Lattice Boltzmann method for rain-induced overland flow

NASA Astrophysics Data System (ADS)

Ding, Yu; Liu, Haifei; Peng, Yong; Xing, Liming

2018-07-01

Complex rainfall situations can generate overland flow with complex hydrodynamic characteristics, affecting the surface configuration (i.e. sheet erosion) and environment to varying degrees. Reliable numerical simulations can provide a scientific method for the optimization of environmental management. A mesoscopic numerical method, the lattice Boltzmann method, was employed to simulate overland flows. To deal with complex rainfall, two schemes were introduced to improve the lattice Boltzmann equation and the local equilibrium function, respectively. Four typical cases with differences in rainfall, bed roughness, and slopes were selected to test the accuracy and applicability of the proposed schemes. It was found that the simulated results were in good agreement with the experimental data, analytical values, and the results produced by other models.

Large-Eddy Simulations of Atmospheric Flows Over Complex Terrain Using the Immersed-Boundary Method in the Weather Research and Forecasting Model

NASA Astrophysics Data System (ADS)

Ma, Yulong; Liu, Heping

2017-12-01

Atmospheric flow over complex terrain, particularly recirculation flows, greatly influences wind-turbine siting, forest-fire behaviour, and trace-gas and pollutant dispersion. However, there is a large uncertainty in the simulation of flow over complex topography, which is attributable to the type of turbulence model, the subgrid-scale (SGS) turbulence parametrization, terrain-following coordinates, and numerical errors in finite-difference methods. Here, we upgrade the large-eddy simulation module within the Weather Research and Forecasting model by incorporating the immersed-boundary method into the module to improve simulations of the flow and recirculation over complex terrain. Simulations over the Bolund Hill indicate improved mean absolute speed-up errors with respect to previous studies, as well an improved simulation of the recirculation zone behind the escarpment of the hill. With regard to the SGS parametrization, the Lagrangian-averaged scale-dependent Smagorinsky model performs better than the classic Smagorinsky model in reproducing both velocity and turbulent kinetic energy. A finer grid resolution also improves the strength of the recirculation in flow simulations, with a higher horizontal grid resolution improving simulations just behind the escarpment, and a higher vertical grid resolution improving results on the lee side of the hill. Our modelling approach has broad applications for the simulation of atmospheric flows over complex topography.

Complex Langevin Simulations of QCD at Finite Density - Progress Report

NASA Astrophysics Data System (ADS)

Sinclair, D. K.; Kogut, J. B.

2018-03-01

We simulate lattice QCD at finite quark-number chemical potential to study nuclear matter, using the complex Langevin equation (CLE). The CLE is used because the fermion determinant is complex so that standard methods relying on importance sampling fail. Adaptive methods and gauge-cooling are used to prevent runaway solutions. Even then, the CLE is not guaranteed to give correct results. We are therefore performing extensive testing to determine under what, if any, conditions we can achieve reliable results. Our earlier simulations at β = 6/g2 = 5.6, m = 0.025 on a 124 lattice reproduced the expected phase structure but failed in the details. Our current simulations at β = 5.7 on a 164 lattice fail in similar ways while showing some improvement. We are therefore moving to even weaker couplings to see if the CLE might produce the correct results in the continuum (weak-coupling) limit, or, if it still fails, whether it might reproduce the results of the phase-quenched theory. We also discuss action (and other dynamics) modifications which might improve the performance of the CLE.

Rainfall runoff modelling of the Upper Ganga and Brahmaputra basins using PERSiST.

PubMed

Futter, M N; Whitehead, P G; Sarkar, S; Rodda, H; Crossman, J

2015-06-01

There are ongoing discussions about the appropriate level of complexity and sources of uncertainty in rainfall runoff models. Simulations for operational hydrology, flood forecasting or nutrient transport all warrant different levels of complexity in the modelling approach. More complex model structures are appropriate for simulations of land-cover dependent nutrient transport while more parsimonious model structures may be adequate for runoff simulation. The appropriate level of complexity is also dependent on data availability. Here, we use PERSiST; a simple, semi-distributed dynamic rainfall-runoff modelling toolkit to simulate flows in the Upper Ganges and Brahmaputra rivers. We present two sets of simulations driven by single time series of daily precipitation and temperature using simple (A) and complex (B) model structures based on uniform and hydrochemically relevant land covers respectively. Models were compared based on ensembles of Bayesian Information Criterion (BIC) statistics. Equifinality was observed for parameters but not for model structures. Model performance was better for the more complex (B) structural representations than for parsimonious model structures. The results show that structural uncertainty is more important than parameter uncertainty. The ensembles of BIC statistics suggested that neither structural representation was preferable in a statistical sense. Simulations presented here confirm that relatively simple models with limited data requirements can be used to credibly simulate flows and water balance components needed for nutrient flux modelling in large, data-poor basins.

Prototyping and Simulation of Robot Group Intelligence using Kohonen Networks.

PubMed

Wang, Zhijun; Mirdamadi, Reza; Wang, Qing

2016-01-01

Intelligent agents such as robots can form ad hoc networks and replace human being in many dangerous scenarios such as a complicated disaster relief site. This project prototypes and builds a computer simulator to simulate robot kinetics, unsupervised learning using Kohonen networks, as well as group intelligence when an ad hoc network is formed. Each robot is modeled using an object with a simple set of attributes and methods that define its internal states and possible actions it may take under certain circumstances. As the result, simple, reliable, and affordable robots can be deployed to form the network. The simulator simulates a group of robots as an unsupervised learning unit and tests the learning results under scenarios with different complexities. The simulation results show that a group of robots could demonstrate highly collaborative behavior on a complex terrain. This study could potentially provide a software simulation platform for testing individual and group capability of robots before the design process and manufacturing of robots. Therefore, results of the project have the potential to reduce the cost and improve the efficiency of robot design and building.

Prototyping and Simulation of Robot Group Intelligence using Kohonen Networks

PubMed Central

Wang, Zhijun; Mirdamadi, Reza; Wang, Qing

2016-01-01

Intelligent agents such as robots can form ad hoc networks and replace human being in many dangerous scenarios such as a complicated disaster relief site. This project prototypes and builds a computer simulator to simulate robot kinetics, unsupervised learning using Kohonen networks, as well as group intelligence when an ad hoc network is formed. Each robot is modeled using an object with a simple set of attributes and methods that define its internal states and possible actions it may take under certain circumstances. As the result, simple, reliable, and affordable robots can be deployed to form the network. The simulator simulates a group of robots as an unsupervised learning unit and tests the learning results under scenarios with different complexities. The simulation results show that a group of robots could demonstrate highly collaborative behavior on a complex terrain. This study could potentially provide a software simulation platform for testing individual and group capability of robots before the design process and manufacturing of robots. Therefore, results of the project have the potential to reduce the cost and improve the efficiency of robot design and building. PMID:28540284

Simulating Mass Removal of Groundwater Contaminant Plumes with Complex and Simple Models

NASA Astrophysics Data System (ADS)

Lopez, J.; Guo, Z.; Fogg, G. E.

2016-12-01

Chlorinated solvents used in industrial, commercial, and other applications continue to pose significant threats to human health through contamination of groundwater resources. A recent National Research Council report concludes that it is unlikely that remediation of these complex sites will be achieved in a time frame of 50-100 years under current methods and standards (NRC, 2013). Pump and treat has been a common strategy at many sites to contain and treat groundwater contamination. In these sites, extensive retention of contaminant mass in low-permeability materials (tailing) has been observed after years or decades of pumping. Although transport models can be built that contain enough of the complex, 3D heterogeneity to simulate the tailing and long cleanup times, this is seldom done because of the large data and computational burdens. Hence, useful, reliable models to simulate various cleanup strategies are rare. The purpose of this study is to explore other potential ways to simulate the mass-removal processes with shorter time and less cost but still produce robust results by capturing effects of the heterogeneity and long-term retention of mass. A site containing a trichloroethylene groundwater plume was selected as the study area. The plume is located within alluvial sediments in the Tucson Basin. A fully heterogeneous domain is generated first and MODFLOW is used to simulate the flow field. Contaminant transport is simulated using both MT3D and RWHet for the fully heterogeneous model. Other approaches, including dual-domain mass transfer and heterogeneous chemical reactions, are manipulated to simulate the mass removal in a less heterogeneous, or homogeneous, domain and results are compared to the results obtained from complex models. The capability of these simpler models to simulate remediation processes, especially capture the late-time tailing, are examined.

Scale-Dependent Rates of Uranyl Surface Complexation Reaction in Sediments

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

Liu, Chongxuan; Shang, Jianying; Kerisit, Sebastien N.

Scale-dependency of uranyl[U(VI)] surface complexation rates was investigated in stirred flow-cell and column systems using a U(VI)-contaminated sediment from the US Department of Energy, Hanford site, WA. The experimental results were used to estimate the apparent rate of U(VI) surface complexation at the grain-scale and in porous media. Numerical simulations using molecular, pore-scale, and continuum models were performed to provide insights into and to estimate the rate constants of U(VI) surface complexation at the different scales. The results showed that the grain-scale rate constant of U(VI) surface complexation was over 3 to 10 orders of magnitude smaller, dependent on themore » temporal scale, than the rate constant calculated using the molecular simulations. The grain-scale rate was faster initially and slower with time, showing the temporal scale-dependency. The largest rate constant at the grain-scale decreased additional 2 orders of magnitude when the rate was scaled to the porous media in the column. The scaling effect from the grain-scale to the porous media became less important for the slower sorption sites. Pore-scale simulations revealed the importance of coupled mass transport and reactions in both intragranular and inter-granular domains, which caused both spatial and temporal dependence of U(VI) surface complexation rates in the sediment. Pore-scale simulations also revealed a new rate-limiting mechanism in the intragranular porous domains that the rate of coupled diffusion and surface complexation reaction was slower than either process alone. The results provided important implications for developing models to scale geochemical/biogeochemical reactions.« less

Promoting Conceptual Change for Complex Systems Understanding: Outcomes of an Agent-Based Participatory Simulation

NASA Astrophysics Data System (ADS)

Rates, Christopher A.; Mulvey, Bridget K.; Feldon, David F.

2016-08-01

Components of complex systems apply across multiple subject areas, and teaching these components may help students build unifying conceptual links. Students, however, often have difficulty learning these components, and limited research exists to understand what types of interventions may best help improve understanding. We investigated 32 high school students' understandings of complex systems components and whether an agent-based simulation could improve their understandings. Pretest and posttest essays were coded for changes in six components to determine whether students showed more expert thinking about the complex system of the Chesapeake Bay watershed. Results showed significant improvement for the components Emergence ( r = .26, p = .03), Order ( r = .37, p = .002), and Tradeoffs ( r = .44, p = .001). Implications include that the experiential nature of the simulation has the potential to support conceptual change for some complex systems components, presenting a promising option for complex systems instruction.

Thrive or overload? The effect of task complexity on novices' simulation-based learning.

PubMed

Haji, Faizal A; Cheung, Jeffrey J H; Woods, Nicole; Regehr, Glenn; de Ribaupierre, Sandrine; Dubrowski, Adam

2016-09-01

Fidelity is widely viewed as an important element of simulation instructional design based on its purported relationship with transfer of learning. However, higher levels of fidelity may increase task complexity to a point at which novices' cognitive resources become overloaded. In this experiment, we investigate the effects of variations in task complexity on novices' cognitive load and learning during simulation-based procedural skills training. Thirty-eight medical students were randomly assigned to simulation training on a simple or complex lumbar puncture (LP) task. Participants completed four practice trials on this task (skill acquisition). After 10 days of rest, all participants completed one additional trial on their assigned task (retention) and one trial on a 'very complex' simulation designed to be similar to the complex task (transfer). We assessed LP performance and cognitive load on each trial using multiple measures. In both groups, LP performance improved significantly during skill acquisition (p ≤ 0.047, f = 0.29-0.96) and was maintained at retention. The simple task group demonstrated superior performance compared with the complex task group throughout these phases (p ≤ 0.002, d = 1.13-2.31). Cognitive load declined significantly in the simple task group (p < 0.009, f = 0.48-0.76), but not in the complex task group during skill acquisition, and remained lower at retention (p ≤ 0.024, d = 0.78-1.39). Between retention and transfer, LP performance declined and cognitive load increased in the simple task group, whereas both remained stable in the complex task group. At transfer, no group differences were observed in LP performance and cognitive load, except that the simple task group made significantly fewer breaches of sterility (p = 0.023, d = 0.80). Reduced task complexity was associated with superior LP performance and lower cognitive load during skill acquisition and retention, but mixed results on transfer to a more complex task. These results indicate that task complexity is an important factor that may mediate (via cognitive overload) the relationship between instructional design elements (e.g. fidelity) and simulation-based learning outcomes. © 2016 John Wiley & Sons Ltd and The Association for the Study of Medical Education.

Virtual planning for craniomaxillofacial surgery--7 years of experience.

PubMed

Adolphs, Nicolai; Haberl, Ernst-Johannes; Liu, Weichen; Keeve, Erwin; Menneking, Horst; Hoffmeister, Bodo

2014-07-01

Contemporary computer-assisted surgery systems more and more allow for virtual simulation of even complex surgical procedures with increasingly realistic predictions. Preoperative workflows are established and different commercially software solutions are available. Potential and feasibility of virtual craniomaxillofacial surgery as an additional planning tool was assessed retrospectively by comparing predictions and surgical results. Since 2006 virtual simulation has been performed in selected patient cases affected by complex craniomaxillofacial disorders (n = 8) in addition to standard surgical planning based on patient specific 3d-models. Virtual planning could be performed for all levels of the craniomaxillofacial framework within a reasonable preoperative workflow. Simulation of even complex skeletal displacements corresponded well with the real surgical result and soft tissue simulation proved to be helpful. In combination with classic 3d-models showing the underlying skeletal pathology virtual simulation improved planning and transfer of craniomaxillofacial corrections. Additional work and expenses may be justified by increased possibilities of visualisation, information, instruction and documentation in selected craniomaxillofacial procedures. Copyright © 2013 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

SimulaTE: simulating complex landscapes of transposable elements of populations.

PubMed

Kofler, Robert

2018-04-15

Estimating the abundance of transposable elements (TEs) in populations (or tissues) promises to answer many open research questions. However, progress is hampered by the lack of concordance between different approaches for TE identification and thus potentially unreliable results. To address this problem, we developed SimulaTE a tool that generates TE landscapes for populations using a newly developed domain specific language (DSL). The simple syntax of our DSL allows for easily building even complex TE landscapes that have, for example, nested, truncated and highly diverged TE insertions. Reads may be simulated for the populations using different sequencing technologies (PacBio, Illumina paired-ends) and strategies (sequencing individuals and pooled populations). The comparison between the expected (i.e. simulated) and the observed results will guide researchers in finding the most suitable approach for a particular research question. SimulaTE is implemented in Python and available at https://sourceforge.net/projects/simulates/. Manual https://sourceforge.net/p/simulates/wiki/Home/#manual; Test data and tutorials https://sourceforge.net/p/simulates/wiki/Home/#walkthrough; Validation https://sourceforge.net/p/simulates/wiki/Home/#validation. robert.kofler@vetmeduni.ac.at.

Metrics for comparing dynamic earthquake rupture simulations

USGS Publications Warehouse

Barall, Michael; Harris, Ruth A.

2014-01-01

Earthquakes are complex events that involve a myriad of interactions among multiple geologic features and processes. One of the tools that is available to assist with their study is computer simulation, particularly dynamic rupture simulation. A dynamic rupture simulation is a numerical model of the physical processes that occur during an earthquake. Starting with the fault geometry, friction constitutive law, initial stress conditions, and assumptions about the condition and response of the near‐fault rocks, a dynamic earthquake rupture simulation calculates the evolution of fault slip and stress over time as part of the elastodynamic numerical solution (Ⓔ see the simulation description in the electronic supplement to this article). The complexity of the computations in a dynamic rupture simulation make it challenging to verify that the computer code is operating as intended, because there are no exact analytic solutions against which these codes’ results can be directly compared. One approach for checking if dynamic rupture computer codes are working satisfactorily is to compare each code’s results with the results of other dynamic rupture codes running the same earthquake simulation benchmark. To perform such a comparison consistently, it is necessary to have quantitative metrics. In this paper, we present a new method for quantitatively comparing the results of dynamic earthquake rupture computer simulation codes.

Building an Open-source Simulation Platform of Acoustic Radiation Force-based Breast Elastography

PubMed Central

Wang, Yu; Peng, Bo; Jiang, Jingfeng

2017-01-01

Ultrasound-based elastography including strain elastography (SE), acoustic radiation force Impulse (ARFI) imaging, point shear wave elastography (pSWE) and supersonic shear imaging (SSI) have been used to differentiate breast tumors among other clinical applications. The objective of this study is to extend a previously published virtual simulation platform built for ultrasound quasi-static breast elastography toward acoustic radiation force-based breast elastography. Consequently, the extended virtual breast elastography simulation platform can be used to validate image pixels with known underlying soft tissue properties (i.e. “ground truth”) in complex, heterogeneous media, enhancing confidence in elastographic image interpretations. The proposed virtual breast elastography system inherited four key components from the previously published virtual simulation platform: an ultrasound simulator (Field II), a mesh generator (Tetgen), a finite element solver (FEBio) and a visualization and data processing package (VTK). Using a simple message passing mechanism, functionalities have now been extended to acoustic radiation force-based elastography simulations. Examples involving three different numerical breast models with increasing complexity – one uniform model, one simple inclusion model and one virtual complex breast model derived from magnetic resonance imaging data, were used to demonstrate capabilities of this extended virtual platform. Overall, simulation results were compared with the published results. In the uniform model, the estimated shear wave speed (SWS) values were within 4% compared to the predetermined SWS values. In the simple inclusion and the complex breast models, SWS values of all hard inclusions in soft backgrounds were slightly underestimated, similar to what has been reported. The elastic contrast values and visual observation show that ARFI images have higher spatial resolution, while SSI images can provide higher inclusion-to-background contrast. In summary, our initial results were consistent with our expectations and what have been reported in the literature. The proposed (open-source) simulation platform can serve as a single gateway to perform many elastographic simulations in a transparent manner, thereby promoting collaborative developments. PMID:28075330

Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields.

PubMed

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

2015-12-10

We report an extensive set of explicit solvent molecular dynamics (MD) simulations (∼25 μs of accumulated simulation time) of the RNA kissing-loop complex of the HIV-1 virus initiation dimerization site. Despite many structural investigations by X-ray, NMR, and MD techniques, the position of the bulged purines of the kissing complex has not been unambiguously resolved. The X-ray structures consistently show bulged-out positions of the unpaired bases, while several NMR studies show bulged-in conformations. The NMR studies are, however, mutually inconsistent regarding the exact orientations of the bases. The earlier simulation studies predicted the bulged-out conformation; however, this finding could have been biased by the short simulation time scales. Our microsecond-long simulations reveal that all unpaired bases of the kissing-loop complex stay preferably in the interior of the kissing-loop complex. The MD results are discussed in the context of the available experimental data and we suggest that both conformations are biochemically relevant. We also show that MD provides a quite satisfactory description of this RNA system, contrasting recent reports of unsatisfactory performance of the RNA force fields for smaller systems such as tetranucleotides and tetraloops. We explain this by the fact that the kissing complex is primarily stabilized by an extensive network of Watson-Crick interactions which are rather well described by the force fields. We tested several different sets of water/ion parameters but they all lead to consistent results. However, we demonstrate that a recently suggested modification of van der Waals interactions of the Cornell et al. force field deteriorates the description of the kissing complex by the loss of key stacking interactions stabilizing the interhelical junction and excessive hydrogen-bonding interactions.

Characterization of the Interaction between Gallic Acid and Lysozyme by Molecular Dynamics Simulation and Optical Spectroscopy

PubMed Central

Zhan, Minzhong; Guo, Ming; Jiang, Yanke; Wang, Xiaomeng

2015-01-01

The binding interaction between gallic acid (GA) and lysozyme (LYS) was investigated and compared by molecular dynamics (MD) simulation and spectral techniques. The results from spectroscopy indicate that GA binds to LYS to generate a static complex. The binding constants and thermodynamic parameters were calculated. MD simulation revealed that the main driving forces for GA binding to LYS are hydrogen bonding and hydrophobic interactions. The root-mean-square deviation verified that GA and LYS bind to form a stable complex, while the root-mean-square fluctuation results showed that the stability of the GA-LYS complex at 298 K was higher than that at 310 K. The calculated free binding energies from the molecular mechanics/Poisson-Boltzmann surface area method showed that van der Waals forces and electrostatic interactions are the predominant intermolecular forces. The MD simulation was consistent with the spectral experiments. This study provides a reference for future study of the pharmacological mechanism of GA. PMID:26140374

Characterization of the Interaction between Gallic Acid and Lysozyme by Molecular Dynamics Simulation and Optical Spectroscopy.

PubMed

Zhan, Minzhong; Guo, Ming; Jiang, Yanke; Wang, Xiaomeng

2015-07-01

The binding interaction between gallic acid (GA) and lysozyme (LYS) was investigated and compared by molecular dynamics (MD) simulation and spectral techniques. The results from spectroscopy indicate that GA binds to LYS to generate a static complex. The binding constants and thermodynamic parameters were calculated. MD simulation revealed that the main driving forces for GA binding to LYS are hydrogen bonding and hydrophobic interactions. The root-mean-square deviation verified that GA and LYS bind to form a stable complex, while the root-mean-square fluctuation results showed that the stability of the GA-LYS complex at 298 K was higher than that at 310 K. The calculated free binding energies from the molecular mechanics/Poisson-Boltzmann surface area method showed that van der Waals forces and electrostatic interactions are the predominant intermolecular forces. The MD simulation was consistent with the spectral experiments. This study provides a reference for future study of the pharmacological mechanism of GA.

Global exponential periodicity and stability of discrete-time complex-valued recurrent neural networks with time-delays.

PubMed

Hu, Jin; Wang, Jun

2015-06-01

In recent years, complex-valued recurrent neural networks have been developed and analysed in-depth in view of that they have good modelling performance for some applications involving complex-valued elements. In implementing continuous-time dynamical systems for simulation or computational purposes, it is quite necessary to utilize a discrete-time model which is an analogue of the continuous-time system. In this paper, we analyse a discrete-time complex-valued recurrent neural network model and obtain the sufficient conditions on its global exponential periodicity and exponential stability. Simulation results of several numerical examples are delineated to illustrate the theoretical results and an application on associative memory is also given. Copyright © 2015 Elsevier Ltd. All rights reserved.

Efficient evaluation of wireless real-time control networks.

PubMed

Horvath, Peter; Yampolskiy, Mark; Koutsoukos, Xenofon

2015-02-11

In this paper, we present a system simulation framework for the design and performance evaluation of complex wireless cyber-physical systems. We describe the simulator architecture and the specific developments that are required to simulate cyber-physical systems relying on multi-channel, multihop mesh networks. We introduce realistic and efficient physical layer models and a system simulation methodology, which provides statistically significant performance evaluation results with low computational complexity. The capabilities of the proposed framework are illustrated in the example of WirelessHART, a centralized, real-time, multi-hop mesh network designed for industrial control and monitor applications.

FLAME: A platform for high performance computing of complex systems, applied for three case studies

DOE PAGES

Kiran, Mariam; Bicak, Mesude; Maleki-Dizaji, Saeedeh; ...

2011-01-01

FLAME allows complex models to be automatically parallelised on High Performance Computing (HPC) grids enabling large number of agents to be simulated over short periods of time. Modellers are hindered by complexities of porting models on parallel platforms and time taken to run large simulations on a single machine, which FLAME overcomes. Three case studies from different disciplines were modelled using FLAME, and are presented along with their performance results on a grid.

Simulations of DNA stretching by flow field in microchannels with complex geometry.

PubMed

Huang, Chiou-De; Kang, Dun-Yen; Hsieh, Chih-Chen

2014-01-01

Recently, we have reported the experimental results of DNA stretching by flow field in three microchannels (C. H. Lee and C. C. Hsieh, Biomicrofluidics 7(1), 014109 (2013)) designed specifically for the purpose of preconditioning DNA conformation for easier stretching. The experimental results do not only demonstrate the superiority of the new devices but also provides detailed observation of DNA behavior in complex flow field that was not available before. In this study, we use Brownian dynamics-finite element method (BD-FEM) to simulate DNA behavior in these microchannels, and compare the results against the experiments. Although the hydrodynamic interaction (HI) between DNA segments and between DNA and the device boundaries was not included in the simulations, the simulation results are in fairly good agreement with the experimental data from either the aspect of the single molecule behavior or from the aspect of ensemble averaged properties. The discrepancy between the simulation and the experimental results can be explained by the neglect of HI effect in the simulations. Considering the huge savings on the computational cost from neglecting HI, we conclude that BD-FEM can be used as an efficient and economic designing tool for developing new microfluidic device for DNA manipulation.

Design and validation of inert homemade explosive simulants for ground penetrating radar

NASA Astrophysics Data System (ADS)

VanderGaast, Brian W.; McFee, John E.; Russell, Kevin L.; Faust, Anthony A.

2015-05-01

The Canadian Armed Forces (CAF) identified a requirement for inert simulants to act as improvised, or homemade, explosives (IEs) when training on, or evaluating, ground penetrating radar (GPR) systems commonly used in the detection of buried landmines and improvised explosive devices (IEDs). In response, Defence R and D Canada (DRDC) initiated a project to develop IE simulant formulations using commonly available inert materials. These simulants are intended to approximate the expected GPR response of common ammonium nitrate-based IEs, in particular ammonium nitrate/fuel oil (ANFO) and ammonium nitrate/aluminum (ANAl). The complex permittivity over the range of electromagnetic frequencies relevant to standard GPR systems was measured for bulk quantities of these three IEs that had been fabricated at DRDC Suffield Research Centre. Following these measurements, published literature was examined to find benign materials with both a similar complex permittivity, as well as other physical properties deemed desirable - such as low-toxicity, thermal stability, and commercial availability - in order to select candidates for subsequent simulant formulation. Suitable simulant formulations were identified for ANFO, with resulting complex permittivities measured to be within acceptable limits of target values. These IE formulations will now undergo end-user trials with CAF operators in order to confirm their utility. Investigations into ANAl simulants continues. This progress report outlines the development program, simulant design, and current validation results.

Comparison of Measured and Numerically Simulated Turbulence Statistics in a Convective Boundary Layer Over Complex Terrain

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

Rai, Raj K.; Berg, Larry K.; Kosović, Branko

High resolution numerical simulation can provide insight into important physical processes that occur within the planetary boundary layer (PBL). The present work employs large eddy simulation (LES) using the Weather Forecasting and Research (WRF) model, with the LES domain nested within mesoscale simulation, to simulate real conditions in the convective PBL over an area of complex terrain. A multiple nesting approach has been used to downsize the grid spacing from 12.15 km (mesoscale) to 0.03 km (LES). A careful selection of grid spacing in the WRF Meso domain has been conducted to minimize artifacts in the WRF-LES solutions. The WRF-LESmore » results have been evaluated with in situ and remote sensing observations collected during the US Department of Energy-supported Columbia BasinWind Energy Study (CBWES). Comparison of the first- and second-order moments, turbulence spectrum, and probability density function (PDF) of wind speed shows good agreement between the simulations and data. Furthermore, the WRF-LES variables show a great deal of variability in space and time caused by the complex topography in the LES domain. The WRF-LES results show that the flow structures, such as roll vortices and convective cells, vary depending on both the location and time of day. In addition to basic studies related to boundary-layer meteorology, results from these simulations can be used in other applications, such as studying wind energy resources, atmospheric dispersion, fire weather etc.« less

Simulation of the human-telerobot interface

NASA Technical Reports Server (NTRS)

Stuart, Mark A.; Smith, Randy L.

1988-01-01

A part of NASA's Space Station will be a Flight Telerobotic Servicer (FTS) used to help assemble, service, and maintain the Space Station. Since the human operator will be required to control the FTS, the design of the human-telerobot interface must be optimized from a human factors perspective. Simulation has been used as an aid in the development of complex systems. Simulation has been especially useful when it has been applied to the development of complex systems. Simulation should ensure that the hardware and software components of the human-telerobot interface have been designed and selected so that the operator's capabilities and limitations have been accommodated for since this is a complex system where few direct comparisons to existent systems can be made. Three broad areas of the human-telerobot interface where simulation can be of assistance are described. The use of simulation not only can result in a well-designed human-telerobot interface, but also can be used to ensure that components have been selected to best meet system's goals, and for operator training.

Stabilizing a spinning Skylab

NASA Technical Reports Server (NTRS)

Seltzer, S. M.; Patel, J. S.; Justice, D. W.; Schweitzer, G. E.

1972-01-01

The results are presented of a study of the dynamics of a spinning Skylab space station. The stability of motion of several simplified models with flexible appendages was investigated. A digital simulation model that more accurately portrays the complex Skylab vehicle is described, and simulation results are compared with analytically derived results.

Numerical investigation of coupled density-driven flow and hydrogeochemical processes below playas

NASA Astrophysics Data System (ADS)

Hamann, Enrico; Post, Vincent; Kohfahl, Claus; Prommer, Henning; Simmons, Craig T.

2015-11-01

Numerical modeling approaches with varying complexity were explored to investigate coupled groundwater flow and geochemical processes in saline basins. Long-term model simulations of a playa system gain insights into the complex feedback mechanisms between density-driven flow and the spatiotemporal patterns of precipitating evaporites and evolving brines. Using a reactive multicomponent transport model approach, the simulations reproduced, for the first time in a numerical study, the evaporite precipitation sequences frequently observed in saline basins ("bull's eyes"). Playa-specific flow, evapoconcentration, and chemical divides were found to be the primary controls for the location of evaporites formed, and the resulting brine chemistry. Comparative simulations with the computationally far less demanding surrogate single-species transport models showed that these were still able to replicate the major flow patterns obtained by the more complex reactive transport simulations. However, the simulated degree of salinization was clearly lower than in reactive multicomponent transport simulations. For example, in the late stages of the simulations, when the brine becomes halite-saturated, the nonreactive simulation overestimated the solute mass by almost 20%. The simulations highlight the importance of the consideration of reactive transport processes for understanding and quantifying geochemical patterns, concentrations of individual dissolved solutes, and evaporite evolution.

Building a virtual simulation platform for quasistatic breast ultrasound elastography using open source software: A preliminary investigation

PubMed Central

Wang, Yu; Helminen, Emily; Jiang, Jingfeng

2015-01-01

Purpose: Quasistatic ultrasound elastography (QUE) is being used to augment in vivo characterization of breast lesions. Results from early clinical trials indicated that there was a lack of confidence in image interpretation. Such confidence can only be gained through rigorous imaging tests using complex, heterogeneous but known media. The objective of this study is to build a virtual breast QUE simulation platform in the public domain that can be used not only for innovative QUE research but also for rigorous imaging tests. Methods: The main thrust of this work is to streamline biomedical ultrasound simulations by leveraging existing open source software packages including Field II (ultrasound simulator), VTK (geometrical visualization and processing), FEBio [finite element (FE) analysis], and Tetgen (mesh generator). However, integration of these open source packages is nontrivial and requires interdisciplinary knowledge. In the first step, a virtual breast model containing complex anatomical geometries was created through a novel combination of image-based landmark structures and randomly distributed (small) structures. Image-based landmark structures were based on data from the NIH Visible Human Project. Subsequently, an unstructured FE-mesh was created by Tetgen. In the second step, randomly positioned point scatterers were placed within the meshed breast model through an octree-based algorithm to make a virtual breast ultrasound phantom. In the third step, an ultrasound simulator (Field II) was used to interrogate the virtual breast phantom to obtain simulated ultrasound echo data. Of note, tissue deformation generated using a FE-simulator (FEBio) was the basis of deforming the original virtual breast phantom in order to obtain the postdeformation breast phantom for subsequent ultrasound simulations. Using the procedures described above, a full cycle of QUE simulations involving complex and highly heterogeneous virtual breast phantoms can be accomplished for the first time. Results: Representative examples were used to demonstrate capabilities of this virtual simulation platform. In the first set of three ultrasound simulation examples, three heterogeneous volumes of interest were selected from a virtual breast ultrasound phantom to perform sophisticated ultrasound simulations. These resultant B-mode images realistically represented the underlying complex but known media. In the second set of three QUE examples, advanced applications in QUE were simulated. The first QUE example was to show breast tumors with complex shapes and/or compositions. The resultant strain images showed complex patterns that were normally seen in freehand clinical ultrasound data. The second and third QUE examples demonstrated (deformation-dependent) nonlinear strain imaging and time-dependent strain imaging, respectively. Conclusions: The proposed virtual QUE platform was implemented and successfully tested in this study. Through show-case examples, the proposed work has demonstrated its capabilities of creating sophisticated QUE data in a way that cannot be done through the manufacture of physical tissue-mimicking phantoms and other software. This open software architecture will soon be made available in the public domain and can be readily adapted to meet specific needs of different research groups to drive innovations in QUE. PMID:26328994

Coarse-grained simulations of polyelectrolyte complexes: MARTINI models for poly(styrene sulfonate) and poly(diallyldimethylammonium)

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

Vögele, Martin; Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt a. M.; Holm, Christian

2015-12-28

We present simulations of aqueous polyelectrolyte complexes with new MARTINI models for the charged polymers poly(styrene sulfonate) and poly(diallyldimethylammonium). Our coarse-grained polyelectrolyte models allow us to study large length and long time scales with regard to chemical details and thermodynamic properties. The results are compared to the outcomes of previous atomistic molecular dynamics simulations and verify that electrostatic properties are reproduced by our MARTINI coarse-grained approach with reasonable accuracy. Structural similarity between the atomistic and the coarse-grained results is indicated by a comparison between the pair radial distribution functions and the cumulative number of surrounding particles. Our coarse-grained models aremore » able to quantitatively reproduce previous findings like the correct charge compensation mechanism and a reduced dielectric constant of water. These results can be interpreted as the underlying reason for the stability of polyelectrolyte multilayers and complexes and validate the robustness of the proposed models.« less

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

Siranosian, Antranik Antonio; Schembri, Philip Edward; Miller, Nathan Andrew

The Benchmark Extensible Tractable Testbed Engineering Resource (BETTER) is proposed as a family of modular test bodies that are intended to support engineering capability development by helping to identify weaknesses and needs. Weapon systems, subassemblies, and components are often complex and difficult to test and analyze, resulting in low confidence and high uncertainties in experimental and simulated results. The complexities make it difficult to distinguish between inherent uncertainties and errors due to insufficient capabilities. BETTER test bodies will first use simplified geometries and materials such that testing, data collection, modeling and simulation can be accomplished with high confidence and lowmore » uncertainty. Modifications and combinations of simple and well-characterized BETTER test bodies can then be used to increase complexity in order to reproduce relevant mechanics and identify weaknesses. BETTER can provide both immediate and long-term improvements in testing and simulation capabilities. This document presents the motivation, concept, benefits and examples for BETTER.« less

Building a virtual simulation platform for quasistatic breast ultrasound elastography using open source software: A preliminary investigation.

PubMed

Wang, Yu; Helminen, Emily; Jiang, Jingfeng

2015-09-01

Quasistatic ultrasound elastography (QUE) is being used to augment in vivo characterization of breast lesions. Results from early clinical trials indicated that there was a lack of confidence in image interpretation. Such confidence can only be gained through rigorous imaging tests using complex, heterogeneous but known media. The objective of this study is to build a virtual breast QUE simulation platform in the public domain that can be used not only for innovative QUE research but also for rigorous imaging tests. The main thrust of this work is to streamline biomedical ultrasound simulations by leveraging existing open source software packages including Field II (ultrasound simulator), VTK (geometrical visualization and processing), FEBio [finite element (FE) analysis], and Tetgen (mesh generator). However, integration of these open source packages is nontrivial and requires interdisciplinary knowledge. In the first step, a virtual breast model containing complex anatomical geometries was created through a novel combination of image-based landmark structures and randomly distributed (small) structures. Image-based landmark structures were based on data from the NIH Visible Human Project. Subsequently, an unstructured FE-mesh was created by Tetgen. In the second step, randomly positioned point scatterers were placed within the meshed breast model through an octree-based algorithm to make a virtual breast ultrasound phantom. In the third step, an ultrasound simulator (Field II) was used to interrogate the virtual breast phantom to obtain simulated ultrasound echo data. Of note, tissue deformation generated using a FE-simulator (FEBio) was the basis of deforming the original virtual breast phantom in order to obtain the postdeformation breast phantom for subsequent ultrasound simulations. Using the procedures described above, a full cycle of QUE simulations involving complex and highly heterogeneous virtual breast phantoms can be accomplished for the first time. Representative examples were used to demonstrate capabilities of this virtual simulation platform. In the first set of three ultrasound simulation examples, three heterogeneous volumes of interest were selected from a virtual breast ultrasound phantom to perform sophisticated ultrasound simulations. These resultant B-mode images realistically represented the underlying complex but known media. In the second set of three QUE examples, advanced applications in QUE were simulated. The first QUE example was to show breast tumors with complex shapes and/or compositions. The resultant strain images showed complex patterns that were normally seen in freehand clinical ultrasound data. The second and third QUE examples demonstrated (deformation-dependent) nonlinear strain imaging and time-dependent strain imaging, respectively. The proposed virtual QUE platform was implemented and successfully tested in this study. Through show-case examples, the proposed work has demonstrated its capabilities of creating sophisticated QUE data in a way that cannot be done through the manufacture of physical tissue-mimicking phantoms and other software. This open software architecture will soon be made available in the public domain and can be readily adapted to meet specific needs of different research groups to drive innovations in QUE.

Monte Carlo simulations of flexible polyanions complexing with whey proteins at their isoelectric point

NASA Astrophysics Data System (ADS)

de Vries, R.

2004-02-01

Electrostatic complexation of flexible polyanions with the whey proteins α-lactalbumin and β-lactoglobulin is studied using Monte Carlo simulations. The proteins are considered at their respective isoelectric points. Discrete charges on the model polyelectrolytes and proteins interact through Debye-Hückel potentials. Protein excluded volume is taken into account through a coarse-grained model of the protein shape. Consistent with experimental results, it is found that α-lactalbumin complexes much more strongly than β-lactoglobulin. For α-lactalbumin, strong complexation is due to localized binding to a single large positive "charge patch," whereas for β-lactoglobulin, weak complexation is due to diffuse binding to multiple smaller charge patches.

Second-Year Pharmacy Students’ Perceptions of Adhering to a Complex Simulated Medication Regimen

PubMed Central

Hamer, David; Lehotsky, Kristin

2012-01-01

Objective. To conduct a simulated medication regimen with second-year pharmacy students to determine their anticipated versus actual difficulty in adhering to it. Methods. Second-year pharmacy students were given 6 fictitious medications (jellybeans) and a drug regimen to adhere to for 6 days. Pre- and post-intervention surveys were conducted to compare participants anticipated vs. actual difficulty with adherence and changes in empathy toward patients. Results. The 69 (96%) students who participated in the study missed on average 16% of all simulated medication doses and noted that adhering to the complex medication regimen was more difficult than they had anticipated. Eighty-nine percent of students agreed or strongly agreed the project was valuable in developing empathy towards patients taking complex medication regimens. Conclusions. Pharmacy students participating in a simulated medication regimen missed a notable number of doses and reported a greater level of empathy for patients taking complex medication regiments. Finding meaningful ways to integrate adherence into the curriculum is essential. PMID:22412210

Learning Performance with Interactive Simulations in Medical Education: Lessons Learned from Results of Learning Complex Physiological Models with the HAEMOdynamics SIMulator

ERIC Educational Resources Information Center

Holzinger, Andreas; Kickmeier-Rust, Michael D.; Wassertheurer, Sigi; Hessinger, Michael

2009-01-01

Objective: Since simulations are often accepted uncritically, with excessive emphasis being placed on technological sophistication at the expense of underlying psychological and educational theories, we evaluated the learning performance of simulation software, in order to gain insight into the proper use of simulations for application in medical…

A multiple-point geostatistical approach to quantifying uncertainty for flow and transport simulation in geologically complex environments

NASA Astrophysics Data System (ADS)

Cronkite-Ratcliff, C.; Phelps, G. A.; Boucher, A.

2011-12-01

In many geologic settings, the pathways of groundwater flow are controlled by geologic heterogeneities which have complex geometries. Models of these geologic heterogeneities, and consequently, their effects on the simulated pathways of groundwater flow, are characterized by uncertainty. Multiple-point geostatistics, which uses a training image to represent complex geometric descriptions of geologic heterogeneity, provides a stochastic approach to the analysis of geologic uncertainty. Incorporating multiple-point geostatistics into numerical models provides a way to extend this analysis to the effects of geologic uncertainty on the results of flow simulations. We present two case studies to demonstrate the application of multiple-point geostatistics to numerical flow simulation in complex geologic settings with both static and dynamic conditioning data. Both cases involve the development of a training image from a complex geometric description of the geologic environment. Geologic heterogeneity is modeled stochastically by generating multiple equally-probable realizations, all consistent with the training image. Numerical flow simulation for each stochastic realization provides the basis for analyzing the effects of geologic uncertainty on simulated hydraulic response. The first case study is a hypothetical geologic scenario developed using data from the alluvial deposits in Yucca Flat, Nevada. The SNESIM algorithm is used to stochastically model geologic heterogeneity conditioned to the mapped surface geology as well as vertical drill-hole data. Numerical simulation of groundwater flow and contaminant transport through geologic models produces a distribution of hydraulic responses and contaminant concentration results. From this distribution of results, the probability of exceeding a given contaminant concentration threshold can be used as an indicator of uncertainty about the location of the contaminant plume boundary. The second case study considers a characteristic lava-flow aquifer system in Pahute Mesa, Nevada. A 3D training image is developed by using object-based simulation of parametric shapes to represent the key morphologic features of rhyolite lava flows embedded within ash-flow tuffs. In addition to vertical drill-hole data, transient pressure head data from aquifer tests can be used to constrain the stochastic model outcomes. The use of both static and dynamic conditioning data allows the identification of potential geologic structures that control hydraulic response. These case studies demonstrate the flexibility of the multiple-point geostatistics approach for considering multiple types of data and for developing sophisticated models of geologic heterogeneities that can be incorporated into numerical flow simulations.

SIM_EXPLORE: Software for Directed Exploration of Complex Systems

NASA Technical Reports Server (NTRS)

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

2013-01-01

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

Hyper-Parallel Tempering Monte Carlo Method and It's Applications

NASA Astrophysics Data System (ADS)

Yan, Qiliang; de Pablo, Juan

2000-03-01

A new generalized hyper-parallel tempering Monte Carlo molecular simulation method is presented for study of complex fluids. The method is particularly useful for simulation of many-molecule complex systems, where rough energy landscapes and inherently long characteristic relaxation times can pose formidable obstacles to effective sampling of relevant regions of configuration space. The method combines several key elements from expanded ensemble formalisms, parallel-tempering, open ensemble simulations, configurational bias techniques, and histogram reweighting analysis of results. It is found to accelerate significantly the diffusion of a complex system through phase-space. In this presentation, we demonstrate the effectiveness of the new method by implementing it in grand canonical ensembles for a Lennard-Jones fluid, for the restricted primitive model of electrolyte solutions (RPM), and for polymer solutions and blends. Our results indicate that the new algorithm is capable of overcoming the large free energy barriers associated with phase transitions, thereby greatly facilitating the simulation of coexistence properties. It is also shown that the method can be orders of magnitude more efficient than previously available techniques. More importantly, the method is relatively simple and can be incorporated into existing simulation codes with minor efforts.

Using Metal Complex Ion-Molecule Reactions in a Miniature Rectilinear Ion Trap Mass Spectrometer to Detect Chemical Warfare Agents

NASA Astrophysics Data System (ADS)

Graichen, Adam M.; Vachet, Richard W.

2013-06-01

The gas-phase reactions of a series of coordinatively unsaturated [Ni(L)n]y+ complexes, where L is a nitrogen-containing ligand, with chemical warfare agent (CWA) simulants in a miniature rectilinear ion trap mass spectrometer were investigated as part of a new approach to detect CWAs. Results show that upon entering the vacuum system via a poly(dimethylsiloxane) (PDMS) membrane introduction, low concentrations of several CWA simulants, including dipropyl sulfide (simulant for mustard gas), acetonitrile (simulant for the nerve agent tabun), and diethyl phosphite (simulant for nerve agents sarin, soman, tabun, and VX), can react with metal complex ions generated by electrospray ionization (ESI), thereby providing a sensitive means of detecting these compounds. The [Ni(L)n]2+ complexes are found to be particularly reactive with the simulants of mustard gas and tabun, allowing their detection at low parts-per-billion (ppb) levels. These detection limits are well below reported exposure limits for these CWAs, which indicates the applicability of this new approach, and are about two orders of magnitude lower than electron ionization detection limits on the same mass spectrometer. The use of coordinatively unsaturated metal complexes as reagent ions offers the possibility of further tuning the ion-molecule chemistry so that desired compounds can be detected selectively or at even lower concentrations.

Simulation of the mobility of metal - EDTA complexes in groundwater: The influence of contaminant metals

USGS Publications Warehouse

Friedly, J.C.; Kent, D.B.; Davis, J.A.

