ADS)
Kozanecka, D.; Kozanecki, Z.; Łagodziński, J.
2011-05-01
In rotor dynamics, the bearing characteristics exerts a decisive influence on dynamics of the rotating shaft. The research and application experience have led to active magnetic bearings (AMBs), which allow for unique applications in rotating systems. The paper presents the investigations concerning optimization of the magnetic bearing construction. An active magnetic bearing operates as a radial, auxiliary damper, which cooperates with the long, flexible shaft line (aircraft industry applications) and modifies its dynamic properties. In the developed concept of AMBs for aviation purposes, a necessity of increasing its bearing load capacity and damping has occurred. The second important criterion is a weight reduction. This advanced problem leads to specific requirements on the design and materials for the AMB. To achieve these goals, some simulations have been performed. The experimental results are presented as well.
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Soil Organic Matter (SOM): Molecular Simulations
DOE Office of Scientific and Technical Information (OSTI.GOV)
Andersen, Amity
Molecular simulation is a powerful tool used to gain an atomistic, molecular, and nanoscale level understanding of the structure, dynamics, and interactions from adsorption on minerals and assembly in aggregates of soil organic matter (SOM). Given the importance of SOM fate and persistence in soils and the current knowledge gaps, applications of atomistic scale simulations to study the complex compounds in SOM and their interactions in self-assembled aggregates composed of different organic matter compounds and with mineral surfaces of different types common in soils are few and far between. Here, we describe various molecular simulation methods that are currently inmore » use in various areas and applicable to SOM research, followed by a brief survey of specific applications to SOM research and an illustration with our own recent efforts in this area. We conclude with an outlook and the challenges for future research in this area.« less
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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.
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NASA Astrophysics Data System (ADS)
Pierre, Sadrach; Duke, Jessica R.; Hele, Timothy J. H.; Ananth, Nandini
2017-12-01
We investigate the mechanisms of condensed phase proton-coupled electron transfer (PCET) using Mapping-Variable Ring Polymer Molecular Dynamics (MV-RPMD), a recently developed method that employs an ensemble of classical trajectories to simulate nonadiabatic excited state dynamics. Here, we construct a series of system-bath model Hamiltonians for the PCET, where four localized electron-proton states are coupled to a thermal bath via a single solvent mode, and we employ MV-RPMD to simulate state population dynamics. Specifically, for each model, we identify the dominant PCET mechanism, and by comparing against rate theory calculations, we verify that our simulations correctly distinguish between concerted PCET, where the electron and proton transfer together, and sequential PCET, where either the electron or the proton transfers first. This work represents a first application of MV-RPMD to multi-level condensed phase systems; we introduce a modified MV-RPMD expression that is derived using a symmetric rather than asymmetric Trotter discretization scheme and an initialization protocol that uses a recently derived population estimator to constrain trajectories to a dividing surface. We also demonstrate that, as expected, the PCET mechanisms predicted by our simulations are robust to an arbitrary choice of the initial dividing surface.
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Integration of Continuous-Time Dynamics in a Spiking Neural Network Simulator.
Hahne, Jan; Dahmen, David; Schuecker, Jannis; Frommer, Andreas; Bolten, Matthias; Helias, Moritz; Diesmann, Markus
2017-01-01
Contemporary modeling approaches to the dynamics of neural networks include two important classes of models: biologically grounded spiking neuron models and functionally inspired rate-based units. We present a unified simulation framework that supports the combination of the two for multi-scale modeling, enables the quantitative validation of mean-field approaches by spiking network simulations, and provides an increase in reliability by usage of the same simulation code and the same network model specifications for both model classes. While most spiking simulations rely on the communication of discrete events, rate models require time-continuous interactions between neurons. Exploiting the conceptual similarity to the inclusion of gap junctions in spiking network simulations, we arrive at a reference implementation of instantaneous and delayed interactions between rate-based models in a spiking network simulator. The separation of rate dynamics from the general connection and communication infrastructure ensures flexibility of the framework. In addition to the standard implementation we present an iterative approach based on waveform-relaxation techniques to reduce communication and increase performance for large-scale simulations of rate-based models with instantaneous interactions. Finally we demonstrate the broad applicability of the framework by considering various examples from the literature, ranging from random networks to neural-field models. The study provides the prerequisite for interactions between rate-based and spiking models in a joint simulation.