2002-01-01

Reactive transport simulations were conducted to model chemical reactions between metal - EDTA (ethylenediaminetetraacetic acid) complexes during transport in a mildly acidic quartz - sand aquifer. Simulations were compared with the results of small-scale tracer tests wherein nickel-, zinc-, and calcium - EDTA complexes and free EDTA were injected into three distinct chemical zones of a plume of sewage-contaminated groundwater. One zone had a large mass of adsorbed, sewage-derived zinc; one zone had a large mass of adsorbed manganese resulting from mildly reducing conditions created bythe sewage plume; and one zone had significantly less adsorbed manganese and negligible zinc background. The chemical model assumed that the dissolution of iron(III) from metal - hydroxypolymer coatings on the aquifer sediments by the metal - EDTA complexes was kinetically restricted. All other reactions, including metal - EDTA complexation, zinc and manganese adsorption, and aluminum hydroxide dissolution were assumed to reach equilibrium on the time scale of transport; equilibrium constants were either taken from the literature or determined independently in the laboratory. A single iron(III) dissolution rate constant was used to fit the breakthrough curves observed in the zone with negligible zinc background. Simulation results agreed well with the experimental data in all three zones, which included temporal moments derived from breakthrough curves at different distances downgradient from the injections and spatial moments calculated from synoptic samplings conducted at different times. Results show that the tracer cloud was near equilibrium with respect to Fe in the sediment after 11 m of transport in the Zn-contaminated region but remained far from equilibrium in the other two zones. Sensitivity studies showed that the relative rate of iron(III) dissolution by the different metal - EDTA complexes was less important than the fact that these reactions are rate controlled. Results suggest that the published solubility for ferrihydrite reasonably approximates the Fe solubility of the hydroxypolymer coatings on the sediments. Aluminum may be somewhat more soluble than represented by the equilibrium constant for gibbsite, and its dissolution may be rate controlled when reacting with Ca - EDTA complexes.

Lattice Boltzmann simulations of immiscible displacement process with large viscosity ratios

NASA Astrophysics Data System (ADS)

Rao, Parthib; Schaefer, Laura

2017-11-01

Immiscible displacement is a key physical mechanism involved in enhanced oil recovery and carbon sequestration processes. This multiphase flow phenomenon involves a complex interplay of viscous, capillary, inertial and wettability effects. The lattice Boltzmann (LB) method is an accurate and efficient technique for modeling and simulating multiphase/multicomponent flows especially in complex flow configurations and media. In this presentation we present numerical simulation results of displacement process in thin long channels. The results are based on a new psuedo-potential multicomponent LB model with multiple relaxation time collision (MRT) model and explicit forcing scheme. We demonstrate that the proposed model is capable of accurately simulating the displacement process involving fluids with a wider range of viscosity ratios (>100) and which also leads to viscosity-independent interfacial tension and reduction of some important numerical artifacts.

Recommendations on Model Fidelity for Wind Turbine Gearbox Simulations; NREL (National Renewable Energy Laboratory)

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

Keller, J.; Lacava, W.; Austin, J.

2015-02-01

This work investigates the minimum level of fidelity required to accurately simulate wind turbine gearboxes using state-of-the-art design tools. Excessive model fidelity including drivetrain complexity, gearbox complexity, excitation sources, and imperfections, significantly increases computational time, but may not provide a commensurate increase in the value of the results. Essential designparameters are evaluated, including the planetary load-sharing factor, gear tooth load distribution, and sun orbit motion. Based on the sensitivity study results, recommendations for the minimum model fidelities are provided.

Are gamers better crossers? An examination of action video game experience and dual task effects in a simulated street crossing task.

PubMed

Gaspar, John G; Neider, Mark B; Crowell, James A; Lutz, Aubrey; Kaczmarski, Henry; Kramer, Arthur F

2014-05-01

A high-fidelity street crossing simulator was used to test the hypothesis that experienced action video game players are less vulnerable than non-gamers to dual task costs in complex tasks. Previous research has shown that action video game players outperform nonplayers on many single task measures of perception and attention. It is unclear, however, whether action video game players outperform nonplayers in complex, divided attention tasks. Experienced action video game players and nongamers completed a street crossing task in a high-fidelity simulator. Participants walked on a manual treadmill to cross the street. During some crossings, a cognitively demanding working memory task was added. Dividing attention resulted in more collisions and increased decision making time. Of importance, these dual task costs were equivalent for the action video game players and the nongamers. These results suggest that action video game players are equally susceptible to the costs of dividing attention in a complex task. Perceptual and attentional benefits associated with action video game experience may not translate to performance benefits in complex, real-world tasks.

Summarizing Simulation Results using Causally-relevant States

PubMed Central

Parikh, Nidhi; Marathe, Madhav; Swarup, Samarth

2016-01-01

As increasingly large-scale multiagent simulations are being implemented, new methods are becoming necessary to make sense of the results of these simulations. Even concisely summarizing the results of a given simulation run is a challenge. Here we pose this as the problem of simulation summarization: how to extract the causally-relevant descriptions of the trajectories of the agents in the simulation. We present a simple algorithm to compress agent trajectories through state space by identifying the state transitions which are relevant to determining the distribution of outcomes at the end of the simulation. We present a toy-example to illustrate the working of the algorithm, and then apply it to a complex simulation of a major disaster in an urban area. PMID:28042620

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

NASA Technical Reports Server (NTRS)

Hoffman, J. A.

1979-01-01

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

Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex

PubMed Central

Van Eerden, Floris J.; Melo, Manuel N.; Frederix, Pim W. J. M.; Periole, Xavier; Marrink, Siewert J.

2017-01-01

Plastoquinone (PLQ) acts as an electron carrier between photosystem II (PSII) and the cytochrome b6f complex. To understand how PLQ enters and leaves PSII, here we show results of coarse grained molecular dynamics simulations of PSII embedded in the thylakoid membrane, covering a total simulation time of more than 0.5 ms. The long time scale allows the observation of many spontaneous entries of PLQ into PSII, and the unbinding of plastoquinol (PLQol) from the complex. In addition to the two known channels, we observe a third channel for PLQ/PLQol diffusion between the thylakoid membrane and the PLQ binding sites. Our simulations point to a promiscuous diffusion mechanism in which all three channels function as entry and exit channels. The exchange cavity serves as a PLQ reservoir. Our simulations provide a direct view on the exchange of electron carriers, a key step of the photosynthesis machinery. PMID:28489071

Monte Carlo simulations of flexible polyanions complexing with whey proteins at their isoelectric point.

PubMed

de Vries, R

2004-02-15

Electrostatic complexation of flexible polyanions with the whey proteins alpha-lactalbumin and beta-lactoglobulin is studied using Monte Carlo simulations. The proteins are considered at their respective isoelectric points. Discrete charges on the model polyelectrolytes and proteins interact through Debye-Huckel potentials. Protein excluded volume is taken into account through a coarse-grained model of the protein shape. Consistent with experimental results, it is found that alpha-lactalbumin complexes much more strongly than beta-lactoglobulin. For alpha-lactalbumin, strong complexation is due to localized binding to a single large positive "charge patch," whereas for beta-lactoglobulin, weak complexation is due to diffuse binding to multiple smaller charge patches. Copyright 2004 American Institute of Physics

Large eddy simulation modeling of particle-laden flows in complex terrain

NASA Astrophysics Data System (ADS)

Salesky, S.; Giometto, M. G.; Chamecki, M.; Lehning, M.; Parlange, M. B.

2017-12-01

The transport, deposition, and erosion of heavy particles over complex terrain in the atmospheric boundary layer is an important process for hydrology, air quality forecasting, biology, and geomorphology. However, in situ observations can be challenging in complex terrain due to spatial heterogeneity. Furthermore, there is a need to develop numerical tools that can accurately represent the physics of these multiphase flows over complex surfaces. We present a new numerical approach to accurately model the transport and deposition of heavy particles in complex terrain using large eddy simulation (LES). Particle transport is represented through solution of the advection-diffusion equation including terms that represent gravitational settling and inertia. The particle conservation equation is discretized in a cut-cell finite volume framework in order to accurately enforce mass conservation. Simulation results will be validated with experimental data, and numerical considerations required to enforce boundary conditions at the surface will be discussed. Applications will be presented in the context of snow deposition and transport, as well as urban dispersion.

Vehicle Animation Software (VAS) to Animate Results Obtained from Vehicle Handling and Rollover Simulations and Tests

DOT National Transportation Integrated Search

1991-04-01

Results from vehicle computer simulations usually take the form of numeric data or graphs. While these graphs provide the investigator with the insight into vehicle behavior, it may be difficult to use these graphs to assess complex vehicle motion. C...

MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories

PubMed Central

2014-01-01

Background Molecular Dynamics (MD) simulations of protein complexes suffer from the lack of specific tools in the analysis step. Analyses of MD trajectories of protein complexes indeed generally rely on classical measures, such as the RMSD, RMSF and gyration radius, conceived and developed for single macromolecules. As a matter of fact, instead, researchers engaged in simulating the dynamics of a protein complex are mainly interested in characterizing the conservation/variation of its biological interface. Results On these bases, herein we propose a novel approach to the analysis of MD trajectories or other conformational ensembles of protein complexes, MDcons, which uses the conservation of inter-residue contacts at the interface as a measure of the similarity between different snapshots. A "consensus contact map" is also provided, where the conservation of the different contacts is drawn in a grey scale. Finally, the interface area of the complex is monitored during the simulations. To show its utility, we used this novel approach to study two protein-protein complexes with interfaces of comparable size and both dominated by hydrophilic interactions, but having binding affinities at the extremes of the experimental range. MDcons is demonstrated to be extremely useful to analyse the MD trajectories of the investigated complexes, adding important insight into the dynamic behavior of their biological interface. Conclusions MDcons specifically allows the user to highlight and characterize the dynamics of the interface in protein complexes and can thus be used as a complementary tool for the analysis of MD simulations of both experimental and predicted structures of protein complexes. PMID:25077693

High-fidelity meshes from tissue samples for diffusion MRI simulations.

PubMed

Panagiotaki, Eleftheria; Hall, Matt G; Zhang, Hui; Siow, Bernard; Lythgoe, Mark F; Alexander, Daniel C

2010-01-01

This paper presents a method for constructing detailed geometric models of tissue microstructure for synthesizing realistic diffusion MRI data. We construct three-dimensional mesh models from confocal microscopy image stacks using the marching cubes algorithm. Random-walk simulations within the resulting meshes provide synthetic diffusion MRI measurements. Experiments optimise simulation parameters and complexity of the meshes to achieve accuracy and reproducibility while minimizing computation time. Finally we assess the quality of the synthesized data from the mesh models by comparison with scanner data as well as synthetic data from simple geometric models and simplified meshes that vary only in two dimensions. The results support the extra complexity of the three-dimensional mesh compared to simpler models although sensitivity to the mesh resolution is quite robust.

Performance evaluation of GPU parallelization, space-time adaptive algorithms, and their combination for simulating cardiac electrophysiology.

PubMed

Sachetto Oliveira, Rafael; Martins Rocha, Bernardo; Burgarelli, Denise; Meira, Wagner; Constantinides, Christakis; Weber Dos Santos, Rodrigo

2018-02-01

The use of computer models as a tool for the study and understanding of the complex phenomena of cardiac electrophysiology has attained increased importance nowadays. At the same time, the increased complexity of the biophysical processes translates into complex computational and mathematical models. To speed up cardiac simulations and to allow more precise and realistic uses, 2 different techniques have been traditionally exploited: parallel computing and sophisticated numerical methods. In this work, we combine a modern parallel computing technique based on multicore and graphics processing units (GPUs) and a sophisticated numerical method based on a new space-time adaptive algorithm. We evaluate each technique alone and in different combinations: multicore and GPU, multicore and GPU and space adaptivity, multicore and GPU and space adaptivity and time adaptivity. All the techniques and combinations were evaluated under different scenarios: 3D simulations on slabs, 3D simulations on a ventricular mouse mesh, ie, complex geometry, sinus-rhythm, and arrhythmic conditions. Our results suggest that multicore and GPU accelerate the simulations by an approximate factor of 33×, whereas the speedups attained by the space-time adaptive algorithms were approximately 48. Nevertheless, by combining all the techniques, we obtained speedups that ranged between 165 and 498. The tested methods were able to reduce the execution time of a simulation by more than 498× for a complex cellular model in a slab geometry and by 165× in a realistic heart geometry simulating spiral waves. The proposed methods will allow faster and more realistic simulations in a feasible time with no significant loss of accuracy. Copyright © 2017 John Wiley & Sons, Ltd.

A Review of Numerical Simulation and Analytical Modeling for Medical Devices Safety in MRI

PubMed Central

Kabil, J.; Belguerras, L.; Trattnig, S.; Pasquier, C.; Missoffe, A.

2016-01-01

Summary Objectives To review past and present challenges and ongoing trends in numerical simulation for MRI (Magnetic Resonance Imaging) safety evaluation of medical devices. Methods A wide literature review on numerical and analytical simulation on simple or complex medical devices in MRI electromagnetic fields shows the evolutions through time and a growing concern for MRI safety over the years. Major issues and achievements are described, as well as current trends and perspectives in this research field. Results Numerical simulation of medical devices is constantly evolving, supported by calculation methods now well-established. Implants with simple geometry can often be simulated in a computational human model, but one issue remaining today is the experimental validation of these human models. A great concern is to assess RF heating on implants too complex to be traditionally simulated, like pacemaker leads. Thus, ongoing researches focus on alternative hybrids methods, both numerical and experimental, with for example a transfer function method. For the static field and gradient fields, analytical models can be used for dimensioning simple implants shapes, but limited for complex geometries that cannot be studied with simplifying assumptions. Conclusions Numerical simulation is an essential tool for MRI safety testing of medical devices. The main issues remain the accuracy of simulations compared to real life and the studies of complex devices; but as the research field is constantly evolving, some promising ideas are now under investigation to take up the challenges. PMID:27830244

The QuakeSim Project: Numerical Simulations for Active Tectonic Processes

NASA Technical Reports Server (NTRS)

Donnellan, Andrea; Parker, Jay; Lyzenga, Greg; Granat, Robert; Fox, Geoffrey; Pierce, Marlon; Rundle, John; McLeod, Dennis; Grant, Lisa; Tullis, Terry

2004-01-01

In order to develop a solid earth science framework for understanding and studying of active tectonic and earthquake processes, this task develops simulation and analysis tools to study the physics of earthquakes using state-of-the art modeling, data manipulation, and pattern recognition technologies. We develop clearly defined accessible data formats and code protocols as inputs to the simulations. these are adapted to high-performance computers because the solid earth system is extremely complex and nonlinear resulting in computationally intensive problems with millions of unknowns. With these tools it will be possible to construct the more complex models and simulations necessary to develop hazard assessment systems critical for reducing future losses from major earthquakes.

Dispersion Analysis Using Particle Tracking Simulations Through Heterogeneity Based on Outcrop Lidar Imagery

NASA Astrophysics Data System (ADS)

Klise, K. A.; Weissmann, G. S.; McKenna, S. A.; Tidwell, V. C.; Frechette, J. D.; Wawrzyniec, T. F.

2007-12-01

Solute plumes are believed to disperse in a non-Fickian manner due to small-scale heterogeneity and variable velocities that create preferential pathways. In order to accurately predict dispersion in naturally complex geologic media, the connection between heterogeneity and dispersion must be better understood. Since aquifer properties can not be measured at every location, it is common to simulate small-scale heterogeneity with random field generators based on a two-point covariance (e.g., through use of sequential simulation algorithms). While these random fields can produce preferential flow pathways, it is unknown how well the results simulate solute dispersion through natural heterogeneous media. To evaluate the influence that complex heterogeneity has on dispersion, we utilize high-resolution terrestrial lidar to identify and model lithofacies from outcrop for application in particle tracking solute transport simulations using RWHet. The lidar scan data are used to produce a lab (meter) scale two-dimensional model that captures 2-8 mm scale natural heterogeneity. Numerical simulations utilize various methods to populate the outcrop structure captured by the lidar-based image with reasonable hydraulic conductivity values. The particle tracking simulations result in residence time distributions used to evaluate the nature of dispersion through complex media. Particle tracking simulations through conductivity fields produced from the lidar images are then compared to particle tracking simulations through hydraulic conductivity fields produced from sequential simulation algorithms. Based on this comparison, the study aims to quantify the difference in dispersion when using realistic and simplified representations of aquifer heterogeneity. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Wealth distribution on complex networks

NASA Astrophysics Data System (ADS)

Ichinomiya, Takashi

2012-12-01

We study the wealth distribution of the Bouchaud-Mézard model on complex networks. It is known from numerical simulations that this distribution depends on the topology of the network; however, no one has succeeded in explaining it. Using “adiabatic” and “independent” assumptions along with the central-limit theorem, we derive equations that determine the probability distribution function. The results are compared to those of simulations for various networks. We find good agreement between our theory and the simulations, except for the case of Watts-Strogatz networks with a low rewiring rate due to the breakdown of independent assumption.

Simulating Scenario Floods for Hazard Assessment on the Lower Bicol Floodplain, the Philippines

NASA Astrophysics Data System (ADS)

Usamah, Muhibuddin Bin; Alkema, Dinand

This paper describes the first results from a study to the behavior of floods in the lower Bicol area, the Philippines. A 1D2D dynamic hydraulic model was applied to simulate a set of scenario floods through the complex topography of the city Naga and surrounding area. The simulation results are integrated into a multi-parameter hazard zonation for the five scenario floods.

Investigation of Different Constituent Encoders in a Turbo-code Scheme for Reduced Decoder Complexity

NASA Technical Reports Server (NTRS)

Kwatra, S. C.

1998-01-01

A large number of papers have been published attempting to give some analytical basis for the performance of Turbo-codes. It has been shown that performance improves with increased interleaver length. Also procedures have been given to pick the best constituent recursive systematic convolutional codes (RSCC's). However testing by computer simulation is still required to verify these results. This thesis begins by describing the encoding and decoding schemes used. Next simulation results on several memory 4 RSCC's are shown. It is found that the best BER performance at low E(sub b)/N(sub o) is not given by the RSCC's that were found using the analytic techniques given so far. Next the results are given from simulations using a smaller memory RSCC for one of the constituent encoders. Significant reduction in decoding complexity is obtained with minimal loss in performance. Simulation results are then given for a rate 1/3 Turbo-code with the result that this code performed as well as a rate 1/2 Turbo-code as measured by the distance from their respective Shannon limits. Finally the results of simulations where an inaccurate noise variance measurement was used are given. From this it was observed that Turbo-decoding is fairly stable with regard to noise variance measurement.

On validating remote sensing simulations using coincident real data

NASA Astrophysics Data System (ADS)

Wang, Mingming; Yao, Wei; Brown, Scott; Goodenough, Adam; van Aardt, Jan

2016-05-01

The remote sensing community often requires data simulation, either via spectral/spatial downsampling or through virtual, physics-based models, to assess systems and algorithms. The Digital Imaging and Remote Sensing Image Generation (DIRSIG) model is one such first-principles, physics-based model for simulating imagery for a range of modalities. Complex simulation of vegetation environments subsequently has become possible, as scene rendering technology and software advanced. This in turn has created questions related to the validity of such complex models, with potential multiple scattering, bidirectional distribution function (BRDF), etc. phenomena that could impact results in the case of complex vegetation scenes. We selected three sites, located in the Pacific Southwest domain (Fresno, CA) of the National Ecological Observatory Network (NEON). These sites represent oak savanna, hardwood forests, and conifer-manzanita-mixed forests. We constructed corresponding virtual scenes, using airborne LiDAR and imaging spectroscopy data from NEON, ground-based LiDAR data, and field-collected spectra to characterize the scenes. Imaging spectroscopy data for these virtual sites then were generated using the DIRSIG simulation environment. This simulated imagery was compared to real AVIRIS imagery (15m spatial resolution; 12 pixels/scene) and NEON Airborne Observation Platform (AOP) data (1m spatial resolution; 180 pixels/scene). These tests were performed using a distribution-comparison approach for select spectral statistics, e.g., established the spectra's shape, for each simulated versus real distribution pair. The initial comparison results of the spectral distributions indicated that the shapes of spectra between the virtual and real sites were closely matched.

Occupational exposure of personnel operating military radio equipment: measurements and simulation.

PubMed

Paljanos, Annamaria; Miclaus, Simona; Munteanu, Calin

2015-09-01

Technical literature provides numerous studies concerning radiofrequency exposure measurements for various radio communication devices, but there are few studies related to exposure of personnel operating military radio equipment. In order to evaluate exposure and identify cases when safety requirements are not entirely met, both measurements and simulations are needed for accurate results. Moreover, given the technical characteristics of the radio devices used in the military, personnel mainly operate in the near-field region so both measurements and simulation becomes more complex. Measurements were made in situ using a broadband personal exposimeter equipped with two isotropic probes for both electric and magnetic components of the field. The experiment was designed for three different operating frequencies of the same radio equipment, while simulations were made in FEKO software using hybrid numerical methods to solve complex electromagnetic field problems. The paper aims to discuss the comparative results of the measurements and simulation, as well as comparing them to reference levels specified in military or civilian radiofrequency exposure standards.

Comparison of AERMOD and CALPUFF models for simulating SO2 concentrations in a gas refinery.

PubMed

Atabi, Farideh; Jafarigol, Farzaneh; Moattar, Faramarz; Nouri, Jafar

2016-09-01

In this study, concentration of SO2 from a gas refinery located in complex terrain was calculated by the steady-state, AERMOD model, and nonsteady-state CALPUFF model. First, in four seasons, SO2 concentrations emitted from 16 refinery stacks, in nine receptors, were obtained by field measurements, and then the performance of both models was evaluated. Then, the simulated results for SO2 ambient concentrations made by each model were compared with the results of the observed concentrations, and model results were compared among themselves. The evaluation of the two models to simulate SO2 concentrations was based on the statistical analysis and Q-Q plots. Review of statistical parameters and Q-Q plots has shown that, according to the evaluation of estimations made, performance of both models to simulate the concentration of SO2 in the region can be considered acceptable. The results showed the AERMOD composite ratio between simulated values made by models and the observed values in various receptors for all four average times is 0.72, whereas CALPUFF's ratio is 0.89. However, in the complex conditions of topography, CALPUFF offers better agreement with the observed concentrations.

Modeling software systems by domains

NASA Technical Reports Server (NTRS)

Dippolito, Richard; Lee, Kenneth

1992-01-01

The Software Architectures Engineering (SAE) Project at the Software Engineering Institute (SEI) has developed engineering modeling techniques that both reduce the complexity of software for domain-specific computer systems and result in systems that are easier to build and maintain. These techniques allow maximum freedom for system developers to apply their domain expertise to software. We have applied these techniques to several types of applications, including training simulators operating in real time, engineering simulators operating in non-real time, and real-time embedded computer systems. Our modeling techniques result in software that mirrors both the complexity of the application and the domain knowledge requirements. We submit that the proper measure of software complexity reflects neither the number of software component units nor the code count, but the locus of and amount of domain knowledge. As a result of using these techniques, domain knowledge is isolated by fields of engineering expertise and removed from the concern of the software engineer. In this paper, we will describe kinds of domain expertise, describe engineering by domains, and provide relevant examples of software developed for simulator applications using the techniques.

Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible ‘seed-less’ targets

PubMed Central

Xia, Zhen; Clark, Peter; Huynh, Tien; Loher, Phillipe; Zhao, Yue; Chen, Huang-Wen; Rigoutsos, Isidore; Zhou, Ruhong

2012-01-01

To better understand the recognition mechanism of RISC and the repertoire of guide-target interactions we introduced G:U wobbles and mismatches at various positions of the microRNA (miRNA) ‘seed’ region and performed all-atom molecular dynamics simulations of the resulting Ago-miRNA:mRNA ternary complexes. Our simulations reveal that many modifications, including combinations of multiple G:U wobbles and mismatches in the seed region, are admissible and result in only minor structural fluctuations that do not affect overall complex stability. These results are further supported by analyses of HITS-CLIP data. Lastly, introduction of disruptive mutations revealed a bending motion of the PAZ domain along the L1/L2 ‘hinge’ and a subsequent opening of the nucleic-acid-binding channel. Our findings suggest that the spectrum of a miRNA's admissible targets is different from what is currently anticipated by the canonical seed-model. Moreover, they provide a likely explanation for the previously reported sequence-dependent regulation of unintended targeting by siRNAs. PMID:22888400

Availability Simulation of AGT Systems

DOT National Transportation Integrated Search

1975-02-01

The report discusses the analytical and simulation procedures that were used to evaluate the effects of failure in a complex dual mode transportation system based on a worst case study-state condition. The computed results are an availability figure ...

[Design of Complex Cavity Structure in Air Route System of Automated Peritoneal Dialysis Machine].

PubMed

Quan, Xiaoliang

2017-07-30

This paper introduced problems about Automated Peritoneal Dialysis machine(APD) that the lack of technical issues such as the structural design of the complex cavities. To study the flow characteristics of this special structure, the application of ANSYS CFX software is used with k-ε turbulence model as the theoretical basis of fluid mechanics. The numerical simulation of flow field simulation result in the internal model can be gotten after the complex structure model is imported into ANSYS CFX module. Then, it will present the distribution of complex cavities inside the flow field and the flow characteristics parameter, which will provide an important reference design for APD design.

Molecular dynamic simulation of weakly magnetized complex plasmas

NASA Astrophysics Data System (ADS)

Funk, Dylan; Konopka, Uwe; Thomas, Edward

2017-10-01

A complex plasma consists of the usual plasma components (electrons, ions and neutrals), as well as a heavier component made of solid, micrometer-sized particles. The particles are in general highly charged as a result of the interaction with the other plasma components. The static and dynamic properties of a complex plasma such as its crystal structure or wave properties are influenced by many forces acting on the individual particles such as the dust particle interaction (a screened Coulomb interaction), neutral (Epstein) drag, the particle inertia and various plasma drag or thermophoretic forces. To study the behavior of complex plasmas we setup an experiment accompanying molecular dynamic simulation. We will present the approach taken in our simulation and give an overview of experimental situations that we want to cover with our simulation such as the particle charge under microgravity condition as performed on the PK-4 space experiment, or to study the detailed influences of high magnetic fields. This work was supported by the US Dept. of Energy (DE-SC0016330), NSF (PHY-1613087) and JPL/NASA (JPL-RSA 1571699).

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

NASA Astrophysics Data System (ADS)

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

2015-08-01

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

Numerical Simulation of Electrical Properties of Carbonate Reservoir Rocks Using µCT Images

NASA Astrophysics Data System (ADS)

Colgin, J.; Niu, Q.; Zhang, C.; Zhang, F.

2017-12-01

Digital rock physics involves the modern microscopic imaging of geomaterials, digitalization of the microstructure, and numerical simulation of physical properties of rocks. This physics-based approach can give important insight into understanding properties of reservoir rocks, and help reveal the link between intrinsic rock properties and macroscopic geophysical responses. The focus of this study is the simulation of the complex conductivity of carbonate reservoir rocks using reconstructed 3D rock structures from high-resolution X-ray micro computed tomography (µCT). Carbonate core samples with varying lithofacies and pore structures from the Cambro-Ordovician Arbuckle Group and the Upper Pennsylvanian Lansing-Kansas City Group in Kansas are used in this study. The wide variations in pore geometry and connectivity of these samples were imaged using µCT. A two-phase segmentation method was used to reconstruct a digital rock of solid particles and pores. We then calculate the effective electrical conductivity of the digital rock volume using a pore-scale numerical approach. The complex conductivity of geomaterials is influenced by the electrical properties and geometry of each phase, i.e., the solid and fluid phases. In addition, the electrical double layer that forms between the solid and fluid phases can also affect the effective conductivity of the material. In the numerical modeling, the influence of the electrical double layer is quantified by a complex surface conductance and converted to an apparent volumetric complex conductivity of either solid particles or pore fluid. The effective complex conductivity resulting from numerical simulations based on µCT images will be compared to results from laboratory experiments on equivalent rock samples. The imaging and digital segmentation method, assumptions in the numerical simulation, and trends as compared to laboratory results will be discussed. This study will help us understand how microscale physics affects macroscale electrical conductivity in porous media.

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

PubMed

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

2015-01-01

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

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

PubMed Central

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

2015-01-01

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

First-principles molecular dynamics simulation of the Ca 2UO 2(CO 3) 3 complex in water

DOE PAGES

Priest, Chad; Tian, Ziqi; Jiang, De-en

2016-01-22

Recent experiments have shown that the neutral Ca 2UO 2(CO 3) 3 complex is the dominant species of uranium in many uranyl-containing streams. However, the structure and solvation of such a species in water has not been investigated from first principles. Herein we present a first principles molecular dynamics perspective of the Ca 2UO 2(CO 3) 3 complex in water based on density functional theory and Born–Oppenheimer approximation. We find that the Ca 2UO 2(CO 3) 3 complex is very stable in our simulation timeframe for three different concentrations considered and that the key distances from our simulation are inmore » good agreement with the experimental data from extended X-ray absorption fine structure (EXAFS) spectroscopy. More important, we find that the two Ca ions bind differently in the complex, as a result of the hydrogen-bonding network around the whole complex. Furthermore, this finding invites confirmation from time-resolved EXAFS and has implications in understanding the dissociative equilibrium of the Ca 2UO 2(CO 3) 3 complex in water.« less

Encapsulating model complexity and landscape-scale analyses of state-and-transition simulation models: an application of ecoinformatics and juniper encroachment in sagebrush steppe ecosystems

USGS Publications Warehouse

O'Donnell, Michael

2015-01-01

State-and-transition simulation modeling relies on knowledge of vegetation composition and structure (states) that describe community conditions, mechanistic feedbacks such as fire that can affect vegetation establishment, and ecological processes that drive community conditions as well as the transitions between these states. However, as the need for modeling larger and more complex landscapes increase, a more advanced awareness of computing resources becomes essential. The objectives of this study include identifying challenges of executing state-and-transition simulation models, identifying common bottlenecks of computing resources, developing a workflow and software that enable parallel processing of Monte Carlo simulations, and identifying the advantages and disadvantages of different computing resources. To address these objectives, this study used the ApexRMS® SyncroSim software and embarrassingly parallel tasks of Monte Carlo simulations on a single multicore computer and on distributed computing systems. The results demonstrated that state-and-transition simulation models scale best in distributed computing environments, such as high-throughput and high-performance computing, because these environments disseminate the workloads across many compute nodes, thereby supporting analysis of larger landscapes, higher spatial resolution vegetation products, and more complex models. Using a case study and five different computing environments, the top result (high-throughput computing versus serial computations) indicated an approximate 96.6% decrease of computing time. With a single, multicore compute node (bottom result), the computing time indicated an 81.8% decrease relative to using serial computations. These results provide insight into the tradeoffs of using different computing resources when research necessitates advanced integration of ecoinformatics incorporating large and complicated data inputs and models. - See more at: http://aimspress.com/aimses/ch/reader/view_abstract.aspx?file_no=Environ2015030&flag=1#sthash.p1XKDtF8.dpuf

A CellML simulation compiler and code generator using ODE solving schemes

PubMed Central

2012-01-01

Models written in description languages such as CellML are becoming a popular solution to the handling of complex cellular physiological models in biological function simulations. However, in order to fully simulate a model, boundary conditions and ordinary differential equation (ODE) solving schemes have to be combined with it. Though boundary conditions can be described in CellML, it is difficult to explicitly specify ODE solving schemes using existing tools. In this study, we define an ODE solving scheme description language-based on XML and propose a code generation system for biological function simulations. In the proposed system, biological simulation programs using various ODE solving schemes can be easily generated. We designed a two-stage approach where the system generates the equation set associating the physiological model variable values at a certain time t with values at t + Δt in the first stage. The second stage generates the simulation code for the model. This approach enables the flexible construction of code generation modules that can support complex sets of formulas. We evaluate the relationship between models and their calculation accuracies by simulating complex biological models using various ODE solving schemes. Using the FHN model simulation, results showed good qualitative and quantitative correspondence with the theoretical predictions. Results for the Luo-Rudy 1991 model showed that only first order precision was achieved. In addition, running the generated code in parallel on a GPU made it possible to speed up the calculation time by a factor of 50. The CellML Compiler source code is available for download at http://sourceforge.net/projects/cellmlcompiler. PMID:23083065

Simulating tracer transport in variably saturated soils and shallow groundwater

USDA-ARS?s Scientific Manuscript database

The objective of this study was to develop a realistic model to simulate the complex processes of flow and tracer transport in variably saturated soils and to compare simulation results with the detailed monitoring observations. The USDA-ARS OPE3 field site was selected for the case study due to ava...

Real-Time Agent-Based Modeling Simulation with in-situ Visualization of Complex Biological Systems: A Case Study on Vocal Fold Inflammation and Healing.

PubMed

Seekhao, Nuttiiya; Shung, Caroline; JaJa, Joseph; Mongeau, Luc; Li-Jessen, Nicole Y K

2016-05-01

We present an efficient and scalable scheme for implementing agent-based modeling (ABM) simulation with In Situ visualization of large complex systems on heterogeneous computing platforms. The scheme is designed to make optimal use of the resources available on a heterogeneous platform consisting of a multicore CPU and a GPU, resulting in minimal to no resource idle time. Furthermore, the scheme was implemented under a client-server paradigm that enables remote users to visualize and analyze simulation data as it is being generated at each time step of the model. Performance of a simulation case study of vocal fold inflammation and wound healing with 3.8 million agents shows 35× and 7× speedup in execution time over single-core and multi-core CPU respectively. Each iteration of the model took less than 200 ms to simulate, visualize and send the results to the client. This enables users to monitor the simulation in real-time and modify its course as needed.

Winds, Mountains, and Wildland Fire: Improved Understanding of Coupled Atmosphere-Topography-Fire Interactions Through Large-Eddy Simulation

NASA Astrophysics Data System (ADS)

Munoz-Esparza, D.; Sauer, J.; Linn, R.

2015-12-01

Anomalous and unexpected fire behavior in complex terrain continues to result in substantial loss of property and extremely dangerous conditions for firefighting field personnel. We briefly discuss proposed hypotheses of fire interactions with atmospheric flows over complex terrain that can lead to poorly-understood and potentially catastrophic scenarios. Then, our recent results of numerical investigations via large-eddy simulation of coupled atmosphere-topography-fire phenomenology with the Los Alamos National Laboratory, HiGrad-Firetec model are presented as an example of the potential for increased understanding of these complex processes. This investigation focuses on the influence of downslope surface wind enhancement through stably stratified flow over an isolated hill, and the resulting dramatic changes in fire behavior including spread rate, and intensity. Implications with respect to counter-intuitive fire behavior and extreme fire events are discussed. This work demonstrates a tremendous opportunity to immediately create safer and more effective policy for field personnel through improved predictability of atmospheric conditions over complex terrain

In silico Interrogation of Insect Central Complex Suggests Computational Roles for the Ellipsoid Body in Spatial Navigation.

PubMed

Fiore, Vincenzo G; Kottler, Benjamin; Gu, Xiaosi; Hirth, Frank

2017-01-01

The central complex in the insect brain is a composite of midline neuropils involved in processing sensory cues and mediating behavioral outputs to orchestrate spatial navigation. Despite recent advances, however, the neural mechanisms underlying sensory integration and motor action selections have remained largely elusive. In particular, it is not yet understood how the central complex exploits sensory inputs to realize motor functions associated with spatial navigation. Here we report an in silico interrogation of central complex-mediated spatial navigation with a special emphasis on the ellipsoid body. Based on known connectivity and function, we developed a computational model to test how the local connectome of the central complex can mediate sensorimotor integration to guide different forms of behavioral outputs. Our simulations show integration of multiple sensory sources can be effectively performed in the ellipsoid body. This processed information is used to trigger continuous sequences of action selections resulting in self-motion, obstacle avoidance and the navigation of simulated environments of varying complexity. The motor responses to perceived sensory stimuli can be stored in the neural structure of the central complex to simulate navigation relying on a collective of guidance cues, akin to sensory-driven innate or habitual behaviors. By comparing behaviors under different conditions of accessible sources of input information, we show the simulated insect computes visual inputs and body posture to estimate its position in space. Finally, we tested whether the local connectome of the central complex might also allow the flexibility required to recall an intentional behavioral sequence, among different courses of actions. Our simulations suggest that the central complex can encode combined representations of motor and spatial information to pursue a goal and thus successfully guide orientation behavior. Together, the observed computational features identify central complex circuitry, and especially the ellipsoid body, as a key neural correlate involved in spatial navigation.

In silico Interrogation of Insect Central Complex Suggests Computational Roles for the Ellipsoid Body in Spatial Navigation

PubMed Central

Fiore, Vincenzo G.; Kottler, Benjamin; Gu, Xiaosi; Hirth, Frank

2017-01-01

The central complex in the insect brain is a composite of midline neuropils involved in processing sensory cues and mediating behavioral outputs to orchestrate spatial navigation. Despite recent advances, however, the neural mechanisms underlying sensory integration and motor action selections have remained largely elusive. In particular, it is not yet understood how the central complex exploits sensory inputs to realize motor functions associated with spatial navigation. Here we report an in silico interrogation of central complex-mediated spatial navigation with a special emphasis on the ellipsoid body. Based on known connectivity and function, we developed a computational model to test how the local connectome of the central complex can mediate sensorimotor integration to guide different forms of behavioral outputs. Our simulations show integration of multiple sensory sources can be effectively performed in the ellipsoid body. This processed information is used to trigger continuous sequences of action selections resulting in self-motion, obstacle avoidance and the navigation of simulated environments of varying complexity. The motor responses to perceived sensory stimuli can be stored in the neural structure of the central complex to simulate navigation relying on a collective of guidance cues, akin to sensory-driven innate or habitual behaviors. By comparing behaviors under different conditions of accessible sources of input information, we show the simulated insect computes visual inputs and body posture to estimate its position in space. Finally, we tested whether the local connectome of the central complex might also allow the flexibility required to recall an intentional behavioral sequence, among different courses of actions. Our simulations suggest that the central complex can encode combined representations of motor and spatial information to pursue a goal and thus successfully guide orientation behavior. Together, the observed computational features identify central complex circuitry, and especially the ellipsoid body, as a key neural correlate involved in spatial navigation. PMID:28824390

Effect of moisture on disintegration kinetics during anaerobic digestion of complex organic substrates.

PubMed

Liotta, Flavia; d'Antonio, Giuseppe; Esposito, Giovanni; Fabbricino, Massimiliano; Frunzo, Luigi; van Hullebusch, Eric D; Lens, Piet N L; Pirozzi, Francesco

2014-01-01

The role of the moisture content and particle size (PS) on the disintegration of complex organic matter during the wet anaerobic digestion (AD) process was investigated. A range of total solids (TS) from 5% to 11.3% and PS from 0.25 to 15 mm was evaluated using carrot waste as model complex organic matter. The experimental results showed that the methane production rate decreased with higher TS and PS. A modified version of the AD model no.1 for complex organic substrates was used to model the experimental data. The simulations showed a decrease of the disintegration rate constants with increasing TS and PS. The results of the biomethanation tests were used to calibrate and validate the applied model. In particular, the values of the disintegration constant for various TS and PS were determined. The simulations showed good agreement between the numerical and observed data.

Convective Weather Avoidance with Uncertain Weather Forecasts

NASA Technical Reports Server (NTRS)

Karahan, Sinan; Windhorst, Robert D.

2009-01-01

Convective weather events have a disruptive impact on air traffic both in terminal area and in en-route airspaces. In order to make sure that the national air transportation system is safe and efficient, it is essential to respond to convective weather events effectively. Traffic flow control initiatives in response to convective weather include ground delay, airborne delay, miles-in-trail restrictions as well as tactical and strategic rerouting. The rerouting initiatives can potentially increase traffic density and complexity in regions neighboring the convective weather activity. There is a need to perform rerouting in an intelligent and efficient way such that the disruptive effects of rerouting are minimized. An important area of research is to study the interaction of in-flight rerouting with traffic congestion or complexity and developing methods that quantitatively measure this interaction. Furthermore, it is necessary to find rerouting solutions that account for uncertainties in weather forecasts. These are important steps toward managing complexity during rerouting operations, and the paper is motivated by these research questions. An automated system is developed for rerouting air traffic in order to avoid convective weather regions during the 20- minute - 2-hour time horizon. Such a system is envisioned to work in concert with separation assurance (0 - 20-minute time horizon), and longer term air traffic management (2-hours and beyond) to provide a more comprehensive solution to complexity and safety management. In this study, weather is dynamic and uncertain; it is represented as regions of airspace that pilots are likely to avoid. Algorithms are implemented in an air traffic simulation environment to support the research study. The algorithms used are deterministic but periodically revise reroutes to account for weather forecast updates. In contrast to previous studies, in this study convective weather is represented as regions of airspace that pilots are likely to avoid. The automated system periodically updates forecasts and reassesses rerouting decisions in order to account for changing weather predictions. The main objectives are to reroute flights to avoid convective weather regions and determine the resulting complexity due to rerouting. The eventual goal is to control and reduce complexity while rerouting flights during the 20 minute - 2 hour planning period. A three-hour simulation is conducted using 4800 flights in the national airspace. The study compares several metrics against a baseline scenario using the same traffic and weather but with rerouting disabled. The results show that rerouting can have a negative impact on congestion in some sectors, as expected. The rerouting system provides accurate measurements of the resulting complexity in the congested sectors. Furthermore, although rerouting is performed only in the 20-minute - 2-hour range, it results in a 30% reduction in encounters with nowcast weather polygons (100% being the ideal for perfectly predictable and accurate weather). In the simulations, rerouting was performed for the 20-minute - 2-hour flight time horizon, and for the en-route segment of air traffic. The implementation uses CWAM, a set of polygons that represent probabilities of pilot deviation around weather. The algorithms were implemented in a software-based air traffic simulation system. Initial results of the system's performance and effectiveness were encouraging. Simulation results showed that when flights were rerouted in the 20-minute - 2-hour flight time horizon of air traffic, there were fewer weather encounters in the first 20 minutes than for flights that were not rerouted. Some preliminary results were also obtained that showed that rerouting will also increase complexity. More simulations will be conducted in order to report conclusive results on the effects of rerouting on complexity. Thus, the use of the 20-minute - 2-hour flight time horizon weather avoidance teniques performed in the simulation is expected to provide benefits for short-term weather avoidance.

Understanding self-assembly of charged-neutral block copolymer (BCP) and surfactant complexes using molecular dynamics (MD) simulation

NASA Astrophysics Data System (ADS)

Goswami, Monojoy; Sumpter, Bobby; Kilbey, Michael

Here we report the formation of phase separated BCP-surfactant complexes resulting from the electrostatic self-assembly of charge-neutral block copolymers with oppositely charged surfactants. Complexation behaviors of oppositely charged polyelectrolytes has gained considerable attention in the field of soft condensed matter physics due to their potential application as functional nanomaterials for batteries, wastewater treatment and drug delivery systems. Numerous experiments have examined the self-assembled structures resulting from complexation of charge-neutral BCP and surfactants, however, there is a lack of comprehensive understanding at the fundamental level. To help bridge this gap, we use, MD simulations to study self-assembly and dynamics of the BCP-surfactant complex at the molecular level. Our results show an overcharging effect in BCPs with hydrophobic neutral blocks and a formation of core-shell colloidal structure. Hydrophilic neutral blocks, on the other hand, show stable, hairy colloidal structures with neutral blocks forming a loosely-bound, fuzzy outer layer. Our results qualitatively agree with previous SANS and SAXS experiments. This work was supported by the U.S. Department of Energy (DOE), Office of Basic Energy Sciences, Materials Science and Engineering Division.

Latin hypercube sampling and geostatistical modeling of spatial uncertainty in a spatially explicit forest landscape model simulation

Treesearch

Chonggang Xu; Hong S. He; Yuanman Hu; Yu Chang; Xiuzhen Li; Rencang Bu

2005-01-01

Geostatistical stochastic simulation is always combined with Monte Carlo method to quantify the uncertainty in spatial model simulations. However, due to the relatively long running time of spatially explicit forest models as a result of their complexity, it is always infeasible to generate hundreds or thousands of Monte Carlo simulations. Thus, it is of great...

Building an open-source simulation platform of acoustic radiation force-based breast elastography

NASA Astrophysics Data System (ADS)

Wang, Yu; Peng, Bo; Jiang, Jingfeng

2017-03-01

Ultrasound-based elastography including strain elastography, acoustic radiation force impulse (ARFI) imaging, point shear wave elastography and supersonic shear imaging (SSI) have been used to differentiate breast tumors among other clinical applications. The objective of this study is to extend a previously published virtual simulation platform built for ultrasound quasi-static breast elastography toward acoustic radiation force-based breast elastography. Consequently, the extended virtual breast elastography simulation platform can be used to validate image pixels with known underlying soft tissue properties (i.e. ‘ground truth’) in complex, heterogeneous media, enhancing confidence in elastographic image interpretations. The proposed virtual breast elastography system inherited four key components from the previously published virtual simulation platform: an ultrasound simulator (Field II), a mesh generator (Tetgen), a finite element solver (FEBio) and a visualization and data processing package (VTK). Using a simple message passing mechanism, functionalities have now been extended to acoustic radiation force-based elastography simulations. Examples involving three different numerical breast models with increasing complexity—one uniform model, one simple inclusion model and one virtual complex breast model derived from magnetic resonance imaging data, were used to demonstrate capabilities of this extended virtual platform. Overall, simulation results were compared with the published results. In the uniform model, the estimated shear wave speed (SWS) values were within 4% compared to the predetermined SWS values. In the simple inclusion and the complex breast models, SWS values of all hard inclusions in soft backgrounds were slightly underestimated, similar to what has been reported. The elastic contrast values and visual observation show that ARFI images have higher spatial resolution, while SSI images can provide higher inclusion-to-background contrast. In summary, our initial results were consistent with our expectations and what have been reported in the literature. The proposed (open-source) simulation platform can serve as a single gateway to perform many elastographic simulations in a transparent manner, thereby promoting collaborative developments.

Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations.