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Integration of Continuous-Time Dynamics in a Spiking Neural Network Simulator
Hahne, Jan; Dahmen, David; Schuecker, Jannis; Frommer, Andreas; Bolten, Matthias; Helias, Moritz; Diesmann, Markus
2017-01-01
Contemporary modeling approaches to the dynamics of neural networks include two important classes of models: biologically grounded spiking neuron models and functionally inspired rate-based units. We present a unified simulation framework that supports the combination of the two for multi-scale modeling, enables the quantitative validation of mean-field approaches by spiking network simulations, and provides an increase in reliability by usage of the same simulation code and the same network model specifications for both model classes. While most spiking simulations rely on the communication of discrete events, rate models require time-continuous interactions between neurons. Exploiting the conceptual similarity to the inclusion of gap junctions in spiking network simulations, we arrive at a reference implementation of instantaneous and delayed interactions between rate-based models in a spiking network simulator. The separation of rate dynamics from the general connection and communication infrastructure ensures flexibility of the framework. In addition to the standard implementation we present an iterative approach based on waveform-relaxation techniques to reduce communication and increase performance for large-scale simulations of rate-based models with instantaneous interactions. Finally we demonstrate the broad applicability of the framework by considering various examples from the literature, ranging from random networks to neural-field models. The study provides the prerequisite for interactions between rate-based and spiking models in a joint simulation. PMID:28596730
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Use of System Dynamics Modeling in Medical Education and Research Projects.
Bozikov, Jadranka; Relic, Danko; Dezelic, Gjuro
2018-01-01
The paper reviews experiences and accomplishments in application of system dynamics modeling in education, training and research projects at the Andrija Stampar School of Public Health, a branch of the Zagreb University School of Medicine, Croatia. A number of simulation models developed over the past 40 years are briefly described with regard to real problems concerned, objectives and modeling methods and techniques used. Many of them have been developed as the individual students' projects as a part of their graduation, MSc or PhD theses and subsequently published in journals or conference proceedings. Some of them were later used in teaching and simulation training. System dynamics modeling proved to be not only powerful method for research and decision making but also a useful tool in medical and nursing education enabling better understanding of dynamic systems' behavior.
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Pal, Sandeep; Milano, Giuseppe; Roccatano, Danilo
2006-12-28
The understanding of interactions of poly(ethylene glycol) (PEG) or poly(ethylene oxide) (PEO) with biological interfaces has important technological application in industry and in medicine. In this paper, structural and dynamical properties of PEO at the dimyristoylphospatidylcholine (DMPC) bilayer/water interface have been investigated by molecular dynamics (MD) and steered molecular dynamics (SMD) simulations. The structural properties of a PEO chain in bulk water, at the water/vacuum interface, and in the presence of the membrane were compared with available experimental data. The presence of a barrier for the PEO penetration into the DMPC bilayer has been found. A qualitative estimation of the barrier provided a value equal to approximately 19 kJ/mol, that is, 7 times the value of kT at 310 K.
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NASA Astrophysics Data System (ADS)
Reyes López, Yaidel; Roose, Dirk; Recarey Morfa, Carlos
2013-05-01
In this paper, we present a dynamic refinement algorithm for the smoothed particle Hydrodynamics (SPH) method. An SPH particle is refined by replacing it with smaller daughter particles, which positions are calculated by using a square pattern centered at the position of the refined particle. We determine both the optimal separation and the smoothing distance of the new particles such that the error produced by the refinement in the gradient of the kernel is small and possible numerical instabilities are reduced. We implemented the dynamic refinement procedure into two different models: one for free surface flows, and one for post-failure flow of non-cohesive soil. The results obtained for the test problems indicate that using the dynamic refinement procedure provides a good trade-off between the accuracy and the cost of the simulations.