PubMed

Di Palma, Francesco; Bottaro, Sandro; Bussi, Giovanni

2015-01-01

Riboswitches are cis-acting regulatory RNA elements prevalently located in the leader sequences of bacterial mRNA. An adenine sensing riboswitch cis-regulates adeninosine deaminase gene (add) in Vibrio vulnificus. The structural mechanism regulating its conformational changes upon ligand binding mostly remains to be elucidated. In this open framework it has been suggested that the ligand stabilizes the interaction of the distal "kissing loop" complex. Using accurate full-atom molecular dynamics with explicit solvent in combination with enhanced sampling techniques and advanced analysis methods it could be possible to provide a more detailed perspective on the formation of these tertiary contacts. In this work, we used umbrella sampling simulations to study the thermodynamics of the kissing loop complex in the presence and in the absence of the cognate ligand. We enforced the breaking/formation of the loop-loop interaction restraining the distance between the two loops. We also assessed the convergence of the results by using two alternative initialization protocols. A structural analysis was performed using a novel approach to analyze base contacts. Contacts between the two loops were progressively lost when larger inter-loop distances were enforced. Inter-loop Watson-Crick contacts survived at larger separation when compared with non-canonical pairing and stacking interactions. Intra-loop stacking contacts remained formed upon loop undocking. Our simulations qualitatively indicated that the ligand could stabilize the kissing loop complex. We also compared with previously published simulation studies. Kissing complex stabilization given by the ligand was compatible with available experimental data. However, the dependence of its value on the initialization protocol of the umbrella sampling simulations posed some questions on the quantitative interpretation of the results and called for better converged enhanced sampling simulations.

Towards a complex systems approach in sports injury research: simulating running-related injury development with agent-based modelling.

PubMed

Hulme, Adam; Thompson, Jason; Nielsen, Rasmus Oestergaard; Read, Gemma J M; Salmon, Paul M

2018-06-18

There have been recent calls for the application of the complex systems approach in sports injury research. However, beyond theoretical description and static models of complexity, little progress has been made towards formalising this approach in way that is practical to sports injury scientists and clinicians. Therefore, our objective was to use a computational modelling method and develop a dynamic simulation in sports injury research. Agent-based modelling (ABM) was used to model the occurrence of sports injury in a synthetic athlete population. The ABM was developed based on sports injury causal frameworks and was applied in the context of distance running-related injury (RRI). Using the acute:chronic workload ratio (ACWR), we simulated the dynamic relationship between changes in weekly running distance and RRI through the manipulation of various 'athlete management tools'. The findings confirmed that building weekly running distances over time, even within the reported ACWR 'sweet spot', will eventually result in RRI as athletes reach and surpass their individual physical workload limits. Introducing training-related error into the simulation and the modelling of a 'hard ceiling' dynamic resulted in a higher RRI incidence proportion across the population at higher absolute workloads. The presented simulation offers a practical starting point to further apply more sophisticated computational models that can account for the complex nature of sports injury aetiology. Alongside traditional forms of scientific inquiry, the use of ABM and other simulation-based techniques could be considered as a complementary and alternative methodological approach in sports injury research. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Selected-node stochastic simulation algorithm

NASA Astrophysics Data System (ADS)

Duso, Lorenzo; Zechner, Christoph

2018-04-01

Stochastic simulations of biochemical networks are of vital importance for understanding complex dynamics in cells and tissues. However, existing methods to perform such simulations are associated with computational difficulties and addressing those remains a daunting challenge to the present. Here we introduce the selected-node stochastic simulation algorithm (snSSA), which allows us to exclusively simulate an arbitrary, selected subset of molecular species of a possibly large and complex reaction network. The algorithm is based on an analytical elimination of chemical species, thereby avoiding explicit simulation of the associated chemical events. These species are instead described continuously in terms of statistical moments derived from a stochastic filtering equation, resulting in a substantial speedup when compared to Gillespie's stochastic simulation algorithm (SSA). Moreover, we show that statistics obtained via snSSA profit from a variance reduction, which can significantly lower the number of Monte Carlo samples needed to achieve a certain performance. We demonstrate the algorithm using several biological case studies for which the simulation time could be reduced by orders of magnitude.

Free energy surface of the Michaelis complex of lactate dehydrogenase: a network analysis of microsecond simulations.

PubMed

Pan, Xiaoliang; Schwartz, Steven D

2015-04-30

It has long been recognized that the structure of a protein creates a hierarchy of conformations interconverting on multiple time scales. The conformational heterogeneity of the Michaelis complex is of particular interest in the context of enzymatic catalysis in which the reactant is usually represented by a single conformation of the enzyme/substrate complex. Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate with concomitant interconversion of two forms of the cofactor nicotinamide adenine dinucleotide (NADH and NAD(+)). Recent experimental results suggest that multiple substates exist within the Michaelis complex of LDH, and they show a strong variance in their propensity toward the on-enzyme chemical step. In this study, microsecond-scale all-atom molecular dynamics simulations were performed on LDH to explore the free energy landscape of the Michaelis complex, and network analysis was used to characterize the distribution of the conformations. Our results provide a detailed view of the kinetic network of the Michaelis complex and the structures of the substates at atomistic scales. They also shed light on the complete picture of the catalytic mechanism of LDH.

Determination of elastomeric foam parameters for simulations of complex loading.

PubMed

Petre, M T; Erdemir, A; Cavanagh, P R

2006-08-01

Finite element (FE) analysis has shown promise for the evaluation of elastomeric foam personal protection devices. Although appropriate representation of foam materials is necessary in order to obtain realistic simulation results, material definitions used in the literature vary widely and often fail to account for the multi-mode loading experienced by these devices. This study aims to provide a library of elastomeric foam material parameters that can be used in FE simulations of complex loading scenarios. Twelve foam materials used in footwear were tested in uni-axial compression, simple shear and volumetric compression. For each material, parameters for a common compressible hyperelastic material model used in FE analysis were determined using: (a) compression; (b) compression and shear data; and (c) data from all three tests. Material parameters and Drucker stability limits for the best fits are provided with their associated errors. The material model was able to reproduce deformation modes for which data was provided during parameter determination but was unable to predict behavior in other deformation modes. Simulation results were found to be highly dependent on the extent of the test data used to determine the parameters in the material definition. This finding calls into question the many published results of simulations of complex loading that use foam material parameters obtained from a single mode of testing. The library of foam parameters developed here presents associated errors in three deformation modes that should provide for a more informed selection of material parameters.

Simulation methods to estimate design power: an overview for applied research

PubMed Central

2011-01-01

Background Estimating the required sample size and statistical power for a study is an integral part of study design. For standard designs, power equations provide an efficient solution to the problem, but they are unavailable for many complex study designs that arise in practice. For such complex study designs, computer simulation is a useful alternative for estimating study power. Although this approach is well known among statisticians, in our experience many epidemiologists and social scientists are unfamiliar with the technique. This article aims to address this knowledge gap. Methods We review an approach to estimate study power for individual- or cluster-randomized designs using computer simulation. This flexible approach arises naturally from the model used to derive conventional power equations, but extends those methods to accommodate arbitrarily complex designs. The method is universally applicable to a broad range of designs and outcomes, and we present the material in a way that is approachable for quantitative, applied researchers. We illustrate the method using two examples (one simple, one complex) based on sanitation and nutritional interventions to improve child growth. Results We first show how simulation reproduces conventional power estimates for simple randomized designs over a broad range of sample scenarios to familiarize the reader with the approach. We then demonstrate how to extend the simulation approach to more complex designs. Finally, we discuss extensions to the examples in the article, and provide computer code to efficiently run the example simulations in both R and Stata. Conclusions Simulation methods offer a flexible option to estimate statistical power for standard and non-traditional study designs and parameters of interest. The approach we have described is universally applicable for evaluating study designs used in epidemiologic and social science research. PMID:21689447

WE-H-BRA-04: Biological Geometries for the Monte Carlo Simulation Toolkit TOPASNBio

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

McNamara, A; Held, K; Paganetti, H

2016-06-15

Purpose: New advances in radiation therapy are most likely to come from the complex interface of physics, chemistry and biology. Computational simulations offer a powerful tool for quantitatively investigating radiation interactions with biological tissue and can thus help bridge the gap between physics and biology. The aim of TOPAS-nBio is to provide a comprehensive tool to generate advanced radiobiology simulations. Methods: TOPAS wraps and extends the Geant4 Monte Carlo (MC) simulation toolkit. TOPAS-nBio is an extension to TOPAS which utilizes the physics processes in Geant4-DNA to model biological damage from very low energy secondary electrons. Specialized cell, organelle and molecularmore » geometries were designed for the toolkit. Results: TOPAS-nBio gives the user the capability of simulating biological geometries, ranging from the micron-scale (e.g. cells and organelles) to complex nano-scale geometries (e.g. DNA and proteins). The user interacts with TOPAS-nBio through easy-to-use input parameter files. For example, in a simple cell simulation the user can specify the cell type and size as well as the type, number and size of included organelles. For more detailed nuclear simulations, the user can specify chromosome territories containing chromatin fiber loops, the later comprised of nucleosomes on a double helix. The chromatin fibers can be arranged in simple rigid geometries or within factual globules, mimicking realistic chromosome territories. TOPAS-nBio also provides users with the capability of reading protein data bank 3D structural files to simulate radiation damage to proteins or nucleic acids e.g. histones or RNA. TOPAS-nBio has been validated by comparing results to other track structure simulation software and published experimental measurements. Conclusion: TOPAS-nBio provides users with a comprehensive MC simulation tool for radiobiological simulations, giving users without advanced programming skills the ability to design and run complex simulations.« less

Study of intermolecular contacts in the proline-rich homeodomain (PRH)-DNA complex using molecular dynamics simulations.

PubMed

Jalili, Seifollah; Karami, Leila

2012-03-01

The proline-rich homeodomain (PRH)-DNA complex consists of a protein with 60 residues and a 13-base-pair DNA. The PRH protein is a transcription factor that plays a key role in the regulation of gene expression. PRH is a significant member of the Q50 class of homeodomain proteins. The homeodomain section of PRH is essential for binding to DNA and mediates sequence-specific DNA binding. Three 20-ns molecular dynamics (MD) simulations (free protein, free DNA and protein-DNA complex) in explicit solvent water were performed to elucidate the intermolecular contacts in the PRH-DNA complex and the role of dynamics of water molecules forming water-mediated contacts. The simulation provides a detailed explanation of the trajectory of hydration water molecules. The simulations show that some water molecules in the protein-DNA interface exchange with bulk waters. The simulation identifies that most of the contacts consisted of direct interactions between the protein and DNA including specific and non-specific contacts, but several water-mediated polar contacts were also observed. The specific interaction between Gln50 and C18 and water-mediated hydrogen bond between Gln50 and T7 were found to be present during almost the entire time of the simulation. These results show good consistency with experimental and previous computational studies. Structural properties such as root-mean-square deviations (RMSD), root-mean-square fluctuations (RMSF) and secondary structure were also analyzed as a function of time. Analyses of the trajectories showed that the dynamic fluctuations of both the protein and the DNA were lowered by the complex formation.

Large eddy simulation of forest canopy flow for wildland fire modeling

Treesearch

Eric Mueller; William Mell; Albert Simeoni

2014-01-01

Large eddy simulation (LES) based computational fluid dynamics (CFD) simulators have obtained increasing attention in the wildland fire research community, as these tools allow the inclusion of important driving physics. However, due to the complexity of the models, individual aspects must be isolated and tested rigorously to ensure meaningful results. As wind is a...

Simulation of land use change in the three gorges reservoir area based on CART-CA

NASA Astrophysics Data System (ADS)

Yuan, Min

2018-05-01

This study proposes a new method to simulate spatiotemporal complex multiple land uses by using classification and regression tree algorithm (CART) based CA model. In this model, we use classification and regression tree algorithm to calculate land class conversion probability, and combine neighborhood factor, random factor to extract cellular transformation rules. The overall Kappa coefficient is 0.8014 and the overall accuracy is 0.8821 in the land dynamic simulation results of the three gorges reservoir area from 2000 to 2010, and the simulation results are satisfactory.

Collaborative simulation method with spatiotemporal synchronization process control

NASA Astrophysics Data System (ADS)

Zou, Yisheng; Ding, Guofu; Zhang, Weihua; Zhang, Jian; Qin, Shengfeng; Tan, John Kian

2016-10-01

When designing a complex mechatronics system, such as high speed trains, it is relatively difficult to effectively simulate the entire system's dynamic behaviors because it involves multi-disciplinary subsystems. Currently,a most practical approach for multi-disciplinary simulation is interface based coupling simulation method, but it faces a twofold challenge: spatial and time unsynchronizations among multi-directional coupling simulation of subsystems. A new collaborative simulation method with spatiotemporal synchronization process control is proposed for coupling simulating a given complex mechatronics system across multiple subsystems on different platforms. The method consists of 1) a coupler-based coupling mechanisms to define the interfacing and interaction mechanisms among subsystems, and 2) a simulation process control algorithm to realize the coupling simulation in a spatiotemporal synchronized manner. The test results from a case study show that the proposed method 1) can certainly be used to simulate the sub-systems interactions under different simulation conditions in an engineering system, and 2) effectively supports multi-directional coupling simulation among multi-disciplinary subsystems. This method has been successfully applied in China high speed train design and development processes, demonstrating that it can be applied in a wide range of engineering systems design and simulation with improved efficiency and effectiveness.

Statistical analysis of dimer formation in supersaturated metal vapor based on molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Korenchenko, Anna E.; Vorontsov, Alexander G.; Gelchinski, Boris R.; Sannikov, Grigorii P.

2018-04-01

We discuss the problem of dimer formation during the homogeneous nucleation of atomic metal vapor in an inert gas environment. We simulated nucleation with molecular dynamics and carried out the statistical analysis of double- and triple-atomic collisions as the two ways of long-lived diatomic complex formation. Close pair of atoms with lifetime greater than the mean time interval between atom-atom collisions is called a long-lived diatomic complex. We found that double- and triple-atomic collisions gave approximately the same probabilities of long-lived diatomic complex formation, but internal energy of the resulted state was essentially lower in the second case. Some diatomic complexes formed in three-particle collisions are stable enough to be a critical nucleus.

Neoclassical toroidal viscosity calculations in tokamaks using a δf Monte Carlo simulation and their verifications.

PubMed

Satake, S; Park, J-K; Sugama, H; Kanno, R

2011-07-29

Neoclassical toroidal viscosities (NTVs) in tokamaks are investigated using a δf Monte Carlo simulation, and are successfully verified with a combined analytic theory over a wide range of collisionality. A Monte Carlo simulation has been required in the study of NTV since the complexities in guiding-center orbits of particles and their collisions cannot be fully investigated by any means of analytic theories alone. Results yielded the details of the complex NTV dependency on particle precessions and collisions, which were predicted roughly in a combined analytic theory. Both numerical and analytic methods can be utilized and extended based on these successful verifications.

OBJECT KINETIC MONTE CARLO SIMULATIONS OF MICROSTRUCTURE EVOLUTION

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

Nandipati, Giridhar; Setyawan, Wahyu; Heinisch, Howard L.

2013-09-30

The objective is to report the development of the flexible object kinetic Monte Carlo (OKMC) simulation code KSOME (kinetic simulation of microstructure evolution) which can be used to simulate microstructure evolution of complex systems under irradiation. In this report we briefly describe the capabilities of KSOME and present preliminary results for short term annealing of single cascades in tungsten at various primary-knock-on atom (PKA) energies and temperatures.

Quantum Gauss-Jordan Elimination and Simulation of Accounting Principles on Quantum Computers

NASA Astrophysics Data System (ADS)

Diep, Do Ngoc; Giang, Do Hoang; Van Minh, Nguyen

2017-06-01

The paper is devoted to a version of Quantum Gauss-Jordan Elimination and its applications. In the first part, we construct the Quantum Gauss-Jordan Elimination (QGJE) Algorithm and estimate the complexity of computation of Reduced Row Echelon Form (RREF) of N × N matrices. The main result asserts that QGJE has computation time is of order 2 N/2. The second part is devoted to a new idea of simulation of accounting by quantum computing. We first expose the actual accounting principles in a pure mathematics language. Then, we simulate the accounting principles on quantum computers. We show that, all accounting actions are exhousted by the described basic actions. The main problems of accounting are reduced to some system of linear equations in the economic model of Leontief. In this simulation, we use our constructed Quantum Gauss-Jordan Elimination to solve the problems and the complexity of quantum computing is a square root order faster than the complexity in classical computing.

Multi-Agent-Based Simulation of a Complex Ecosystem of Mental Health Care.

PubMed

Kalton, Alan; Falconer, Erin; Docherty, John; Alevras, Dimitris; Brann, David; Johnson, Kyle

2016-02-01

This paper discusses the creation of an Agent-Based Simulation that modeled the introduction of care coordination capabilities into a complex system of care for patients with Serious and Persistent Mental Illness. The model describes the engagement between patients and the medical, social and criminal justice services they interact with in a complex ecosystem of care. We outline the challenges involved in developing the model, including process mapping and the collection and synthesis of data to support parametric estimates, and describe the controls built into the model to support analysis of potential changes to the system. We also describe the approach taken to calibrate the model to an observable level of system performance. Preliminary results from application of the simulation are provided to demonstrate how it can provide insights into potential improvements deriving from introduction of care coordination technology.

A Combined Theoretical and Experimental Study for Silver Electroplating

PubMed Central

Liu, Anmin; Ren, Xuefeng; An, Maozhong; Zhang, Jinqiu; Yang, Peixia; Wang, Bo; Zhu, Yongming; Wang, Chong

2014-01-01

A novel method combined theoretical and experimental study for environmental friendly silver electroplating was introduced. Quantum chemical calculations and molecular dynamic (MD) simulations were employed for predicting the behaviour and function of the complexing agents. Electronic properties, orbital information, and single point energies of the 5,5-dimethylhydantoin (DMH), nicotinic acid (NA), as well as their silver(I)-complexes were provided by quantum chemical calculations based on density functional theory (DFT). Adsorption behaviors of the agents on copper and silver surfaces were investigated using MD simulations. Basing on the data of quantum chemical calculations and MD simulations, we believed that DMH and NA could be the promising complexing agents for silver electroplating. The experimental results, including of electrochemical measurement and silver electroplating, further confirmed the above prediction. This efficient and versatile method thus opens a new window to study or design complexing agents for generalized metal electroplating and will vigorously promote the level of this research region. PMID:24452389

Effects of Different Quantum Coherence on the Pump-Probe Polarization Anisotropy of Photosynthetic Light-Harvesting Complexes: A Computational Study.

PubMed

Bai, Shuming; Song, Kai; Shi, Qiang

2015-05-21

Observations of oscillatory features in the 2D spectra of several photosynthetic complexes have led to diverged opinions on their origins, including electronic coherence, vibrational coherence, and vibronic coherence. In this work, effects of these different types of quantum coherence on ultrafast pump-probe polarization anisotropy are investigated and distinguished. We first simulate the isotropic pump-probe signal and anisotropy decay of the Fenna-Matthews-Olson (FMO) complex using a model with only electronic coherence at low temperature and obtain the same coherence time as in the previous experiment. Then, three model dimer systems with different prespecified quantum coherence are simulated, and the results show that their different spectral characteristics can be used to determine the type of coherence during the spectral process. Finally, we simulate model systems with different electronic-vibrational couplings and reveal the condition in which long time vibronic coherence can be observed in systems like the FMO complex.

EMU Suit Performance Simulation

NASA Technical Reports Server (NTRS)

Cowley, Matthew S.; Benson, Elizabeth; Harvill, Lauren; Rajulu, Sudhakar

2014-01-01

Introduction: Designing a planetary suit is very complex and often requires difficult trade-offs between performance, cost, mass, and system complexity. To verify that new suit designs meet requirements, full prototypes must be built and tested with human subjects. However, numerous design iterations will occur before the hardware meets those requirements. Traditional draw-prototype-test paradigms for research and development are prohibitively expensive with today's shrinking Government budgets. Personnel at NASA are developing modern simulation techniques that focus on a human-centric design paradigm. These new techniques make use of virtual prototype simulations and fully adjustable physical prototypes of suit hardware. This is extremely advantageous and enables comprehensive design down-selections to be made early in the design process. Objectives: The primary objective was to test modern simulation techniques for evaluating the human performance component of two EMU suit concepts, pivoted and planar style hard upper torso (HUT). Methods: This project simulated variations in EVA suit shoulder joint design and subject anthropometry and then measured the differences in shoulder mobility caused by the modifications. These estimations were compared to human-in-the-loop test data gathered during past suited testing using four subjects (two large males, two small females). Results: Results demonstrated that EVA suit modeling and simulation are feasible design tools for evaluating and optimizing suit design based on simulated performance. The suit simulation model was found to be advantageous in its ability to visually represent complex motions and volumetric reach zones in three dimensions, giving designers a faster and deeper comprehension of suit component performance vs. human performance. Suit models were able to discern differing movement capabilities between EMU HUT configurations, generic suit fit concerns, and specific suit fit concerns for crewmembers based on individual anthropometry

Method for decreasing CT simulation time of complex phantoms and systems through separation of material specific projection data

NASA Astrophysics Data System (ADS)

Divel, Sarah E.; Christensen, Soren; Wintermark, Max; Lansberg, Maarten G.; Pelc, Norbert J.

2017-03-01

Computer simulation is a powerful tool in CT; however, long simulation times of complex phantoms and systems, especially when modeling many physical aspects (e.g., spectrum, finite detector and source size), hinder the ability to realistically and efficiently evaluate and optimize CT techniques. Long simulation times primarily result from the tracing of hundreds of line integrals through each of the hundreds of geometrical shapes defined within the phantom. However, when the goal is to perform dynamic simulations or test many scan protocols using a particular phantom, traditional simulation methods inefficiently and repeatedly calculate line integrals through the same set of structures although only a few parameters change in each new case. In this work, we have developed a new simulation framework that overcomes such inefficiencies by dividing the phantom into material specific regions with the same time attenuation profiles, acquiring and storing monoenergetic projections of the regions, and subsequently scaling and combining the projections to create equivalent polyenergetic sinograms. The simulation framework is especially efficient for the validation and optimization of CT perfusion which requires analysis of many stroke cases and testing hundreds of scan protocols on a realistic and complex numerical brain phantom. Using this updated framework to conduct a 31-time point simulation with 80 mm of z-coverage of a brain phantom on two 16-core Linux serves, we have reduced the simulation time from 62 hours to under 2.6 hours, a 95% reduction.

Evaluation of tocopherol recovery through simulation of molecular distillation process.

PubMed

Moraes, E B; Batistella, C B; Alvarez, M E Torres; Filho, Rubens Maciel; Maciel, M R Wolf

2004-01-01

DISMOL simulator was used to determine the best possible operating conditions to guide, in future studies, experimental works. This simulator needs several physical-chemical properties and often it is very difficult to determine them because of the complexity of the involved components. Their determinations must be made through correlations and/or predictions, in order to characterize the system and calculate it. The first try is to have simulation results of a system that later can be validated with experimental data. To implement, in the simulator, the necessary parameters of complex systems is a difficult task. In this work, we aimed to determe these properties in order to evaluate the tocopherol (vitamin E) recovery using a DISMOL simulator. The raw material used was the crude deodorizer distillate of soya oil. With this procedure, it is possible to determine the best operating conditions for experimental works and to evaluate the process in the separation of new systems, analyzing the profiles obtained from these simulations for the falling film molecular distillator.

New Communitarianism Movements and Complex Utopia

NASA Astrophysics Data System (ADS)

Akdeniz, K. Gediz

Simulation is a rapidly growing field in social sciences. Simulation theories in social sciences are considered to critique social dynamics and societies which are mostly simulated by media, cinema, TV, internet, etc. Recently we (Akdeniz KG, Disorder in complex human system. In: Fritzsch H, Phua KK (eds) Singapore: proceedings of the conference in Honour of Murray Gell-Mann's 80th birthday quantum mechanics, elementary particles, quantum cosmology and complexity. World Scientific Publishing, Hackensack, pp 630-637, 2009) purposed a simulation theory as a critique theory to investigate disordered human behaviors. In this theory, "Disorder-Sensitive Human Behaviors (DSHB) Simulation Theory", chaotic awareness is also considered as a reality principle in simulation world to complete Baudrillard Simulation Theory (Baudrillard J, Simulacra and simulation. University of Michigan Press, Michigan, 1995). We call the emergence of this reality as zuhur which is different than simulacra. More recently we proposed the complex utopia (Akdeniz KG, From Simulacra to Zuhur in Complex Utopia. 11th International Conference of the Utopian Studies Society, Lublin, 2010; Akdeniz KG, The new identities of the physicist: cyborg-physicist and post-physicist. In: Proceedings of the conference of world international conference of technology and education, Beirut, 2010) to critique the complex societies and communities in simulation world. The challenging agents in the complex utopia are both simulacra and zuhur. In this paper we would like to review "What is the complex utopia?" And we shall critique some global events in framework of complex utopia with particular examples in socio-economic and political contexts.

Performance Predictions for Proposed ILS Facilities at St. Louis Municipal Airport

DOT National Transportation Integrated Search

1978-01-01

The results of computer simulations of performance of proposed ILS facilities on Runway 12L/30R at St. Louis Municipal Airport (Lambert Field) are reported. These simulations indicate that an existing industrial complex located near the runway is com...

The electronically excited states of LH2 complexes from Rhodopseudomonas acidophila strain 10050 studied by time-resolved spectroscopy and dynamic Monte Carlo simulations. II. Homo-arrays of LH2 complexes reconstituted into phospholipid model membranes.

PubMed

Pflock, Tobias J; Oellerich, Silke; Krapf, Lisa; Southall, June; Cogdell, Richard J; Ullmann, G Matthias; Köhler, Jürgen

2011-07-21

We performed time-resolved spectroscopy on homoarrays of LH2 complexes from the photosynthetic purple bacterium Rhodopseudomonas acidophila. Variations of the fluorescence transients were monitored as a function of the excitation fluence and the repetition rate of the excitation. These parameters are directly related to the excitation density within the array and to the number of LH2 complexes that still carry a triplet state prior to the next excitation. Comparison of the experimental observations with results from dynamic Monte Carlo simulations for a model cluster of LH2 complexes yields qualitative agreement without the need for any free parameter and reveals the mutual relationship between energy transfer and annihilation processes.

Complexity Analysis of Traffic in Corridors-in-the-Sky

NASA Technical Reports Server (NTRS)

Xue, Min; Zelinski, Shannon Jean

2010-01-01

The corridors-in-the-sky concept imitates the highway system in ground transportation. The benefit expected from a corridor relies on its capability of handling high density traffic with negligible controller workload, the acceptance of extra fuel or distance, and the complexity reduction in underlying sectors. This work evaluates a selected corridor from these perspectives through simulations. To examine traffic inside the corridor, a corridor traffic simulation tool that can resolve conflicts is developed using C language. Prescribed conflict resolution maneuvers mimic corridor users behaviors and conflict resolution counts measure complexity. Different lane options and operational policies are proposed to examine their impacts on complexity. Fuel consumption is calculated and compared for corridor traffic. On the other hand, to investigate the complexity of non-corridor traffic in underlying sectors, the existing Airspace Concept Evaluation System tool is utilized along with the Automated Airspace Concept tool. The number of conflict resolutions is examined and treated as the complexity measurement. The results show heavy traffic can be managed with low complexity for a historical traffic schedule simulated with appropriate operational policies and lane options. For instance, with 608 flights and peak aircraft count of 100, only 84 actions need to be taken in a 24-hour period to resolve the conflicts for an 8-lane corridor. Compared with the fuel consumptions with great circle trajectories, the simulation of corridor traffic shows that the total extra fuel for corridor flights is 26,373 gallons, or 2.76%, which is 0.38% less than flying filed flight plans. Without taking climb and descent portions of corridor traffic, the complexity of underlying sectors is reduced by 17.71%. However the climb and descent portions will eliminate the reduction and the overall complexity of sectors is actually increased by 9.14%.

Three-dimensional curved grid finite-difference modelling for non-planar rupture dynamics

NASA Astrophysics Data System (ADS)

Zhang, Zhenguo; Zhang, Wei; Chen, Xiaofei

2014-11-01

In this study, we present a new method for simulating the 3-D dynamic rupture process occurring on a non-planar fault. The method is based on the curved-grid finite-difference method (CG-FDM) proposed by Zhang & Chen and Zhang et al. to simulate the propagation of seismic waves in media with arbitrary irregular surface topography. While keeping the advantages of conventional FDM, that is computational efficiency and easy implementation, the CG-FDM also is flexible in modelling the complex fault model by using general curvilinear grids, and thus is able to model the rupture dynamics of a fault with complex geometry, such as oblique dipping fault, non-planar fault, fault with step-over, fault branching, even if irregular topography exists. The accuracy and robustness of this new method have been validated by comparing with the previous results of Day et al., and benchmarks for rupture dynamics simulations. Finally, two simulations of rupture dynamics with complex fault geometry, that is a non-planar fault and a fault rupturing a free surface with topography, are presented. A very interesting phenomenon was observed that topography can weaken the tendency for supershear transition to occur when rupture breaks out at a free surface. Undoubtedly, this new method provides an effective, at least an alternative, tool to simulate the rupture dynamics of a complex non-planar fault, and can be applied to model the rupture dynamics of a real earthquake with complex geometry.

Piloted Evaluation of a UH-60 Mixer Equivalent Turbulence Simulation Model

NASA Technical Reports Server (NTRS)

Lusardi, Jeff A.; Blanken, Chris L.; Tischeler, Mark B.

2002-01-01

A simulation study of a recently developed hover/low speed Mixer Equivalent Turbulence Simulation (METS) model for the UH-60 Black Hawk helicopter was conducted in the NASA Ames Research Center Vertical Motion Simulator (VMS). The experiment was a continuation of previous work to develop a simple, but validated, turbulence model for hovering rotorcraft. To validate the METS model, two experienced test pilots replicated precision hover tasks that had been conducted in an instrumented UH-60 helicopter in turbulence. Objective simulation data were collected for comparison with flight test data, and subjective data were collected that included handling qualities ratings and pilot comments for increasing levels of turbulence. Analyses of the simulation results show good analytic agreement between the METS model and flight test data, with favorable pilot perception of the simulated turbulence. Precision hover tasks were also repeated using the more complex rotating-frame SORBET (Simulation Of Rotor Blade Element Turbulence) model to generate turbulence. Comparisons of the empirically derived METS model with the theoretical SORBET model show good agreement providing validation of the more complex blade element method of simulating turbulence.

Gray: a ray tracing-based Monte Carlo simulator for PET

NASA Astrophysics Data System (ADS)

Freese, David L.; Olcott, Peter D.; Buss, Samuel R.; Levin, Craig S.

2018-05-01

Monte Carlo simulation software plays a critical role in PET system design. Performing complex, repeated Monte Carlo simulations can be computationally prohibitive, as even a single simulation can require a large amount of time and a computing cluster to complete. Here we introduce Gray, a Monte Carlo simulation software for PET systems. Gray exploits ray tracing methods used in the computer graphics community to greatly accelerate simulations of PET systems with complex geometries. We demonstrate the implementation of models for positron range, annihilation acolinearity, photoelectric absorption, Compton scatter, and Rayleigh scatter. For validation, we simulate the GATE PET benchmark, and compare energy, distribution of hits, coincidences, and run time. We show a speedup using Gray, compared to GATE for the same simulation, while demonstrating nearly identical results. We additionally simulate the Siemens Biograph mCT system with both the NEMA NU-2 scatter phantom and sensitivity phantom. We estimate the total sensitivity within % when accounting for differences in peak NECR. We also estimate the peak NECR to be kcps, or within % of published experimental data. The activity concentration of the peak is also estimated within 1.3%.

Calibration of an Unsteady Groundwater Flow Model for a Complex, Strongly Heterogeneous Aquifer

NASA Astrophysics Data System (ADS)

Curtis, Z. K.; Liao, H.; Li, S. G.; Phanikumar, M. S.; Lusch, D.

2016-12-01

Modeling of groundwater systems characterized by complex three-dimensional structure and heterogeneity remains a significant challenge. Most of today's groundwater models are developed based on relatively simple conceptual representations in favor of model calibratibility. As more complexities are modeled, e.g., by adding more layers and/or zones, or introducing transient processes, more parameters have to be estimated and issues related to ill-posed groundwater problems and non-unique calibration arise. Here, we explore the use of an alternative conceptual representation for groundwater modeling that is fully three-dimensional and can capture complex 3D heterogeneity (both systematic and "random") without over-parameterizing the aquifer system. In particular, we apply Transition Probability (TP) geostatistics on high resolution borehole data from a water well database to characterize the complex 3D geology. Different aquifer material classes, e.g., `AQ' (aquifer material), `MAQ' (marginal aquifer material'), `PCM' (partially confining material), and `CM' (confining material), are simulated, with the hydraulic properties of each material type as tuning parameters during calibration. The TP-based approach is applied to simulate unsteady groundwater flow in a large, complex, and strongly heterogeneous glacial aquifer system in Michigan across multiple spatial and temporal scales. The resulting model is calibrated to observed static water level data over a time span of 50 years. The results show that the TP-based conceptualization enables much more accurate and robust calibration/simulation than that based on conventional deterministic layer/zone based conceptual representations.

Module-based multiscale simulation of angiogenesis in skeletal muscle

PubMed Central

2011-01-01

Background Mathematical modeling of angiogenesis has been gaining momentum as a means to shed new light on the biological complexity underlying blood vessel growth. A variety of computational models have been developed, each focusing on different aspects of the angiogenesis process and occurring at different biological scales, ranging from the molecular to the tissue levels. Integration of models at different scales is a challenging and currently unsolved problem. Results We present an object-oriented module-based computational integration strategy to build a multiscale model of angiogenesis that links currently available models. As an example case, we use this approach to integrate modules representing microvascular blood flow, oxygen transport, vascular endothelial growth factor transport and endothelial cell behavior (sensing, migration and proliferation). Modeling methodologies in these modules include algebraic equations, partial differential equations and agent-based models with complex logical rules. We apply this integrated model to simulate exercise-induced angiogenesis in skeletal muscle. The simulation results compare capillary growth patterns between different exercise conditions for a single bout of exercise. Results demonstrate how the computational infrastructure can effectively integrate multiple modules by coordinating their connectivity and data exchange. Model parameterization offers simulation flexibility and a platform for performing sensitivity analysis. Conclusions This systems biology strategy can be applied to larger scale integration of computational models of angiogenesis in skeletal muscle, or other complex processes in other tissues under physiological and pathological conditions. PMID:21463529

Insights into the functional role of protonation states in the HIV-1 protease-BEA369 complex: molecular dynamics simulations and free energy calculations.

PubMed

Chen, Jianzhong; Yang, Maoyou; Hu, Guodong; Shi, Shuhua; Yi, Changhong; Zhang, Qinggang

2009-10-01

The molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method combined with molecular dynamics (MD) simulations were used to investigate the functional role of protonation in human immunodeficiency virus type 1 (HIV-1) protease complexed with the inhibitor BEA369. Our results demonstrate that protonation of two aspartic acids (Asp25/Asp25') has a strong influence on the dynamics behavior of the complex, the binding free energy of BEA369, and inhibitor-residue interactions. Relative binding free energies calculated using the MM-PBSA method show that protonation of Asp25 results in the strongest binding of BEA369 to HIV-1 protease. Inhibitor-residue interactions computed by the theory of free energy decomposition also indicate that protonation of Asp25 has the most favorable effect on binding of BEA369. In addition, hydrogen-bond analysis based on the trajectories of the MD simulations shows that protonation of Asp25 strongly influences the water-mediated link of a conserved water molecule, Wat301. We expect that the results of this study will contribute significantly to binding calculations for BEA369, and to the design of high affinity inhibitors.

Simplified and advanced modelling of traction control systems of heavy-haul locomotives

NASA Astrophysics Data System (ADS)

Spiryagin, Maksym; Wolfs, Peter; Szanto, Frank; Cole, Colin

2015-05-01

Improving tractive effort is a very complex task in locomotive design. It requires the development of not only mechanical systems but also power systems, traction machines and traction algorithms. At the initial design stage, traction algorithms can be verified by means of a simulation approach. A simple single wheelset simulation approach is not sufficient because all locomotive dynamics are not fully taken into consideration. Given that many traction control strategies exist, the best solution is to use more advanced approaches for such studies. This paper describes the modelling of a locomotive with a bogie traction control strategy based on a co-simulation approach in order to deliver more accurate results. The simplified and advanced modelling approaches of a locomotive electric power system are compared in this paper in order to answer a fundamental question. What level of modelling complexity is necessary for the investigation of the dynamic behaviours of a heavy-haul locomotive running under traction? The simulation results obtained provide some recommendations on simulation processes and the further implementation of advanced and simplified modelling approaches.

Synthesis Al complex and investigating effect of doped ZnO nanoparticles in the electrical and optical efficiency of OLEDS

NASA Astrophysics Data System (ADS)

Shahedi, Zahra; Jafari, Mohammad Reza

2017-01-01

In this study, an organometallic complex based on aluminum ions is synthesized. And it is utilized as fluorescent material in the organic light-emitting diodes (OLEDs). The synthesized complex was characterized using XRD, UV-Vis, FT-IR as well as PL spectroscopy analyses. The energy levels of Al complex were determined by cyclic voltammetry measurements. Then, the effects of ZnO nanoparticles (NPs) of poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate), PEDOT:PSS, on the electrical and optical performance of the organic light-emitting diodes have been investigated. For this purpose, two samples containing ITO/PEDOT:PSS/PVK/Alq3/PBD/Al with two different concentration and two samples containing ITO/PEDOT:PSS:ZnO/PVK/Alq3/PBD/Al with two different concentration were prepared. Then, hole transport, electron transport and emissive layers were deposited by the spin coating method and the cathode layer (Al) was deposited by the thermal evaporation method. The OLED simulation was also done by constructing the model and choosing appropriate parameters. Then, the experimental data were collected and the results interpreted both qualitatively and quantitatively. The results of the simulations were compared with experimental data of the J-V spectra. Comparing experimental data and simulation results showed that the electrical and optical efficiency of the samples with ZnO NPs is appreciably higher than the samples without ZnO NPs.

C-1311 (Symadex), a potential anti-cancer drug, intercalates into DNA between A and G moieties. NMR-derived and MD-refined stereostructure of the d(GAGGCCTC)2:C-1311 complex

NASA Astrophysics Data System (ADS)

Laskowski, Tomasz; Borzyszkowska, Julia; Grynda, Jakub; Mazerski, Jan

2017-08-01

Imidazoacridinone C-1311 (Symadex®) is an antitumor agent which has been recommended for Phase II clinical trials a few years ago. Previously, it was shown experimentally that during the initial stage of its action C-1311 forms stable intercalation complexes with DNA duplexes. Herein, a NMR-derived stereostructure of d(GAGGCCTC)2:C-1311 complex was reported. The ligand was found locating itself between A and G moieties, forming symmetrical DNA:drug 1:2 mol/mol complex. Intercalation site was located upon the DNA-ligand proton/proton dipolar couplings observed in the NOESY spectrum and the performed MD simulations. NMR-derived stereostructure was hence refined by restrained MD using distance restraints obtained from the NOESY data and the result was compared with MD-derived structure of the proposed complex, obtained from the calculations performed with distance restraints applied only for hydrogen bonds in the terminal GC base pairs. The results of both simulations were coherent. Basing on the observed C-1311's intercalation sites and on our previous results concerning the d(CGATCG)2:C-1311 complex, we stated that AG/GA sequences are the preferred binding sites of imidazoacridinone C-1311.

Numerical simulations of water flow and tracer transport in soils at the USDA-ARS Beltsville OPE3 field site

USDA-ARS?s Scientific Manuscript database

The objective of this study was to develop a realistic model to simulate the complex processes of flow and tracer transport in USDA-ARS OPE3 field site and to compare simulation results with the detailed monitoring observations. The site has been studied for over 10 years with the extensive availabl...

Optimizing Cognitive Load for Learning from Computer-Based Science Simulations

ERIC Educational Resources Information Center

Lee, Hyunjeong; Plass, Jan L.; Homer, Bruce D.

2006-01-01

How can cognitive load in visual displays of computer simulations be optimized? Middle-school chemistry students (N = 257) learned with a simulation of the ideal gas law. Visual complexity was manipulated by separating the display of the simulations in two screens (low complexity) or presenting all information on one screen (high complexity). The…

Zinc complexation in chloride-rich hydrothermal fluids (25-600 °C): A thermodynamic model derived from ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Mei, Yuan; Sherman, David M.; Liu, Weihua; Etschmann, Barbara; Testemale, Denis; Brugger, Joël

2015-02-01

The solubility of zinc minerals in hydrothermal fluids is enhanced by chloride complexation of Zn2+. Thermodynamic models of these complexation reactions are central to models of Zn transport and ore formation. However, existing thermodynamic models, derived from solubility measurements, are inconsistent with spectroscopic measurements of Zn speciation. Here, we used ab initio molecular dynamics simulations (with the PBE exchange-correlation functional) to predict the speciation of Zn-Cl complexes from 25 to 600 °C. We also obtained in situ XAS measurements of Zn-Cl solutions at 30-600 °C. Qualitatively, the simulations reproduced the main features derived from in situ XANES and EXAFS measurements: octahedral to tetrahedral transition with increasing temperature and salinity, stability of ZnCl42- at high chloride concentration up to ⩾500 °C, and increasing stability of the trigonal planar [ZnCl3]- complex at high temperature. Having confirmed the dominant species, we directly determined the stability constants for the Zn-Cl complexes using thermodynamic integration along constrained Zn-Cl distances in a series of MD simulations. We corrected our stability constants to infinite dilution using the b-dot model for the activity coefficients of the solute species. In order to compare the ab initio results with experiments, we need to re-model the existing solubility data using the species we identified in our MD simulations. The stability constants derived from refitting published experimental data are in reasonable agreement with those we obtained using ab initio MD simulations. Our new thermodynamic model accurately predicts the experimentally observed changes in ZnO(s) and ZnCO3(s) solubility as a function of chloride concentration from 200 (Psat) to 600 °C (2000 bar). This study demonstrates that metal speciation and geologically useful stability constants can be derived for species in hydrothermal fluids from ab initio MD simulations even at the generalized gradient approximation for exchange-correlation. We caution, however, that simulations are mostly reliable at high T where ligand exchange is fast enough to yield thermodynamic averages over the timescales of the simulations.

Variable forgetting factor mechanisms for diffusion recursive least squares algorithm in sensor networks

NASA Astrophysics Data System (ADS)

Zhang, Ling; Cai, Yunlong; Li, Chunguang; de Lamare, Rodrigo C.

2017-12-01

In this work, we present low-complexity variable forgetting factor (VFF) techniques for diffusion recursive least squares (DRLS) algorithms. Particularly, we propose low-complexity VFF-DRLS algorithms for distributed parameter and spectrum estimation in sensor networks. For the proposed algorithms, they can adjust the forgetting factor automatically according to the posteriori error signal. We develop detailed analyses in terms of mean and mean square performance for the proposed algorithms and derive mathematical expressions for the mean square deviation (MSD) and the excess mean square error (EMSE). The simulation results show that the proposed low-complexity VFF-DRLS algorithms achieve superior performance to the existing DRLS algorithm with fixed forgetting factor when applied to scenarios of distributed parameter and spectrum estimation. Besides, the simulation results also demonstrate a good match for our proposed analytical expressions.

An ecohydrologic model for a shallow groundwater urban environment.

PubMed

Arden, Sam; Ma, Xin Cissy; Brown, Mark

2014-01-01

The urban environment is a patchwork of natural and artificial surfaces that results in complex interactions with and impacts to natural hydrologic cycles. Evapotranspiration is a major hydrologic flow that is often altered through urbanization, although the mechanisms of change are sometimes difficult to tease out due to difficulty in effectively simulating soil-plant-atmosphere interactions. This paper introduces a simplified yet realistic model that is a combination of existing surface runoff and ecohydrology models designed to increase the quantitative understanding of complex urban hydrologic processes. Results demonstrate that the model is capable of simulating the long-term variability of major hydrologic fluxes as a function of impervious surface, temperature, water table elevation, canopy interception, soil characteristics, precipitation and complex mechanisms of plant water uptake. These understandings have potential implications for holistic urban water system management.

Aspect of ECMWF downscaled Regional Climate Modeling in simulating Indian summer monsoon rainfall and dependencies on lateral boundary conditions

NASA Astrophysics Data System (ADS)

Ghosh, Soumik; Bhatla, R.; Mall, R. K.; Srivastava, Prashant K.; Sahai, A. K.

2018-03-01

Climate model faces considerable difficulties in simulating the rainfall characteristics of southwest summer monsoon. In this study, the dynamical downscaling of European Centre for Medium-Range Weather Forecast's (ECMWF's) ERA-Interim (EIN15) has been utilized for the simulation of Indian summer monsoon (ISM) through the Regional Climate Model version 4.3 (RegCM-4.3) over the South Asia Co-Ordinated Regional Climate Downscaling EXperiment (CORDEX) domain. The complexities of model simulation over a particular terrain are generally influenced by factors such as complex topography, coastal boundary, and lack of unbiased initial and lateral boundary conditions. In order to overcome some of these limitations, the RegCM-4.3 is employed for simulating the rainfall characteristics over the complex topographical conditions. For reliable rainfall simulation, implementations of numerous lower boundary conditions are forced in the RegCM-4.3 with specific horizontal grid resolution of 50 km over South Asia CORDEX domain. The analysis is considered for 30 years of climatological simulation of rainfall, outgoing longwave radiation (OLR), mean sea level pressure (MSLP), and wind with different vertical levels over the specified region. The dependency of model simulation with the forcing of EIN15 initial and lateral boundary conditions is used to understand the impact of simulated rainfall characteristics during different phases of summer monsoon. The results obtained from this study are used to evaluate the activity of initial conditions of zonal wind circulation speed, which causes an increase in the uncertainty of regional model output over the region under investigation. Further, the results showed that the EIN15 zonal wind circulation lacks sufficient speed over the specified region in a particular time, which was carried forward by the RegCM output and leads to a disrupted regional simulation in the climate model.

Analysis of the solution structure of Thermosynechococcus elongatus photosystem I in n-dodecyl-β-d-maltoside using small-angle neutron scattering and molecular dynamics simulation

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

Le, Rosemary K.; Harris, Bradley J.; Iwuchukwu, Ifeyinwa J.