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Dynamic Resource Allocation for IEEE802.16e
NASA Astrophysics Data System (ADS)
Nascimento, Alberto; Rodriguez, Jonathan
Mobile communications has witnessed an exponential increase in the amount of users, services and applications. New high bandwidth consuming applications are targeted for B3G networks raising more stringent requirements for Dynamic Resource Allocation (DRA) architectures and packet schedulers that must be spectrum efficient and deliver QoS for heterogeneous applications and services. In this paper we propose a new cross layer-based architecture framework embedded in a newly designed DRA architecture for the Mobile WiMAX standard. System level simulation results show that the proposed architecture can be considered a viable candidate solution for supporting mixed services in a cost-effective manner in contrast to existing approaches.
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Space Station Common Berthing Mechanism, a multi-body simulation application
NASA Technical Reports Server (NTRS)
Searle, Ian
1993-01-01
This paper discusses an application of multi-body dynamic analysis conducted at the Boeing Company in connection with the Space Station (SS) Common Berthing Mechanism (CBM). After introducing the hardware and analytical objectives we will focus on some of the day-to-day computational issues associated with this type of analysis.
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Development of a rotorcraft. Propulsion dynamics interface analysis, volume 2
NASA Technical Reports Server (NTRS)
Hull, R.
1982-01-01
A study was conducted to establish a coupled rotor/propulsion analysis that would be applicable to a wide range of rotorcraft systems. The effort included the following tasks: (1) development of a model structure suitable for simulating a wide range of rotorcraft configurations; (2) defined a methodology for parameterizing the model structure to represent a particular rotorcraft; (3) constructing a nonlinear coupled rotor/propulsion model as a test case to use in analyzing coupled system dynamics; and (4) an attempt to develop a mostly linear coupled model derived from the complete nonlinear simulations. Documentation of the computer models developed is presented.
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Vectorization of a Monte Carlo simulation scheme for nonequilibrium gas dynamics
NASA Technical Reports Server (NTRS)
Boyd, Iain D.
1991-01-01
Significant improvement has been obtained in the numerical performance of a Monte Carlo scheme for the analysis of nonequilibrium gas dynamics through an implementation of the algorithm which takes advantage of vector hardware, as presently demonstrated through application to three different problems. These are (1) a 1D standing-shock wave; (2) the flow of an expanding gas through an axisymmetric nozzle; and (3) the hypersonic flow of Ar gas over a 3D wedge. Problem (3) is illustrative of the greatly increased number of molecules which the simulation may involve, thanks to improved algorithm performance.
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Accelerated simulations of aromatic polymers: application to polyether ether ketone (PEEK)
NASA Astrophysics Data System (ADS)
Broadbent, Richard J.; Spencer, James S.; Mostofi, Arash A.; Sutton, Adrian P.
2014-10-01
For aromatic polymers, the out-of-plane oscillations of aromatic groups limit the maximum accessible time step in a molecular dynamics simulation. We present a systematic approach to removing such high-frequency oscillations from planar groups along aromatic polymer backbones, while preserving the dynamical properties of the system. We consider, as an example, the industrially important polymer, polyether ether ketone (PEEK), and show that this coarse graining technique maintains excellent agreement with the fully flexible all-atom and all-atom rigid bond models whilst allowing the time step to increase fivefold to 5 fs.
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NASA Astrophysics Data System (ADS)
Gupta, Neha; Parihar, Priyanka; Neema, Vaibhav
2018-04-01
Researchers have proposed many circuit techniques to reduce leakage power dissipation in memory cells. If we want to reduce the overall power in the memory system, we have to work on the input circuitry of memory architecture i.e. row and column decoder. In this research work, low leakage power with a high speed row and column decoder for memory array application is designed and four new techniques are proposed. In this work, the comparison of cluster DECODER, body bias DECODER, source bias DECODER, and source coupling DECODER are designed and analyzed for memory array application. Simulation is performed for the comparative analysis of different DECODER design parameters at 180 nm GPDK technology file using the CADENCE tool. Simulation results show that the proposed source bias DECODER circuit technique decreases the leakage current by 99.92% and static energy by 99.92% at a supply voltage of 1.2 V. The proposed circuit also improves dynamic power dissipation by 5.69%, dynamic PDP/EDP 65.03% and delay 57.25% at 1.2 V supply voltage.