2014-05-01

Small-angle neutron scattering (SANS) and molecular dynamics (MD) simulation were used to investigate the structure of trimeric photosystem I (PSI) from Thermosynechococcus elongatus (T. elongatus) stabilized in n-dodecyl-β-d-maltoside (DDM) detergent solution. Scattering curves of detergent and protein–detergent complexes were measured at 18% D2O, the contrast match point for the detergent, and 100% D2O, allowing observation of the structures of protein/detergent complexes. It was determined that the maximum dimension of the PSI–DDM complex was consistent with the presence of a monolayer belt of detergent around the periphery of PSI. A dummy-atom reconstruction of the shape of the complex from the SANSmore » data indicates that the detergent envelope has an irregular shape around the hydrophobic periphery of the PSI trimer rather than a uniform, toroidal belt around the complex. A 50 ns MD simulation model (a DDM ring surrounding the PSI complex with extra interstitial DDM) of the PSI–DDM complex was developed for comparison with the SANS data. The results suggest that DDM undergoes additional structuring around the membrane-spanning surface of the complex instead of a simple, relatively uniform belt, as is generally assumed for studies that use detergents to solubilize membrane proteins.« less

Simulation and optimization of an experimental membrane wastewater treatment plant using computational intelligence methods.

PubMed

Ludwig, T; Kern, P; Bongards, M; Wolf, C

2011-01-01

The optimization of relaxation and filtration times of submerged microfiltration flat modules in membrane bioreactors used for municipal wastewater treatment is essential for efficient plant operation. However, the optimization and control of such plants and their filtration processes is a challenging problem due to the underlying highly nonlinear and complex processes. This paper presents the use of genetic algorithms for this optimization problem in conjunction with a fully calibrated simulation model, as computational intelligence methods are perfectly suited to the nonconvex multi-objective nature of the optimization problems posed by these complex systems. The simulation model is developed and calibrated using membrane modules from the wastewater simulation software GPS-X based on the Activated Sludge Model No.1 (ASM1). Simulation results have been validated at a technical reference plant. They clearly show that filtration process costs for cleaning and energy can be reduced significantly by intelligent process optimization.

Free energy landscape of the Michaelis complex of lactate dehydrogenase: A network analysis of atomistic simulations

NASA Astrophysics Data System (ADS)

Pan, Xiaoliang; Schwartz, Steven

2015-03-01

It has long been recognized that the structure of a protein is a hierarchy of conformations interconverting on multiple time scales. However, the conformational heterogeneity is rarely considered in the context of enzymatic catalysis in which the reactant is usually represented by a single conformation of the enzyme/substrate complex. Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate with concomitant interconversion of two forms of the cofactor nicotinamide adenine dinucleotide (NADH and NAD+). Recent experimental results suggest that multiple substates exist within the Michaelis complex of LDH, and they are catalytic competent at different reaction rates. In this study, millisecond-scale all-atom molecular dynamics simulations were performed on LDH to explore the free energy landscape of the Michaelis complex, and network analysis was used to characterize the distribution of the conformations. Our results provide a detailed view of the kinetic network the Michaelis complex and the structures of the substates at atomistic scale. It also shed some light on understanding the complete picture of the catalytic mechanism of LDH.

Prediction of Ordered Water Molecules in Protein Binding Sites from Molecular Dynamics Simulations: The Impact of Ligand Binding on Hydration Networks.

PubMed

Rudling, Axel; Orro, Adolfo; Carlsson, Jens

2018-02-26

Water plays a major role in ligand binding and is attracting increasing attention in structure-based drug design. Water molecules can make large contributions to binding affinity by bridging protein-ligand interactions or by being displaced upon complex formation, but these phenomena are challenging to model at the molecular level. Herein, networks of ordered water molecules in protein binding sites were analyzed by clustering of molecular dynamics (MD) simulation trajectories. Locations of ordered waters (hydration sites) were first identified from simulations of high resolution crystal structures of 13 protein-ligand complexes. The MD-derived hydration sites reproduced 73% of the binding site water molecules observed in the crystal structures. If the simulations were repeated without the cocrystallized ligands, a majority (58%) of the crystal waters in the binding sites were still predicted. In addition, comparison of the hydration sites obtained from simulations carried out in the absence of ligands to those identified for the complexes revealed that the networks of ordered water molecules were preserved to a large extent, suggesting that the locations of waters in a protein-ligand interface are mainly dictated by the protein. Analysis of >1000 crystal structures showed that hydration sites bridged protein-ligand interactions in complexes with different ligands, and those with high MD-derived occupancies were more likely to correspond to experimentally observed ordered water molecules. The results demonstrate that ordered water molecules relevant for modeling of protein-ligand complexes can be identified from MD simulations. Our findings could contribute to development of improved methods for structure-based virtual screening and lead optimization.

Diamond-like nanoparticles influence on flavonoids transport: molecular modelling

NASA Astrophysics Data System (ADS)

Plastun, Inna L.; Agandeeva, Ksenia E.; Bokarev, Andrey N.; Zenkin, Nikita S.

2017-03-01

Intermolecular interaction of diamond-like nanoparticles and flavonoids is investigated by numerical simulation. Using molecular modelling by the density functional theory method, we analyze hydrogen bonds formation and their influence on IR - spectra and structure of molecular complex which is formed due to interaction between flavonoids and nanodiamonds surrounded with carboxylic groups. Enriched adamantane (1,3,5,7 - adamantanetetracarboxylic acid) is used as an example of diamond-like nanoparticles. Intermolecular forces and structure of hydrogen bonds are investigated. IR - spectra and structure parameters of quercetin - adamantanetetracarboxylic acid molecular complex are obtained by numerical simulation using the Gaussian software complex. Received data coincide well with experimental results. Intermolecular interactions and hydrogen bonding structure in the obtained molecular complex are examined. Possibilities of flavonoids interaction with DNA at the molecular level are also considered.

High performance computing in biology: multimillion atom simulations of nanoscale systems

PubMed Central

Sanbonmatsu, K. Y.; Tung, C.-S.

2007-01-01

Computational methods have been used in biology for sequence analysis (bioinformatics), all-atom simulation (molecular dynamics and quantum calculations), and more recently for modeling biological networks (systems biology). Of these three techniques, all-atom simulation is currently the most computationally demanding, in terms of compute load, communication speed, and memory load. Breakthroughs in electrostatic force calculation and dynamic load balancing have enabled molecular dynamics simulations of large biomolecular complexes. Here, we report simulation results for the ribosome, using approximately 2.64 million atoms, the largest all-atom biomolecular simulation published to date. Several other nanoscale systems with different numbers of atoms were studied to measure the performance of the NAMD molecular dynamics simulation program on the Los Alamos National Laboratory Q Machine. We demonstrate that multimillion atom systems represent a 'sweet spot' for the NAMD code on large supercomputers. NAMD displays an unprecedented 85% parallel scaling efficiency for the ribosome system on 1024 CPUs. We also review recent targeted molecular dynamics simulations of the ribosome that prove useful for studying conformational changes of this large biomolecular complex in atomic detail. PMID:17187988

Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation

NASA Astrophysics Data System (ADS)

Matsushita, Y.; Murakawa, T.; Shimamura, K.; Oishi, M.; Ohyama, T.; Kurita, N.

2015-02-01

The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.

Effects of in-sewer processes: a stochastic model approach.

PubMed

Vollertsen, J; Nielsen, A H; Yang, W; Hvitved-Jacobsen, T

2005-01-01

Transformations of organic matter, nitrogen and sulfur in sewers can be simulated taking into account the relevant transformation and transport processes. One objective of such simulation is the assessment and management of hydrogen sulfide formation and corrosion. Sulfide is formed in the biofilms and sediments of the water phase, but corrosion occurs on the moist surfaces of the sewer gas phase. Consequently, both phases and the transport of volatile substances between these phases must be included. Furthermore, wastewater composition and transformations in sewers are complex and subject to high, natural variability. This paper presents the latest developments of the WATS model concept, allowing integrated aerobic, anoxic and anaerobic simulation of the water phase and of gas phase processes. The resulting model is complex and with high parameter variability. An example applying stochastic modeling shows how this complexity and variability can be taken into account.

Simulating Valence-to-Core X-ray Emission Spectroscopy of Transition Metal Complexes with Time-Dependent Density Functional Theory.

PubMed

Zhang, Yu; Mukamel, Shaul; Khalil, Munira; Govind, Niranjan

2015-12-08

Valence-to-core (VtC) X-ray emission spectroscopy (XES) has emerged as a powerful technique for the structural characterization of complex organometallic compounds in realistic environments. Since the spectrum represents electronic transitions from the ligand molecular orbitals to the core holes of the metal centers, the approach is more chemically sensitive to the metal-ligand bonding character compared with conventional X-ray absorption techniques. In this paper we study how linear-response time-dependent density functional theory (LR-TDDFT) can be harnessed to simulate K-edge VtC X-ray emission spectra reliably. LR-TDDFT allows one to go beyond the single-particle picture that has been extensively used to simulate VtC-XES. We consider seven low- and high-spin model complexes involving chromium, manganese, and iron transition metal centers. Our results are in good agreement with experiment.

Charge Inversion by Electrostatic Complexation: Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Faraudo, Jordi; Travesset, Alex

2007-03-01

Ions near interfaces play an important role in many biological and physico-chemical processes and exhibit a fascinating diverse range of phenomena. A relevant example is charge inversion, where interfacial charges attract counterions in excess of their own nominal charge, thus leading to an inversion of the sign of the interfacial charge. In this work, we argue that in the case of amphiphilic interfaces, charge inversion can be generated by complexation, that is, electrostatic complexes containing several counterions bound to amphiphilic molecules. The formation of these complexes require the presence at the interface of groups with conformational degrees of freedom with many electronegative atoms. We illustrate this mechanism by analyzing all atomic molecular dynamics simulations of a DMPA (Dimirystoil-Phosphatidic acid) phospholipid monolayer in contact with divalent counterions. The results are found to be in agreement with recent experimental results on Langmuir monolayers. We also discuss the implications for biological systems, as Phosphatidic acid is emerging as a key signaling phospholipid.

Interaction investigations of HipA binding to HipB dimer and HipB dimer + DNA complex: a molecular dynamics simulation study.

PubMed

Li, Chaoqun; Wang, Yaru; Wang, Yan; Chen, Guangju

2013-11-01

We carried out molecular dynamics simulations and free energy calculations for a series of ternary and diplex models for the HipA protein, HipB dimer, and DNA molecule to address the mechanism of HipA sequestration and the binding order of events from apo HipB/HipA to 2HipA + HipB dimer + DNA complex. The results revealed that the combination of DNA with the HipB dimer is energetically favorable for the combination of HipB dimer with HipA protein. The binding of DNA to HipB dimer induces a long-range allosteric communication from the HipB2 -DNA interface to the HipA-HipB2 interface, which involves the closeness of α1 helices of HipB dimer to HipA protein and formations of extra hydrogen bonds in the HipA-HipB2 interface through the extension of α2/3 helices in the HipB dimer. These simulated results suggested that the DNA molecule, as a regulative media, modulates the HipB dimer conformation, consequently increasing the interactions of HipB dimer with the HipA proteins, which explains the mechanism of HipA sequestration reported by the previous experiment. Simultaneously, these simulations also explored that the thermodynamic binding order in a simulated physiological environment, that is, the HipB dimer first bind to DNA to form HipB dimer + DNA complex, then capturing strongly the HipA proteins to form a ternary complex, 2HipA + HipB dimer + DNA, for sequestrating HipA in the nucleoid. Copyright © 2013 John Wiley & Sons, Ltd.

Identification of the dominant hydrological process and appropriate model structure of a karst catchment through stepwise simplification of a complex conceptual model

NASA Astrophysics Data System (ADS)

Chang, Yong; Wu, Jichun; Jiang, Guanghui; Kang, Zhiqiang

2017-05-01

Conceptual models often suffer from the over-parameterization problem due to limited available data for the calibration. This leads to the problem of parameter nonuniqueness and equifinality, which may bring much uncertainty of the simulation result. How to find out the appropriate model structure supported by the available data to simulate the catchment is still a big challenge in the hydrological research. In this paper, we adopt a multi-model framework to identify the dominant hydrological process and appropriate model structure of a karst spring, located in Guilin city, China. For this catchment, the spring discharge is the only available data for the model calibration. This framework starts with a relative complex conceptual model according to the perception of the catchment and then this complex is simplified into several different models by gradually removing the model component. The multi-objective approach is used to compare the performance of these different models and the regional sensitivity analysis (RSA) is used to investigate the parameter identifiability. The results show this karst spring is mainly controlled by two different hydrological processes and one of the processes is threshold-driven which is consistent with the fieldwork investigation. However, the appropriate model structure to simulate the discharge of this spring is much simpler than the actual aquifer structure and hydrological processes understanding from the fieldwork investigation. A simple linear reservoir with two different outlets is enough to simulate this spring discharge. The detail runoff process in the catchment is not needed in the conceptual model to simulate the spring discharge. More complex model should need more other additional data to avoid serious deterioration of model predictions.

Structural characterization and bioavailability of ternary nanoparticles consisting of amylose, α-linoleic acid and β-lactoglobulin complexed with naringin.

PubMed

Feng, Tao; Wang, Ke; Liu, Fangfang; Ye, Ran; Zhu, Xiao; Zhuang, Haining; Xu, Zhimin

2017-06-01

Naringin is a bioflavonoid that is rich in citrus plants and possesses enormous health benefits. However, the use of naringin as a nutraceutical is significantly limited by its low bioavailability. In this study, a novel water-soluble ternary nanoparticle material consisting of amylose, α-linoleic acid and β-lactoglobulin was developed to encapsulate naringin to improve its bioavailability. The physicochemical characteristics of the ternary nanoparticle-naringin inclusion complex were analysed by ultraviolet-visible spectroscopy (UV), Fourier transform infrared spectroscopy (FT-IR), differential scanning calorimetry (DSC), high-resolution transmission electron microscopy (TEM), X-ray diffractometry (XRD) and particle size distribution. The results confirmed the formation of the ternary nanoparticle-naringin inclusion complex. The encapsulation efficiency (EE) and loading content (LC) of the ternary nanoparticle-naringin inclusion complex were 78.73±4.17% and 14.51±3.43%, respectively. In addition, the results of the ternary nanoparticle-naringin inclusion complex in simulated gastric fluid (SGF) and simulated intestinal fluid (SIF) demonstrated that naringin can be gradually released from the complex. In conclusion, ternary nanoparticles are considered promising carriers to effectively improve the bioavailability of naringin. Copyright © 2017 Elsevier B.V. All rights reserved.

Combined quantum mechanics/molecular mechanics (QM/MM) simulations for protein-ligand complexes: free energies of binding of water molecules in influenza neuraminidase.

PubMed

Woods, Christopher J; Shaw, Katherine E; Mulholland, Adrian J

2015-01-22

The applicability of combined quantum mechanics/molecular mechanics (QM/MM) methods for the calculation of absolute binding free energies of conserved water molecules in protein/ligand complexes is demonstrated. Here, we apply QM/MM Monte Carlo simulations to investigate binding of water molecules to influenza neuraminidase. We investigate five different complexes, including those with the drugs oseltamivir and peramivir. We investigate water molecules in two different environments, one more hydrophobic and one hydrophilic. We calculate the free-energy change for perturbation of a QM to MM representation of the bound water molecule. The calculations are performed at the BLYP/aVDZ (QM) and TIP4P (MM) levels of theory, which we have previously demonstrated to be consistent with one another for QM/MM modeling. The results show that the QM to MM perturbation is significant in both environments (greater than 1 kcal mol(-1)) and larger in the more hydrophilic site. Comparison with the same perturbation in bulk water shows that this makes a contribution to binding. The results quantify how electronic polarization differences in different environments affect binding affinity and also demonstrate that extensive, converged QM/MM free-energy simulations, with good levels of QM theory, are now practical for protein/ligand complexes.

The Toxicological Geochemistry of Dusts, Soils, and Other Earth Materials: Insights From In Vitro Physiologically-based Geochemical Leach Tests

NASA Astrophysics Data System (ADS)

Plumlee, G. S.; Ziegler, T. L.; Lamothe, P.; Meeker, G. P.; Sutley, S.

2003-12-01

Exposure to mineral dusts, soils, and other earth materials results in chemical reactions between the materials and different body fluids that include, depending upon the exposure route, lung fluids, gastrointestinal fluids, and perspiration. In vitro physiologically-based geochemical leach tests provide useful insights into these chemical reactions and their potential toxicological implications. We have conducted such leach tests on a variety of earth materials, including asbestos, volcanic ash, dusts from dry lake beds, mine wastes, wastes left from the roasting of mercury ores, mineral processing wastes, coal dusts and coal fly ash, various soils, and complex dusts generated by the World Trade Center collapse. Size-fractionated samples of earth materials that have been well-characterized mineralogically and chemically are reacted at body temperature (37 C) for periods from 2 hours up to multiple days with various proportions of simulated lung, gastric, intestinal, and/or plasma-based fluids. Results indicate that different earth materials may have quite different solubility and dissolution behavior in vivo, depending upon a) the mineralogic makeup of the material, and b) the exposure route. For example, biodurable minerals such as asbestos and volcanic ash particles, whose health effects result because they dissolve very slowly in vivo, bleed off low levels of trace metals into the simulated lung fluids; these include metals such as Fe and Cr that are suspected by health scientists of contributing to the generation of reactive oxygen species and resulting DNA damage in vivo. In contrast, dry lake bed dusts and concrete-rich dusts are highly alkaline and bioreactive, and cause substantial pH increases and other chemical changes in the simulated body fluids. Many of the earth materials tested contain a variety of metals that can be quite soluble (bioaccessible), depending upon the material and the simulated body fluid composition. For example, due to their acidic pH and high chloride concentrations, simulated gastric fluids are most efficient at solubilizing metals such as Hg, Pb, Zn, and others that form strong chloride complexes; although these metals tend to partially reprecipitate in the near-neutral simulated intestinal fluids, complexes with organic ligands (i.e., amino and carboxylic acids) enhance their solubility. These metals are also quite soluble in near-neutral, protein-rich plasma-based fluids because they form strong complexes with the proteins. In contrast, metalloids that form oxyanion species (such as As, Cr, Mo, W) are commonly more soluble in near-neutral pH simulated lung fluids than in simulated gastric fluids.

The electronically excited states of LH2 complexes from Rhodopseudomonas acidophila strain 10050 studied by time-resolved spectroscopy and dynamic Monte Carlo simulations. I. Isolated, non-interacting LH2 complexes.

PubMed

Pflock, Tobias J; Oellerich, Silke; Southall, June; Cogdell, Richard J; Ullmann, G Matthias; Köhler, Jürgen

2011-07-21

We have employed time-resolved spectroscopy on the picosecond time scale in combination with dynamic Monte Carlo simulations to investigate the photophysical properties of light-harvesting 2 (LH2) complexes from the purple photosynthetic bacterium Rhodopseudomonas acidophila. The variations of the fluorescence transients were studied as a function of the excitation fluence, the repetition rate of the excitation and the sample preparation conditions. Here we present the results obtained on detergent solubilized LH2 complexes, i.e., avoiding intercomplex interactions, and show that a simple four-state model is sufficient to grasp the experimental observations quantitatively without the need for any free parameters. This approach allows us to obtain a quantitative measure for the singlet-triplet annihilation rate in isolated, noninteracting LH2 complexes.

Leadership as an Emergent Feature in Social Organizations: Insights from A Laboratory Simulation Experiment.

PubMed

Curral, Luis; Marques-Quinteiro, Pedro; Gomes, Catarina; Lind, Pedro G

2016-01-01

Recent theoretical contributions have suggested a theory of leadership that is grounded in complexity theory, hence regarding leadership as a complex process (i.e., nonlinear; emergent). This article tests if complexity leadership theory promotes efficiency in work groups. 40 groups of five participants each had to complete four decision making tasks using the city simulation game SimCity4. Before engaging in the four decision making tasks, participants received information regarding what sort of leadership behaviors were more adequate to help them perform better. Results suggest that if complexity leadership theory is applied, groups can achieve higher efficiency over time, when compared with other groups where complexity leadership is not applied. This study goes beyond traditional views of leadership as a centralized form of control, and presents new evidence suggesting that leadership is a collective and emergent phenomenon, anchored in simple rules of behavior.

Leadership as an Emergent Feature in Social Organizations: Insights from A Laboratory Simulation Experiment

PubMed Central

Marques-Quinteiro, Pedro; Gomes, Catarina; Lind, Pedro G.

2016-01-01

Recent theoretical contributions have suggested a theory of leadership that is grounded in complexity theory, hence regarding leadership as a complex process (i.e., nonlinear; emergent). This article tests if complexity leadership theory promotes efficiency in work groups. 40 groups of five participants each had to complete four decision making tasks using the city simulation game SimCity4. Before engaging in the four decision making tasks, participants received information regarding what sort of leadership behaviors were more adequate to help them perform better. Results suggest that if complexity leadership theory is applied, groups can achieve higher efficiency over time, when compared with other groups where complexity leadership is not applied. This study goes beyond traditional views of leadership as a centralized form of control, and presents new evidence suggesting that leadership is a collective and emergent phenomenon, anchored in simple rules of behavior. PMID:27973596

Complexation of Cd, Ni, and Zn by DOC in polluted groundwater: A comparison of approaches using resin exchange, aquifer material sorption, and computer speciation models (WHAM and MINTEQA2)

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

Christensen, J.B.; Christensen, T.H.

1999-11-01

Complexation of cadmium (Cd), nickel (Ni), and zinc (Zn) by dissolved organic carbon (DOC) in leachate-polluted groundwater was measured using a resin equilibrium method and an aquifer material sorption technique. The first method is commonly used in complexation studies, while the second method better represents aquifer conditions. The two approaches gave similar results. Metal-DOC complexation was measured over a range of DOC concentrations using the resin equilibrium method, and the results were compared to simulations made by two speciation models containing default databases on metal-DOC complexes (WHAM and MINTEQA2). The WHAM model gave reasonable estimates of Cd and Ni complexationmore » by DOC for both leachate-polluted groundwater samples. The estimated effect of complexation differed less than 50% from the experimental values corresponding to a deviation on the activity of the free metal ion of a factor of 2.5. The effect of DOC complexation for Zn was largely overestimated by the WHAM model, and it was found that using a binding constant of 1.7 instead of the default value of 1.3 would improve the fit between the simulations and experimental data. The MINTEQA2 model gave reasonable predictions of the complexation of Cd and Zn by DOC, whereas deviations in the estimated activity of the free Ni{sup 2+} ion as compared to experimental results are up to a factor of 5.« less

Computational modeling of carbohydrate recognition in protein complex

NASA Astrophysics Data System (ADS)

Ishida, Toyokazu

2017-11-01

To understand the mechanistic principle of carbohydrate recognition in proteins, we propose a systematic computational modeling strategy to identify complex carbohydrate chain onto the reduced 2D free energy surface (2D-FES), determined by MD sampling combined with QM/MM energy corrections. In this article, we first report a detailed atomistic simulation study of the norovirus capsid proteins with carbohydrate antigens based on ab initio QM/MM combined with MD-FEP simulations. The present result clearly shows that the binding geometries of complex carbohydrate antigen are determined not by one single, rigid carbohydrate structure, but rather by the sum of averaged conformations mapped onto the minimum free energy region of QM/MM 2D-FES.

Toward a detailed description of the pathways of allosteric communication in the GroEL chaperonin through atomistic simulation.

PubMed

Piggot, Thomas J; Sessions, Richard B; Burston, Steven G

2012-02-28

GroEL, along with its coprotein GroES, is essential for ensuring the correct folding of unfolded or newly synthesized proteins in bacteria. GroEL is a complex, allosteric molecule, composed of two heptameric rings stacked back to back, that undergoes large structural changes during its reaction cycle. These structural changes are driven by the cooperative binding and subsequent hydrolysis of ATP, by GroEL. Despite numerous previous studies, the precise mechanisms of allosteric communication and the associated structural changes remain elusive. In this paper, we describe a series of all-atom, unbiased, molecular dynamics simulations over relatively long (50-100 ns) time scales of a single, isolated GroEL subunit and also a heptameric GroEL ring, in the presence and absence of ATP. Combined with results from a distance restraint-biased simulation of the single ring, the atomistic details of the earliest stages of ATP-driven structural changes within this complex molecule are illuminated. Our results are in broad agreement with previous modeling studies of isolated subunits and with a coarse-grained, forcing simulation of the single ring. These are the first reported all-atom simulations of the GroEL single-ring complex and provide a unique insight into the role of charged residues K80, K277, R284, R285, and E388 at the subunit interface in transmission of the allosteric signal. These simulations also demonstrate the feasibility of performing all-atom simulations of very large systems on sufficiently long time scales on typical high performance computing facilities to show the origins of the earliest events in biologically relevant processes.

Multiscale Mathematics for Biomass Conversion to Renewable Hydrogen

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

Plechac, Petr; Vlachos, Dionisios; Katsoulakis, Markos

2013-09-05

The overall objective of this project is to develop multiscale models for understanding and eventually designing complex processes for renewables. To the best of our knowledge, our work is the first attempt at modeling complex reacting systems, whose performance relies on underlying multiscale mathematics. Our specific application lies at the heart of biofuels initiatives of DOE and entails modeling of catalytic systems, to enable economic, environmentally benign, and efficient conversion of biomass into either hydrogen or valuable chemicals. Specific goals include: (i) Development of rigorous spatio-temporal coarse-grained kinetic Monte Carlo (KMC) mathematics and simulation for microscopic processes encountered in biomassmore » transformation. (ii) Development of hybrid multiscale simulation that links stochastic simulation to a deterministic partial differential equation (PDE) model for an entire reactor. (iii) Development of hybrid multiscale simulation that links KMC simulation with quantum density functional theory (DFT) calculations. (iv) Development of parallelization of models of (i)-(iii) to take advantage of Petaflop computing and enable real world applications of complex, multiscale models. In this NCE period, we continued addressing these objectives and completed the proposed work. Main initiatives, key results, and activities are outlined.« less

Exponential stability of stochastic complex networks with multi-weights based on graph theory

NASA Astrophysics Data System (ADS)

Zhang, Chunmei; Chen, Tianrui

2018-04-01

In this paper, a novel approach to exponential stability of stochastic complex networks with multi-weights is investigated by means of the graph-theoretical method. New sufficient conditions are provided to ascertain the moment exponential stability and almost surely exponential stability of stochastic complex networks with multiple weights. It is noted that our stability results are closely related with multi-weights and the intensity of stochastic disturbance. Numerical simulations are also presented to substantiate the theoretical results.

Aerial Survey of Ames Research Center - Flight Simulation Complex' Flight simulators create an

NASA Technical Reports Server (NTRS)

1967-01-01

Aerial Survey of Ames Research Center - Flight Simulation Complex' Flight simulators create an authentic aircraft environment by generating the appropriate physical cues that provide the sensations of flight.

Adding Complex Terrain and Stable Atmospheric Condition Capability to the OpenFOAM-based Flow Solver of the Simulator for On/Offshore Wind Farm Applications (SOWFA): Preprint

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

Churchfield, M. J.; Sang, L.; Moriarty, P. J.

This paper describes changes made to NREL's OpenFOAM-based wind plant aerodynamics solver such that it can compute the stably stratified atmospheric boundary layer and flow over terrain. Background about the flow solver, the Simulator for Off/Onshore Wind Farm Applications (SOWFA) is given, followed by details of the stable stratification/complex terrain modifications to SOWFA, along with somepreliminary results calculations of a stable atmospheric boundary layer and flow over a simply set of hills.

Adding Complex Terrain and Stable Atmospheric Condition Capability to the Simulator for On/Offshore Wind Farm Applications (SOWFA) (Presentation)

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

Churchfield, M. J.

This presentation describes changes made to NREL's OpenFOAM-based wind plant aerodynamics solver so that it can compute the stably stratified atmospheric boundary layer and flow over terrain. Background about the flow solver, the Simulator for Off/Onshore Wind Farm Applications (SOWFA) is given, followed by details of the stable stratification/complex terrain modifications to SOWFA, along with some preliminary results calculations of a stable atmospheric boundary layer and flow over a simple set of hills.

Theoretical and simulated performance for a novel frequency estimation technique

NASA Technical Reports Server (NTRS)

Crozier, Stewart N.

1993-01-01

A low complexity, open-loop, discrete-time, delay-multiply-average (DMA) technique for estimating the frequency offset for digitally modulated MPSK signals is investigated. A nonlinearity is used to remove the MPSK modulation and generate the carrier component to be extracted. Theoretical and simulated performance results are presented and compared to the Cramer-Rao lower bound (CRLB) for the variance of the frequency estimation error. For all signal-to-noise ratios (SNR's) above threshold, it is shown that the CRLB can essentially be achieved with linear complexity.

CFD simulation of a screw compressor including leakage flows and rotor heating

NASA Astrophysics Data System (ADS)

Spille-Kohoff, Andreas, Dr.; Hesse, Jan; El Shorbagy, Ahmed

2015-08-01

Computational Fluid Dynamics (CFD) simulations have promising potential to become an important part in the development process of positive displacement (PD) machines. CFD delivers deep insights into the flow and thermodynamic behaviour of PD machines. However, the numerical simulation of such machines is more complex compared to dynamic pumps like turbines or fans. The fluid transport in size-changing chambers with very small clearances between the rotors, and between rotors and casing, demands complex meshes that change with each time step. Additionally, the losses due to leakage flows and the heat transfer to the rotors need high-quality meshes so that automatic remeshing is almost impossible. In this paper, setup steps and results for the simulation of a dry screw compressor are shown. The rotating parts are meshed with TwinMesh, a special hexahedral meshing program for gear pumps, gerotors, lobe pumps and screw compressors. In particular, these meshes include axial and radial clearances between housing and rotors, and beside the fluid volume the rotor solids are also meshed. The CFD simulation accounts for gas flow with compressibility and turbulence effects, heat transfer between gas and rotors, and leakage flows through the clearances. We show time- resolved results for torques, forces, interlobe pressure, mass flow, and heat flow between gas and rotors, as well as time- and space-resolved results for pressure, velocity, temperature etc. for different discharge ports and working points of the screw compressor. These results are also used as thermal loads for deformation simulations of the rotors.

Stress Training and Simulator Complexity: Why Sometimes More Is Less

ERIC Educational Resources Information Center

Tichon, Jennifer G.; Wallis, Guy M.

2010-01-01

Through repeated practice under conditions similar to those in real-world settings, simulator training prepares an individual to maintain effective performance under stressful work conditions. Interfaces offering high fidelity and immersion can more closely reproduce real-world experiences and are generally believed to result in better learning…

To Cooperate or Not to Cooperate: Why Behavioural Mechanisms Matter

PubMed Central

2016-01-01

Mutualistic cooperation often requires multiple individuals to behave in a coordinated fashion. Hence, while the evolutionary stability of mutualistic cooperation poses no particular theoretical difficulty, its evolutionary emergence faces a chicken and egg problem: an individual cannot benefit from cooperating unless other individuals already do so. Here, we use evolutionary robotic simulations to study the consequences of this problem for the evolution of cooperation. In contrast with standard game-theoretic results, we find that the transition from solitary to cooperative strategies is very unlikely, whether interacting individuals are genetically related (cooperation evolves in 20% of all simulations) or unrelated (only 3% of all simulations). We also observe that successful cooperation between individuals requires the evolution of a specific and rather complex behaviour. This behavioural complexity creates a large fitness valley between solitary and cooperative strategies, making the evolutionary transition difficult. These results reveal the need for research on biological mechanisms which may facilitate this transition. PMID:27148874

Numerical Simulation of Regional Circulation in the Monterey Bay Region

NASA Technical Reports Server (NTRS)

Tseng, Y. H.; Dietrich, D. E.; Ferziger, J. H.

2003-01-01

The objective of this study is to produce a high-resolution numerical model of Mon- terey Bay area in which the dynamics are determined by the complex geometry of the coastline, steep bathymetry, and the in uence of the water masses that constitute the CCS. Our goal is to simulate the regional-scale ocean response with realistic dynamics (annual cycle), forcing, and domain. In particular, we focus on non-hydrostatic e ects (by comparing the results of hydrostatic and non-hydrostatic models) and the role of complex geometry, i.e. the bay and submarine canyon, on the nearshore circulation. To the best of our knowledge, the current study is the rst to simulate the regional circulation in the vicinity of Monterey Bay using a non-hydrostatic model. Section 2 introduces the high resolution Monterey Bay area regional model (MBARM). Section 3 provides the results and veri cation with mooring and satellite data. Section 4 compares the results of hydrostatic and non-hydrostatic models.

Three-dimensional plant architecture and sunlit-shaded patterns: a stochastic model of light dynamics in canopies.

PubMed

Retkute, Renata; Townsend, Alexandra J; Murchie, Erik H; Jensen, Oliver E; Preston, Simon P

2018-05-25

Diurnal changes in solar position and intensity combined with the structural complexity of plant architecture result in highly variable and dynamic light patterns within the plant canopy. This affects productivity through the complex ways that photosynthesis responds to changes in light intensity. Current methods to characterize light dynamics, such as ray-tracing, are able to produce data with excellent spatio-temporal resolution but are computationally intensive and the resulting data are complex and high-dimensional. This necessitates development of more economical models for summarizing the data and for simulating realistic light patterns over the course of a day. High-resolution reconstructions of field-grown plants are assembled in various configurations to form canopies, and a forward ray-tracing algorithm is applied to the canopies to compute light dynamics at high (1 min) temporal resolution. From the ray-tracer output, the sunlit or shaded state for each patch on the plants is determined, and these data are used to develop a novel stochastic model for the sunlit-shaded patterns. The model is designed to be straightforward to fit to data using maximum likelihood estimation, and fast to simulate from. For a wide range of contrasting 3-D canopies, the stochastic model is able to summarize, and replicate in simulations, key features of the light dynamics. When light patterns simulated from the stochastic model are used as input to a model of photoinhibition, the predicted reduction in carbon gain is similar to that from calculations based on the (extremely costly) ray-tracer data. The model provides a way to summarize highly complex data in a small number of parameters, and a cost-effective way to simulate realistic light patterns. Simulations from the model will be particularly useful for feeding into larger-scale photosynthesis models for calculating how light dynamics affects the photosynthetic productivity of canopies.

Adaptive control for a class of nonlinear complex dynamical systems with uncertain complex parameters and perturbations

PubMed Central

Liu, Jian; Liu, Kexin; Liu, Shutang

2017-01-01

In this paper, adaptive control is extended from real space to complex space, resulting in a new control scheme for a class of n-dimensional time-dependent strict-feedback complex-variable chaotic (hyperchaotic) systems (CVCSs) in the presence of uncertain complex parameters and perturbations, which has not been previously reported in the literature. In detail, we have developed a unified framework for designing the adaptive complex scalar controller to ensure this type of CVCSs asymptotically stable and for selecting complex update laws to estimate unknown complex parameters. In particular, combining Lyapunov functions dependent on complex-valued vectors and back-stepping technique, sufficient criteria on stabilization of CVCSs are derived in the sense of Wirtinger calculus in complex space. Finally, numerical simulation is presented to validate our theoretical results. PMID:28467431

Adaptive control for a class of nonlinear complex dynamical systems with uncertain complex parameters and perturbations.

PubMed

Liu, Jian; Liu, Kexin; Liu, Shutang

2017-01-01

In this paper, adaptive control is extended from real space to complex space, resulting in a new control scheme for a class of n-dimensional time-dependent strict-feedback complex-variable chaotic (hyperchaotic) systems (CVCSs) in the presence of uncertain complex parameters and perturbations, which has not been previously reported in the literature. In detail, we have developed a unified framework for designing the adaptive complex scalar controller to ensure this type of CVCSs asymptotically stable and for selecting complex update laws to estimate unknown complex parameters. In particular, combining Lyapunov functions dependent on complex-valued vectors and back-stepping technique, sufficient criteria on stabilization of CVCSs are derived in the sense of Wirtinger calculus in complex space. Finally, numerical simulation is presented to validate our theoretical results.

Modeling and Simulation for Mission Operations Work System Design

NASA Technical Reports Server (NTRS)

Sierhuis, Maarten; Clancey, William J.; Seah, Chin; Trimble, Jay P.; Sims, Michael H.

2003-01-01

Work System analysis and design is complex and non-deterministic. In this paper we describe Brahms, a multiagent modeling and simulation environment for designing complex interactions in human-machine systems. Brahms was originally conceived as a business process design tool that simulates work practices, including social systems of work. We describe our modeling and simulation method for mission operations work systems design, based on a research case study in which we used Brahms to design mission operations for a proposed discovery mission to the Moon. We then describe the results of an actual method application project-the Brahms Mars Exploration Rover. Space mission operations are similar to operations of traditional organizations; we show that the application of Brahms for space mission operations design is relevant and transferable to other types of business processes in organizations.

Structure and dynamics of complex liquid water: Molecular dynamics simulation

NASA Astrophysics Data System (ADS)

S, Indrajith V.; Natesan, Baskaran

2015-06-01

We have carried out detailed structure and dynamical studies of complex liquid water using molecular dynamics simulations. Three different model potentials, namely, TIP3P, TIP4P and SPC-E have been used in the simulations, in order to arrive at the best possible potential function that could reproduce the structure of experimental bulk water. All the simulations were performed in the NVE micro canonical ensemble using LAMMPS. The radial distribution functions, gOO, gOH and gHH and the self diffusion coefficient, Ds, were calculated for all three models. We conclude from our results that the structure and dynamical parameters obtained for SPC-E model matched well with the experimental values, suggesting that among the models studied here, the SPC-E model gives the best structure and dynamics of bulk water.

On the Simulation-Based Reliability of Complex Emergency Logistics Networks in Post-Accident Rescues.

PubMed

Wang, Wei; Huang, Li; Liang, Xuedong

2018-01-06

This paper investigates the reliability of complex emergency logistics networks, as reliability is crucial to reducing environmental and public health losses in post-accident emergency rescues. Such networks' statistical characteristics are analyzed first. After the connected reliability and evaluation indices for complex emergency logistics networks are effectively defined, simulation analyses of network reliability are conducted under two different attack modes using a particular emergency logistics network as an example. The simulation analyses obtain the varying trends in emergency supply times and the ratio of effective nodes and validates the effects of network characteristics and different types of attacks on network reliability. The results demonstrate that this emergency logistics network is both a small-world and a scale-free network. When facing random attacks, the emergency logistics network steadily changes, whereas it is very fragile when facing selective attacks. Therefore, special attention should be paid to the protection of supply nodes and nodes with high connectivity. The simulation method provides a new tool for studying emergency logistics networks and a reference for similar studies.

On the Simulation-Based Reliability of Complex Emergency Logistics Networks in Post-Accident Rescues

PubMed Central

Wang, Wei; Huang, Li; Liang, Xuedong

2018-01-01

This paper investigates the reliability of complex emergency logistics networks, as reliability is crucial to reducing environmental and public health losses in post-accident emergency rescues. Such networks’ statistical characteristics are analyzed first. After the connected reliability and evaluation indices for complex emergency logistics networks are effectively defined, simulation analyses of network reliability are conducted under two different attack modes using a particular emergency logistics network as an example. The simulation analyses obtain the varying trends in emergency supply times and the ratio of effective nodes and validates the effects of network characteristics and different types of attacks on network reliability. The results demonstrate that this emergency logistics network is both a small-world and a scale-free network. When facing random attacks, the emergency logistics network steadily changes, whereas it is very fragile when facing selective attacks. Therefore, special attention should be paid to the protection of supply nodes and nodes with high connectivity. The simulation method provides a new tool for studying emergency logistics networks and a reference for similar studies. PMID:29316614

Molecular Cloning Designer Simulator (MCDS): All-in-one molecular cloning and genetic engineering design, simulation and management software for complex synthetic biology and metabolic engineering projects.

PubMed

Shi, Zhenyu; Vickers, Claudia E

2016-12-01

Molecular Cloning Designer Simulator (MCDS) is a powerful new all-in-one cloning and genetic engineering design, simulation and management software platform developed for complex synthetic biology and metabolic engineering projects. In addition to standard functions, it has a number of features that are either unique, or are not found in combination in any one software package: (1) it has a novel interactive flow-chart user interface for complex multi-step processes, allowing an integrated overview of the whole project; (2) it can perform a user-defined workflow of cloning steps in a single execution of the software; (3) it can handle multiple types of genetic recombineering, a technique that is rapidly replacing classical cloning for many applications; (4) it includes experimental information to conveniently guide wet lab work; and (5) it can store results and comments to allow the tracking and management of the whole project in one platform. MCDS is freely available from https://mcds.codeplex.com.

Siderophores in Cloud Waters and Potential Impact on Atmospheric Chemistry: Photoreactivity of Iron Complexes under Sun-Simulated Conditions.

PubMed

Passananti, Monica; Vinatier, Virginie; Delort, Anne-Marie; Mailhot, Gilles; Brigante, Marcello

2016-09-06

In the present work, the photoreactivity of a mixture of iron(III)–pyoverdin (Fe(III)–Pyo) complexes was investigated under simulated cloud conditions. Pyoverdins are expected to complex ferric ions naturally present in cloudwater, thus modifying their availability and photoreactivity. The spectroscopic properties and photoreactivity of Fe(III)-Pyo were investigated, with particular attention to their fate under solar irradiation, also studied through simulations. The photolysis of the Fe(III)–Pyo complex leads to the generation of Fe(II), with rates of formation (RFe(II)f) of 6.98 and 3.96 × 10–9 M s–1 at pH 4.0 and 6.0, respectively. Interestingly, acetate formation was observed during the iron-complex photolysis, suggesting that fragmentation can occur after the ligand-to-metal charge transfer (LMCT) via a complex reaction mechanism. Moreover, photogenerated Fe(II) represent an important source of hydroxyl radical via the Fenton reaction in cloudwater. This reactivity might be relevant for the estimation of the rates of formation and steady-state concentrations of the hydroxyl radical by cloud chemistry models and for organic matter speciation in the cloud aqueous phase. In fact, the conventional models, which describe the iron photoreactivity in terms of iron–aqua and oxalate complexes, are not in accordance with our results.

Numerical Simulation of Nocturnal Drainage Flows in Idealized Valley-Tributary Systems.

NASA Astrophysics Data System (ADS)

O'Steen, Lance B.

2000-11-01

Numerical simulations of nocturnal drainage flow and transport in idealized valley-tributary systems are compared with the Atmospheric Science in Complex Terrain (ASCOT) meteorological field data and tracer studies from the Brush Creek valley of western Colorado. Much of the general valley-tributary flow behavior deduced from observations is qualitatively reproduced in the numerical results. The spatially complex, unsteady nature of the tributary flow found in the field data is also seen in the simulations. Oscillations in the simulated tributary flow are similar to some field observations. However, observed oscillations in the valley flow at the mouth of the tributary could not be reproduced in the numerical results. Thus, hypotheses of strongly coupled valley-tributary flow oscillations, based on field data, cannot be supported by these simulations. Along-valley mass flux calculations based on model results for the valley-tributary system indicate an increase of 5%-10% over a valley without a tributary. Enhanced valley mass fluxes were found from 8 km above the tributary to almost the valley mouth. However, the valley mass fluxes for topography with and without a tributary were nearly equal at the valley outflow. ASCOT field data suggested a tributary mass flow contribution of 5%-15% for a Brush Creek tributary of similar drainage area to the model tributary employed here. Numerical simulations of transport in the nocturnal valley-tributary flow strongly support ASCOT tracer studies in the Pack Canyon tributary of Brush Creek. These results suggest that the valley-tributary interaction can significantly increase plume dispersion under stable conditions. Overall, the simulation results presented here indicate that simple terrain geometries are able to capture many of the salient features of drainage flow in real valley-tributary systems.

Gray: a ray tracing-based Monte Carlo simulator for PET.

PubMed

Freese, David L; Olcott, Peter D; Buss, Samuel R; Levin, Craig S

2018-05-21

Monte Carlo simulation software plays a critical role in PET system design. Performing complex, repeated Monte Carlo simulations can be computationally prohibitive, as even a single simulation can require a large amount of time and a computing cluster to complete. Here we introduce Gray, a Monte Carlo simulation software for PET systems. Gray exploits ray tracing methods used in the computer graphics community to greatly accelerate simulations of PET systems with complex geometries. We demonstrate the implementation of models for positron range, annihilation acolinearity, photoelectric absorption, Compton scatter, and Rayleigh scatter. For validation, we simulate the GATE PET benchmark, and compare energy, distribution of hits, coincidences, and run time. We show a [Formula: see text] speedup using Gray, compared to GATE for the same simulation, while demonstrating nearly identical results. We additionally simulate the Siemens Biograph mCT system with both the NEMA NU-2 scatter phantom and sensitivity phantom. We estimate the total sensitivity within [Formula: see text]% when accounting for differences in peak NECR. We also estimate the peak NECR to be [Formula: see text] kcps, or within [Formula: see text]% of published experimental data. The activity concentration of the peak is also estimated within 1.3%.

Implementation of quantum key distribution network simulation module in the network simulator NS-3

NASA Astrophysics Data System (ADS)

Mehic, Miralem; Maurhart, Oliver; Rass, Stefan; Voznak, Miroslav

2017-10-01

As the research in quantum key distribution (QKD) technology grows larger and becomes more complex, the need for highly accurate and scalable simulation technologies becomes important to assess the practical feasibility and foresee difficulties in the practical implementation of theoretical achievements. Due to the specificity of the QKD link which requires optical and Internet connection between the network nodes, to deploy a complete testbed containing multiple network hosts and links to validate and verify a certain network algorithm or protocol would be very costly. Network simulators in these circumstances save vast amounts of money and time in accomplishing such a task. The simulation environment offers the creation of complex network topologies, a high degree of control and repeatable experiments, which in turn allows researchers to conduct experiments and confirm their results. In this paper, we described the design of the QKD network simulation module which was developed in the network simulator of version 3 (NS-3). The module supports simulation of the QKD network in an overlay mode or in a single TCP/IP mode. Therefore, it can be used to simulate other network technologies regardless of QKD.

Computer simulations of dendrimer-polyelectrolyte complexes.

PubMed

Pandav, Gunja; Ganesan, Venkat

2014-08-28

We carry out a systematic analysis of static properties of the clusters formed by complexation between charged dendrimers and linear polyelectrolyte (LPE) chains in a dilute solution under good solvent conditions. We use single chain in mean-field simulations and analyze the structure of the clusters through radial distribution functions of the dendrimer, cluster size, and charge distributions. The effects of LPE length, charge ratio between LPE and dendrimer, the influence of salt concentration, and the dendrimer generation number are examined. Systems with short LPEs showed a reduced propensity for aggregation with dendrimers, leading to formation of smaller clusters. In contrast, larger dendrimers and longer LPEs lead to larger clusters with significant bridging. Increasing salt concentration was seen to reduce aggregation between dendrimers as a result of screening of electrostatic interactions. Generally, maximum complexation was observed in systems with an equal amount of net dendrimer and LPE charges, whereas either excess LPE or dendrimer concentrations resulted in reduced clustering between dendrimers.

Next-generation purex flowsheets with acetohydroxamic acid as complexant for FBR and thermal-fuel reprocessing

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

Kumar, Shekhar; Koganti, S.B.

2008-07-01

Acetohydroxamic acid (AHA) is a novel complexant for recycle of nuclear-fuel materials. It can be used in ordinary centrifugal extractors, eliminating the need for electro-redox equipment or complex maintenance requirements in a remotely maintained hot cell. In this work, the effect of AHA on Pu(IV) distribution ratios in 30% TBP system was quantified, modeled, and integrated in SIMPSEX code. Two sets of batch experiments involving macro Pu concentrations (conducted at IGCAR) and one high-Pu flowsheet (literature) were simulated for AHA based U-Pu separation. Based on the simulation and validation results, AHA based next-generation reprocessing flowsheets are proposed for co-processing basedmore » FBR and thermal-fuel reprocessing as well as evaporator-less macro-level Pu concentration process required for MOX fuel fabrication. Utilization of AHA results in significant simplification in plant design and simpler technology implementations with significant cost savings. (authors)« less

Complex Langevin simulation of a random matrix model at nonzero chemical potential

NASA Astrophysics Data System (ADS)

Bloch, J.; Glesaaen, J.; Verbaarschot, J. J. M.; Zafeiropoulos, S.

2018-03-01

In this paper we test the complex Langevin algorithm for numerical simulations of a random matrix model of QCD with a first order phase transition to a phase of finite baryon density. We observe that a naive implementation of the algorithm leads to phase quenched results, which were also derived analytically in this article. We test several fixes for the convergence issues of the algorithm, in particular the method of gauge cooling, the shifted representation, the deformation technique and reweighted complex Langevin, but only the latter method reproduces the correct analytical results in the region where the quark mass is inside the domain of the eigenvalues. In order to shed more light on the issues of the methods we also apply them to a similar random matrix model with a milder sign problem and no phase transition, and in that case gauge cooling solves the convergence problems as was shown before in the literature.

Differential die-away instrument: Report on comparison of fuel assembly experiments and simulations

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

Goodsell, Alison Victoria; Henzl, Vladimir; Swinhoe, Martyn Thomas

2015-01-14

Experimental results of the assay of mock-up (fresh) fuel with the differential die-away (DDA) instrument were compared to the Monte Carlo N-Particle eXtended (MCNPX) simulation results. Most principal experimental observables, the die-away time and the in tegral of the DDA signal in several time domains, have been found in good agreement with the MCNPX simulation results. The remaining discrepancies between the simulation and experimental results are likely due to small differences between the actual experimental setup and the simulated geometry, including uncertainty in the DT neutron generator yield. Within this report we also present a sensitivity study of the DDAmore » instrument which is a complex and sensitive system and demonstrate to what degree it can be impacted by geometry, material composition, and electronics performance.« less

Evaluation of integration methods for hybrid simulation of complex structural systems through collapse

NASA Astrophysics Data System (ADS)

Del Carpio R., Maikol; Hashemi, M. Javad; Mosqueda, Gilberto

2017-10-01

This study examines the performance of integration methods for hybrid simulation of large and complex structural systems in the context of structural collapse due to seismic excitations. The target application is not necessarily for real-time testing, but rather for models that involve large-scale physical sub-structures and highly nonlinear numerical models. Four case studies are presented and discussed. In the first case study, the accuracy of integration schemes including two widely used methods, namely, modified version of the implicit Newmark with fixed-number of iteration (iterative) and the operator-splitting (non-iterative) is examined through pure numerical simulations. The second case study presents the results of 10 hybrid simulations repeated with the two aforementioned integration methods considering various time steps and fixed-number of iterations for the iterative integration method. The physical sub-structure in these tests consists of a single-degree-of-freedom (SDOF) cantilever column with replaceable steel coupons that provides repeatable highlynonlinear behavior including fracture-type strength and stiffness degradations. In case study three, the implicit Newmark with fixed-number of iterations is applied for hybrid simulations of a 1:2 scale steel moment frame that includes a relatively complex nonlinear numerical substructure. Lastly, a more complex numerical substructure is considered by constructing a nonlinear computational model of a moment frame coupled to a hybrid model of a 1:2 scale steel gravity frame. The last two case studies are conducted on the same porotype structure and the selection of time steps and fixed number of iterations are closely examined in pre-test simulations. The generated unbalance forces is used as an index to track the equilibrium error and predict the accuracy and stability of the simulations.

Computational composite mechanics for aerospace propulsion structures

NASA Technical Reports Server (NTRS)

Chamis, C. C.

1986-01-01

Specialty methods are presented for the computational simulation of specific composite behavior. These methods encompass all aspects of composite mechanics, impact, progressive fracture and component specific simulation. Some of these methods are structured to computationally simulate, in parallel, the composite behavior and history from the initial fabrication through several missions and even to fracture. Select methods and typical results obtained from such simulations are described in detail in order to demonstrate the effectiveness of computationally simulating (1) complex composite structural behavior in general and (2) specific aerospace propulsion structural components in particular.

Computational composite mechanics for aerospace propulsion structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

1987-01-01

Specialty methods are presented for the computational simulation of specific composite behavior. These methods encompass all aspects of composite mechanics, impact, progressive fracture and component specific simulation. Some of these methods are structured to computationally simulate, in parallel, the composite behavior and history from the initial frabrication through several missions and even to fracture. Select methods and typical results obtained from such simulations are described in detail in order to demonstrate the effectiveness of computationally simulating: (1) complex composite structural behavior in general, and (2) specific aerospace propulsion structural components in particular.

A computational study of the chemokine receptor CXCR1 bound with interleukin-8

NASA Astrophysics Data System (ADS)

Wang, Yang; Severin Lupala, Cecylia; Wang, Ting; Li, Xuanxuan; Yun, Ji-Hye; Park, Jae-hyun; Jin, Zeyu; Lee, Weontae; Tan, Leihan; Liu, Haiguang

2018-03-01

CXCR1 is a G-protein coupled receptor, transducing signals from chemokines, in particular the interleukin-8 (IL8) molecules. This study combines homology modeling and molecular dynamics simulation methods to study the structure of CXCR1-IL8 complex. By using CXCR4-vMIP-II crystallography structure as the homologous template, CXCR1-IL8 complex structure was constructed, and then refined using all-atom molecular dynamics simulations. Through extensive simulations, CXCR1-IL8 binding poses were investigated in detail. Furthermore, the role of the N-terminal of CXCR1 receptor was studied by comparing four complex models differing in the N-terminal sequences. The results indicate that the receptor N-terminal affects the binding of IL8 significantly. With a shorter N-terminal domain, the binding of IL8 to CXCR1 becomes unstable. The homology modeling and simulations also reveal the key receptor-ligand residues involved in the electrostatic interactions known to be vital for complex formation. Project supported by the National Natural Science Foundation of China (Grant Nos. 11575021, U1530401, and U1430237) and the National Research Foundation of Korea (Grant Nos. NRF-2017R1A2B2008483 and NRF-2016R1A6A3A04010213).

Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and their Complexes with Proteins

PubMed Central

Nguyen, Hai; Pérez, Alberto; Bermeo, Sherry; Simmerling, Carlos

2016-01-01

The Generalized Born (GB) implicit solvent model has undergone significant improvements in accuracy for modeling of proteins and small molecules. However, GB still remains a less widely explored option for nucleic acid simulations, in part because fast GB models are often unable to maintain stable nucleic acid structures, or they introduce structural bias in proteins, leading to difficulty in application of GB models in simulations of protein-nucleic acid complexes. Recently, GB-neck2 was developed to improve the behavior of protein simulations. In an effort to create a more accurate model for nucleic acids, a similar procedure to the development of GB-neck2 is described here for nucleic acids. The resulting parameter set significantly reduces absolute and relative energy error relative to Poisson Boltzmann for both nucleic acids and nucleic acid-protein complexes, when compared to its predecessor GB-neck model. This improvement in solvation energy calculation translates to increased structural stability for simulations of DNA and RNA duplexes, quadruplexes, and protein-nucleic acid complexes. The GB-neck2 model also enables successful folding of small DNA and RNA hairpins to near native structures as determined from comparison with experiment. The functional form and all required parameters are provided here and also implemented in the AMBER software. PMID:26574454

Investigating Complexity Using Excel and Visual Basic.

ERIC Educational Resources Information Center

Zetie, K. P.

2001-01-01

Shows how some of the simple ideas in complexity can be investigated using a spreadsheet and a macro written in Visual Basic. Shows how the sandpile model of Bak, Chao, and Wiesenfeld can be simulated and animated. The model produces results that cannot easily be predicted from its properties. (Author/MM)

Modular, high power, variable R dynamic electrical load simulator

NASA Technical Reports Server (NTRS)

Joncas, K. P.

1974-01-01

The design of a previously developed basic variable R load simulator was entended to increase its power dissipation and transient handling capabilities. The delivered units satisfy all design requirements, and provides for a high power, modular simulation capability uniquely suited to the simulation of complex load responses. In addition to presenting conclusions and recommendations and pertinent background information, the report covers program accomplishments; describes the simulator basic circuits, transfer characteristic, protective features, assembly, and specifications; indicates the results of simulator evaluation, including burn-in and acceptance testing; provides acceptance test data; and summarizes the monthly progress reports.

Free energy calculation of single molecular interaction using Jarzynski's identity method: the case of HIV-1 protease inhibitor system

NASA Astrophysics Data System (ADS)

Li, De-Chang; Ji, Bao-Hua

2012-06-01

Jarzynski' identity (JI) method was suggested a promising tool for reconstructing free energy landscape of biomolecular interactions in numerical simulations and experiments. However, JI method has not yet been well tested in complex systems such as ligand-receptor molecular pairs. In this paper, we applied a huge number of steered molecular dynamics (SMD) simulations to dissociate the protease of human immunodeficiency type I virus (HIV-1 protease) and its inhibitors. We showed that because of intrinsic complexity of the ligand-receptor system, the energy barrier predicted by JI method at high pulling rates is much higher than experimental results. However, with a slower pulling rate and fewer switch times of simulations, the predictions of JI method can approach to the experiments. These results suggested that the JI method is more appropriate for reconstructing free energy landscape using the data taken from experiments, since the pulling rates used in experiments are often much slower than those in SMD simulations. Furthermore, we showed that a higher loading stiffness can produce higher precision of calculation of energy landscape because it yields a lower mean value and narrower bandwidth of work distribution in SMD simulations.

Check-Cases for Verification of 6-Degree-of-Freedom Flight Vehicle Simulations. Volume 2; Appendices

NASA Technical Reports Server (NTRS)

Murri, Daniel G.; Jackson, E. Bruce; Shelton, Robert O.

2015-01-01

This NASA Engineering and Safety Center (NESC) assessment was established to develop a set of time histories for the flight behavior of increasingly complex example aerospacecraft that could be used to partially validate various simulation frameworks. The assessment was conducted by representatives from several NASA Centers and an open-source simulation project. This document contains details on models, implementation, and results.

FLASH hydrodynamic simulations of experiments to explore the generation of cosmological magnetic fields

NASA Astrophysics Data System (ADS)

Scopatz, A.; Fatenejad, M.; Flocke, N.; Gregori, G.; Koenig, M.; Lamb, D. Q.; Lee, D.; Meinecke, J.; Ravasio, A.; Tzeferacos, P.; Weide, K.; Yurchak, R.

2013-03-01

We report the results of FLASH hydrodynamic simulations of the experiments conducted by the University of Oxford High Energy Density Laboratory Astrophysics group and its collaborators at the Laboratoire pour l'Utilisation de Lasers Intenses (LULI). In these experiments, a long-pulse laser illuminates a target in a chamber filled with Argon gas, producing shock waves that generate magnetic fields via the Biermann battery mechanism. The simulations show that the result of the laser illuminating the target is a series of complex hydrodynamic phenomena.

Simulation of blast action on civil structures using ANSYS Autodyn

NASA Astrophysics Data System (ADS)

Fedorova, N. N.; Valger, S. A.; Fedorov, A. V.

2016-10-01

The paper presents the results of 3D numerical simulations of shock wave spreading in cityscape area. ANSYS Autodyne software is used for the computations. Different test cases are investigated numerically. On the basis of the computations, the complex transient flowfield structure formed in the vicinity of prismatic bodies was obtained and analyzed. The simulation results have been compared to the experimental data. The ability of two numerical schemes is studied to correctly predict the pressure history in several gauges placed on walls of the obstacles.

Applications of the Lattice Boltzmann Method to Complex and Turbulent Flows

NASA Technical Reports Server (NTRS)

Luo, Li-Shi; Qi, Dewei; Wang, Lian-Ping; Bushnell, Dennis M. (Technical Monitor)

2002-01-01

We briefly review the method of the lattice Boltzmann equation (LBE). We show the three-dimensional LBE simulation results for a non-spherical particle in Couette flow and 16 particles in sedimentation in fluid. We compare the LBE simulation of the three-dimensional homogeneous isotropic turbulence flow in a periodic cubic box of the size 1283 with the pseudo-spectral simulation, and find that the two results agree well with each other but the LBE method is more dissipative than the pseudo-spectral method in small scales, as expected.

Study of orotidine 5'-monophosphate decarboxylase in complex with the top three OMP, BMP, and PMP ligands by molecular dynamics simulation.

PubMed

Jamshidi, Shirin; Jalili, Seifollah; Rafii-Tabar, Hashem

2015-01-01

Catalytic mechanism of orotidine 5'-monophosphate decarboxylase (OMPDC), one of the nature most proficient enzymes which provides large rate enhancement, has not been fully understood yet. A series of 30 ns molecular dynamics (MD) simulations were run on X-ray structure of the OMPDC from Saccharomyces cerevisiae in its free form as well as in complex with different ligands, namely 1-(5'-phospho-D-ribofuranosyl) barbituric acid (BMP), orotidine 5'-monophosphate (OMP), and 6-phosphonouridine 5'-monophosphate (PMP). The importance of this biological system is justified both by its high rate enhancement and its potential use as a target in chemotherapy. This work focuses on comparing two physicochemical states of the enzyme (protonated and deprotonated Asp91) and three ligands (substrate OMP, inhibitor, and transition state analog BMP and substrate analog PMP). Detailed analysis of the active site geometry and its interactions is properly put in context by extensive comparison with relevant experimental works. Our overall results show that in terms of hydrogen bond occupancy, electrostatic interactions, dihedral angles, active site configuration, and movement of loops, notable differences among different complexes are observed. Comparison of the results obtained from these simulations provides some detailed structural data for the complexes, the enzyme, and the ligands, as well as useful insights into the inhibition mechanism of the OMPDC enzyme. Furthermore, these simulations are applied to clarify the ambiguous mechanism of the OMPDC enzyme, and imply that the substrate destabilization and transition state stabilization contribute to the mechanism of action of the most proficient enzyme, OMPDC.

Solute transport with equilibrium aqueous complexation and either sorption or ion exchange: Simulation methodology and applications

USGS Publications Warehouse

Lewis, F.M.; Voss, C.I.; Rubin, J.

1987-01-01

Methodologies that account for specific types of chemical reactions in the simulation of solute transport can be developed so they are compatible with solution algorithms employed in existing transport codes. This enables the simulation of reactive transport in complex multidimensional flow regimes, and provides a means for existing codes to account for some of the fundamental chemical processes that occur among transported solutes. Two equilibrium-controlled reaction systems demonstrate a methodology for accommodating chemical interaction into models of solute transport. One system involves the sorption of a given chemical species, as well as two aqueous complexations in which the sorbing species is a participant. The other reaction set involves binary ion exchange coupled with aqueous complexation involving one of the exchanging species. The methodology accommodates these reaction systems through the addition of nonlinear terms to the transport equations for the sorbing species. Example simulation results show (1) the effect equilibrium chemical parameters have on the spatial distributions of concentration for complexing solutes; (2) that an interrelationship exists between mechanical dispersion and the various reaction processes; (3) that dispersive parameters of the porous media cannot be determined from reactive concentration distributions unless the reaction is accounted for or the influence of the reaction is negligible; (4) how the concentration of a chemical species may be significantly affected by its participation in an aqueous complex with a second species which also sorbs; and (5) that these coupled chemical processes influencing reactive transport can be demonstrated in two-dimensional flow regimes. ?? 1987.

Aromatic sulfonation with sulfur trioxide: mechanism and kinetic model.

PubMed

Moors, Samuel L C; Deraet, Xavier; Van Assche, Guy; Geerlings, Paul; De Proft, Frank

2017-01-01

Electrophilic aromatic sulfonation of benzene with sulfur trioxide is studied with ab initio molecular dynamics simulations in gas phase, and in explicit noncomplexing (CCl 3 F) and complexing (CH 3 NO 2 ) solvent models. We investigate different possible reaction pathways, the number of SO 3 molecules participating in the reaction, and the influence of the solvent. Our simulations confirm the existence of a low-energy concerted pathway with formation of a cyclic transition state with two SO 3 molecules. Based on the simulation results, we propose a sequence of elementary reaction steps and a kinetic model compatible with experimental data. Furthermore, a new alternative reaction pathway is proposed in complexing solvent, involving two SO 3 and one CH 3 NO 2 .

Cluster-Expansion Model for Complex Quinary Alloys: Application to Alnico Permanent Magnets

NASA Astrophysics Data System (ADS)

Nguyen, Manh Cuong; Zhou, Lin; Tang, Wei; Kramer, Matthew J.; Anderson, Iver E.; Wang, Cai-Zhuang; Ho, Kai-Ming

2017-11-01

An accurate and transferable cluster-expansion model for complex quinary alloys is developed. Lattice Monte Carlo simulation enabled by this cluster-expansion model is used to investigate temperature-dependent atomic structure of alnico alloys, which are considered as promising high-performance non-rare-earth permanent-magnet materials for high-temperature applications. The results of the Monte Carlo simulations are consistent with available experimental data and provide useful insights into phase decomposition, selection, and chemical ordering in alnico. The simulations also reveal a previously unrecognized D 03 alloy phase. This phase is very rich in Ni and exhibits very weak magnetization. Manipulating the size and location of this phase provides a possible route to improve the magnetic properties of alnico, especially coercivity.

Dual simulation of the massless lattice Schwinger model with topological term and non-zero chemical potential

NASA Astrophysics Data System (ADS)

Göschl, Daniel

2018-03-01

We discuss simulation strategies for the massless lattice Schwinger model with a topological term and finite chemical potential. The simulation is done in a dual representation where the complex action problem is solved and the partition function is a sum over fermion loops, fermion dimers and plaquette-occupation numbers. We explore strategies to update the fermion loops coupled to the gauge degrees of freedom and check our results with conventional simulations (without topological term and at zero chemical potential), as well as with exact summation on small volumes. Some physical implications of the results are discussed.

CFD simulation and experimental validation of a GM type double inlet pulse tube refrigerator

NASA Astrophysics Data System (ADS)

Banjare, Y. P.; Sahoo, R. K.; Sarangi, S. K.

2010-04-01

Pulse tube refrigerator has the advantages of long life and low vibration over the conventional cryocoolers, such as GM and stirling coolers because of the absence of moving parts in low temperature. This paper performs a three-dimensional computational fluid dynamic (CFD) simulation of a GM type double inlet pulse tube refrigerator (DIPTR) vertically aligned, operating under a variety of thermal boundary conditions. A commercial computational fluid dynamics (CFD) software package, Fluent 6.1 is used to model the oscillating flow inside a pulse tube refrigerator. The simulation represents fully coupled systems operating in steady-periodic mode. The externally imposed boundary conditions are sinusoidal pressure inlet by user defined function at one end of the tube and constant temperature or heat flux boundaries at the external walls of the cold-end heat exchangers. The experimental method to evaluate the optimum parameters of DIPTR is difficult. On the other hand, developing a computer code for CFD analysis is equally complex. The objectives of the present investigations are to ascertain the suitability of CFD based commercial package, Fluent for study of energy and fluid flow in DIPTR and to validate the CFD simulation results with available experimental data. The general results, such as the cool down behaviours of the system, phase relation between mass flow rate and pressure at cold end, the temperature profile along the wall of the cooler and refrigeration load are presented for different boundary conditions of the system. The results confirm that CFD based Fluent simulations are capable of elucidating complex periodic processes in DIPTR. The results also show that there is an excellent agreement between CFD simulation results and experimental results.

Development of axisymmetric lattice Boltzmann flux solver for complex multiphase flows

NASA Astrophysics Data System (ADS)

Wang, Yan; Shu, Chang; Yang, Li-Ming; Yuan, Hai-Zhuan

2018-05-01

This paper presents an axisymmetric lattice Boltzmann flux solver (LBFS) for simulating axisymmetric multiphase flows. In the solver, the two-dimensional (2D) multiphase LBFS is applied to reconstruct macroscopic fluxes excluding axisymmetric effects. Source terms accounting for axisymmetric effects are introduced directly into the governing equations. As compared to conventional axisymmetric multiphase lattice Boltzmann (LB) method, the present solver has the kinetic feature for flux evaluation and avoids complex derivations of external forcing terms. In addition, the present solver also saves considerable computational efforts in comparison with three-dimensional (3D) computations. The capability of the proposed solver in simulating complex multiphase flows is demonstrated by studying single bubble rising in a circular tube. The obtained results compare well with the published data.

Development of an Output-based Adaptive Method for Multi-Dimensional Euler and Navier-Stokes Simulations

NASA Technical Reports Server (NTRS)

Darmofal, David L.

2003-01-01

The use of computational simulations in the prediction of complex aerodynamic flows is becoming increasingly prevalent in the design process within the aerospace industry. Continuing advancements in both computing technology and algorithmic development are ultimately leading to attempts at simulating ever-larger, more complex problems. However, by increasing the reliance on computational simulations in the design cycle, we must also increase the accuracy of these simulations in order to maintain or improve the reliability arid safety of the resulting aircraft. At the same time, large-scale computational simulations must be made more affordable so that their potential benefits can be fully realized within the design cycle. Thus, a continuing need exists for increasing the accuracy and efficiency of computational algorithms such that computational fluid dynamics can become a viable tool in the design of more reliable, safer aircraft. The objective of this research was the development of an error estimation and grid adaptive strategy for reducing simulation errors in integral outputs (functionals) such as lift or drag from from multi-dimensional Euler and Navier-Stokes simulations. In this final report, we summarize our work during this grant.

Space station Simulation Computer System (SCS) study for NASA/MSFC. Volume 1: Overview and summary

NASA Technical Reports Server (NTRS)

1989-01-01

NASA's Space Station Freedom Program (SSFP) planning efforts have identified a need for a payload training simulator system to serve as both a training facility and as a demonstrator to validate operational concepts. The envisioned Marshall Space Flight Center (MSFC) Payload Training Complex (PTC) required to meet this need will train the space station payload scientists, station scientists, and ground controllers to operate the wide variety of experiments that will be onboard the Space Station Freedom. The Simulation Computer System (SCS) is the computer hardware, software, and workstations that will support the Payload Training Complex at MSFC. The purpose of this SCS study is to investigate issues related to the SCS, alternative requirements, simulator approaches, and state-of-the-art technologies to develop candidate concepts and designs. This study was performed August 1988 to October 1989. Thus, the results are based on the SSFP August 1989 baseline, i.e., pre-Langley configuration/budget review (C/BR) baseline. Some terms, e.g., combined trainer, are being redefined. An overview of the study activities and a summary of study results are given here.

Methods for Generating Complex Networks with Selected Structural Properties for Simulations: A Review and Tutorial for Neuroscientists

PubMed Central

Prettejohn, Brenton J.; Berryman, Matthew J.; McDonnell, Mark D.

2011-01-01

Many simulations of networks in computational neuroscience assume completely homogenous random networks of the Erdös–Rényi type, or regular networks, despite it being recognized for some time that anatomical brain networks are more complex in their connectivity and can, for example, exhibit the “scale-free” and “small-world” properties. We review the most well known algorithms for constructing networks with given non-homogeneous statistical properties and provide simple pseudo-code for reproducing such networks in software simulations. We also review some useful mathematical results and approximations associated with the statistics that describe these network models, including degree distribution, average path length, and clustering coefficient. We demonstrate how such results can be used as partial verification and validation of implementations. Finally, we discuss a sometimes overlooked modeling choice that can be crucially important for the properties of simulated networks: that of network directedness. The most well known network algorithms produce undirected networks, and we emphasize this point by highlighting how simple adaptations can instead produce directed networks. PMID:21441986

Efficient Analysis of Complex Structures

NASA Technical Reports Server (NTRS)

Kapania, Rakesh K.

2000-01-01

Last various accomplishments achieved during this project are : (1) A Survey of Neural Network (NN) applications using MATLAB NN Toolbox on structural engineering especially on equivalent continuum models (Appendix A). (2) Application of NN and GAs to simulate and synthesize substructures: 1-D and 2-D beam problems (Appendix B). (3) Development of an equivalent plate-model analysis method (EPA) for static and vibration analysis of general trapezoidal built-up wing structures composed of skins, spars and ribs. Calculation of all sorts of test cases and comparison with measurements or FEA results. (Appendix C). (4) Basic work on using second order sensitivities on simulating wing modal response, discussion of sensitivity evaluation approaches, and some results (Appendix D). (5) Establishing a general methodology of simulating the modal responses by direct application of NN and by sensitivity techniques, in a design space composed of a number of design points. Comparison is made through examples using these two methods (Appendix E). (6) Establishing a general methodology of efficient analysis of complex wing structures by indirect application of NN: the NN-aided Equivalent Plate Analysis. Training of the Neural Networks for this purpose in several cases of design spaces, which can be applicable for actual design of complex wings (Appendix F).

Mathematical simulation of water and salt transfer in geosystems of solonetzic soils in the Northern Caspian region

NASA Astrophysics Data System (ADS)

Golovanov, A. I.; Sotneva, N. I.

2009-03-01

The Dzhanybek two-dimensional radial-axial mathematical model was developed for water and salt transfer in geosystems of solonetzic complexes of the Northern Caspian region; the model is capable of considering the geochemical links and revealing the features of migration processes between the conjugated elements of the microcatena. The simulation results suggested that the stabilization of salinization-desalinization processes occurs under stable weather conditions within approximately 100 years. When the weather conditions changed (the total moisture pool of the area increased from 1978), the simulation results indicated a tendency toward salinization of dark-colored soils in microdepressions and removal of salts in the upper 1-m thick soil layer on microhighs and microslopes. Predictions for 2040 showed that a deep accumulation of salts in microdepressions and desalinization of soils of microhighs and microslopes will occur under the current weather conditions. Thus, the changes in the halogeochemical capacity of geosystems of solonetzic complexes primarily depend on the climatic conditions, although the capacity value remains almost constant with increasing total water reserves; the changes occur only between the conjugated soils of solonetzic complexes, which is of great importance for predicting the soil-geochemical status of the entire landscape.

Parametric Analysis of a Hover Test Vehicle using Advanced Test Generation and Data Analysis

NASA Technical Reports Server (NTRS)

Gundy-Burlet, Karen; Schumann, Johann; Menzies, Tim; Barrett, Tony

2009-01-01

Large complex aerospace systems are generally validated in regions local to anticipated operating points rather than through characterization of the entire feasible operational envelope of the system. This is due to the large parameter space, and complex, highly coupled nonlinear nature of the different systems that contribute to the performance of the aerospace system. We have addressed the factors deterring such an analysis by applying a combination of technologies to the area of flight envelop assessment. We utilize n-factor (2,3) combinatorial parameter variations to limit the number of cases, but still explore important interactions in the parameter space in a systematic fashion. The data generated is automatically analyzed through a combination of unsupervised learning using a Bayesian multivariate clustering technique (AutoBayes) and supervised learning of critical parameter ranges using the machine-learning tool TAR3, a treatment learner. Covariance analysis with scatter plots and likelihood contours are used to visualize correlations between simulation parameters and simulation results, a task that requires tool support, especially for large and complex models. We present results of simulation experiments for a cold-gas-powered hover test vehicle.

Elucidation of Enzymatic Mechanism of Phenazine Biosynthetic Protein PhzF Using QM/MM and MD Simulations

PubMed Central

Liu, Fei; Zhao, Yi-Lei; Wang, Xiaolei; Hu, Hongbo; Peng, Huasong; Wang, Wei; Wang, Jing-Fang; Zhang, Xuehong

2015-01-01

The phenazine biosynthetic pathway is of considerable importance for the pharmaceutical industry. The pathway produces two products: phenazine-1,6-dicarboxylic acid and phenazine-1-carboxylic acid. PhzF is an isomerase that catalyzes trans-2,3-dihydro-3-hydroxyanthranilic acid isomerization and plays an essential role in the phenazine biosynthetic pathway. Although the PhzF crystal structure has been determined recently, an understanding of the detailed catalytic mechanism and the roles of key catalytic residues are still lacking. In this study, a computational strategy using a combination of molecular modeling, molecular dynamics simulations, and quantum mechanics/molecular mechanics simulations was used to elucidate these important issues. The Apo enzyme, enzyme–substrate complexes with negatively charged Glu45, enzyme–transition state analog inhibitor complexes with neutral Glu45, and enzyme–product complexes with negatively charged Glu45 structures were optimized and modeled using a 200 ns molecular dynamics simulation. Residues such as Gly73, His74, Asp208, Gly212, Ser213, and water, which play important roles in ligand binding and the isomerization reaction, were comprehensively investigated. Our results suggest that the Glu45 residue at the active site of PhzF acts as a general base/acid catalyst during proton transfer. This study provides new insights into the detailed catalytic mechanism of PhzF and the results have important implications for PhzF modification. PMID:26414009

An investigation of molecular dynamics simulation and molecular docking: interaction of citrus flavonoids and bovine β-lactoglobulin in focus.

PubMed

Sahihi, M; Ghayeb, Y

2014-08-01

Citrus flavonoids are natural compounds with important health benefits. The study of their interaction with a transport protein, such as bovine β-lactoglobulin (BLG), at the atomic level could be a valuable factor to control their transport to biological sites. In the present study, molecular docking and molecular dynamics simulation methods were used to investigate the interaction of hesperetin, naringenin, nobiletin and tangeretin as citrus flavonoids and BLG as transport protein. The molecular docking results revealed that these flavonoids bind in the internal cavity of BLG and the BLG affinity for binding the flavonoids follows naringenin>hesperetin>tangeretin>nobiletin. The docking results also indicated that the BLG-flavonoid complexes are stabilized through hydrophobic interactions, hydrogen bond interactions and π-π stacking interactions. The analysis of molecular dynamics (MD) simulation trajectories showed that the root mean square deviation (RMSD) of various systems reaches equilibrium and fluctuates around the mean value at various times. Time evolution of the radius of gyration, total solvent accessible surface of the protein and the second structure of protein showed as well that BLG and BLG-flavonoid complexes were stable around 2500ps, and there was not any conformational change as for BLG-flavonoid complexes. Further, the profiles of atomic fluctuations indicated the rigidity of the ligand binding site during the simulation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Working alone or in the presence of others: exploring social facilitation in baggage X-ray security screening tasks.

PubMed

Yu, Rui-feng; Wu, Xin

2015-01-01

This study investigated whether the mere presence of a human audience would evoke a social facilitation effect in baggage X-ray security screening tasks. A 2 (target presence: present vs. absent) ×  2 (task complexity: simple vs. complex) ×  2 (social presence: alone vs. human audience) within-subject experiment simulating a real baggage screening task was conducted. This experiment included 20 male participants. The participants' search performance in this task was recorded. The results showed that the presence of a human audience speeded up responses in simple tasks and slowed down responses in complex tasks. However, the social facilitation effect produced by the presence of a human audience had no effect on response accuracy. These findings suggested that the complexity of screening tasks should be considered when designing work organisation modes for security screening tasks. Practitioner summary: This study investigated whether the presence of a human audience could evoke a social facilitation effect in baggage X-ray security screening tasks. An experimental simulation was conducted. The results showed that the presence of a human audience facilitated the search performance of simple tasks and inhibited the performance of complex tasks.

Sensitivity Analysis of Multidisciplinary Rotorcraft Simulations

NASA Technical Reports Server (NTRS)

Wang, Li; Diskin, Boris; Biedron, Robert T.; Nielsen, Eric J.; Bauchau, Olivier A.

2017-01-01

A multidisciplinary sensitivity analysis of rotorcraft simulations involving tightly coupled high-fidelity computational fluid dynamics and comprehensive analysis solvers is presented and evaluated. An unstructured sensitivity-enabled Navier-Stokes solver, FUN3D, and a nonlinear flexible multibody dynamics solver, DYMORE, are coupled to predict the aerodynamic loads and structural responses of helicopter rotor blades. A discretely-consistent adjoint-based sensitivity analysis available in FUN3D provides sensitivities arising from unsteady turbulent flows and unstructured dynamic overset meshes, while a complex-variable approach is used to compute DYMORE structural sensitivities with respect to aerodynamic loads. The multidisciplinary sensitivity analysis is conducted through integrating the sensitivity components from each discipline of the coupled system. Numerical results verify accuracy of the FUN3D/DYMORE system by conducting simulations for a benchmark rotorcraft test model and comparing solutions with established analyses and experimental data. Complex-variable implementation of sensitivity analysis of DYMORE and the coupled FUN3D/DYMORE system is verified by comparing with real-valued analysis and sensitivities. Correctness of adjoint formulations for FUN3D/DYMORE interfaces is verified by comparing adjoint-based and complex-variable sensitivities. Finally, sensitivities of the lift and drag functions obtained by complex-variable FUN3D/DYMORE simulations are compared with sensitivities computed by the multidisciplinary sensitivity analysis, which couples adjoint-based flow and grid sensitivities of FUN3D and FUN3D/DYMORE interfaces with complex-variable sensitivities of DYMORE structural responses.

Advanced Simulation and Computing Business Plan

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

Rummel, E.

To maintain a credible nuclear weapons program, the National Nuclear Security Administration’s (NNSA’s) Office of Defense Programs (DP) needs to make certain that the capabilities, tools, and expert staff are in place and are able to deliver validated assessments. This requires a complete and robust simulation environment backed by an experimental program to test ASC Program models. This ASC Business Plan document encapsulates a complex set of elements, each of which is essential to the success of the simulation component of the Nuclear Security Enterprise. The ASC Business Plan addresses the hiring, mentoring, and retaining of programmatic technical staff responsiblemore » for building the simulation tools of the nuclear security complex. The ASC Business Plan describes how the ASC Program engages with industry partners—partners upon whom the ASC Program relies on for today’s and tomorrow’s high performance architectures. Each piece in this chain is essential to assure policymakers, who must make decisions based on the results of simulations, that they are receiving all the actionable information they need.« less

A 3D virtual reality simulator for training of minimally invasive surgery.

PubMed

Mi, Shao-Hua; Hou, Zeng-Gunag; Yang, Fan; Xie, Xiao-Liang; Bian, Gui-Bin

2014-01-01

For the last decade, remarkable progress has been made in the field of cardiovascular disease treatment. However, these complex medical procedures require a combination of rich experience and technical skills. In this paper, a 3D virtual reality simulator for core skills training in minimally invasive surgery is presented. The system can generate realistic 3D vascular models segmented from patient datasets, including a beating heart, and provide a real-time computation of force and force feedback module for surgical simulation. Instruments, such as a catheter or guide wire, are represented by a multi-body mass-spring model. In addition, a realistic user interface with multiple windows and real-time 3D views are developed. Moreover, the simulator is also provided with a human-machine interaction module that gives doctors the sense of touch during the surgery training, enables them to control the motion of a virtual catheter/guide wire inside a complex vascular model. Experimental results show that the simulator is suitable for minimally invasive surgery training.

MOLNs: A CLOUD PLATFORM FOR INTERACTIVE, REPRODUCIBLE, AND SCALABLE SPATIAL STOCHASTIC COMPUTATIONAL EXPERIMENTS IN SYSTEMS BIOLOGY USING PyURDME.

PubMed

Drawert, Brian; Trogdon, Michael; Toor, Salman; Petzold, Linda; Hellander, Andreas

2016-01-01

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools and a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments.

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

PubMed

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

2013-01-01

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

Development of a physically-based planar inductors VHDL-AMS model for integrated power converter design

NASA Astrophysics Data System (ADS)

Ammouri, Aymen; Ben Salah, Walid; Khachroumi, Sofiane; Ben Salah, Tarek; Kourda, Ferid; Morel, Hervé

2014-05-01

Design of integrated power converters needs prototype-less approaches. Specific simulations are required for investigation and validation process. Simulation relies on active and passive device models. Models of planar devices, for instance, are still not available in power simulator tools. There is, thus, a specific limitation during the simulation process of integrated power systems. The paper focuses on the development of a physically-based planar inductor model and its validation inside a power converter during transient switching. The planar inductor model remains a complex device to model, particularly when the skin, the proximity and the parasitic capacitances effects are taken into account. Heterogeneous simulation scheme, including circuit and device models, is successfully implemented in VHDL-AMS language and simulated in Simplorer platform. The mixed simulation results has been favorably tested and compared with practical measurements. It is found that the multi-domain simulation results and measurements data are in close agreement.

Protein-Protein Interactions of Azurin Complex by Coarse-Grained Simulations with a Gō-Like Model

NASA Astrophysics Data System (ADS)

Rusmerryani, Micke; Takasu, Masako; Kawaguchi, Kazutomo; Saito, Hiroaki; Nagao, Hidemi

Proteins usually perform their biological functions by forming a complex with other proteins. It is very important to study the protein-protein interactions since these interactions are crucial in many processes of a living organism. In this study, we develop a coarse grained model to simulate protein complex in liquid system. We carry out molecular dynamics simulations with topology-based potential interactions to simulate dynamical properties of Pseudomonas Aeruginosa azurin complex systems. Azurin is known to play an essential role as an anticancer agent and bind many important intracellular molecules. Some physical properties are monitored during simulation time to get a better understanding of the influence of protein-protein interactions to the azurin complex dynamics. These studies will provide valuable insights for further investigation on protein-protein interactions in more realistic system.

Neuronvisio: A Graphical User Interface with 3D Capabilities for NEURON.

PubMed

Mattioni, Michele; Cohen, Uri; Le Novère, Nicolas

2012-01-01

The NEURON simulation environment is a commonly used tool to perform electrical simulation of neurons and neuronal networks. The NEURON User Interface, based on the now discontinued InterViews library, provides some limited facilities to explore models and to plot their simulation results. Other limitations include the inability to generate a three-dimensional visualization, no standard mean to save the results of simulations, or to store the model geometry within the results. Neuronvisio (http://neuronvisio.org) aims to address these deficiencies through a set of well designed python APIs and provides an improved UI, allowing users to explore and interact with the model. Neuronvisio also facilitates access to previously published models, allowing users to browse, download, and locally run NEURON models stored in ModelDB. Neuronvisio uses the matplotlib library to plot simulation results and uses the HDF standard format to store simulation results. Neuronvisio can be viewed as an extension of NEURON, facilitating typical user workflows such as model browsing, selection, download, compilation, and simulation. The 3D viewer simplifies the exploration of complex model structure, while matplotlib permits the plotting of high-quality graphs. The newly introduced ability of saving numerical results allows users to perform additional analysis on their previous simulations.

FEA Simulation of Free-Bending - a Preforming Step in the Hydroforming Process Chain

NASA Astrophysics Data System (ADS)

Beulich, N.; Craighero, P.; Volk, W.

2017-09-01

High-strength steel and aluminum alloys are essential for developing innovative, lightly-weighted space frame concepts. The intended design is built from car body parts with high geometrical complexity and reduced material-thickness. Over the past few years, many complex car body parts have been produced using hydroforming. To increase the accuracy of hydroforming in relation to prospective car concepts, the virtual manufacturing of forming becomes more important. As a part of process digitalization, it is necessary to develop a simulation model for the hydroforming process chain. The preforming of longitudinal welded tubes is therefore implemented by the use of three-dimensional free-bending. This technique is able to reproduce complex deflection curves in combination with innovative low-thickness material design for hydroforming processes. As a first step to the complete process simulation, the content of this paper deals with the development of a finite element simulation model for the free-bending process with 6 degrees of freedom. A mandrel built from spherical segments connected by a steel rope is located inside of the tube to prevent geometrical instability. Critical parameters for the result of the bending process are therefore evaluated and optimized. The simulation model is verified by surface measurements of a two-dimensional bending test.

General Relativistic MHD Simulations of Jet Formation

NASA Technical Reports Server (NTRS)

Mizuno, Y.; Nishikawa, K.-I.; Hardee, P.; Koide, S.; Fishman, G. J.

2005-01-01

We have performed 3-dimensional general relativistic magnetohydrodynamic (GRMHD) simulations of jet formation from an accretion disk with/without initial perturbation around a rotating black hole. We input a sinusoidal perturbation (m = 5 mode) in the rotation velocity of the accretion disk. The simulation results show the formation of a relativistic jet from the accretion disk. Although the initial perturbation becomes weakened by the coupling among different modes, it survives and triggers lower modes. As a result, complex non-axisymmetric density structure develops in the disk and the jet. Newtonian MHD simulations of jet formation with a non-axisymmetric mode show the growth of the m = 2 mode but GRMHD simulations cannot see the clear growth of the m = 2 mode.

Model Checking Satellite Operational Procedures

NASA Astrophysics Data System (ADS)

Cavaliere, Federico; Mari, Federico; Melatti, Igor; Minei, Giovanni; Salvo, Ivano; Tronci, Enrico; Verzino, Giovanni; Yushtein, Yuri

2011-08-01

We present a model checking approach for the automatic verification of satellite operational procedures (OPs). Building a model for a complex system as a satellite is a hard task. We overcome this obstruction by using a suitable simulator (SIMSAT) for the satellite. Our approach aims at improving OP quality assurance by automatic exhaustive exploration of all possible simulation scenarios. Moreover, our solution decreases OP verification costs by using a model checker (CMurphi) to automatically drive the simulator. We model OPs as user-executed programs observing the simulator telemetries and sending telecommands to the simulator. In order to assess feasibility of our approach we present experimental results on a simple meaningful scenario. Our results show that we can save up to 90% of verification time.

Surfactants at Single-Walled Carbon Nanotube-Water Interface: Physics of Surfactants, Counter-Ions, and Hydration Shell

NASA Astrophysics Data System (ADS)

Khare, Ketan S.; Phelan, Frederick R., Jr.

Specialized applications of single-walled carbon nanotubes (SWCNTs) require an efficient and reliable method to sort these materials into monodisperse fractions with respect to their defining metrics (chirality, length, etc.) while retaining their physical and chemical integrity. A popular method to achieve this goal is to use surfactants that individually disperse SWCNTs in water and then to separate the resulting colloidal mixture into fractions that are enriched in monodisperse SWCNTs. Recently, experiments at NIST have shown that subtle point mutations of chemical groups in bile salt surfactants have a large impact on the hydrodynamic properties of SWCNT-surfactant complexes during ultracentrifugation. These results provide strong motivation for understanding the rich physics underlying the assembly of surfactants around SWCNTs, the structure and dynamics of counter ions around the resulting complex, and propagation of these effects into the first hydration shell. Here, all-atom molecular dynamics simulations are used to investigate the thermodynamics of SWCNT-bile salt surfactant complexes in water with an emphasis on the buoyant characteristics of the SWCNT-surfactant complexes. Simulation results will be presented along with a comparison with experimental data. Official contribution of the National Institute of Standards and Technology; not subject to copyright in the United States.

Applying Biomimetic Algorithms for Extra-Terrestrial Habitat Generation

NASA Technical Reports Server (NTRS)

Birge, Brian

2012-01-01

The objective is to simulate and optimize distributed cooperation among a network of robots tasked with cooperative excavation on an extra-terrestrial surface. Additionally to examine the concept of directed Emergence among a group of limited artificially intelligent agents. Emergence is the concept of achieving complex results from very simple rules or interactions. For example, in a termite mound each individual termite does not carry a blueprint of how to make their home in a global sense, but their interactions based strictly on local desires create a complex superstructure. Leveraging this Emergence concept applied to a simulation of cooperative agents (robots) will allow an examination of the success of non-directed group strategy achieving specific results. Specifically the simulation will be a testbed to evaluate population based robotic exploration and cooperative strategies while leveraging the evolutionary teamwork approach in the face of uncertainty about the environment and partial loss of sensors. Checking against a cost function and 'social' constraints will optimize cooperation when excavating a simulated tunnel. Agents will act locally with non-local results. The rules by which the simulated robots interact will be optimized to the simplest possible for the desired result, leveraging Emergence. Sensor malfunction and line of sight issues will be incorporated into the simulation. This approach falls under Swarm Robotics, a subset of robot control concerned with finding ways to control large groups of robots. Swarm Robotics often contains biologically inspired approaches, research comes from social insect observation but also data from among groups of herding, schooling, and flocking animals. Biomimetic algorithms applied to manned space exploration is the method under consideration for further study.