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Simulation-driven machine learning: Bearing fault classification
NASA Astrophysics Data System (ADS)
Sobie, Cameron; Freitas, Carina; Nicolai, Mike
2018-01-01
Increasing the accuracy of mechanical fault detection has the potential to improve system safety and economic performance by minimizing scheduled maintenance and the probability of unexpected system failure. Advances in computational performance have enabled the application of machine learning algorithms across numerous applications including condition monitoring and failure detection. Past applications of machine learning to physical failure have relied explicitly on historical data, which limits the feasibility of this approach to in-service components with extended service histories. Furthermore, recorded failure data is often only valid for the specific circumstances and components for which it was collected. This work directly addresses these challenges for roller bearings with race faults by generating training data using information gained from high resolution simulations of roller bearing dynamics, which is used to train machine learning algorithms that are then validated against four experimental datasets. Several different machine learning methodologies are compared starting from well-established statistical feature-based methods to convolutional neural networks, and a novel application of dynamic time warping (DTW) to bearing fault classification is proposed as a robust, parameter free method for race fault detection.
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NASA Astrophysics Data System (ADS)
Perdigão, Rui A. P.; Hall, Julia; Pires, Carlos A. L.; Blöschl, Günter
2017-04-01
Classical and stochastic dynamical system theories assume structural coherence and dynamic recurrence with invariants of motion that are not necessarily so. These are grounded on the unproven assumption of universality in the dynamic laws derived from statistical kinematic evaluation of non-representative empirical records. As a consequence, the associated formulations revolve around a restrictive set of configurations and intermittencies e.g. in an ergodic setting, beyond which any predictability is essentially elusive. Moreover, dynamical systems are fundamentally framed around dynamic codependence among intervening processes, i.e. entail essentially redundant interactions such as couplings and feedbacks. That precludes synergistic cooperation among processes that, whilst independent from each other, jointly produce emerging dynamic behaviour not present in any of the intervening parties. In order to overcome these fundamental limitations, we introduce a broad class of non-recursive dynamical systems that formulate dynamic emergence of unprecedented states in a fundamental synergistic manner, with fundamental principles in mind. The overall theory enables innovations to be predicted from the internal system dynamics before any a priori information is provided about the associated dynamical properties. The theory is then illustrated to anticipate, from non-emergent records, the spatiotemporal emergence of multiscale hyper chaotic regimes, critical transitions and structural coevolutionary changes in synthetic and real-world complex systems. Example applications are provided within the hydro-climatic context, formulating and dynamically forecasting evolving hydro-climatic distributions, including the emergence of extreme precipitation and flooding in a structurally changing hydro-climate system. Validation is then conducted with a posteriori verification of the simulated dynamics against observational records. Agreement between simulations and observations is confirmed with robust nonlinear information diagnostics.
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Studying the flow dynamics of a karst aquifer system with an equivalent porous medium model.
Abusaada, Muath; Sauter, Martin
2013-01-01
The modeling of groundwater flow in karst aquifers is a challenge due to the extreme heterogeneity of its hydraulic parameters and the duality in their discharge behavior, that is, rapid response of highly conductive karst conduits and delayed drainage of the low-permeability fractured matrix after recharge events. There are a number of different modeling approaches for the simulation of the karst groundwater dynamics, applicable to different aquifer as well as modeling problem types, ranging from continuum models to double continuum models to discrete and hybrid models. This study presents the application of an equivalent porous model approach (EPM, single continuum model) to construct a steady-state numerical flow model for an important karst aquifer, that is, the Western Mountain Aquifer Basin (WMAB), shared by Israel and the West-Bank, using MODFLOW2000. The WMAB was used as a catchment since it is a well-constrained catchment with well-defined recharge and discharge components and therefore allows a control on the modeling approach, a very rare opportunity for karst aquifer modeling. The model demonstrates the applicability of equivalent porous medium models for the simulation of karst systems, despite their large contrast in hydraulic conductivities. As long as the simulated saturated volume is large enough to average out the local influence of karst conduits and as long as transport velocities are not an issue, EPM models excellently simulate the observed head distribution. The model serves as a starting basis that will be used as a reference for developing a long-term dynamic model for the WMAB, starting from the pre-development period (i.e., 1940s) up to date. © 2012, The Author(s). GroundWater © 2012, National Ground Water Association.
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Communication Simulations for Power System Applications
DOE Office of Scientific and Technical Information (OSTI.GOV)
Fuller, Jason C.; Ciraci, Selim; Daily, Jeffrey A.
2013-05-29
New smart grid technologies and concepts, such as dynamic pricing, demand response, dynamic state estimation, and wide area monitoring, protection, and control, are expected to require considerable communication resources. As the cost of retrofit can be high, future power grids will require the integration of high-speed, secure connections with legacy communication systems, while still providing adequate system control and security. While considerable work has been performed to create co-simulators for the power domain with load models and market operations, limited work has been performed in integrating communications directly into a power domain solver. The simulation of communication and power systemsmore » will become more important as the two systems become more inter-related. This paper will discuss ongoing work at Pacific Northwest National Laboratory to create a flexible, high-speed power and communication system co-simulator for smart grid applications. The framework for the software will be described, including architecture considerations for modular, high performance computing and large-scale scalability (serialization, load balancing, partitioning, cross-platform support, etc.). The current simulator supports the ns-3 (telecommunications) and GridLAB-D (distribution systems) simulators. Ongoing and future work will be described, including planned future expansions for a traditional transmission solver. A test case using the co-simulator, utilizing a transactive demand response system created for the Olympic Peninsula and AEP gridSMART demonstrations, requiring two-way communication between distributed and centralized market devices, will be used to demonstrate the value and intended purpose of the co-simulation environment.« less
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The design of nonlinear observers for wind turbine dynamic state and parameter estimation
NASA Astrophysics Data System (ADS)
Ritter, B.; Schild, A.; Feldt, M.; Konigorski, U.
2016-09-01
This contribution addresses the dynamic state and parameter estimation problem which arises with more advanced wind turbine controllers. These control devices need precise information about the system's current state to outperform conventional industrial controllers effectively. First, the necessity of a profound scientific treatment on nonlinear observers for wind turbine application is highlighted. Secondly, the full estimation problem is introduced and the variety of nonlinear filters is discussed. Finally, a tailored observer architecture is proposed and estimation results of an illustrative application example from a complex simulation set-up are presented.
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NASA Technical Reports Server (NTRS)
Kandil, Osama A.
1993-01-01
Research on Navier-Stokes, dynamics, and aeroelastic computations for vortical flows, buffet, and flutter applications was performed. Progress during the period from 1 Oct. 1992 to 30 Sep. 1993 is included. Papers on the following topics are included: vertical tail buffet in vortex breakdown flows; simulation of tail buffet using delta wing-vertical tail configuration; shock-vortex interaction over a 65-degree delta wing in transonic flow; supersonic vortex breakdown over a delta wing in transonic flow; and prediction and control of slender wing rock.
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Functionalized lipids and surfactants for specific applications.
Kepczynski, Mariusz; Róg, Tomasz
2016-10-01
Synthetic lipids and surfactants that do not exist in biological systems have been used for the last few decades in both basic and applied science. The most notable applications for synthetic lipids and surfactants are drug delivery, gene transfection, as reporting molecules, and as support for structural lipid biology. In this review, we describe the potential of the synergistic combination of computational and experimental methodologies to study the behavior of synthetic lipids and surfactants embedded in lipid membranes and liposomes. We focused on select cases in which molecular dynamics simulations were used to complement experimental studies aiming to understand the structure and properties of new compounds at the atomistic level. We also describe cases in which molecular dynamics simulations were used to design new synthetic lipids and surfactants, as well as emerging fields for the application of these compounds. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg. Copyright © 2016 Elsevier B.V. All rights reserved.