Monte Carlo radiotherapy simulations of accelerated repopulation and reoxygenation for hypoxic head and neck cancer

PubMed Central

Harriss-Phillips, W M; Bezak, E; Yeoh, E K

2011-01-01

Objective A temporal Monte Carlo tumour growth and radiotherapy effect model (HYP-RT) simulating hypoxia in head and neck cancer has been developed and used to analyse parameters influencing cell kill during conventionally fractionated radiotherapy. The model was designed to simulate individual cell division up to 108 cells, while incorporating radiobiological effects, including accelerated repopulation and reoxygenation during treatment. Method Reoxygenation of hypoxic tumours has been modelled using randomised increments of oxygen to tumour cells after each treatment fraction. The process of accelerated repopulation has been modelled by increasing the symmetrical stem cell division probability. Both phenomena were onset immediately or after a number of weeks of simulated treatment. Results The extra dose required to control (total cell kill) hypoxic vs oxic tumours was 15–25% (8–20 Gy for 5×2 Gy per week) depending on the timing of accelerated repopulation onset. Reoxygenation of hypoxic tumours resulted in resensitisation and reduction in total dose required by approximately 10%, depending on the time of onset. When modelled simultaneously, accelerated repopulation and reoxygenation affected cell kill in hypoxic tumours in a similar manner to when the phenomena were modelled individually; however, the degree was altered, with non-additive results. Simulation results were in good agreement with standard linear quadratic theory; however, differed for more complex comparisons where hypoxia, reoxygenation as well as accelerated repopulation effects were considered. Conclusion Simulations have quantitatively confirmed the need for patient individualisation in radiotherapy for hypoxic head and neck tumours, and have shown the benefits of modelling complex and dynamic processes using Monte Carlo methods. PMID:21933980

Constructing Scientific Arguments Using Evidence from Dynamic Computational Climate Models

NASA Astrophysics Data System (ADS)

Pallant, Amy; Lee, Hee-Sun

2015-04-01

Modeling and argumentation are two important scientific practices students need to develop throughout school years. In this paper, we investigated how middle and high school students ( N = 512) construct a scientific argument based on evidence from computational models with which they simulated climate change. We designed scientific argumentation tasks with three increasingly complex dynamic climate models. Each scientific argumentation task consisted of four parts: multiple-choice claim, openended explanation, five-point Likert scale uncertainty rating, and open-ended uncertainty rationale. We coded 1,294 scientific arguments in terms of a claim's consistency with current scientific consensus, whether explanations were model based or knowledge based and categorized the sources of uncertainty (personal vs. scientific). We used chi-square and ANOVA tests to identify significant patterns. Results indicate that (1) a majority of students incorporated models as evidence to support their claims, (2) most students used model output results shown on graphs to confirm their claim rather than to explain simulated molecular processes, (3) students' dependence on model results and their uncertainty rating diminished as the dynamic climate models became more and more complex, (4) some students' misconceptions interfered with observing and interpreting model results or simulated processes, and (5) students' uncertainty sources reflected more frequently on their assessment of personal knowledge or abilities related to the tasks than on their critical examination of scientific evidence resulting from models. These findings have implications for teaching and research related to the integration of scientific argumentation and modeling practices to address complex Earth systems.

Simulation of noise involved in synthetic aperture radar

NASA Astrophysics Data System (ADS)

Grandchamp, Myriam; Cavassilas, Jean-Francois

1996-08-01

The synthetic aperture radr (SAR) returns from a linear distribution of scatterers are simulated and processed in order to estimate the reflectivity coefficients of the ground. An original expression of this estimate is given, which establishes the relation between the terms of signal and noise. Both are compared. One application of this formulation consists of detecting a surface ship wake on a complex SAR image. A smoothing is first accomplished on the complex image. The choice of the integration area is determined by the preceding mathematical formulation. Then a differential filter is applied, and results are shown for two parts of the wake.

Role of electrostatic interactions in binding of peptides and intrinsically disordered proteins to their folded targets. 1. NMR and MD characterization of the complex between the c-Crk N-SH3 domain and the peptide Sos.

PubMed

Xue, Yi; Yuwen, Tairan; Zhu, Fangqiang; Skrynnikov, Nikolai R

2014-10-21

Intrinsically disordered proteins (IDPs) often rely on electrostatic interactions to bind their structured targets. To obtain insight into the mechanism of formation of the electrostatic encounter complex, we investigated the binding of the peptide Sos (PPPVPPRRRR), which serves as a minimal model for an IDP, to the c-Crk N-terminal SH3 domain. Initially, we measured ¹⁵N relaxation rates at two magnetic field strengths and determined the binding shifts for the complex of Sos with wild-type SH3. We have also recorded a 3 μs molecular dynamics (MD) trajectory of this complex using the Amber ff99SB*-ILDN force field. The comparison of the experimental and simulated data shows that MD simulation consistently overestimates the strength of salt bridge interactions at the binding interface. The series of simulations using other advanced force fields also failed to produce any satisfactory results. To address this issue, we have devised an empirical correction to the Amber ff99SB*-ILDN force field whereby the Lennard-Jones equilibrium distance for the nitrogen-oxygen pair across the Arg-to-Asp and Arg-to-Glu salt bridges has been increased by 3%. Implementing this correction resulted in a good agreement between the simulations and the experiment. Adjusting the strength of salt bridge interactions removed a certain amount of strain contained in the original MD model, thus improving the binding of the hydrophobic N-terminal portion of the peptide. The arginine-rich C-terminal portion of the peptide, freed from the effect of the overstabilized salt bridges, was found to interconvert more rapidly between its multiple conformational states. The modified MD protocol has also been successfully used to simulate the entire binding process. In doing so, the peptide was initially placed high above the protein surface. It then arrived at the correct bound pose within ∼2 Å of the crystallographic coordinates. This simulation allowed us to analyze the details of the dynamic binding intermediate, i.e., the electrostatic encounter complex. However, an experimental characterization of this transient, weakly populated state remains out of reach. To overcome this problem, we designed the double mutant of c-Crk N-SH3 in which mutations Y186L and W169F abrogate tight Sos binding and shift the equilibrium toward the intermediate state resembling the electrostatic encounter complex. The results of the combined NMR and MD study of this engineered system will be reported in the next part of this paper.

Analysis and Description of HOLTIN Service Provision for AECG monitoring in Complex Indoor Environments

PubMed Central

Led, Santiago; Azpilicueta, Leire; Aguirre, Erik; de Espronceda, Miguel Martínez; Serrano, Luis; Falcone, Francisco

2013-01-01

In this work, a novel ambulatory ECG monitoring device developed in-house called HOLTIN is analyzed when operating in complex indoor scenarios. The HOLTIN system is described, from the technological platform level to its functional model. In addition, by using in-house 3D ray launching simulation code, the wireless channel behavior, which enables ubiquitous operation, is performed. The effect of human body presence is taken into account by a novel simplified model embedded within the 3D Ray Launching code. Simulation as well as measurement results are presented, showing good agreement. These results may aid in the adequate deployment of this novel device to automate conventional medical processes, increasing the coverage radius and optimizing energy consumption. PMID:23584122

Inference, simulation, modeling, and analysis of complex networks, with special emphasis on complex networks in systems biology

NASA Astrophysics Data System (ADS)

Christensen, Claire Petra

Across diverse fields ranging from physics to biology, sociology, and economics, the technological advances of the past decade have engendered an unprecedented explosion of data on highly complex systems with thousands, if not millions of interacting components. These systems exist at many scales of size and complexity, and it is becoming ever-more apparent that they are, in fact, universal, arising in every field of study. Moreover, they share fundamental properties---chief among these, that the individual interactions of their constituent parts may be well-understood, but the characteristic behaviour produced by the confluence of these interactions---by these complex networks---is unpredictable; in a nutshell, the whole is more than the sum of its parts. There is, perhaps, no better illustration of this concept than the discoveries being made regarding complex networks in the biological sciences. In particular, though the sequencing of the human genome in 2003 was a remarkable feat, scientists understand that the "cellular-level blueprints" for the human being are cellular-level parts lists, but they say nothing (explicitly) about cellular-level processes. The challenge of modern molecular biology is to understand these processes in terms of the networks of parts---in terms of the interactions among proteins, enzymes, genes, and metabolites---as it is these processes that ultimately differentiate animate from inanimate, giving rise to life! It is the goal of systems biology---an umbrella field encapsulating everything from molecular biology to epidemiology in social systems---to understand processes in terms of fundamental networks of core biological parts, be they proteins or people. By virtue of the fact that there are literally countless complex systems, not to mention tools and techniques used to infer, simulate, analyze, and model these systems, it is impossible to give a truly comprehensive account of the history and study of complex systems. The author's own publications have contributed network inference, simulation, modeling, and analysis methods to the much larger body of work in systems biology, and indeed, in network science. The aim of this thesis is therefore twofold: to present this original work in the historical context of network science, but also to provide sufficient review and reference regarding complex systems (with an emphasis on complex networks in systems biology) and tools and techniques for their inference, simulation, analysis, and modeling, such that the reader will be comfortable in seeking out further information on the subject. The review-like Chapters 1, 2, and 4 are intended to convey the co-evolution of network science and the slow but noticeable breakdown of boundaries between disciplines in academia as research and comparison of diverse systems has brought to light the shared properties of these systems. It is the author's hope that theses chapters impart some sense of the remarkable and rapid progress in complex systems research that has led to this unprecedented academic synergy. Chapters 3 and 5 detail the author's original work in the context of complex systems research. Chapter 3 presents the methods and results of a two-stage modeling process that generates candidate gene-regulatory networks of the bacterium B.subtilis from experimentally obtained, yet mathematically underdetermined microchip array data. These networks are then analyzed from a graph theoretical perspective, and their biological viability is critiqued by comparing the networks' graph theoretical properties to those of other biological systems. The results of topological perturbation analyses revealing commonalities in behavior at multiple levels of complexity are also presented, and are shown to be an invaluable means by which to ascertain the level of complexity to which the network inference process is robust to noise. Chapter 5 outlines a learning algorithm for the development of a realistic, evolving social network (a city) into which a disease is introduced. The results of simulations in populations spanning two orders of magnitude are compared to prevaccine era measles data for England and Wales and demonstrate that the simulations are able to capture the quantitative and qualitative features of epidemics in populations as small as 10,000 people. The work presented in Chapter 5 validates the utility of network simulation in concurrently probing contact network dynamics and disease dynamics.

Large-eddy simulation, fuel rod vibration and grid-to-rod fretting in pressurized water reactors

DOE PAGES

Christon, Mark A.; Lu, Roger; Bakosi, Jozsef; ...

2016-10-01

Grid-to-rod fretting (GTRF) in pressurized water reactors is a flow-induced vibration phenomenon that results in wear and fretting of the cladding material on fuel rods. GTRF is responsible for over 70% of the fuel failures in pressurized water reactors in the United States. Predicting the GTRF wear and concomitant interval between failures is important because of the large costs associated with reactor shutdown and replacement of fuel rod assemblies. The GTRF-induced wear process involves turbulent flow, mechanical vibration, tribology, and time-varying irradiated material properties in complex fuel assembly geometries. This paper presents a new approach for predicting GTRF induced fuelmore » rod wear that uses high-resolution implicit large-eddy simulation to drive nonlinear transient dynamics computations. The GTRF fluid–structure problem is separated into the simulation of the turbulent flow field in the complex-geometry fuel-rod bundles using implicit large-eddy simulation, the calculation of statistics of the resulting fluctuating structural forces, and the nonlinear transient dynamics analysis of the fuel rod. Ultimately, the methods developed here, can be used, in conjunction with operational management, to improve reactor core designs in which fuel rod failures are minimized or potentially eliminated. Furthermore, robustness of the behavior of both the structural forces computed from the turbulent flow simulations and the results from the transient dynamics analyses highlight the progress made towards achieving a predictive simulation capability for the GTRF problem.« less

Large-eddy simulation, fuel rod vibration and grid-to-rod fretting in pressurized water reactors

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

Christon, Mark A.; Lu, Roger; Bakosi, Jozsef

Grid-to-rod fretting (GTRF) in pressurized water reactors is a flow-induced vibration phenomenon that results in wear and fretting of the cladding material on fuel rods. GTRF is responsible for over 70% of the fuel failures in pressurized water reactors in the United States. Predicting the GTRF wear and concomitant interval between failures is important because of the large costs associated with reactor shutdown and replacement of fuel rod assemblies. The GTRF-induced wear process involves turbulent flow, mechanical vibration, tribology, and time-varying irradiated material properties in complex fuel assembly geometries. This paper presents a new approach for predicting GTRF induced fuelmore » rod wear that uses high-resolution implicit large-eddy simulation to drive nonlinear transient dynamics computations. The GTRF fluid–structure problem is separated into the simulation of the turbulent flow field in the complex-geometry fuel-rod bundles using implicit large-eddy simulation, the calculation of statistics of the resulting fluctuating structural forces, and the nonlinear transient dynamics analysis of the fuel rod. Ultimately, the methods developed here, can be used, in conjunction with operational management, to improve reactor core designs in which fuel rod failures are minimized or potentially eliminated. Furthermore, robustness of the behavior of both the structural forces computed from the turbulent flow simulations and the results from the transient dynamics analyses highlight the progress made towards achieving a predictive simulation capability for the GTRF problem.« less

Numerical propulsion system simulation: An interdisciplinary approach

NASA Technical Reports Server (NTRS)

Nichols, Lester D.; Chamis, Christos C.

1991-01-01

The tremendous progress being made in computational engineering and the rapid growth in computing power that is resulting from parallel processing now make it feasible to consider the use of computer simulations to gain insights into the complex interactions in aerospace propulsion systems and to evaluate new concepts early in the design process before a commitment to hardware is made. Described here is a NASA initiative to develop a Numerical Propulsion System Simulation (NPSS) capability.

Numerical propulsion system simulation - An interdisciplinary approach

NASA Technical Reports Server (NTRS)

Nichols, Lester D.; Chamis, Christos C.

1991-01-01

The tremendous progress being made in computational engineering and the rapid growth in computing power that is resulting from parallel processing now make it feasible to consider the use of computer simulations to gain insights into the complex interactions in aerospace propulsion systems and to evaluate new concepts early in the design process before a commitment to hardware is made. Described here is a NASA initiative to develop a Numerical Propulsion System Simulation (NPSS) capability.

Development of a calculation method for estimating specific energy distribution in complex radiation fields.

PubMed

Sato, Tatsuhiko; Watanabe, Ritsuko; Niita, Koji

2006-01-01

Estimation of the specific energy distribution in a human body exposed to complex radiation fields is of great importance in the planning of long-term space missions and heavy ion cancer therapies. With the aim of developing a tool for this estimation, the specific energy distributions in liquid water around the tracks of several HZE particles with energies up to 100 GeV n(-1) were calculated by performing track structure simulation with the Monte Carlo technique. In the simulation, the targets were assumed to be spherical sites with diameters from 1 nm to 1 microm. An analytical function to reproduce the simulation results was developed in order to predict the distributions of all kinds of heavy ions over a wide energy range. The incorporation of this function into the Particle and Heavy Ion Transport code System (PHITS) enables us to calculate the specific energy distributions in complex radiation fields in a short computational time.

Computer modeling describes gravity-related adaptation in cell cultures.

PubMed

Alexandrov, Ludmil B; Alexandrova, Stoyana; Usheva, Anny

2009-12-16

Questions about the changes of biological systems in response to hostile environmental factors are important but not easy to answer. Often, the traditional description with differential equations is difficult due to the overwhelming complexity of the living systems. Another way to describe complex systems is by simulating them with phenomenological models such as the well-known evolutionary agent-based model (EABM). Here we developed an EABM to simulate cell colonies as a multi-agent system that adapts to hyper-gravity in starvation conditions. In the model, the cell's heritable characteristics are generated and transferred randomly to offspring cells. After a qualitative validation of the model at normal gravity, we simulate cellular growth in hyper-gravity conditions. The obtained data are consistent with previously confirmed theoretical and experimental findings for bacterial behavior in environmental changes, including the experimental data from the microgravity Atlantis and the Hypergravity 3000 experiments. Our results demonstrate that it is possible to utilize an EABM with realistic qualitative description to examine the effects of hypergravity and starvation on complex cellular entities.

Molecular dynamics simulation of interactions between a sodium dodecyl sulfate micelle and a poly(ethylene oxide) polymer.

PubMed

Shang, Barry Z; Wang, Zuowei; Larson, Ronald G

2008-03-13

We have performed atomistic molecular dynamics simulations of an anionic sodium dodecyl sulfate (SDS) micelle and a nonionic poly(ethylene oxide) (PEO) polymer in aqueous solution. The micelle consisted of 60 surfactant molecules, and the polymer chain lengths varied from 20 to 40 monomers. The force field parameters for PEO were adjusted by using 1,2-dimethoxymethane (DME) as a model compound and matching its hydration enthalpy and conformational behavior to experiment. Excellent agreement with previous experimental and simulation work was obtained through these modifications. The simulated scaling behavior of the PEO radius of gyration was also in close agreement with experimental results. The SDS-PEO simulations show that the polymer resides on the micelle surface and at the hydrocarbon-water interface, leading to a selective reduction in the hydrophobic contribution to the solvent-accessible surface area of the micelle. The association is mainly driven by hydrophobic interactions between the polymer and surfactant tails, while the interaction between the polymer and sulfate headgroups on the micelle surface is weak. The 40-monomer chain is mostly wrapped around the micelle, and nearly 90% of the monomers are adsorbed at low PEO concentration. Simulations were also performed with multiple 20-monomer chains, and gradual addition of polymer indicates that about 120 monomers are required to saturate the micelle surface. The stoichiometry of the resulting complex is in close agreement with experimental results, and the commonly accepted "beaded necklace" structure of the SDS-PEO complex is recovered by our simulations.

Nesting large-eddy simulations within mesoscale simulations for wind energy applications

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

Lundquist, J K; Mirocha, J D; Chow, F K

2008-09-08

With increasing demand for more accurate atmospheric simulations for wind turbine micrositing, for operational wind power forecasting, and for more reliable turbine design, simulations of atmospheric flow with resolution of tens of meters or higher are required. These time-dependent large-eddy simulations (LES), which resolve individual atmospheric eddies on length scales smaller than turbine blades and account for complex terrain, are possible with a range of commercial and open-source software, including the Weather Research and Forecasting (WRF) model. In addition to 'local' sources of turbulence within an LES domain, changing weather conditions outside the domain can also affect flow, suggesting thatmore » a mesoscale model provide boundary conditions to the large-eddy simulations. Nesting a large-eddy simulation within a mesoscale model requires nuanced representations of turbulence. Our group has improved the Weather and Research Forecasting model's (WRF) LES capability by implementing the Nonlinear Backscatter and Anisotropy (NBA) subfilter stress model following Kosovic (1997) and an explicit filtering and reconstruction technique to compute the Resolvable Subfilter-Scale (RSFS) stresses (following Chow et al, 2005). We have also implemented an immersed boundary method (IBM) in WRF to accommodate complex terrain. These new models improve WRF's LES capabilities over complex terrain and in stable atmospheric conditions. We demonstrate approaches to nesting LES within a mesoscale simulation for farms of wind turbines in hilly regions. Results are sensitive to the nesting method, indicating that care must be taken to provide appropriate boundary conditions, and to allow adequate spin-up of turbulence in the LES domain.« less

Software for Simulating a Complex Robot

NASA Technical Reports Server (NTRS)

Goza, S. Michael

2003-01-01

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

Simulating Vibrations in a Complex Loaded Structure

NASA Technical Reports Server (NTRS)

Cao, Tim T.

2005-01-01

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

Towards a supported common NEAMS software stack

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

Cormac Garvey

2012-04-01

The NEAMS IPSC's are developing multidimensional, multiphysics, multiscale simulation codes based on first principles that will be capable of predicting all aspects of current and future nuclear reactor systems. These new breeds of simulation codes will include rigorous verification, validation and uncertainty quantification checks to quantify the accuracy and quality of the simulation results. The resulting NEAMS IPSC simulation codes will be an invaluable tool in designing the next generation of Nuclear Reactors and also contribute to a more speedy process in the acquisition of licenses from the NRC for new Reactor designs. Due to the high resolution of themore » models, the complexity of the physics and the added computational resources to quantify the accuracy/quality of the results, the NEAMS IPSC codes will require large HPC resources to carry out the production simulation runs.« less

Modeling complex and multi-component food systems in molecular dynamics simulations on the example of chocolate conching.

PubMed

Greiner, Maximilian; Sonnleitner, Bettina; Mailänder, Markus; Briesen, Heiko

2014-02-01

Additional benefits of foods are an increasing factor in the consumer's purchase. To produce foods with the properties the consumer demands, understanding the micro- and nanostructure is becoming more important in food research today. We present molecular dynamics (MD) simulations as a tool to study complex and multi-component food systems on the example of chocolate conching. The process of conching is chosen because of the interesting challenges it provides: the components (fats, emulsifiers and carbohydrates) contain diverse functional groups, are naturally fluctuating in their chemical composition, and have a high number of internal degrees of freedom. Further, slow diffusion in the non-aqueous medium is expected. All of these challenges are typical to food systems in general. Simulation results show the suitability of present force fields to correctly model the liquid and crystal density of cocoa butter and sucrose, respectively. Amphiphilic properties of emulsifiers are observed by micelle formation in water. For non-aqueous media, pulling simulations reveal high energy barriers for motion in the viscous cocoa butter. The work for detachment of an emulsifier from the sucrose crystal is calculated and matched with detachment of the head and tail groups separately. Hydrogen bonding is shown to be the dominant interaction between the emulsifier and the crystal surface. Thus, MD simulations are suited to model the interaction between the emulsifier and sugar crystal interface in non-aqueous media, revealing detailed information about the structuring and interactions on a molecular level. With interaction parameters being available for a wide variety of chemical groups, MD simulations are a valuable tool to understand complex and multi-component food systems in general. MD simulations provide a substantial benefit to researchers to verify their hypothesis in dynamic simulations with an atomistic resolution. Rapid rise of computational resources successively increases the complexity and the size of the systems that can be studied.

Controls of multi-modal wave conditions in a complex coastal setting

USGS Publications Warehouse

Hegermiller, Christie; Rueda, Ana C.; Erikson, Li H.; Barnard, Patrick L.; Antolinez, J.A.A.; Mendez, Fernando J.

2017-01-01

Coastal hazards emerge from the combined effect of wave conditions and sea level anomalies associated with storms or low-frequency atmosphere-ocean oscillations. Rigorous characterization of wave climate is limited by the availability of spectral wave observations, the computational cost of dynamical simulations, and the ability to link wave-generating atmospheric patterns with coastal conditions. We present a hybrid statistical-dynamical approach to simulating nearshore wave climate in complex coastal settings, demonstrated in the Southern California Bight, where waves arriving from distant, disparate locations are refracted over complex bathymetry and shadowed by offshore islands. Contributions of wave families and large-scale atmospheric drivers to nearshore wave energy flux are analyzed. Results highlight the variability of influences controlling wave conditions along neighboring coastlines. The universal method demonstrated here can be applied to complex coastal settings worldwide, facilitating analysis of the effects of climate change on nearshore wave climate.

Controls of Multimodal Wave Conditions in a Complex Coastal Setting

NASA Astrophysics Data System (ADS)

Hegermiller, C. A.; Rueda, A.; Erikson, L. H.; Barnard, P. L.; Antolinez, J. A. A.; Mendez, F. J.

2017-12-01

Coastal hazards emerge from the combined effect of wave conditions and sea level anomalies associated with storms or low-frequency atmosphere-ocean oscillations. Rigorous characterization of wave climate is limited by the availability of spectral wave observations, the computational cost of dynamical simulations, and the ability to link wave-generating atmospheric patterns with coastal conditions. We present a hybrid statistical-dynamical approach to simulating nearshore wave climate in complex coastal settings, demonstrated in the Southern California Bight, where waves arriving from distant, disparate locations are refracted over complex bathymetry and shadowed by offshore islands. Contributions of wave families and large-scale atmospheric drivers to nearshore wave energy flux are analyzed. Results highlight the variability of influences controlling wave conditions along neighboring coastlines. The universal method demonstrated here can be applied to complex coastal settings worldwide, facilitating analysis of the effects of climate change on nearshore wave climate.

A New Low Complexity Angle of Arrival Algorithm for 1D and 2D Direction Estimation in MIMO Smart Antenna Systems

PubMed Central

Al-Sadoon, Mohammed A. G.; Zuid, Abdulkareim; Jones, Stephen M. R.; Noras, James M.

2017-01-01

This paper proposes a new low complexity angle of arrival (AOA) method for signal direction estimation in multi-element smart wireless communication systems. The new method estimates the AOAs of the received signals directly from the received signals with significantly reduced complexity since it does not need to construct the correlation matrix, invert the matrix or apply eigen-decomposition, which are computationally expensive. A mathematical model of the proposed method is illustrated and then verified using extensive computer simulations. Both linear and circular sensors arrays are studied using various numerical examples. The method is systematically compared with other common and recently introduced AOA methods over a wide range of scenarios. The simulated results show that the new method has several advantages in terms of reduced complexity and improved accuracy under the assumptions of correlated signals and limited numbers of snapshots. PMID:29140313

A New Low Complexity Angle of Arrival Algorithm for 1D and 2D Direction Estimation in MIMO Smart Antenna Systems.

PubMed

Al-Sadoon, Mohammed A G; Ali, Nazar T; Dama, Yousf; Zuid, Abdulkareim; Jones, Stephen M R; Abd-Alhameed, Raed A; Noras, James M

2017-11-15

This paper proposes a new low complexity angle of arrival (AOA) method for signal direction estimation in multi-element smart wireless communication systems. The new method estimates the AOAs of the received signals directly from the received signals with significantly reduced complexity since it does not need to construct the correlation matrix, invert the matrix or apply eigen-decomposition, which are computationally expensive. A mathematical model of the proposed method is illustrated and then verified using extensive computer simulations. Both linear and circular sensors arrays are studied using various numerical examples. The method is systematically compared with other common and recently introduced AOA methods over a wide range of scenarios. The simulated results show that the new method has several advantages in terms of reduced complexity and improved accuracy under the assumptions of correlated signals and limited numbers of snapshots.

Validation of a Monte Carlo model used for simulating tube current modulation in computed tomography over a wide range of phantom conditions/challenges

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

Bostani, Maryam, E-mail: mbostani@mednet.ucla.edu; McMillan, Kyle; Cagnon, Chris H.

2014-11-01

Purpose: Monte Carlo (MC) simulation methods have been widely used in patient dosimetry in computed tomography (CT), including estimating patient organ doses. However, most simulation methods have undergone a limited set of validations, often using homogeneous phantoms with simple geometries. As clinical scanning has become more complex and the use of tube current modulation (TCM) has become pervasive in the clinic, MC simulations should include these techniques in their methodologies and therefore should also be validated using a variety of phantoms with different shapes and material compositions to result in a variety of differently modulated tube current profiles. The purposemore » of this work is to perform the measurements and simulations to validate a Monte Carlo model under a variety of test conditions where fixed tube current (FTC) and TCM were used. Methods: A previously developed MC model for estimating dose from CT scans that models TCM, built using the platform of MCNPX, was used for CT dose quantification. In order to validate the suitability of this model to accurately simulate patient dose from FTC and TCM CT scan, measurements and simulations were compared over a wide range of conditions. Phantoms used for testing range from simple geometries with homogeneous composition (16 and 32 cm computed tomography dose index phantoms) to more complex phantoms including a rectangular homogeneous water equivalent phantom, an elliptical shaped phantom with three sections (where each section was a homogeneous, but different material), and a heterogeneous, complex geometry anthropomorphic phantom. Each phantom requires varying levels of x-, y- and z-modulation. Each phantom was scanned on a multidetector row CT (Sensation 64) scanner under the conditions of both FTC and TCM. Dose measurements were made at various surface and depth positions within each phantom. Simulations using each phantom were performed for FTC, detailed x–y–z TCM, and z-axis-only TCM to obtain dose estimates. This allowed direct comparisons between measured and simulated dose values under each condition of phantom, location, and scan to be made. Results: For FTC scans, the percent root mean square (RMS) difference between measurements and simulations was within 5% across all phantoms. For TCM scans, the percent RMS of the difference between measured and simulated values when using detailed TCM and z-axis-only TCM simulations was 4.5% and 13.2%, respectively. For the anthropomorphic phantom, the difference between TCM measurements and detailed TCM and z-axis-only TCM simulations was 1.2% and 8.9%, respectively. For FTC measurements and simulations, the percent RMS of the difference was 5.0%. Conclusions: This work demonstrated that the Monte Carlo model developed provided good agreement between measured and simulated values under both simple and complex geometries including an anthropomorphic phantom. This work also showed the increased dose differences for z-axis-only TCM simulations, where considerable modulation in the x–y plane was present due to the shape of the rectangular water phantom. Results from this investigation highlight details that need to be included in Monte Carlo simulations of TCM CT scans in order to yield accurate, clinically viable assessments of patient dosimetry.« less

Modeling complexity in engineered infrastructure system: Water distribution network as an example

NASA Astrophysics Data System (ADS)

Zeng, Fang; Li, Xiang; Li, Ke

2017-02-01

The complex topology and adaptive behavior of infrastructure systems are driven by both self-organization of the demand and rigid engineering solutions. Therefore, engineering complex systems requires a method balancing holism and reductionism. To model the growth of water distribution networks, a complex network model was developed following the combination of local optimization rules and engineering considerations. The demand node generation is dynamic and follows the scaling law of urban growth. The proposed model can generate a water distribution network (WDN) similar to reported real-world WDNs on some structural properties. Comparison with different modeling approaches indicates that a realistic demand node distribution and co-evolvement of demand node and network are important for the simulation of real complex networks. The simulation results indicate that the efficiency of water distribution networks is exponentially affected by the urban growth pattern. On the contrary, the improvement of efficiency by engineering optimization is limited and relatively insignificant. The redundancy and robustness, on another aspect, can be significantly improved through engineering methods.

Application of two hydrologic models with different runoff mechanisms to a hillslope dominated watershed in the northeastern US: A comparison of HSPF and SMR

USGS Publications Warehouse

Johnson, M.S.; Coon, W.F.; Mehta, V.K.; Steenhuis, T.S.; Brooks, E.S.; Boll, J.

2003-01-01

Differences in the simulation of hydrologic processes by watershed models directly affect the accuracy of results. Surface runoff generation can be simulated as either: (1) infiltration-excess (or Hortonian) overland flow, or (2) saturation-excess overland flow. This study compared the Hydrological Simulation Program - FORTRAN (HSPF) and the Soil Moisture Routing (SMR) models, each representing one of these mechanisms. These two models were applied to a 102 km2 watershed in the upper part of the Irondequoit Creek basin in central New York State over a seven-year simulation period. The models differed in both the complexity of simulating snowmelt and baseflow processes as well as the detail in which the geographic information was preserved by each model. Despite their differences in structure and representation of hydrologic processes, the two models simulated streamflow with almost equal accuracy. Since streamflow is an integral response and depends mainly on the watershed water balance, this was not unexpected. Model efficiency values for the seven-year simulation period were 0.67 and 0.65 for SMR and HSPF, respectively. HSPF simulated winter streamflow slightly better than SMR as a result of its complex snowmelt routine, whereas SMR simulated summer flows better than HSPF as a result of its runoff and baseflow processes. An important difference between model results was the ability to predict the spatial distribution of soil moisture content. HSPF aggregates soil moisture content, which is generally related to a specific pervious land unit across the entire watershed, whereas SMR predictions of moisture content distribution are geographically specific and matched field observations reasonably well. Important is that the saturated area was predicted well by SMR and confirmed the validity of using saturation-excess mechanisms for this hillslope dominated watershed. ?? 2003 Elsevier B.V. All rights reserved.

Separator Reconnection at Earth's Dayside Magnetopause and the Tail: MMS Observations Compared to Global 3D Simulations

NASA Astrophysics Data System (ADS)

Buzulukova, N.; Dorelli, J.; Glocer, A.

2017-12-01

We present the results of global high resolution resistive magnetohydrodynamics (MHD BATS-R-US) simulations of Earth's magnetosphere. We extract location of magnetic separators with RECONX tool and compare the results with observations from the Magnetospheric Multiscale (MMS). A few cases are analysed including a southward IMF magnetopause crossing during October 16, 2015 that was previously identified as an electron diffusion region (EDR) event. The simulation predicts a complex time-dependent magnetic topology consisting of multiple separators and flux ropes. Despite the topological complexity, the predicted distance between MMS and the primary separator is less than 0.5 Earth radii. The simulation shows that the existence of IMF Bx results in a duskward shift of the location of the topological separator. The results are explained by a combined effect of solar wind draping and pile-up effect that modify the current density across the magnetopause and affect the location of the separator. The RECONX tool also is used to extract the separator location in the geomagnetic tail, and relate transient tail structures (bursty bulk flows) to the location of separator. These results suggest that global magnetic topology, rather than local magnetic geometry alone, determines the location of the separator reconnection both at the dayside magnetopause and in the tail. We show that the resistive MHD model helps to understand the global context of local MMS observations.

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

PubMed

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

1997-09-02

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

Grand canonical ensemble Monte Carlo simulation of the dCpG/proflavine crystal hydrate.

PubMed

Resat, H; Mezei, M

1996-09-01

The grand canonical ensemble Monte Carlo molecular simulation method is used to investigate hydration patterns in the crystal hydrate structure of the dCpG/proflavine intercalated complex. The objective of this study is to show by example that the recently advocated grand canonical ensemble simulation is a computationally efficient method for determining the positions of the hydrating water molecules in protein and nucleic acid structures. A detailed molecular simulation convergence analysis and an analogous comparison of the theoretical results with experiments clearly show that the grand ensemble simulations can be far more advantageous than the comparable canonical ensemble simulations.

Complex Langevin simulation of QCD at finite density and low temperature using the deformation technique

NASA Astrophysics Data System (ADS)

Nagata, Keitro; Nishimura, Jun; Shimasaki, Shinji

2018-03-01

We study QCD at finite density and low temperature by using the complex Langevin method. We employ the gauge cooling to control the unitarity norm and intro-duce a deformation parameter in the Dirac operator to avoid the singular-drift problem. The reliability of the obtained results are judged by the probability distribution of the magnitude of the drift term. By making extrapolations with respect to the deformation parameter using only the reliable results, we obtain results for the original system. We perform simulations on a 43 × 8 lattice and show that our method works well even in the region where the reweighing method fails due to the severe sign problem. As a result we observe a delayed onset of the baryon number density as compared with the phase-quenched model, which is a clear sign of the Silver Blaze phenomenon.

Mouse Acetylcholinesterase Unliganded and in Complex with Huperzine A: A Comparison of Molecular Dynamics Simulations

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

Tara, Sylvia; Straatsma, TP; Mccammon, Andy

1999-06-01

A 1 ns molecular dynamics simulation of unliganded mouse acetylcholinesterase (AChE) is compared to a previous simulation of mouse AChE complexed with Huperzine A (HupA). Several common features are observed. In both simulations, the active site gorge fluctuates in size during the 1 ns trajectory, and is completely pinched off several times. Many of the residues in the gorge that formed hydrogen bonds with HupA in the simulation of the complex, now form hydrogen bonds with other protein residues and water molecules in the gorge. The opening of a "backdoor" entrance to the active site that was found in themore » simulation of the complex is also observed in the unliganded simulation. Differences between the two simulations include overall lower structural RMS deviations for residues in the gorge in the unliganded simulation, a smaller diameter of the gorge in the absence of HupA, and the disappearance of a side channel that was frequently present in the liganded simulation. The differences between the two simulations can be attributed, in part, to the interaction of AChE with HupA.« less

The terminal area simulation system. Volume 2: Verification cases

NASA Technical Reports Server (NTRS)

Proctor, F. H.

1987-01-01

The numerical simulation of five case studies are presented and are compared with available data in order to verify the three-dimensional version of the Terminal Area Simulation System (TASS). A spectrum of convective storm types are selected for the case studies. Included are: a High-Plains supercell hailstorm, a small and relatively short-lived High-Plains cumulonimbus, a convective storm which produced the 2 August 1985 DFW microburst, a South Florida convective complex, and a tornadic Oklahoma thunderstorm. For each of the cases the model results compared reasonably well with observed data. In the simulations of the supercell storms many of their characteristic features were modeled, such as the hook echo, BWER, mesocyclone, gust fronts, giant persistent updraft, wall cloud, flanking-line towers, anvil and radar reflectivity overhang, and rightward veering in the storm propagation. In the simulation of the tornadic storm a horseshoe-shaped updraft configuration and cyclic changes in storm intensity and structure were noted. The simulation of the DFW microburst agreed remarkably well with sparse observed data. The simulated outflow rapidly expanded in a nearly symmetrical pattern and was associated with a ringvortex. A South Florida convective complex was simulated and contained updrafts and downdrafts in the form of discrete bubbles. The numerical simulations, in all cases, always remained stable and bounded with no anomalous trends.

Code Samples Used for Complexity and Control

NASA Astrophysics Data System (ADS)

Ivancevic, Vladimir G.; Reid, Darryn J.

2015-11-01

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

Box Model of a Series of Salt Ponds, as Applied to the Alviso Salt Pond Complex, South San Francisco Bay, California

USGS Publications Warehouse

Lionberger, Megan A.; Schoellhamer, David H.; Shellenbarger, Gregory; Orlando, James L.; Ganju, Neil K.

2007-01-01

This report documents the development and application of a box model to simulate water level, salinity, and temperature of the Alviso Salt Pond Complex in South San Francisco Bay. These ponds were purchased for restoration in 2003 and currently are managed by the U.S. Fish and Wildlife Service to maintain existing wildlife habitat and prevent a build up of salt during the development of a long-term restoration plan. The model was developed for the purpose of aiding pond managers during the current interim management period to achieve these goals. A previously developed box model of a salt pond, SPOOM, which calculates daily pond volume and salinity, was reconfigured to simulate multiple connected ponds and a temperature subroutine was added. The updated model simulates rainfall, evaporation, water flowing between the ponds and the adjacent tidal slough network, and water flowing from one pond to the next by gravity and pumps. Theoretical and measured relations between discharge and corresponding differences in water level are used to simulate most flows between ponds and between ponds and sloughs. The principle of conservation of mass is used to calculate daily pond volume and salinity. The model configuration includes management actions specified in the Interim Stewardship Plan for the ponds. The temperature subroutine calculates hourly net heat transfer to or from a pond resulting in a rise or drop in pond temperature and daily average, minimum, and maximum pond temperatures are recorded. Simulated temperature was compared with hourly measured data from pond 3 of the Napa?Sonoma Salt Pond Complex and monthly measured data from pond A14 of the Alviso Salt-Pond Complex. Comparison showed good agreement of measured and simulated pond temperature on the daily and monthly time scales.

Combining a reactive potential with a harmonic approximation for molecular dynamics simulation of failure: construction of a reduced potential

NASA Astrophysics Data System (ADS)

Tejada, I. G.; Brochard, L.; Stoltz, G.; Legoll, F.; Lelièvre, T.; Cancès, E.

2015-01-01

Molecular dynamics is a simulation technique that can be used to study failure in solids, provided the inter-atomic potential energy is able to account for the complex mechanisms at failure. Reactive potentials fitted on ab initio results or on experimental values have the ability to adapt to any complex atomic arrangement and, therefore, are suited to simulate failure. But the complexity of these potentials, together with the size of the systems considered, make simulations computationally expensive. In order to improve the efficiency of numerical simulations, simpler harmonic potentials can be used instead of complex reactive potentials in the regions where the system is close to its ground state and a harmonic approximation reasonably fits the actual reactive potential. However the validity and precision of such an approach has not been investigated in detail yet. We present here a methodology for constructing a reduced potential and combining it with the reactive one. We also report some important features of crack propagation that may be affected by the coupling of reactive and reduced potentials. As an illustrative case, we model a crystalline two-dimensional material (graphene) with a reactive empirical bond-order potential (REBO) or with harmonic potentials made of bond and angle springs that are designed to reproduce the second order approximation of REBO in the ground state. We analyze the consistency of this approximation by comparing the mechanical behavior and the phonon spectra of systems modeled with these potentials. These tests reveal when the anharmonicity effects appear. As anharmonic effects originate from strain, stress or temperature, the latter quantities are the basis for establishing coupling criteria for on the fly substitution in large simulations.

Rule-based spatial modeling with diffusing, geometrically constrained molecules

PubMed Central

2010-01-01

Background We suggest a new type of modeling approach for the coarse grained, particle-based spatial simulation of combinatorially complex chemical reaction systems. In our approach molecules possess a location in the reactor as well as an orientation and geometry, while the reactions are carried out according to a list of implicitly specified reaction rules. Because the reaction rules can contain patterns for molecules, a combinatorially complex or even infinitely sized reaction network can be defined. For our implementation (based on LAMMPS), we have chosen an already existing formalism (BioNetGen) for the implicit specification of the reaction network. This compatibility allows to import existing models easily, i.e., only additional geometry data files have to be provided. Results Our simulations show that the obtained dynamics can be fundamentally different from those simulations that use classical reaction-diffusion approaches like Partial Differential Equations or Gillespie-type spatial stochastic simulation. We show, for example, that the combination of combinatorial complexity and geometric effects leads to the emergence of complex self-assemblies and transportation phenomena happening faster than diffusion (using a model of molecular walkers on microtubules). When the mentioned classical simulation approaches are applied, these aspects of modeled systems cannot be observed without very special treatment. Further more, we show that the geometric information can even change the organizational structure of the reaction system. That is, a set of chemical species that can in principle form a stationary state in a Differential Equation formalism, is potentially unstable when geometry is considered, and vice versa. Conclusions We conclude that our approach provides a new general framework filling a gap in between approaches with no or rigid spatial representation like Partial Differential Equations and specialized coarse-grained spatial simulation systems like those for DNA or virus capsid self-assembly. PMID:20529264

Modeling and simulating networks of interdependent protein interactions.

PubMed

Stöcker, Bianca K; Köster, Johannes; Zamir, Eli; Rahmann, Sven

2018-05-21

Protein interactions are fundamental building blocks of biochemical reaction systems underlying cellular functions. The complexity and functionality of these systems emerge not only from the protein interactions themselves but also from the dependencies between these interactions, as generated by allosteric effects or mutual exclusion due to steric hindrance. Therefore, formal models for integrating and utilizing information about interaction dependencies are of high interest. Here, we describe an approach for endowing protein networks with interaction dependencies using propositional logic, thereby obtaining constrained protein interaction networks ("constrained networks"). The construction of these networks is based on public interaction databases as well as text-mined information about interaction dependencies. We present an efficient data structure and algorithm to simulate protein complex formation in constrained networks. The efficiency of the model allows fast simulation and facilitates the analysis of many proteins in large networks. In addition, this approach enables the simulation of perturbation effects, such as knockout of single or multiple proteins and changes of protein concentrations. We illustrate how our model can be used to analyze a constrained human adhesome protein network, which is responsible for the formation of diverse and dynamic cell-matrix adhesion sites. By comparing protein complex formation under known interaction dependencies versus without dependencies, we investigate how these dependencies shape the resulting repertoire of protein complexes. Furthermore, our model enables investigating how the interplay of network topology with interaction dependencies influences the propagation of perturbation effects across a large biochemical system. Our simulation software CPINSim (for Constrained Protein Interaction Network Simulator) is available under the MIT license at http://github.com/BiancaStoecker/cpinsim and as a Bioconda package (https://bioconda.github.io).

BeeSim: Leveraging Wearable Computers in Participatory Simulations with Young Children

ERIC Educational Resources Information Center

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

2010-01-01

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

Perrhenate complexation by uranyl in traditional solvents and in ionic liquids: a joint molecular dynamics/spectroscopic study.

PubMed

Chaumont, Alain; Klimchuk, Olga; Gaillard, Clotilde; Billard, Isabelle; Ouadi, Ali; Hennig, Christoph; Wipff, Georges

2012-03-15

The complexation of perrhenate (ReO(4)(-)) anions by the uranyl (UO(2)(2+)) cation has been investigated by joint molecular dynamics simulations and spectroscopic (UV-vis, TRLFS, and EXAFS) studies in aqueous solution, acetonitrile, and three ionic liquids (ILs), namely, [Bmi][Tf(2)N], [Me(3)BuN][Tf(2)N], and [Bu(3)MeN][Tf(2)N] that are based on the same Tf(2)N(-) anion (bis(trifluoromethylsulfonyl)imide) and either Bmi(+) (1-butyl,3-methylimidazolium), Me(3)BuN(+), or Bu(3)MeN(+) cations. They show that ReO(4)(-) behaves as a weak ligand in aqueous solution and as a strong ligand in acetonitrile and in the ILs. According to MD simulations in aqueous solution, the UO(2)(ReO(4))(2) complex quickly dissociates to form UO(2)(H(2)O)(5)(2+), while in acetonitrile, a stable UO(2)(ReO(4))(5)(3-) species forms from dissociated ions. In the ILs, the UO(2)(ReO(4))(n)(2-n) complexes (n = 1 to 5) remained stable along the dynamics, and to assess their relative stabilities, we computed the free energy profiles for stepwise ReO(4)(-) complexation to uranyl. In the two studied ILs, complexation is favored, leading to the UO(2)(ReO(4))(5)(3-) species in [Bmi][Tf(2)N] and to UO(2)(ReO(4))(4)(2-) in [Bu(3)MeN][Tf(2)N]. Furthermore, in both acetonitrile and [Bmi][Tf(2)N] solutions, MD and PMF simulations support the formation of dimeric uranyl complexes [UO(2)(ReO(4))(4)](2)(4-) with two bridging ReO(4)(-) ligands. The simulation results are qualitatively consistent with spectroscopic observations in the different solvents, without firmly concluding, however, on the precise composition and structure of the complexes in the solutions. © 2012 American Chemical Society

Software complex for geophysical data visualization

NASA Astrophysics Data System (ADS)

Kryukov, Ilya A.; Tyugin, Dmitry Y.; Kurkin, Andrey A.; Kurkina, Oxana E.