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NASA Technical Reports Server (NTRS)
Harik, Vasyl Michael; Bushnell, Dennis M. (Technical Monitor)
2001-01-01
Ranges of validity for the continuum-beam model, the length-scale effects and continuum assumptions are analyzed in the framework of scaling analysis of NT structure. Two coupled criteria for the applicability of the continuum model are presented. Scaling analysis of NT buckling and geometric parameters (e.g., diameter and length) is carried out to determine the key non-dimensional parameters that control the buckling strains and modes of NT buckling. A model applicability map, which represents two classes of NTs, is constructed in the space of non-dimensional parameters. In an analogy with continuum mechanics, a mechanical law of geometric similitude is presented for two classes of beam-like NTs having different geometries. Expressions for the critical buckling loads and strains are tailored for the distinct groups of NTs and compared with the data provided by the molecular dynamics simulations. Implications for molecular dynamics simulations and the NT-based scanning probes are discussed.
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Path-integral isomorphic Hamiltonian for including nuclear quantum effects in non-adiabatic dynamics
NASA Astrophysics Data System (ADS)
Tao, Xuecheng; Shushkov, Philip; Miller, Thomas F.
2018-03-01
We describe a path-integral approach for including nuclear quantum effects in non-adiabatic chemical dynamics simulations. For a general physical system with multiple electronic energy levels, a corresponding isomorphic Hamiltonian is introduced such that Boltzmann sampling of the isomorphic Hamiltonian with classical nuclear degrees of freedom yields the exact quantum Boltzmann distribution for the original physical system. In the limit of a single electronic energy level, the isomorphic Hamiltonian reduces to the familiar cases of either ring polymer molecular dynamics (RPMD) or centroid molecular dynamics Hamiltonians, depending on the implementation. An advantage of the isomorphic Hamiltonian is that it can easily be combined with existing mixed quantum-classical dynamics methods, such as surface hopping or Ehrenfest dynamics, to enable the simulation of electronically non-adiabatic processes with nuclear quantum effects. We present numerical applications of the isomorphic Hamiltonian to model two- and three-level systems, with encouraging results that include improvement upon a previously reported combination of RPMD with surface hopping in the deep-tunneling regime.
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Dynamic tests of composite panels of an aircraft wing
NASA Astrophysics Data System (ADS)
Splichal, Jan; Pistek, Antonin; Hlinka, Jiri
2015-10-01
The paper describes the analysis of aerospace composite structures under dynamic loading. Today, it is common to use design procedures based on assumption of static loading only, and dynamic loading is rarely assumed and applied in design and certification of aerospace structures. The paper describes the application of dynamic loading for the design of aircraft structures, and the validation of the procedure on a selected structure. The goal is to verify the possibility of reducing the weight through improved design/modelling processes using dynamic loading instead of static loading. The research activity focuses on the modelling and testing of a composite panel representing a local segment of an aircraft wing section, investigating in particular the buckling behavior under dynamic loading. Finite Elements simulation tools are discussed, as well as the advantages of using a digital optical measurement system for the evaluation of the tests. The comparison of the finite element simulations with the results of the tests is presented.
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Enhanced Molecular Dynamics Methods Applied to Drug Design Projects.
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.
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Simulation tools for robotics research and assessment
NASA Astrophysics Data System (ADS)
Fields, MaryAnne; Brewer, Ralph; Edge, Harris L.; Pusey, Jason L.; Weller, Ed; Patel, Dilip G.; DiBerardino, Charles A.