2013-04-01

The effectiveness of current research in geophysics is largely determined by the degree of implementation of the procedure of data processing and visualization with the use of modern information technology. Realistic and informative visualization of the results of three-dimensional modeling of geophysical processes contributes significantly into the naturalness of physical modeling and detailed view of the phenomena. The main difficulty in this case is to interpret the results of the calculations: it is necessary to be able to observe the various parameters of the three-dimensional models, build sections on different planes to evaluate certain characteristics and make a rapid assessment. Programs for interpretation and visualization of simulations are spread all over the world, for example, software systems such as ParaView, Golden Software Surfer, Voxler, Flow Vision and others. However, it is not always possible to solve the problem of visualization with the help of a single software package. Preprocessing, data transfer between the packages and setting up a uniform visualization style can turn into a long and routine work. In addition to this, sometimes special display modes for specific data are required and existing products tend to have more common features and are not always fully applicable to certain special cases. Rendering of dynamic data may require scripting languages that does not relieve the user from writing code. Therefore, the task was to develop a new and original software complex for the visualization of simulation results. Let us briefly list of the primary features that are developed. Software complex is a graphical application with a convenient and simple user interface that displays the results of the simulation. Complex is also able to interactively manage the image, resize the image without loss of quality, apply a two-dimensional and three-dimensional regular grid, set the coordinate axes with data labels and perform slice of data. The feature of geophysical data is their size. Detailed maps used in the simulations are large, thus rendering in real time can be difficult task even for powerful modern computers. Therefore, the performance of the software complex is an important aspect of this work. Complex is based on the latest version of graphic API: Microsoft - DirectX 11, which reduces overhead and harness the power of modern hardware. Each geophysical calculation is the adjustment of the mathematical model for a particular case, so the architecture of the complex visualization is created with the scalability and the ability to customize visualization objects, for better visibility and comfort. In the present study, software complex 'GeoVisual' was developed. One of the main features of this research is the use of bleeding-edge techniques of computer graphics in scientific visualization. The research was supported by The Ministry of education and science of Russian Federation, project 14.B37.21.0642.

Accurate Behavioral Simulator of All-Digital Time-Domain Smart Temperature Sensors by Using SIMULINK

PubMed Central

Chen, Chun-Chi; Chen, Chao-Lieh; Lin, You-Ting

2016-01-01

This study proposes a new behavioral simulator that uses SIMULINK for all-digital CMOS time-domain smart temperature sensors (TDSTSs) for performing rapid and accurate simulations. Inverter-based TDSTSs offer the benefits of low cost and simple structure for temperature-to-digital conversion and have been developed. Typically, electronic design automation tools, such as HSPICE, are used to simulate TDSTSs for performance evaluations. However, such tools require extremely long simulation time and complex procedures to analyze the results and generate figures. In this paper, we organize simple but accurate equations into a temperature-dependent model (TDM) by which the TDSTSs evaluate temperature behavior. Furthermore, temperature-sensing models of a single CMOS NOT gate were devised using HSPICE simulations. Using the TDM and these temperature-sensing models, a novel simulator in SIMULINK environment was developed to substantially accelerate the simulation and simplify the evaluation procedures. Experiments demonstrated that the simulation results of the proposed simulator have favorable agreement with those obtained from HSPICE simulations, showing that the proposed simulator functions successfully. This is the first behavioral simulator addressing the rapid simulation of TDSTSs. PMID:27509507

Brainlab: A Python Toolkit to Aid in the Design, Simulation, and Analysis of Spiking Neural Networks with the NeoCortical Simulator.

PubMed

Drewes, Rich; Zou, Quan; Goodman, Philip H

2009-01-01

Neuroscience modeling experiments often involve multiple complex neural network and cell model variants, complex input stimuli and input protocols, followed by complex data analysis. Coordinating all this complexity becomes a central difficulty for the experimenter. The Python programming language, along with its extensive library packages, has emerged as a leading "glue" tool for managing all sorts of complex programmatic tasks. This paper describes a toolkit called Brainlab, written in Python, that leverages Python's strengths for the task of managing the general complexity of neuroscience modeling experiments. Brainlab was also designed to overcome the major difficulties of working with the NCS (NeoCortical Simulator) environment in particular. Brainlab is an integrated model-building, experimentation, and data analysis environment for the powerful parallel spiking neural network simulator system NCS.

Brainlab: A Python Toolkit to Aid in the Design, Simulation, and Analysis of Spiking Neural Networks with the NeoCortical Simulator

PubMed Central

Drewes, Rich; Zou, Quan; Goodman, Philip H.

2008-01-01

Neuroscience modeling experiments often involve multiple complex neural network and cell model variants, complex input stimuli and input protocols, followed by complex data analysis. Coordinating all this complexity becomes a central difficulty for the experimenter. The Python programming language, along with its extensive library packages, has emerged as a leading “glue” tool for managing all sorts of complex programmatic tasks. This paper describes a toolkit called Brainlab, written in Python, that leverages Python's strengths for the task of managing the general complexity of neuroscience modeling experiments. Brainlab was also designed to overcome the major difficulties of working with the NCS (NeoCortical Simulator) environment in particular. Brainlab is an integrated model-building, experimentation, and data analysis environment for the powerful parallel spiking neural network simulator system NCS. PMID:19506707

Heuristic Identification of Biological Architectures for Simulating Complex Hierarchical Genetic Interactions

PubMed Central

Moore, Jason H; Amos, Ryan; Kiralis, Jeff; Andrews, Peter C

2015-01-01

Simulation plays an essential role in the development of new computational and statistical methods for the genetic analysis of complex traits. Most simulations start with a statistical model using methods such as linear or logistic regression that specify the relationship between genotype and phenotype. This is appealing due to its simplicity and because these statistical methods are commonly used in genetic analysis. It is our working hypothesis that simulations need to move beyond simple statistical models to more realistically represent the biological complexity of genetic architecture. The goal of the present study was to develop a prototype genotype–phenotype simulation method and software that are capable of simulating complex genetic effects within the context of a hierarchical biology-based framework. Specifically, our goal is to simulate multilocus epistasis or gene–gene interaction where the genetic variants are organized within the framework of one or more genes, their regulatory regions and other regulatory loci. We introduce here the Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions (HIBACHI) method and prototype software for simulating data in this manner. This approach combines a biological hierarchy, a flexible mathematical framework, a liability threshold model for defining disease endpoints, and a heuristic search strategy for identifying high-order epistatic models of disease susceptibility. We provide several simulation examples using genetic models exhibiting independent main effects and three-way epistatic effects. PMID:25395175

Tomographic reconstruction of melanin structures of optical coherence tomography via the finite-difference time-domain simulation

NASA Astrophysics Data System (ADS)

Huang, Shi-Hao; Wang, Shiang-Jiu; Tseng, Snow H.

2015-03-01

Optical coherence tomography (OCT) provides high resolution, cross-sectional image of internal microstructure of biological tissue. We use the Finite-Difference Time-Domain method (FDTD) to analyze the data acquired by OCT, which can help us reconstruct the refractive index of the biological tissue. We calculate the refractive index tomography and try to match the simulation with the data acquired by OCT. Specifically, we try to reconstruct the structure of melanin, which has complex refractive indices and is the key component of human pigment system. The results indicate that better reconstruction can be achieved for homogenous sample, whereas the reconstruction is degraded for samples with fine structure or with complex interface. Simulation reconstruction shows structures of the Melanin that may be useful for biomedical optics applications.

Comparison of sub-scaled to full-scaled aircrafts in simulation environment for air traffic management

NASA Astrophysics Data System (ADS)

Elbakary, Mohamed I.; Iftekharuddin, Khan M.; Papelis, Yiannis; Newman, Brett

2017-05-01

Air Traffic Management (ATM) concepts are commonly tested in simulation to obtain preliminary results and validate the concepts before adoption. Recently, the researchers found that simulation is not enough because of complexity associated with ATM concepts. In other words, full-scale tests must eventually take place to provide compelling performance evidence before adopting full implementation. Testing using full-scale aircraft produces a high-cost approach that yields high-confidence results but simulation provides a low-risk/low-cost approach with reduced confidence on the results. One possible approach to increase the confidence of the results and simultaneously reduce the risk and the cost is using unmanned sub-scale aircraft in testing new concepts for ATM. This paper presents the simulation results of using unmanned sub-scale aircraft in implementing ATM concepts compared to the full scale aircraft. The results of simulation show that the performance of sub-scale is quite comparable to that of the full-scale which validates use of the sub-scale in testing new ATM concepts. Keywords: Unmanned

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

ERIC Educational Resources Information Center

Klopfer, Eric; Yoon, Susan; Perry, Judy

2005-01-01

This paper reports on teachers' perceptions of the educational affordances of a handheld application called Participatory Simulations. It presents evidence from five cases representing each of the populations who work with these computational tools. Evidence across multiple data sources yield similar results to previous research evaluations of…

Annual Research Briefs

NASA Technical Reports Server (NTRS)

Spinks, Debra (Compiler)

1997-01-01

This report contains the 1997 annual progress reports of the research fellows and students supported by the Center for Turbulence Research (CTR). Titles include: Invariant modeling in large-eddy simulation of turbulence; Validation of large-eddy simulation in a plain asymmetric diffuser; Progress in large-eddy simulation of trailing-edge turbulence and aeronautics; Resolution requirements in large-eddy simulations of shear flows; A general theory of discrete filtering for LES in complex geometry; On the use of discrete filters for large eddy simulation; Wall models in large eddy simulation of separated flow; Perspectives for ensemble average LES; Anisotropic grid-based formulas for subgrid-scale models; Some modeling requirements for wall models in large eddy simulation; Numerical simulation of 3D turbulent boundary layers using the V2F model; Accurate modeling of impinging jet heat transfer; Application of turbulence models to high-lift airfoils; Advances in structure-based turbulence modeling; Incorporating realistic chemistry into direct numerical simulations of turbulent non-premixed combustion; Effects of small-scale structure on turbulent mixing; Turbulent premixed combustion in the laminar flamelet and the thin reaction zone regime; Large eddy simulation of combustion instabilities in turbulent premixed burners; On the generation of vorticity at a free-surface; Active control of turbulent channel flow; A generalized framework for robust control in fluid mechanics; Combined immersed-boundary/B-spline methods for simulations of flow in complex geometries; and DNS of shock boundary-layer interaction - preliminary results for compression ramp flow.

A finite element model of rigid body structures actuated by dielectric elastomer actuators

NASA Astrophysics Data System (ADS)

Simone, F.; Linnebach, P.; Rizzello, G.; Seelecke, S.

2018-06-01

This paper presents on finite element (FE) modeling and simulation of dielectric elastomer actuators (DEAs) coupled with articulated structures. DEAs have proven to represent an effective transduction technology for the realization of large deformation, low-power consuming, and fast mechatronic actuators. However, the complex dynamic behavior of the material, characterized by nonlinearities and rate-dependent phenomena, makes it difficult to accurately model and design DEA systems. The problem is further complicated in case the DEA is used to activate articulated structures, which increase both system complexity and implementation effort of numerical simulation models. In this paper, we present a model based tool which allows to effectively implement and simulate complex articulated systems actuated by DEAs. A first prototype of a compact switch actuated by DEA membranes is chosen as reference study to introduce the methodology. The commercially available FE software COMSOL is used for implementing and coupling a physics-based dynamic model of the DEA with the external structure, i.e., the switch. The model is then experimentally calibrated and validated in both quasi-static and dynamic loading conditions. Finally, preliminary results on how to use the simulation tool to optimize the design are presented.

A novel medical image data-based multi-physics simulation platform for computational life sciences.

PubMed

Neufeld, Esra; Szczerba, Dominik; Chavannes, Nicolas; Kuster, Niels

2013-04-06

Simulating and modelling complex biological systems in computational life sciences requires specialized software tools that can perform medical image data-based modelling, jointly visualize the data and computational results, and handle large, complex, realistic and often noisy anatomical models. The required novel solvers must provide the power to model the physics, biology and physiology of living tissue within the full complexity of the human anatomy (e.g. neuronal activity, perfusion and ultrasound propagation). A multi-physics simulation platform satisfying these requirements has been developed for applications including device development and optimization, safety assessment, basic research, and treatment planning. This simulation platform consists of detailed, parametrized anatomical models, a segmentation and meshing tool, a wide range of solvers and optimizers, a framework for the rapid development of specialized and parallelized finite element method solvers, a visualization toolkit-based visualization engine, a Python scripting interface for customized applications, a coupling framework, and more. Core components are cross-platform compatible and use open formats. Several examples of applications are presented: hyperthermia cancer treatment planning, tumour growth modelling, evaluating the magneto-haemodynamic effect as a biomarker and physics-based morphing of anatomical models.

Association of the anti-tuberculosis drug rifampicin with a PAMAM dendrimer.

PubMed

Bellini, Reinaldo G; Guimarães, Ana P; Pacheco, Marco A C; Dias, Douglas M; Furtado, Vanessa R; de Alencastro, Ricardo B; Horta, Bruno A C

2015-07-01

The association of the anti-tuberculosis drug rifampicin (RIF) with a 4th-generation poly(amidoamine) (G4-PAMAM) dendrimer was investigated by means of molecular dynamics simulations. The RIF load capacity was estimated to be around 20 RIF per G4-PAMAM at neutral pH. The complex formed by 20 RIF molecules and the dendrimer (RIF20-PAMAM) was subjected to 100 ns molecular dynamics (MD) simulations at two different pH conditions (neutral and acidic). The complex was found to be significantly more stable in the simulation at neutral pH compared to the simulation at low pH in which the RIF molecules were rapidly and almost simultaneously expelled to the solvent bulk. The high stability of the RIF-PAMAM complex under physiological pH and the rapid release of RIF molecules under acidic medium provide an interesting switch for drug targeting since the Mycobacterium resides within acidic domains of the macrophage. Altogether, these results suggest that, at least in terms of stability and pH-dependent release, PAMAM-like dendrimers may be considered suitable drug delivery systems for RIF and derivatives. Copyright © 2015 Elsevier Inc. All rights reserved.

Equilibrium sampling by reweighting nonequilibrium simulation trajectories

NASA Astrophysics Data System (ADS)

Yang, Cheng; Wan, Biao; Xu, Shun; Wang, Yanting; Zhou, Xin

2016-03-01

Based on equilibrium molecular simulations, it is usually difficult to efficiently visit the whole conformational space of complex systems, which are separated into some metastable regions by high free energy barriers. Nonequilibrium simulations could enhance transitions among these metastable regions and then be applied to sample equilibrium distributions in complex systems, since the associated nonequilibrium effects can be removed by employing the Jarzynski equality (JE). Here we present such a systematical method, named reweighted nonequilibrium ensemble dynamics (RNED), to efficiently sample equilibrium conformations. The RNED is a combination of the JE and our previous reweighted ensemble dynamics (RED) method. The original JE reproduces equilibrium from lots of nonequilibrium trajectories but requires that the initial distribution of these trajectories is equilibrium. The RED reweights many equilibrium trajectories from an arbitrary initial distribution to get the equilibrium distribution, whereas the RNED has both advantages of the two methods, reproducing equilibrium from lots of nonequilibrium simulation trajectories with an arbitrary initial conformational distribution. We illustrated the application of the RNED in a toy model and in a Lennard-Jones fluid to detect its liquid-solid phase coexistence. The results indicate that the RNED sufficiently extends the application of both the original JE and the RED in equilibrium sampling of complex systems.

Equilibrium sampling by reweighting nonequilibrium simulation trajectories.

PubMed

Yang, Cheng; Wan, Biao; Xu, Shun; Wang, Yanting; Zhou, Xin

2016-03-01

Based on equilibrium molecular simulations, it is usually difficult to efficiently visit the whole conformational space of complex systems, which are separated into some metastable regions by high free energy barriers. Nonequilibrium simulations could enhance transitions among these metastable regions and then be applied to sample equilibrium distributions in complex systems, since the associated nonequilibrium effects can be removed by employing the Jarzynski equality (JE). Here we present such a systematical method, named reweighted nonequilibrium ensemble dynamics (RNED), to efficiently sample equilibrium conformations. The RNED is a combination of the JE and our previous reweighted ensemble dynamics (RED) method. The original JE reproduces equilibrium from lots of nonequilibrium trajectories but requires that the initial distribution of these trajectories is equilibrium. The RED reweights many equilibrium trajectories from an arbitrary initial distribution to get the equilibrium distribution, whereas the RNED has both advantages of the two methods, reproducing equilibrium from lots of nonequilibrium simulation trajectories with an arbitrary initial conformational distribution. We illustrated the application of the RNED in a toy model and in a Lennard-Jones fluid to detect its liquid-solid phase coexistence. The results indicate that the RNED sufficiently extends the application of both the original JE and the RED in equilibrium sampling of complex systems.

The Formation of Glycine in Hot Cores: New Gas-grain Chemical Simulations of Star-forming Regions

NASA Astrophysics Data System (ADS)

Garrod, Robin

2012-07-01

Organic molecules of increasing complexity have been detected in the warm envelopes of star-forming cores, commonly referred to as "hot cores". Spectroscopic searches at mm/sub-mm wavelengths have uncovered both amines and carboxylic acids in these regions, as well as a range of other compounds including alcohols, ethers, esters, and nitriles. However, the simplest amino acid, glycine (NH2CH2COOH), has not yet been reliably detected in the ISM. There has been much interest in this molecule, due to its importance to the formation of proteins, and to life, while the positive identification of interstellar molecules of similar or greater complexity suggests that its existence in star-forming regions is plausible. I will present the results of recent models of hot-core chemistry that simulate the formation of both simple and complex molecules on the surfaces or within the ice mantles of dust grains. I will also present results from the first gas-grain astrochemical model to approach the question of amino-acid formation in hot cores. The formation of glycine in moderate abundance is found to be as efficient as that for similarly complex species, while its sublimation from the grains occurs at somewhat higher temperatures. However, simulated emission spectra based on the model results show that the degree of compactness of high-abundance regions, and the density and temperature profiles of the cores may be the key variables affecting the future detection of glycine, as well as other amino acids, and may explain its non-detection to date.

Numerical Investigations of Interactions between the Knee-Thigh-Hip Complex with Vehicle Interior Structures.

PubMed

Kim, Yong Sun; Choi, Hyeong Ho; Cho, Young Nam; Park, Yong Jae; Lee, Jong B; Yang, King H; King, Albert I

2005-11-01

Although biomechanical studies on the knee-thigh-hip (KTH) complex have been extensive, interactions between the KTH and various vehicular interior design parameters in frontal automotive crashes for newer models have not been reported in the open literature to the best of our knowledge. A 3D finite element (FE) model of a 50(th) percentile male KTH complex, which includes explicit representations of the iliac wing, acetabulum, pubic rami, sacrum, articular cartilage, femoral head, femoral neck, femoral condyles, patella, and patella tendon, has been developed to simulate injuries such as fracture of the patella, femoral neck, acetabulum, and pubic rami of the KTH complex. Model results compared favorably against regional component test data including a three-point bending test of the femur, axial loading of the isolated knee-patella, axial loading of the KTH complex, axial loading of the femoral head, and lateral loading of the isolated pelvis. The model was further integrated into a Wayne State University upper torso model and validated against data obtained from whole body sled tests. The model was validated against these experimental data over a range of impact speeds, impactor masses and boundary conditions. Using Design Of Experiment (DOE) methods based on Taguchi's approach and the developed FE model of the whole body, including the KTH complex, eight vehicular interior design parameters, namely the load limiter force, seat belt elongation, pretensioner inlet amount, knee-knee bolster distance, knee bolster angle, knee bolster stiffness, toe board angle and impact speed, each with either two or three design levels, were simulated to predict their respective effects on the potential of KTH injury in frontal impacts. Simulation results proposed best design levels for vehicular interior design parameters to reduce the injury potential of the KTH complex due to frontal automotive crashes. This study is limited by the fact that prediction of bony fracture was based on an element elimination method available in the LS-DYNA code. No validation study was conducted to determine if this method is suitable when simulating fractures of biological tissues. More work is still needed to further validate the FE model of the KTH complex to increase its reliability in the assessment of various impact loading conditions associated with vehicular crash scenarios.

Experimental Validation of Various Temperature Modells for Semi-Physical Tyre Model Approaches

NASA Astrophysics Data System (ADS)

Hackl, Andreas; Scherndl, Christoph; Hirschberg, Wolfgang; Lex, Cornelia

2017-10-01

With increasing level of complexity and automation in the area of automotive engineering, the simulation of safety relevant Advanced Driver Assistance Systems (ADAS) leads to increasing accuracy demands in the description of tyre contact forces. In recent years, with improvement in tyre simulation, the needs for coping with tyre temperatures and the resulting changes in tyre characteristics are rising significantly. Therefore, experimental validation of three different temperature model approaches is carried out, discussed and compared in the scope of this article. To investigate or rather evaluate the range of application of the presented approaches in combination with respect of further implementation in semi-physical tyre models, the main focus lies on the a physical parameterisation. Aside from good modelling accuracy, focus is held on computational time and complexity of the parameterisation process. To evaluate this process and discuss the results, measurements from a Hoosier racing tyre 6.0 / 18.0 10 LCO C2000 from an industrial flat test bench are used. Finally the simulation results are compared with the measurement data.

High-order numerical simulations of pulsatile flow in a curved artery model

NASA Astrophysics Data System (ADS)

Cox, Christopher; Liang, Chunlei; Plesniak, Michael W.

2016-11-01

Cardiovascular flows are pulsatile, incompressible and occur in complex geometries with compliant walls. Together, these factors can produce an environment that can affect the progression of cardiovascular disease by altering wall shear stresses. Unstructured high-order CFD methods are well suited for capturing unsteady vortex-dominated viscous flows, and these methods provide high accuracy for similar cost as low-order methods. We use an in-house three-dimensional flux reconstruction Navier-Stokes solver to simulate secondary flows and vortical structures within a rigid 180-degree curved artery model under pulsatile flow of a Newtonian blood-analog fluid. Our simulations use a physiological flowrate waveform taken from the carotid artery. We are particularly interested in the dynamics during the deceleration phase of the waveform, where we observe the deformed-Dean, Dean, Lyne and Wall vortices. Our numerical results reveal the complex nature of these vortices both in space and time and their effect on overall wall shear stress. Numerical results agree with and complement experimental results obtained in our laboratory using particle image velocimetry. Supported by the GW Center for Biomimetics and Bioinspired Engineering.

Amanzi: An Open-Source Multi-process Simulator for Environmental Applications

NASA Astrophysics Data System (ADS)

Moulton, J. D.; Molins, S.; Johnson, J. N.; Coon, E.; Lipnikov, K.; Day, M.; Barker, E.

2014-12-01

The Advanced Simulation Capabililty for Environmental Management (ASCEM) program is developing an approach and open-source tool suite for standardized risk and performance assessments at legacy nuclear waste sites. These assessments begin with simplified models, and add geometric and geologic complexity as understanding is gained. The Platform toolsets (Akuna) generates these conceptual models and Amanzi provides the computational engine to perform the simulations, returning the results for analysis and visualization. In this presentation we highlight key elements of the design, algorithms and implementations used in Amanzi. In particular, the hierarchical and modular design is aligned with the coupled processes being sumulated, and naturally supports a wide range of model complexity. This design leverages a dynamic data manager and the synergy of two graphs (one from the high-level perspective of the models the other from the dependencies of the variables in the model) to enable this flexible model configuration at run time. Moreover, to model sites with complex hydrostratigraphy, as well as engineered systems, we are developing a dual unstructured/structured capability. Recently, these capabilities have been collected in a framework named Arcos, and efforts have begun to improve interoperability between the unstructured and structured AMR approaches in Amanzi. To leverage a range of biogeochemistry capability from the community (e.g., CrunchFlow, PFLOTRAN, etc.), a biogeochemistry interface library was developed called Alquimia. To ensure that Amanzi is truly an open-source community code we require a completely open-source tool chain for our development. We will comment on elements of this tool chain, including the testing and documentation development tools such as docutils, and Sphinx. Finally, we will show simulation results from our phased demonstrations, including the geochemically complex Savannah River F-Area seepage basins.

Evolutionary Agent-Based Simulation of the Introduction of New Technologies in Air Traffic Management

NASA Technical Reports Server (NTRS)

Yliniemi, Logan; Agogino, Adrian K.; Tumer, Kagan

2014-01-01

Accurate simulation of the effects of integrating new technologies into a complex system is critical to the modernization of our antiquated air traffic system, where there exist many layers of interacting procedures, controls, and automation all designed to cooperate with human operators. Additions of even simple new technologies may result in unexpected emergent behavior due to complex human/ machine interactions. One approach is to create high-fidelity human models coming from the field of human factors that can simulate a rich set of behaviors. However, such models are difficult to produce, especially to show unexpected emergent behavior coming from many human operators interacting simultaneously within a complex system. Instead of engineering complex human models, we directly model the emergent behavior by evolving goal directed agents, representing human users. Using evolution we can predict how the agent representing the human user reacts given his/her goals. In this paradigm, each autonomous agent in a system pursues individual goals, and the behavior of the system emerges from the interactions, foreseen or unforeseen, between the agents/actors. We show that this method reflects the integration of new technologies in a historical case, and apply the same methodology for a possible future technology.

Chaos on the conveyor belt.

PubMed

Sándor, Bulcsú; Járai-Szabó, Ferenc; Tél, Tamás; Néda, Zoltán

2013-04-01

The dynamics of a spring-block train placed on a moving conveyor belt is investigated both by simple experiments and computer simulations. The first block is connected by a spring to an external static point and, due to the dragging effect of the belt, the blocks undergo complex stick-slip dynamics. A qualitative agreement with the experimental results can be achieved only by taking into account the spatial inhomogeneity of the friction force on the belt's surface, modeled as noise. As a function of the velocity of the conveyor belt and the noise strength, the system exhibits complex, self-organized critical, sometimes chaotic, dynamics and phase transition-like behavior. Noise-induced chaos and intermittency is also observed. Simulations suggest that the maximum complexity of the dynamical states is achieved for a relatively small number of blocks (around five).

Simulating the dynamics of complex plasmas.

PubMed

Schwabe, M; Graves, D B

2013-08-01

Complex plasmas are low-temperature plasmas that contain micrometer-size particles in addition to the neutral gas particles and the ions and electrons that make up the plasma. The microparticles interact strongly and display a wealth of collective effects. Here we report on linked numerical simulations that reproduce many of the experimental results of complex plasmas. We model a capacitively coupled plasma with a fluid code written for the commercial package comsol. The output of this model is used to calculate forces on microparticles. The microparticles are modeled using the molecular dynamics package lammps, which we extended to include the forces from the plasma. Using this method, we are able to reproduce void formation, the separation of particles of different sizes into layers, lane formation, vortex formation, and other effects.

Complexity, accuracy and practical applicability of different biogeochemical model versions

NASA Astrophysics Data System (ADS)

Los, F. J.; Blaas, M.

2010-04-01

The construction of validated biogeochemical model applications as prognostic tools for the marine environment involves a large number of choices particularly with respect to the level of details of the .physical, chemical and biological aspects. Generally speaking, enhanced complexity might enhance veracity, accuracy and credibility. However, very complex models are not necessarily effective or efficient forecast tools. In this paper, models of varying degrees of complexity are evaluated with respect to their forecast skills. In total 11 biogeochemical model variants have been considered based on four different horizontal grids. The applications vary in spatial resolution, in vertical resolution (2DH versus 3D), in nature of transport, in turbidity and in the number of phytoplankton species. Included models range from 15 year old applications with relatively simple physics up to present state of the art 3D models. With all applications the same year, 2003, has been simulated. During the model intercomparison it has been noticed that the 'OSPAR' Goodness of Fit cost function (Villars and de Vries, 1998) leads to insufficient discrimination of different models. This results in models obtaining similar scores although closer inspection of the results reveals large differences. In this paper therefore, we have adopted the target diagram by Jolliff et al. (2008) which provides a concise and more contrasting picture of model skill on the entire model domain and for the entire period of the simulations. Correctness in prediction of the mean and the variability are separated and thus enhance insight in model functioning. Using the target diagrams it is demonstrated that recent models are more consistent and have smaller biases. Graphical inspection of time series confirms this, as the level of variability appears more realistic, also given the multi-annual background statistics of the observations. Nevertheless, whether the improvements are all genuine for the particular year cannot be judged due to the low sampling frequency of the traditional monitoring data at hand. Specifically, the overall results for chlorophyll- a are rather consistent throughout all models, but regionally recent models are better; resolution is crucial for the accuracy of transport and more important than the nature of the forcing of the transport; SPM strongly affects the biomass simulation and species composition, but even the most recent SPM results do not yet obtain a good overall score; coloured dissolved organic matter (CDOM) should be included in the calculation of the light regime; more complexity in the phytoplankton model improves the chlorophyll- a simulation, but the simulated species composition needs further improvement for some of the functional groups.

Simulation and analysis of a model dinoflagellate predator-prey system

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Structural Mechanism behind Distinct Efficiency of Oct4/Sox2 Proteins in Differentially Spaced DNA Complexes

PubMed Central

Yesudhas, Dhanusha; Anwar, Muhammad Ayaz; Panneerselvam, Suresh; Durai, Prasannavenkatesh; Shah, Masaud; Choi, Sangdun

2016-01-01

The octamer-binding transcription factor 4 (Oct4) and sex-determining region Y (SRY)-box 2 (Sox2) proteins induce various transcriptional regulators to maintain cellular pluripotency. Most Oct4/Sox2 complexes have either 0 base pairs (Oct4/Sox20bp) or 3 base pairs (Oct4/Sox23bp) separation between their DNA-binding sites. Results from previous biochemical studies have shown that the complexes separated by 0 base pairs are associated with a higher pluripotency rate than those separated by 3 base pairs. Here, we performed molecular dynamics (MD) simulations and calculations to determine the binding free energy and per-residue free energy for the Oct4/Sox20bp and Oct4/Sox23bp complexes to identify structural differences that contribute to differences in induction rate. Our MD simulation results showed substantial differences in Oct4/Sox2 domain movements, as well as secondary-structure changes in the Oct4 linker region, suggesting a potential reason underlying the distinct efficiencies of these complexes during reprogramming. Moreover, we identified key residues and hydrogen bonds that potentially facilitate protein-protein and protein-DNA interactions, in agreement with previous experimental findings. Consequently, our results confess that differential spacing of the Oct4/Sox2 DNA binding sites can determine the magnitude of transcription of the targeted genes during reprogramming. PMID:26790000

Motion induced interplay effects for VMAT radiotherapy.

PubMed

Edvardsson, Anneli; Nordström, Fredrik; Ceberg, Crister; Ceberg, Sofie

2018-04-19

The purpose of this study was to develop a method to simulate breathing motion induced interplay effects for volumetric modulated arc therapy (VMAT), to verify the proposed method with measurements, and to use the method to investigate how interplay effects vary with different patient- and machine specific parameters. VMAT treatment plans were created on a virtual phantom in a treatment planning system (TPS). Interplay effects were simulated by dividing each plan into smaller sub-arcs using an in-house developed software and shifting the isocenter for each sub-arc to simulate a sin 6 breathing motion in the superior-inferior direction. The simulations were performed for both flattening-filter (FF) and flattening-filter free (FFF) plans and for different breathing amplitudes, period times, initial breathing phases, dose levels, plan complexities, CTV sizes, and collimator angles. The resulting sub-arcs were calculated in the TPS, generating a dose distribution including the effects of motion. The interplay effects were separated from dose blurring and the relative dose differences to 2% and 98% of the CTV volume (ΔD 98% and ΔD 2% ) were calculated. To verify the simulation method, measurements were carried out, both static and during motion, using a quasi-3D phantom and a motion platform. The results of the verification measurements during motion were comparable to the results of the static measurements. Considerable interplay effects were observed for individual fractions, with the minimum ΔD 98% and maximum ΔD 2% being  -16.7% and 16.2%, respectively. The extent of interplay effects was larger for FFF compared to FF and generally increased for higher breathing amplitudes, larger period times, lower dose levels, and more complex treatment plans. Also, the interplay effects varied considerably with the initial breathing phase, and larger variations were observed for smaller CTV sizes. In conclusion, a method to simulate motion induced interplay effects was developed and verified with measurements, which allowed for a large number of treatment scenarios to be investigated. The simulations showed large interplay effects for individual fractions and that the extent of interplay effects varied with the breathing pattern, FFF/FF, dose level, CTV size, collimator angle, and the complexity of the treatment plan.

Motion induced interplay effects for VMAT radiotherapy

NASA Astrophysics Data System (ADS)

Edvardsson, Anneli; Nordström, Fredrik; Ceberg, Crister; Ceberg, Sofie

2018-04-01

The purpose of this study was to develop a method to simulate breathing motion induced interplay effects for volumetric modulated arc therapy (VMAT), to verify the proposed method with measurements, and to use the method to investigate how interplay effects vary with different patient- and machine specific parameters. VMAT treatment plans were created on a virtual phantom in a treatment planning system (TPS). Interplay effects were simulated by dividing each plan into smaller sub-arcs using an in-house developed software and shifting the isocenter for each sub-arc to simulate a sin6 breathing motion in the superior–inferior direction. The simulations were performed for both flattening-filter (FF) and flattening-filter free (FFF) plans and for different breathing amplitudes, period times, initial breathing phases, dose levels, plan complexities, CTV sizes, and collimator angles. The resulting sub-arcs were calculated in the TPS, generating a dose distribution including the effects of motion. The interplay effects were separated from dose blurring and the relative dose differences to 2% and 98% of the CTV volume (ΔD98% and ΔD2%) were calculated. To verify the simulation method, measurements were carried out, both static and during motion, using a quasi-3D phantom and a motion platform. The results of the verification measurements during motion were comparable to the results of the static measurements. Considerable interplay effects were observed for individual fractions, with the minimum ΔD98% and maximum ΔD2% being  ‑16.7% and 16.2%, respectively. The extent of interplay effects was larger for FFF compared to FF and generally increased for higher breathing amplitudes, larger period times, lower dose levels, and more complex treatment plans. Also, the interplay effects varied considerably with the initial breathing phase, and larger variations were observed for smaller CTV sizes. In conclusion, a method to simulate motion induced interplay effects was developed and verified with measurements, which allowed for a large number of treatment scenarios to be investigated. The simulations showed large interplay effects for individual fractions and that the extent of interplay effects varied with the breathing pattern, FFF/FF, dose level, CTV size, collimator angle, and the complexity of the treatment plan.

[Benchmark experiment to verify radiation transport calculations for dosimetry in radiation therapy].

PubMed

Renner, Franziska

2016-09-01

Monte Carlo simulations are regarded as the most accurate method of solving complex problems in the field of dosimetry and radiation transport. In (external) radiation therapy they are increasingly used for the calculation of dose distributions during treatment planning. In comparison to other algorithms for the calculation of dose distributions, Monte Carlo methods have the capability of improving the accuracy of dose calculations - especially under complex circumstances (e.g. consideration of inhomogeneities). However, there is a lack of knowledge of how accurate the results of Monte Carlo calculations are on an absolute basis. A practical verification of the calculations can be performed by direct comparison with the results of a benchmark experiment. This work presents such a benchmark experiment and compares its results (with detailed consideration of measurement uncertainty) with the results of Monte Carlo calculations using the well-established Monte Carlo code EGSnrc. The experiment was designed to have parallels to external beam radiation therapy with respect to the type and energy of the radiation, the materials used and the kind of dose measurement. Because the properties of the beam have to be well known in order to compare the results of the experiment and the simulation on an absolute basis, the benchmark experiment was performed using the research electron accelerator of the Physikalisch-Technische Bundesanstalt (PTB), whose beam was accurately characterized in advance. The benchmark experiment and the corresponding Monte Carlo simulations were carried out for two different types of ionization chambers and the results were compared. Considering the uncertainty, which is about 0.7 % for the experimental values and about 1.0 % for the Monte Carlo simulation, the results of the simulation and the experiment coincide. Copyright © 2015. Published by Elsevier GmbH.

Learning to manage complexity through simulation: students' challenges and possible strategies.

PubMed

Gormley, Gerard J; Fenwick, Tara

2016-06-01

Many have called for medical students to learn how to manage complexity in healthcare. This study examines the nuances of students' challenges in coping with a complex simulation learning activity, using concepts from complexity theory, and suggests strategies to help them better understand and manage complexity.Wearing video glasses, participants took part in a simulation ward-based exercise that incorporated characteristics of complexity. Video footage was used to elicit interviews, which were transcribed. Using complexity theory as a theoretical lens, an iterative approach was taken to identify the challenges that participants faced and possible coping strategies using both interview transcripts and video footage.Students' challenges in coping with clinical complexity included being: a) unprepared for 'diving in', b) caught in an escalating system, c) captured by the patient, and d) unable to assert boundaries of acceptable practice.Many characteristics of complexity can be recreated in a ward-based simulation learning activity, affording learners an embodied and immersive experience of these complexity challenges. Possible strategies for managing complexity themes include: a) taking time to size up the system, b) attuning to what emerges, c) reducing complexity, d) boundary practices, and e) working with uncertainty. This study signals pedagogical opportunities for recognizing and dealing with complexity.

Recent developments and assessment of a three-dimensional PBL parameterization for improved wind forecasting over complex terrain

NASA Astrophysics Data System (ADS)

Kosovic, B.; Jimenez, P. A.; Haupt, S. E.; Martilli, A.; Olson, J.; Bao, J. W.

2017-12-01

At present, the planetary boundary layer (PBL) parameterizations available in most numerical weather prediction (NWP) models are one-dimensional. One-dimensional parameterizations are based on the assumption of horizontal homogeneity. This homogeneity assumption is appropriate for grid cell sizes greater than 10 km. However, for mesoscale simulations of flows in complex terrain with grid cell sizes below 1 km, the assumption of horizontal homogeneity is violated. Applying a one-dimensional PBL parameterization to high-resolution mesoscale simulations in complex terrain could result in significant error. For high-resolution mesoscale simulations of flows in complex terrain, we have therefore developed and implemented a three-dimensional (3D) PBL parameterization in the Weather Research and Forecasting (WRF) model. The implementation of the 3D PBL scheme is based on the developments outlined by Mellor and Yamada (1974, 1982). Our implementation in the Weather Research and Forecasting (WRF) model uses a pure algebraic model (level 2) to diagnose the turbulent fluxes. To evaluate the performance of the 3D PBL model, we use observations from the Wind Forecast Improvement Project 2 (WFIP2). The WFIP2 field study took place in the Columbia River Gorge area from 2015-2017. We focus on selected cases when physical phenomena of significance for wind energy applications such as mountain waves, topographic wakes, and gap flows were observed. Our assessment of the 3D PBL parameterization also considers a large-eddy simulation (LES). We carried out a nested LES with grid cell sizes of 30 m and 10 m covering a large fraction of the WFIP2 study area. Both LES domains were discretized using 6000 x 3000 x 200 grid cells in zonal, meridional, and vertical direction, respectively. The LES results are used to assess the relative magnitude of horizontal gradients of turbulent stresses and fluxes in comparison to vertical gradients. The presentation will highlight the advantages of the 3D PBL scheme in regions of complex terrain.

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

Lamichhane, N; Johnson, P; Chinea, F

Purpose: To evaluate the correlation between image features and the accuracy of manually drawn target contours on synthetic PET images Methods: A digital PET phantom was used in combination with Monte Carlo simulation to create a set of 26 simulated PET images featuring a variety of tumor shapes and activity heterogeneity. These tumor volumes were used as a gold standard in comparisons with manual contours delineated by 10 radiation oncologist on the simulated PET images. Metrics used to evaluate segmentation accuracy included the dice coefficient, false positive dice, false negative dice, symmetric mean absolute surface distance, and absolute volumetric difference.more » Image features extracted from the simulated tumors consisted of volume, shape complexity, mean curvature, and intensity contrast along with five texture features derived from the gray-level neighborhood difference matrices including contrast, coarseness, busyness, strength, and complexity. Correlation between these features and contouring accuracy were examined. Results: Contour accuracy was reasonably well correlated with a variety of image features. Dice coefficient ranged from 0.7 to 0.90 and was correlated closely with contrast (r=0.43, p=0.02) and complexity (r=0.5, p<0.001). False negative dice ranged from 0.10 to 0.50 and was correlated closely with contrast (r=0.68, p<0.001) and complexity (r=0.66, p<0.001). Absolute volumetric difference ranged from 0.0002 to 0.67 and was correlated closely with coarseness (r=0.46, p=0.02) and complexity (r=0.49, p=0.008). Symmetric mean absolute difference ranged from 0.02 to 1 and was correlated closely with mean curvature (r=0.57, p=0.02) and contrast (r=0.6, p=0.001). Conclusion: The long term goal of this study is to assess whether contouring variability can be reduced by providing feedback to the practitioner based on image feature analysis. The results are encouraging and will be used to develop a statistical model which will enable a prediction of contour accuracy based purely on image feature analysis.« less

Absolute binding free energy calculations of CBClip host–guest systems in the SAMPL5 blind challenge

PubMed Central

Tofoleanu, Florentina; Pickard, Frank C.; König, Gerhard; Huang, Jing; Damjanović, Ana; Baek, Minkyung; Seok, Chaok; Brooks, Bernard R.

2016-01-01

Herein, we report the absolute binding free energy calculations of CBClip complexes in the SAMPL5 blind challenge. Initial conformations of CBClip complexes were obtained using docking and molecular dynamics simulations. Free energy calculations were performed using thermodynamic integration (TI) with soft-core potentials and Bennett’s acceptance ratio (BAR) method based on a serial insertion scheme. We compared the results obtained with TI simulations with soft-core potentials and Hamiltonian replica exchange simulations with the serial insertion method combined with the BAR method. The results show that the difference between the two methods can be mainly attributed to the van der Waals free energies, suggesting that either the simulations used for TI or the simulations used for BAR, or both are not fully converged and the two sets of simulations may have sampled difference phase space regions. The penalty scores of force field parameters of the 10 guest molecules provided by CHARMM Generalized Force Field can be an indicator of the accuracy of binding free energy calculations. Among our submissions, the combination of docking and TI performed best, which yielded the root mean square deviation of 2.94 kcal/mol and an average unsigned error of 3.41 kcal/mol for the ten guest molecules. These values were best overall among all participants. However, our submissions had little correlation with experiments. PMID:27677749

Large eddy simulation for predicting turbulent heat transfer in gas turbines

PubMed Central

Tafti, Danesh K.; He, Long; Nagendra, K.

2014-01-01

Blade cooling technology will play a critical role in the next generation of propulsion and power generation gas turbines. Accurate prediction of blade metal temperature can avoid the use of excessive compressed bypass air and allow higher turbine inlet temperature, increasing fuel efficiency and decreasing emissions. Large eddy simulation (LES) has been established to predict heat transfer coefficients with good accuracy under various non-canonical flows, but is still limited to relatively simple geometries and low Reynolds numbers. It is envisioned that the projected increase in computational power combined with a drop in price-to-performance ratio will make system-level simulations using LES in complex blade geometries at engine conditions accessible to the design process in the coming one to two decades. In making this possible, two key challenges are addressed in this paper: working with complex intricate blade geometries and simulating high-Reynolds-number (Re) flows. It is proposed to use the immersed boundary method (IBM) combined with LES wall functions. A ribbed duct at Re=20 000 is simulated using the IBM, and a two-pass ribbed duct is simulated at Re=100 000 with and without rotation (rotation number Ro=0.2) using LES with wall functions. The results validate that the IBM is a viable alternative to body-conforming grids and that LES with wall functions reproduces experimental results at a much lower computational cost. PMID:25024418

Molecular investigation on the interaction of spermine with proteinase K by multispectroscopic techniques and molecular simulation studies.

PubMed

Hosseini-Koupaei, Mansoore; Shareghi, Behzad; Saboury, Ali Akbar; Davar, Fateme

2017-01-01

The alteration in structure, function and stability of proteinase K in the presence of spermine was investigated using spectroscopic methods and simulation techniques. The stability and enzyme activity of proteinase K-spermine complex were significantly enhanced as compared to that of the pure enzyme. The increase in the value of V max and the catalytic efficiency of Proteinase K in presence of spermine confirmed that the polyamine could bring the enzyme hyperactivation. UV-vis spectroscopy, intrinsic fluorescence and circular dichroism methods demonstrated that the binding of spermine changed the microenvironment and structure of proteinase K. The fluorescence studies, showing that spermine quenched the intensity of proteinase K with static mechanism. Thermodynamic parameters analysis suggested that hydrogen bond and van der Waals forces play a key role in complex stability which is in agreement with modeling studies. The CD spectra represented the secondary structure alteration of proteinase K with an increase in α-helicity and a decrease in β-sheet of proteinase K upon spermine conjugation. The molecular simulation results proposed that spermine could interact with proteinase K spontaneously at single binding site, which is in agreement with spectroscopic results. This agreement between experimental and theoretical results may be a worth method for protein-ligand complex studies. Copyright © 2016 Elsevier B.V. All rights reserved.

Direct simulations of chemically reacting turbulent mixing layers

NASA Technical Reports Server (NTRS)

Riley, J. J.; Metcalfe, R. W.

1984-01-01

The report presents the results of direct numerical simulations of chemically reacting turbulent mixing layers. The work consists of two parts: (1) the development and testing of a spectral numerical computer code that treats the diffusion reaction equations; and (2) the simulation of a series of cases of chemical reactions occurring on mixing layers. The reaction considered is a binary, irreversible reaction with no heat release. The reacting species are nonpremixed. The results of the numerical tests indicate that the high accuracy of the spectral methods observed for rigid body rotation are also obtained when diffusion, reaction, and more complex flows are considered. In the simulations, the effects of vortex rollup and smaller scale turbulence on the overall reaction rates are investigated. The simulation results are found to be in approximate agreement with similarity theory. Comparisons of simulation results with certain modeling hypotheses indicate limitations in these hypotheses. The nondimensional product thickness computed from the simulations is compared with laboratory values and is found to be in reasonable agreement, especially since there are no adjustable constants in the method.