2016-05-01
The Robotics Collaborative Technology Alliance (RCTA) program focuses on four overlapping technology areas: Perception, Intelligence, Human-Robot Interaction (HRI), and Dexterous Manipulation and Unique Mobility (DMUM). In addition, the RCTA program has a requirement to assess progress of this research in standalone as well as integrated form. Since the research is evolving and the robotic platforms with unique mobility and dexterous manipulation are in the early development stage and very expensive, an alternate approach is needed for efficient assessment. Simulation of robotic systems, platforms, sensors, and algorithms, is an attractive alternative to expensive field-based testing. Simulation can provide insight during development and debugging unavailable by many other means. This paper explores the maturity of robotic simulation systems for applications to real-world problems in robotic systems research. Open source (such as Gazebo and Moby), commercial (Simulink, Actin, LMS), government (ANVEL/VANE), and the RCTA-developed RIVET simulation environments are examined with respect to their application in the robotic research domains of Perception, Intelligence, HRI, and DMUM. Tradeoffs for applications to representative problems from each domain are presented, along with known deficiencies and disadvantages. In particular, no single robotic simulation environment adequately covers the needs of the robotic researcher in all of the domains. Simulation for DMUM poses unique constraints on the development of physics-based computational models of the robot, the environment and objects within the environment, and the interactions between them. Most current robot simulations focus on quasi-static systems, but dynamic robotic motion places an increased emphasis on the accuracy of the computational models. In order to understand the interaction of dynamic multi-body systems, such as limbed robots, with the environment, it may be necessary to build component-level computational models to provide the necessary simulation fidelity for accuracy. However, the Perception domain remains the most problematic for adequate simulation performance due to the often cartoon nature of computer rendering and the inability to model realistic electromagnetic radiation effects, such as multiple reflections, in real-time.
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A New Powered Lower Limb Prosthesis Control Framework Based on Adaptive Dynamic Programming.
Wen, Yue; Si, Jennie; Gao, Xiang; Huang, Stephanie; Huang, He Helen
2017-09-01
This brief presents a novel application of adaptive dynamic programming (ADP) for optimal adaptive control of powered lower limb prostheses, a type of wearable robots to assist the motor function of the limb amputees. Current control of these robotic devices typically relies on finite state impedance control (FS-IC), which lacks adaptability to the user's physical condition. As a result, joint impedance settings are often customized manually and heuristically in clinics, which greatly hinder the wide use of these advanced medical devices. This simulation study aimed at demonstrating the feasibility of ADP for automatic tuning of the twelve knee joint impedance parameters during a complete gait cycle to achieve balanced walking. Given that the accurate models of human walking dynamics are difficult to obtain, the model-free ADP control algorithms were considered. First, direct heuristic dynamic programming (dHDP) was applied to the control problem, and its performance was evaluated on OpenSim, an often-used dynamic walking simulator. For the comparison purposes, we selected another established ADP algorithm, the neural fitted Q with continuous action (NFQCA). In both cases, the ADP controllers learned to control the right knee joint and achieved balanced walking, but dHDP outperformed NFQCA in this application during a 200 gait cycle-based testing.
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NASA Astrophysics Data System (ADS)
Wang, Han; Zhang, Linfeng; Han, Jiequn; E, Weinan
2018-07-01
Recent developments in many-body potential energy representation via deep learning have brought new hopes to addressing the accuracy-versus-efficiency dilemma in molecular simulations. Here we describe DeePMD-kit, a package written in Python/C++ that has been designed to minimize the effort required to build deep learning based representation of potential energy and force field and to perform molecular dynamics. Potential applications of DeePMD-kit span from finite molecules to extended systems and from metallic systems to chemically bonded systems. DeePMD-kit is interfaced with TensorFlow, one of the most popular deep learning frameworks, making the training process highly automatic and efficient. On the other end, DeePMD-kit is interfaced with high-performance classical molecular dynamics and quantum (path-integral) molecular dynamics packages, i.e., LAMMPS and the i-PI, respectively. Thus, upon training, the potential energy and force field models can be used to perform efficient molecular simulations for different purposes. As an example of the many potential applications of the package, we use DeePMD-kit to learn the interatomic potential energy and forces of a water model using data obtained from density functional theory. We demonstrate that the resulted molecular dynamics model reproduces accurately the structural information contained in the original model.