Statistical Emulator for Expensive Classification Simulators

NASA Technical Reports Server (NTRS)

Ross, Jerret; Samareh, Jamshid A.

2016-01-01

Expensive simulators prevent any kind of meaningful analysis to be performed on the phenomena they model. To get around this problem the concept of using a statistical emulator as a surrogate representation of the simulator was introduced in the 1980's. Presently, simulators have become more and more complex and as a result running a single example on these simulators is very expensive and can take days to weeks or even months. Many new techniques have been introduced, termed criteria, which sequentially select the next best (most informative to the emulator) point that should be run on the simulator. These criteria methods allow for the creation of an emulator with only a small number of simulator runs. We follow and extend this framework to expensive classification simulators.

A Comparison of Adaptive and Nonadaptive Training Strategies in the Acquisition of a Physically Complex Psychomotor Skill.

ERIC Educational Resources Information Center

Riedel, James A.; And Others

Results of research to determine if an adaptive technique could be used to teach a physically complex psychomotor skill (specifically, performing on an arc welding simulator) more efficiently than the skill could be taught with a nonadaptive technique are presented. Sixty hull maintenance technician firemen and fireman apprentice trainees were…

Using cognitive architectures to study issues in team cognition in a complex task environment

NASA Astrophysics Data System (ADS)

Smart, Paul R.; Sycara, Katia; Tang, Yuqing

2014-05-01

Cognitive social simulation is a computer simulation technique that aims to improve our understanding of the dynamics of socially-situated and socially-distributed cognition. This makes cognitive social simulation techniques particularly appealing as a means to undertake experiments into team cognition. The current paper reports on the results of an ongoing effort to develop a cognitive social simulation capability that can be used to undertake studies into team cognition using the ACT-R cognitive architecture. This capability is intended to support simulation experiments using a team-based problem solving task, which has been used to explore the effect of different organizational environments on collective problem solving performance. The functionality of the ACT-R-based cognitive social simulation capability is presented and a number of areas of future development work are outlined. The paper also describes the motivation for adopting cognitive architectures in the context of social simulation experiments and presents a number of research areas where cognitive social simulation may be useful in developing a better understanding of the dynamics of team cognition. These include the use of cognitive social simulation to study the role of cognitive processes in determining aspects of communicative behavior, as well as the impact of communicative behavior on the shaping of task-relevant cognitive processes (e.g., the social shaping of individual and collective memory as a result of communicative exchanges). We suggest that the ability to perform cognitive social simulation experiments in these areas will help to elucidate some of the complex interactions that exist between cognitive, social, technological and informational factors in the context of team-based problem-solving activities.

An Approach to Experimental Design for the Computer Analysis of Complex Phenomenon

NASA Technical Reports Server (NTRS)

Rutherford, Brian

2000-01-01

The ability to make credible system assessments, predictions and design decisions related to engineered systems and other complex phenomenon is key to a successful program for many large-scale investigations in government and industry. Recently, many of these large-scale analyses have turned to computational simulation to provide much of the required information. Addressing specific goals in the computer analysis of these complex phenomenon is often accomplished through the use of performance measures that are based on system response models. The response models are constructed using computer-generated responses together with physical test results where possible. They are often based on probabilistically defined inputs and generally require estimation of a set of response modeling parameters. As a consequence, the performance measures are themselves distributed quantities reflecting these variabilities and uncertainties. Uncertainty in the values of the performance measures leads to uncertainties in predicted performance and can cloud the decisions required of the analysis. A specific goal of this research has been to develop methodology that will reduce this uncertainty in an analysis environment where limited resources and system complexity together restrict the number of simulations that can be performed. An approach has been developed that is based on evaluation of the potential information provided for each "intelligently selected" candidate set of computer runs. Each candidate is evaluated by partitioning the performance measure uncertainty into two components - one component that could be explained through the additional computational simulation runs and a second that would remain uncertain. The portion explained is estimated using a probabilistic evaluation of likely results for the additional computational analyses based on what is currently known about the system. The set of runs indicating the largest potential reduction in uncertainty is then selected and the computational simulations are performed. Examples are provided to demonstrate this approach on small scale problems. These examples give encouraging results. Directions for further research are indicated.

Complex Langevin simulation of a random matrix model at nonzero chemical potential

DOE PAGES

Bloch, Jacques; Glesaaen, Jonas; Verbaarschot, Jacobus J. M.; ...

2018-03-06

In this study we test the complex Langevin algorithm for numerical simulations of a random matrix model of QCD with a first order phase transition to a phase of finite baryon density. We observe that a naive implementation of the algorithm leads to phase quenched results, which were also derived analytically in this article. We test several fixes for the convergence issues of the algorithm, in particular the method of gauge cooling, the shifted representation, the deformation technique and reweighted complex Langevin, but only the latter method reproduces the correct analytical results in the region where the quark mass ismore » inside the domain of the eigenvalues. In order to shed more light on the issues of the methods we also apply them to a similar random matrix model with a milder sign problem and no phase transition, and in that case gauge cooling solves the convergence problems as was shown before in the literature.« less

Relationship between microscopic dynamics in traffic flow and complexity in networks.

PubMed

Li, Xin-Gang; Gao, Zi-You; Li, Ke-Ping; Zhao, Xiao-Mei

2007-07-01

Complex networks are constructed in the evolution process of traffic flow, and the states of traffic flow are represented by nodes in the network. The traffic dynamics can then be studied by investigating the statistical properties of those networks. According to Kerner's three-phase theory, there are two different phases in congested traffic, synchronized flow and wide moving jam. In the framework of this theory, we study different properties of synchronized flow and moving jam in relation to complex network. Scale-free network is constructed in stop-and-go traffic, i.e., a sequence of moving jams [Chin. Phys. Lett. 10, 2711 (2005)]. In this work, the networks generated in synchronized flow are investigated in detail. Simulation results show that the degree distribution of the networks constructed in synchronized flow has two power law regions, so the distinction in topological structure can really reflect the different dynamics in traffic flow. Furthermore, the real traffic data are investigated by this method, and the results are consistent with the simulations.

Complex Langevin simulation of a random matrix model at nonzero chemical potential

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

Bloch, Jacques; Glesaaen, Jonas; Verbaarschot, Jacobus J. M.

In this study we test the complex Langevin algorithm for numerical simulations of a random matrix model of QCD with a first order phase transition to a phase of finite baryon density. We observe that a naive implementation of the algorithm leads to phase quenched results, which were also derived analytically in this article. We test several fixes for the convergence issues of the algorithm, in particular the method of gauge cooling, the shifted representation, the deformation technique and reweighted complex Langevin, but only the latter method reproduces the correct analytical results in the region where the quark mass ismore » inside the domain of the eigenvalues. In order to shed more light on the issues of the methods we also apply them to a similar random matrix model with a milder sign problem and no phase transition, and in that case gauge cooling solves the convergence problems as was shown before in the literature.« less

Multi-model ensemble hydrological simulation using a BP Neural Network for the upper Yalongjiang River Basin, China

NASA Astrophysics Data System (ADS)

Li, Zhanjie; Yu, Jingshan; Xu, Xinyi; Sun, Wenchao; Pang, Bo; Yue, Jiajia

2018-06-01

Hydrological models are important and effective tools for detecting complex hydrological processes. Different models have different strengths when capturing the various aspects of hydrological processes. Relying on a single model usually leads to simulation uncertainties. Ensemble approaches, based on multi-model hydrological simulations, can improve application performance over single models. In this study, the upper Yalongjiang River Basin was selected for a case study. Three commonly used hydrological models (SWAT, VIC, and BTOPMC) were selected and used for independent simulations with the same input and initial values. Then, the BP neural network method was employed to combine the results from the three models. The results show that the accuracy of BP ensemble simulation is better than that of the single models.

A numerical simulation method and analysis of a complete thermoacoustic-Stirling engine.

PubMed

Ling, Hong; Luo, Ercang; Dai, Wei

2006-12-22

Thermoacoustic prime movers can generate pressure oscillation without any moving parts on self-excited thermoacoustic effect. The details of the numerical simulation methodology for thermoacoustic engines are presented in the paper. First, a four-port network method is used to build the transcendental equation of complex frequency as a criterion to judge if temperature distribution of the whole thermoacoustic system is correct for the case with given heating power. Then, the numerical simulation of a thermoacoustic-Stirling heat engine is carried out. It is proved that the numerical simulation code can run robustly and output what one is interested in. Finally, the calculated results are compared with the experiments of the thermoacoustic-Stirling heat engine (TASHE). It shows that the numerical simulation can agrees with the experimental results with acceptable accuracy.

Estimation of wear in total hip replacement using a ten station hip simulator.

PubMed

Brummitt, K; Hardaker, C S

1996-01-01

The results of hip simulator tests on a total of 16 total hip joints, all of them 22.25 mm Charnley designs, are presented. Wear at up to 6.75 million cycles was assessed by using a coordinate measuring machine. The results gave good agreement with clinical estimates of wear rate on the same design of joint replacement from a number of sources. Good agreement was also obtained when comparison was made with the published results from more sophisticated simulators. The major source of variation in the results was found to occur in the first million cycles where creep predominates. The results of this study support the use of this type of simplified simulator for estimating wear in a total hip prosthesis. The capability to test a significant number of joints simultaneously may make this mechanism preferable to more complex machines in many cases.

STEPS: Modeling and Simulating Complex Reaction-Diffusion Systems with Python

PubMed Central

Wils, Stefan; Schutter, Erik De

2008-01-01

We describe how the use of the Python language improved the user interface of the program STEPS. STEPS is a simulation platform for modeling and stochastic simulation of coupled reaction-diffusion systems with complex 3-dimensional boundary conditions. Setting up such models is a complicated process that consists of many phases. Initial versions of STEPS relied on a static input format that did not cleanly separate these phases, limiting modelers in how they could control the simulation and becoming increasingly complex as new features and new simulation algorithms were added. We solved all of these problems by tightly integrating STEPS with Python, using SWIG to expose our existing simulation code. PMID:19623245

Metabolic flexibility of mitochondrial respiratory chain disorders predicted by computer modelling.

PubMed

Zieliński, Łukasz P; Smith, Anthony C; Smith, Alexander G; Robinson, Alan J

2016-11-01

Mitochondrial respiratory chain dysfunction causes a variety of life-threatening diseases affecting about 1 in 4300 adults. These diseases are genetically heterogeneous, but have the same outcome; reduced activity of mitochondrial respiratory chain complexes causing decreased ATP production and potentially toxic accumulation of metabolites. Severity and tissue specificity of these effects varies between patients by unknown mechanisms and treatment options are limited. So far most research has focused on the complexes themselves, and the impact on overall cellular metabolism is largely unclear. To illustrate how computer modelling can be used to better understand the potential impact of these disorders and inspire new research directions and treatments, we simulated them using a computer model of human cardiomyocyte mitochondrial metabolism containing over 300 characterised reactions and transport steps with experimental parameters taken from the literature. Overall, simulations were consistent with patient symptoms, supporting their biological and medical significance. These simulations predicted: complex I deficiencies could be compensated using multiple pathways; complex II deficiencies had less metabolic flexibility due to impacting both the TCA cycle and the respiratory chain; and complex III and IV deficiencies caused greatest decreases in ATP production with metabolic consequences that parallel hypoxia. Our study demonstrates how results from computer models can be compared to a clinical phenotype and used as a tool for hypothesis generation for subsequent experimental testing. These simulations can enhance understanding of dysfunctional mitochondrial metabolism and suggest new avenues for research into treatment of mitochondrial disease and other areas of mitochondrial dysfunction. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Atomic Simulation of Complex DNA DSBs and the Interactions with the Ku70/80 Heterodimer

NASA Technical Reports Server (NTRS)

Hu, Shaowen; Cucinotta, Francis A.

2011-01-01

DNA double strand breaks (DSBs) induced by ionizing radiation (IR) usually contain modified bases such as 8-oxo-7,8-dihydroguanine (8-oxoG) and thymine glycol, apurinic/apyrimidinic (AP) sites, 2-deoxyribonolactone, or single-strand breaks (SSBs). The presence of such lesions in close proximity to the DSB terminus makes the DNA nicks more difficult to repair and rejoin than endogenously induced simple DSBs, and as such a major determinant of the biological effects of high linear energy transfer (LET) radiation as encountered in space travel. In this study we conducted molecular dynamics simulations on a series of DNA duplexes with various complex lesions of 8-oxoG and AP sites, in an effort to investigate the effects of such lesions to the structural integrity and stability of DNA after insulted by IR. We also simulated the interaction of such complex DSBs with the Ku70/80 heterodimer, the first protein in mammalian cells to embark the non-homologous end joining (NHEJ) DNA repair pathway. The results indicate, compared to DNA with simple DSBs, the complex lesions can enhance the hydrogen bonds opening rate at the DNA terminus, and increase the mobility of the whole duplex, thus they present more deleterious effects to the genome integrity if not captured and repaired promptly in cells. Simulations also demonstrate the binding of Ku drastically reduces structural disruption and flexibility caused by the complex lesions, and the interactions of Ku with complex DSBs have a different potential energy landscape from the bound structure with simple DSB. In all complex DSBs systems, the binding of DSB terminus with Ku70 is softened while the binding of the middle duplex with Ku80 is tightened. This energy shift may help the Ku protein to secure at the DSB terminus for a longer time, so that other end processing factors or repair pathways can proceed at the lesions before NHEJ repair process starts. These atomic simulations may provide valuable new insight into the selective action of repair proteins on damaged DNA.

Benchmarking Geant4 for simulating galactic cosmic ray interactions within planetary bodies

DOE PAGES

Mesick, K. E.; Feldman, W. C.; Coupland, D. D. S.; ...

2018-06-20

Galactic cosmic rays undergo complex nuclear interactions with nuclei within planetary bodies that have little to no atmosphere. Radiation transport simulations are a key tool used in understanding the neutron and gamma-ray albedo coming from these interactions and tracing these signals back to geochemical composition of the target. In this paper, we study the validity of the code Geant4 for simulating such interactions by comparing simulation results to data from the Apollo 17 Lunar Neutron Probe Experiment. Different assumptions regarding the physics are explored to demonstrate how these impact the Geant4 simulation results. In general, all of the Geant4 resultsmore » over-predict the data, however, certain physics lists perform better than others. Finally, in addition, we show that results from the radiation transport code MCNP6 are similar to those obtained using Geant4.« less

Benchmarking Geant4 for simulating galactic cosmic ray interactions within planetary bodies

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

Mesick, K. E.; Feldman, W. C.; Coupland, D. D. S.

Galactic cosmic rays undergo complex nuclear interactions with nuclei within planetary bodies that have little to no atmosphere. Radiation transport simulations are a key tool used in understanding the neutron and gamma-ray albedo coming from these interactions and tracing these signals back to geochemical composition of the target. In this paper, we study the validity of the code Geant4 for simulating such interactions by comparing simulation results to data from the Apollo 17 Lunar Neutron Probe Experiment. Different assumptions regarding the physics are explored to demonstrate how these impact the Geant4 simulation results. In general, all of the Geant4 resultsmore » over-predict the data, however, certain physics lists perform better than others. Finally, in addition, we show that results from the radiation transport code MCNP6 are similar to those obtained using Geant4.« less

Integrated Simulation Design Challenges to Support TPS Repair Operations

NASA Technical Reports Server (NTRS)

Quiocho, Leslie J.; Crues, Edwin Z.; Huynh, An; Nguyen, Hung T.; MacLean, John

2005-01-01

During the Orbiter Repair Maneuver (ORM) operations planned for Return to Flight (RTF), the Shuttle Remote Manipulator System (SRMS) must grapple the International Space Station (ISS), undock the Orbiter, maneuver it through a long duration trajectory, and orient it to an EVA crewman poised at the end of the Space Station Remote Manipulator System (SSRMS) to facilitate the repair of the Thermal Protection System (TPS). Once repair has been completed and confirmed, then the SRMS proceeds back through the trajectory to dock the Orbiter to the Orbiter Docking System. In order to support analysis of the complex dynamic interactions of the integrated system formed by the Orbiter, ISS, SRMS, and SSRMS during the ORM, simulation tools used for previous 'nominal' mission support required substantial enhancements. These upgrades were necessary to provide analysts with the capabilities needed to study integrated system performance. This paper discusses the simulation design challenges encountered while developing simulation capabilities to mirror the ORM operations. The paper also describes the incremental build approach that was utilized, starting with the subsystem simulation elements and integration into increasing more complex simulations until the resulting ORM worksite dynamics simulation had been assembled. Furthermore, the paper presents an overall integrated simulation V&V methodology based upon a subsystem level testing, integrated comparisons, and phased checkout.

Monte Carlo simulation of a simple gene network yields new evolutionary insights.

PubMed

Andrecut, M; Cloud, D; Kauffman, S A

2008-02-07

Monte Carlo simulations of a genetic toggle switch show that its behavior can be more complex than analytic models would suggest. We show here that as a result of the interplay between frequent and infrequent reaction events, such a switch can have more stable states than an analytic model would predict, and that the number and character of these states depend to a large extent on the propensity of transcription factors to bind to and dissociate from promoters. The effects of gene duplications differ even more; in analytic models, these seem to result in the disappearance of bi-stability and thus a loss of the switching function, but a Monte Carlo simulation shows that they can result in the appearance of new stable states without the loss of old ones, and thus in an increase of the complexity of the switch's behavior which may facilitate the evolution of new cellular functions. These differences are of interest with respect to the evolution of gene networks, particularly in clonal lines of cancer cells, where the duplication of active genes is an extremely common event, and often seems to result in the appearance of viable new cellular phenotypes.

Temperature-accelerated molecular dynamics gives insights into globular conformations sampled in the free state of the AC catalytic domain.

PubMed

Selwa, Edithe; Huynh, Tru; Ciccotti, Giovanni; Maragliano, Luca; Malliavin, Thérèse E

2014-10-01

The catalytic domain of the adenyl cyclase (AC) toxin from Bordetella pertussis is activated by interaction with calmodulin (CaM), resulting in cAMP overproduction in the infected cell. In the X-ray crystallographic structure of the complex between AC and the C terminal lobe of CaM, the toxin displays a markedly elongated shape. As for the structure of the isolated protein, experimental results support the hypothesis that more globular conformations are sampled, but information at atomic resolution is still lacking. Here, we use temperature-accelerated molecular dynamics (TAMD) simulations to generate putative all-atom models of globular conformations sampled by CaM-free AC. As collective variables, we use centers of mass coordinates of groups of residues selected from the analysis of standard molecular dynamics (MD) simulations. Results show that TAMD allows extended conformational sampling and generates AC conformations that are more globular than in the complexed state. These structures are then refined via energy minimization and further unrestrained MD simulations to optimize inter-domain packing interactions, thus resulting in the identification of a set of hydrogen bonds present in the globular conformations. © 2014 Wiley Periodicals, Inc.

A meta-model analysis of a finite element simulation for defining poroelastic properties of intervertebral discs.

PubMed

Nikkhoo, Mohammad; Hsu, Yu-Chun; Haghpanahi, Mohammad; Parnianpour, Mohamad; Wang, Jaw-Lin

2013-06-01

Finite element analysis is an effective tool to evaluate the material properties of living tissue. For an interactive optimization procedure, the finite element analysis usually needs many simulations to reach a reasonable solution. The meta-model analysis of finite element simulation can be used to reduce the computation of a structure with complex geometry or a material with composite constitutive equations. The intervertebral disc is a complex, heterogeneous, and hydrated porous structure. A poroelastic finite element model can be used to observe the fluid transferring, pressure deviation, and other properties within the disc. Defining reasonable poroelastic material properties of the anulus fibrosus and nucleus pulposus is critical for the quality of the simulation. We developed a material property updating protocol, which is basically a fitting algorithm consisted of finite element simulations and a quadratic response surface regression. This protocol was used to find the material properties, such as the hydraulic permeability, elastic modulus, and Poisson's ratio, of intact and degenerated porcine discs. The results showed that the in vitro disc experimental deformations were well fitted with limited finite element simulations and a quadratic response surface regression. The comparison of material properties of intact and degenerated discs showed that the hydraulic permeability significantly decreased but Poisson's ratio significantly increased for the degenerated discs. This study shows that the developed protocol is efficient and effective in defining material properties of a complex structure such as the intervertebral disc.

Molecular Dynamics Simulations of the Interfacial Region between Boehmite and Gibbsite Basal Surfaces and High Ionic Strength Aqueous Solutions

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

Shen, Zhizhang; Ilton, Eugene S.; Prange, Micah P.

Classical molecular dynamics (MD) simulations were used to study the interactions of up to 2 M NaCl and NaNO3 aqueous solutions with the presumed inert boehmite (010) and gibbsite (001) surfaces. The force field parameters used in these simulations were validated against density functional theory calculations of Na+ and Cl- hydrated complexes adsorbed at the boehmite (010) surface. In all the classical MD simulations and regardless of the ionic strength or the nature of the anion, Na+ ions were found to preferably form inner-sphere complexes over outer-sphere complexes at the aluminum (oxy)hydroxide surfaces, adsorbing closer to the surface than bothmore » water molecules and anions. In contrast, Cl- ions were distributed almost equally between inner- and outer-sphere positions. The resulting asymmetry in adsorption strengths offers molecular-scale evidence for the observed isoelectric point (IEP) shift to higher pH at high ionic strength for aluminum (oxy)hydroxides. As such, the MD simulations also provided clear evidence against the assumption that the basal surfaces of boehmite and gibbsite are inert to background electrolytes. Finally, the MD simulations indicated that, although the adsorption behavior of Na+ in NaNO3 and NaCl solutions was similar, the different affinities of NO3- and Cl- for the aluminum (oxy)hydroxide surfaces might have macroscopic consequences, such as difference in the sensitivity of the IEP to the electrolyte concentration.« less

Challenges in Integrating a Complex Systems Computer Simulation in Class: An Educational Design Research

ERIC Educational Resources Information Center

Loke, Swee-Kin; Al-Sallami, Hesham S.; Wright, Daniel F. B.; McDonald, Jenny; Jadhav, Sheetal; Duffull, Stephen B.

2012-01-01

Complex systems are typically difficult for students to understand and computer simulations offer a promising way forward. However, integrating such simulations into conventional classes presents numerous challenges. Framed within an educational design research, we studied the use of an in-house built simulation of the coagulation network in four…

A decision tree algorithm for investigation of model biases related to dynamical cores and physical parameterizations: CESM/CAM EVALUATION BY DECISION TREES

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

Soner Yorgun, M.; Rood, Richard B.

An object-based evaluation method using a pattern recognition algorithm (i.e., classification trees) is applied to the simulated orographic precipitation for idealized experimental setups using the National Center of Atmospheric Research (NCAR) Community Atmosphere Model (CAM) with the finite volume (FV) and the Eulerian spectral transform dynamical cores with varying resolutions. Daily simulations were analyzed and three different types of precipitation features were identified by the classification tree algorithm. The statistical characteristics of these features (i.e., maximum value, mean value, and variance) were calculated to quantify the difference between the dynamical cores and changing resolutions. Even with the simple and smoothmore » topography in the idealized setups, complexity in the precipitation fields simulated by the models develops quickly. The classification tree algorithm using objective thresholding successfully detected different types of precipitation features even as the complexity of the precipitation field increased. The results show that the complexity and the bias introduced in small-scale phenomena due to the spectral transform method of CAM Eulerian spectral dynamical core is prominent, and is an important reason for its dissimilarity from the FV dynamical core. The resolvable scales, both in horizontal and vertical dimensions, have significant effect on the simulation of precipitation. The results of this study also suggest that an efficient and informative study about the biases produced by GCMs should involve daily (or even hourly) output (rather than monthly mean) analysis over local scales.« less

A decision tree algorithm for investigation of model biases related to dynamical cores and physical parameterizations: CESM/CAM EVALUATION BY DECISION TREES

DOE PAGES

Soner Yorgun, M.; Rood, Richard B.

2016-11-11

An object-based evaluation method using a pattern recognition algorithm (i.e., classification trees) is applied to the simulated orographic precipitation for idealized experimental setups using the National Center of Atmospheric Research (NCAR) Community Atmosphere Model (CAM) with the finite volume (FV) and the Eulerian spectral transform dynamical cores with varying resolutions. Daily simulations were analyzed and three different types of precipitation features were identified by the classification tree algorithm. The statistical characteristics of these features (i.e., maximum value, mean value, and variance) were calculated to quantify the difference between the dynamical cores and changing resolutions. Even with the simple and smoothmore » topography in the idealized setups, complexity in the precipitation fields simulated by the models develops quickly. The classification tree algorithm using objective thresholding successfully detected different types of precipitation features even as the complexity of the precipitation field increased. The results show that the complexity and the bias introduced in small-scale phenomena due to the spectral transform method of CAM Eulerian spectral dynamical core is prominent, and is an important reason for its dissimilarity from the FV dynamical core. The resolvable scales, both in horizontal and vertical dimensions, have significant effect on the simulation of precipitation. The results of this study also suggest that an efficient and informative study about the biases produced by GCMs should involve daily (or even hourly) output (rather than monthly mean) analysis over local scales.« less

Channel Model Optimization with Reflection Residual Component for Indoor MIMO-VLC System

NASA Astrophysics Data System (ADS)

Chen, Yong; Li, Tengfei; Liu, Huanlin; Li, Yichao

2017-12-01

A fast channel modeling method is studied to solve the problem of reflection channel gain for multiple input multiple output-visible light communications (MIMO-VLC) in the paper. For reducing the computational complexity when associating with the reflection times, no more than 3 reflections are taken into consideration in VLC. We think that higher order reflection link consists of corresponding many times line of sight link and firstly present reflection residual component to characterize higher reflection (more than 2 reflections). We perform computer simulation results for point-to-point channel impulse response, receiving optical power and receiving signal to noise ratio. Based on theoretical analysis and simulation results, the proposed method can effectively reduce the computational complexity of higher order reflection in channel modeling.

Research on complex 3D tree modeling based on L-system

NASA Astrophysics Data System (ADS)

Gang, Chen; Bin, Chen; Yuming, Liu; Hui, Li

2018-03-01

L-system as a fractal iterative system could simulate complex geometric patterns. Based on the field observation data of trees and knowledge of forestry experts, this paper extracted modeling constraint rules and obtained an L-system rules set. Using the self-developed L-system modeling software the L-system rule set was parsed to generate complex tree 3d models.The results showed that the geometrical modeling method based on l-system could be used to describe the morphological structure of complex trees and generate 3D tree models.

Slip-flow in complex porous media as determined by a multi-relaxation-time lattice Boltzmann model

NASA Astrophysics Data System (ADS)

Landry, C. J.; Prodanovic, M.; Eichhubl, P.

2014-12-01

The pores and throats of shales and mudrocks are predominantly found within a range of 1-100 nm, within this size range the flow of gas at reservoir conditions will fall within the slip-flow and low transition-flow regime (0.001 < Kn < 0.5). Currently, the study of slip-flows is for the most part limited to simple tube and channel geometries, however, the geometry of mudrock pores is often sponge-like (organic matter) and/or platy (clays). Molecular dynamics (MD) simulations can be used to predict slip-flow in complex geometries, but due to prohibitive computational demand are generally limited to small volumes (one to several pores). Here we present a multi-relaxation-time lattice Boltzmann model (LBM) parameterized for slip-flow (Guo et al. 2008) and adapted here to complex geometries. LBMs are inherently parallelizable, such that flow in complex geometries of significant (near REV-scale) volumes can be readily simulated at a fraction of the computational cost of MD simulations. At the macroscopic-scale the LBM is parameterized with local effective viscosities at each node to capture the variance of the mean-free-path of gas molecules in a bounded system. The corrected mean-free-path for each lattice node is determined using the mean distance of the node to the pore-wall and Stop's correction for mean-free-paths in an infinite parallel-plate geometry. At the microscopic-scale, a combined bounce-back specular-reflection boundary condition is applied to the pore-wall nodes to capture Maxwellian-slip. The LBM simulation results are first validated in simple tube and channel geometries, where good agreement is found for Knudsen numbers below 0.1, and fair agreement is found for Knudsen numbers between 0.1 and 0.5. More complex geometries are then examined including triangular-ducts and ellipsoid-ducts, both with constant and tapering/expanding cross-sections, as well as a clay pore-network imaged from a hydrocarbon producing shale by sequential focused ion-beam scanning electron microscopy. These results are analyzed to determine grid-independent resolutions, and used to explore the relationship between effective permeability and Knudsen number in complex geometries.

Coupling of Large Eddy Simulations with Meteorological Models to simulate Methane Leaks from Natural Gas Storage Facilities

NASA Astrophysics Data System (ADS)

Prasad, K.

2017-12-01

Atmospheric transport is usually performed with weather models, e.g., the Weather Research and Forecasting (WRF) model that employs a parameterized turbulence model and does not resolve the fine scale dynamics generated by the flow around buildings and features comprising a large city. The NIST Fire Dynamics Simulator (FDS) is a computational fluid dynamics model that utilizes large eddy simulation methods to model flow around buildings at length scales much smaller than is practical with models like WRF. FDS has the potential to evaluate the impact of complex topography on near-field dispersion and mixing that is difficult to simulate with a mesoscale atmospheric model. A methodology has been developed to couple the FDS model with WRF mesoscale transport models. The coupling is based on nudging the FDS flow field towards that computed by WRF, and is currently limited to one way coupling performed in an off-line mode. This approach allows the FDS model to operate as a sub-grid scale model with in a WRF simulation. To test and validate the coupled FDS - WRF model, the methane leak from the Aliso Canyon underground storage facility was simulated. Large eddy simulations were performed over the complex topography of various natural gas storage facilities including Aliso Canyon, Honor Rancho and MacDonald Island at 10 m horizontal and vertical resolution. The goal of these simulations included improving and validating transport models as well as testing leak hypotheses. Forward simulation results were compared with aircraft and tower based in-situ measurements as well as methane plumes observed using the NASA Airborne Visible InfraRed Imaging Spectrometer (AVIRIS) and the next generation instrument AVIRIS-NG. Comparison of simulation results with measurement data demonstrate the capability of the coupled FDS-WRF models to accurately simulate the transport and dispersion of methane plumes over urban domains. Simulated integrated methane enhancements will be presented and compared with results obtained from spectrometer data to estimate the temporally evolving methane flux during the Aliso Canyon blowout.

Modeling Np and Pu transport with a surface complexation model and spatially variant sorption capacities: Implications for reactive transport modeling and performance assessments of nuclear waste disposal sites

USGS Publications Warehouse

Glynn, P.D.

2003-01-01

One-dimensional (1D) geochemical transport modeling is used to demonstrate the effects of speciation and sorption reactions on the ground-water transport of Np and Pu, two redox-sensitive elements. Earlier 1D simulations (Reardon, 1981) considered the kinetically limited dissolution of calcite and its effect on ion-exchange reactions (involving 90Sr, Ca, Na, Mg and K), and documented the spatial variation of a 90Sr partition coefficient under both transient and steady-state chemical conditions. In contrast, the simulations presented here assume local equilibrium for all reactions, and consider sorption on constant potential, rather than constant charge, surfaces. Reardon's (1981) seminal findings on the spatial and temporal variability of partitioning (of 90Sr) are reexamined and found partially caused by his assumption of a kinetically limited reaction. In the present work, sorption is assumed the predominant retardation process controlling Pu and Np transport, and is simulated using a diffuse-double-layer-surface-complexation (DDLSC) model. Transport simulations consider the infiltration of Np- and Pu-contaminated waters into an initially uncontaminated environment, followed by the cleanup of the resultant contamination with uncontaminated water. Simulations are conducted using different spatial distributions of sorption capacities (with the same total potential sorption capacity, but with different variances and spatial correlation structures). Results obtained differ markedly from those that would be obtained in transport simulations using constant Kd, Langmuir or Freundlich sorption models. When possible, simulation results (breakthrough curves) are fitted to a constant K d advection-dispersion transport model and compared. Functional differences often are great enough that they prevent a meaningful fit of the simulation results with a constant K d (or even a Langmuir or Freundlich) model, even in the case of Np, a weakly sorbed radionuclide under the simulation conditions. Functional behaviors that cannot be fit include concentration trend reversals and radionuclide desorption spikes. Other simulation results are fit successfully but the fitted parameters (Kd and dispersivity) vary significantly depending on simulation conditions (e.g. "infiltration" vs. "cleanup" conditions). Notably, an increase in the variance of the specified sorption capacities results in a marked increase in the dispersion of the radionuclides. The results presented have implications for the simulation of radionuclide migration in performance assessments of nuclear waste-disposal sites, for the future monitoring of those sites, and more generally for modeling contaminant transport in ground-water environments. ?? 2003 Published by Elsevier Science Ltd.

Can ligand addition to soil enhance Cd phytoextraction? A mechanistic model study.

PubMed

Lin, Zhongbing; Schneider, André; Nguyen, Christophe; Sterckeman, Thibault

2014-11-01

Phytoextraction is a potential method for cleaning Cd-polluted soils. Ligand addition to soil is expected to enhance Cd phytoextraction. However, experimental results show that this addition has contradictory effects on plant Cd uptake. A mechanistic model simulating the reaction kinetics (adsorption on solid phase, complexation in solution), transport (convection, diffusion) and root absorption (symplastic, apoplastic) of Cd and its complexes in soil was developed. This was used to calculate plant Cd uptake with and without ligand addition in a great number of combinations of soil, ligand and plant characteristics, varying the parameters within defined domains. Ligand addition generally strongly reduced hydrated Cd (Cd(2+)) concentration in soil solution through Cd complexation. Dissociation of Cd complex ([Formula: see text]) could not compensate for this reduction, which greatly lowered Cd(2+) symplastic uptake by roots. The apoplastic uptake of [Formula: see text] was not sufficient to compensate for the decrease in symplastic uptake. This explained why in the majority of the cases, ligand addition resulted in the reduction of the simulated Cd phytoextraction. A few results showed an enhanced phytoextraction in very particular conditions (strong plant transpiration with high apoplastic Cd uptake capacity), but this enhancement was very limited, making chelant-enhanced phytoextraction poorly efficient for Cd.

Molecular Dynamics Simulation of Telomere and TRF1

NASA Astrophysics Data System (ADS)

Kaburagi, Masaaki; Fukuda, Masaki; Yamada, Hironao; Miyakawa, Takeshi; Morikawa, Ryota; Takasu, Masako; Kato, Takamitsu A.; Uesaka, Mitsuru

Telomeres play a central role in determining longevity of a cell. Our study focuses on the interaction between telomeric guanines and TRF1 as a means to observe the telomeric based mechanism of the genome protection. In this research, we performed molecular dynamics simulations of a telomeric DNA and TRF1. Our results show a stable structure with a high affinity for the specific protein. Additionally, we calculated the distance between guanines and the protein in their complex state. From this comparison, we found the calculated values of distance to be very similar, and the angle of guanines in their complex states was larger than that in their single state.

Evaluation of assigned-value uncertainty for complex calibrator value assignment processes: a prealbumin example.

PubMed

Middleton, John; Vaks, Jeffrey E

2007-04-01

Errors of calibrator-assigned values lead to errors in the testing of patient samples. The ability to estimate the uncertainties of calibrator-assigned values and other variables minimizes errors in testing processes. International Organization of Standardization guidelines provide simple equations for the estimation of calibrator uncertainty with simple value-assignment processes, but other methods are needed to estimate uncertainty in complex processes. We estimated the assigned-value uncertainty with a Monte Carlo computer simulation of a complex value-assignment process, based on a formalized description of the process, with measurement parameters estimated experimentally. This method was applied to study uncertainty of a multilevel calibrator value assignment for a prealbumin immunoassay. The simulation results showed that the component of the uncertainty added by the process of value transfer from the reference material CRM470 to the calibrator is smaller than that of the reference material itself (<0.8% vs 3.7%). Varying the process parameters in the simulation model allowed for optimizing the process, while keeping the added uncertainty small. The patient result uncertainty caused by the calibrator uncertainty was also found to be small. This method of estimating uncertainty is a powerful tool that allows for estimation of calibrator uncertainty for optimization of various value assignment processes, with a reduced number of measurements and reagent costs, while satisfying the requirements to uncertainty. The new method expands and augments existing methods to allow estimation of uncertainty in complex processes.

Assessing problem-solving skills in construction education with the virtual construction simulator

NASA Astrophysics Data System (ADS)

Castronovo, Fadi

The ability to solve complex problems is an essential skill that a construction and project manager must possess when entering the architectural, engineering, and construction industry. Such ability requires a mixture of problem-solving skills, ranging from lower to higher order thinking skills, composed of cognitive and metacognitive processes. These skills include the ability to develop and evaluate construction plans and manage the execution of such plans. However, in a typical construction program, introducing students to such complex problems can be a challenge, and most commonly the learner is presented with only part of a complex problem. To support this challenge, the traditional methodology of delivering design, engineering, and construction instruction has been going through a technological revolution, due to the rise of computer-based technology. For example, in construction classrooms, and other disciplines, simulations and educational games are being utilized to support the development of problem-solving skills. Previous engineering education research has illustrated the high potential that simulations and educational games have in engaging in lower and higher order thinking skills. Such research illustrated their capacity to support the development of problem-solving skills. This research presents evidence supporting the theory that educational simulation games can help with the learning and retention of transferable problem-solving skills, which are necessary to solve complex construction problems. The educational simulation game employed in this study is the Virtual Construction Simulator (VCS). The VCS is a game developed to provide students in an engaging learning activity that simulates the planning and managing phases of a construction project. Assessment of the third iteration of the VCS(3) game has shown pedagogical value in promoting students' motivation and a basic understanding of construction concepts. To further evaluate the benefits on problem-solving skills, a new version of the VCS(4) was developed, with new building modules and assessment framework. The design and development of the VCS4 leveraged research in educational psychology, multimedia learning, human-computer interaction, and Building Information Modeling. In this dissertation the researcher aimed to evaluate the pedagogical value of the VCS4 in fostering problem-solving skills. To answer the research questions, a crossover repeated measures quasi-experiment was designed to assess the educational gains that the VCS can provide to construction education. A group of 34 students, attending a fourth-year construction course at a university in the United States was chosen to participate in the experiment. The three learning modules of the VCS were used, which challenged the students to plan and manage the construction process of a wooden pavilion, the steel erection of a dormitory, and the concrete placement of the same dormitory. Based on the results the researcher was able to provide evidence supporting the hypothesis that the chosen sample of construction students were able to gain and retain problem-solving skills necessary to solve complex construction simulation problems, no matter what the sequence with which these modules were played. In conclusion, the presented results provide evidence supporting the theory that educational simulation games can help the learning and retention of transferable problem-solving skills, which are necessary to solve complex construction problems.

morphforge: a toolbox for simulating small networks of biologically detailed neurons in Python

PubMed Central

Hull, Michael J.; Willshaw, David J.

2014-01-01

The broad structure of a modeling study can often be explained over a cup of coffee, but converting this high-level conceptual idea into graphs of the final simulation results may require many weeks of sitting at a computer. Although models themselves can be complex, often many mental resources are wasted working around complexities of the software ecosystem such as fighting to manage files, interfacing between tools and data formats, finding mistakes in code or working out the units of variables. morphforge is a high-level, Python toolbox for building and managing simulations of small populations of multicompartmental biophysical model neurons. An entire in silico experiment, including the definition of neuronal morphologies, channel descriptions, stimuli, visualization and analysis of results can be written within a single short Python script using high-level objects. Multiple independent simulations can be created and run from a single script, allowing parameter spaces to be investigated. Consideration has been given to the reuse of both algorithmic and parameterizable components to allow both specific and stochastic parameter variations. Some other features of the toolbox include: the automatic generation of human-readable documentation (e.g., PDF files) about a simulation; the transparent handling of different biophysical units; a novel mechanism for plotting simulation results based on a system of tags; and an architecture that supports both the use of established formats for defining channels and synapses (e.g., MODL files), and the possibility to support other libraries and standards easily. We hope that this toolbox will allow scientists to quickly build simulations of multicompartmental model neurons for research and serve as a platform for further tool development. PMID:24478690

High performance ultrasonic field simulation on complex geometries

NASA Astrophysics Data System (ADS)

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

2016-02-01

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

ALC: automated reduction of rule-based models

PubMed Central

Koschorreck, Markus; Gilles, Ernst Dieter

2008-01-01

Background Combinatorial complexity is a challenging problem for the modeling of cellular signal transduction since the association of a few proteins can give rise to an enormous amount of feasible protein complexes. The layer-based approach is an approximative, but accurate method for the mathematical modeling of signaling systems with inherent combinatorial complexity. The number of variables in the simulation equations is highly reduced and the resulting dynamic models show a pronounced modularity. Layer-based modeling allows for the modeling of systems not accessible previously. Results ALC (Automated Layer Construction) is a computer program that highly simplifies the building of reduced modular models, according to the layer-based approach. The model is defined using a simple but powerful rule-based syntax that supports the concepts of modularity and macrostates. ALC performs consistency checks on the model definition and provides the model output in different formats (C MEX, MATLAB, Mathematica and SBML) as ready-to-run simulation files. ALC also provides additional documentation files that simplify the publication or presentation of the models. The tool can be used offline or via a form on the ALC website. Conclusion ALC allows for a simple rule-based generation of layer-based reduced models. The model files are given in different formats as ready-to-run simulation files. PMID:18973705

Exploring the mechanism of how tvMyb2 recognizes and binds ap65-1 by molecular dynamics simulations and free energy calculations.

PubMed

Li, Wei-Kang; Zheng, Qing-Chuan; Zhang, Hong-Xing

2016-01-01

TvMyb2, one of the Myb-like transcriptional factors in Trichomonas vaginalis, binds to two closely spaced promoter sites, MRE-1/MRE-2r and MRE-2f, on the ap65-1 gene. However, detailed dynamical structural characteristics of the tvMyb2-ap65-1 complex and a detailed study of the protein in the complex have not been done. Focused on a specific tvMyb2-MRE-2-13 complex (PDB code: ) and a series of mutants K51A, R84A and R87A, we applied molecular dynamics (MD) simulation and molecular mechanics generalized Born surface area (MM-GBSA) free energy calculations to examine the role of the tvMyb2 protein in recognition interaction. The simulation results indicate that tvMyb2 becomes stable when it binds the DNA duplex. A series of mutants, K51A, R84A and R87A, have been followed, and the results of statistical analyses of the H-bond and hydrophobic contacts show that some residues have significant influence on recognition and binding to ap65-1 DNA. Our work gives important information to understand the interactions of tvMyb2 with ap65-1.

Ice Storm Supercomputer

ScienceCinema

None

2018-05-01

A new Idaho National Laboratory supercomputer is helping scientists create more realistic simulations of nuclear fuel. Dubbed "Ice Storm" this 2048-processor machine allows researchers to model and predict the complex physics behind nuclear reactor behavior. And with a new visualization lab, the team can see the results of its simulations on the big screen. For more information about INL research, visit http://www.facebook.com/idahonationallaboratory.

Nested large-eddy simulations of nighttime shear-instability waves and transient warming in a steep valley

NASA Astrophysics Data System (ADS)

Zhou, Bowen; Chow, Fotini

2012-11-01

This numerical study investigates the nighttime flow dynamics in a steep valley. The Owens Valley in California is highly complex, and represents a challenging terrain for large-eddy simulations (LES). To ensure a faithful representation of the nighttime atmospheric boundary layer (ABL), realistic external boundary conditions are provided through grid nesting. The model obtains initial and lateral boundary conditions from reanalysis data, and bottom boundary conditions from a land-surface model. We demonstrate the ability to extend a mesoscale model to LES resolutions through a systematic grid-nesting framework, achieving accurate simulations of the stable ABL over complex terrain. Nighttime cold-air flow was channeled through a gap on the valley sidewall. The resulting katabatic current induced a cross-valley flow. Directional shear against the down-valley flow in the lower layers of the valley led to breaking Kelvin-Helmholtz waves at the interface, which is captured only on the LES grid. Later that night, the flow transitioned from down-slope to down-valley near the western sidewall, leading to a transient warming episode. Simulation results are verified against field observations and reveal good spatial and temporal precision. Supported by NSF grant ATM-0645784.

Patient-Specific Simulation of Cardiac Blood Flow From High-Resolution Computed Tomography.

PubMed

Lantz, Jonas; Henriksson, Lilian; Persson, Anders; Karlsson, Matts; Ebbers, Tino

2016-12-01

Cardiac hemodynamics can be computed from medical imaging data, and results could potentially aid in cardiac diagnosis and treatment optimization. However, simulations are often based on simplified geometries, ignoring features such as papillary muscles and trabeculae due to their complex shape, limitations in image acquisitions, and challenges in computational modeling. This severely hampers the use of computational fluid dynamics in clinical practice. The overall aim of this study was to develop a novel numerical framework that incorporated these geometrical features. The model included the left atrium, ventricle, ascending aorta, and heart valves. The framework used image registration to obtain patient-specific wall motion, automatic remeshing to handle topological changes due to the complex trabeculae motion, and a fast interpolation routine to obtain intermediate meshes during the simulations. Velocity fields and residence time were evaluated, and they indicated that papillary muscles and trabeculae strongly interacted with the blood, which could not be observed in a simplified model. The framework resulted in a model with outstanding geometrical detail, demonstrating the feasibility as well as the importance of a framework that is capable of simulating blood flow in physiologically realistic hearts.

A novel grid multiwing chaotic system with only non-hyperbolic equilibria

NASA Astrophysics Data System (ADS)

Zhang, Sen; Zeng, Yicheng; Li, Zhijun; Wang, Mengjiao; Xiong, Le

2018-05-01

The structure of the chaotic attractor of a system is mainly determined by the nonlinear functions in system equations. By using a new saw-tooth wave function and a new stair function, a novel complex grid multiwing chaotic system which belongs to non-Shil'nikov chaotic system with non-hyperbolic equilibrium points is proposed in this paper. It is particularly interesting that the complex grid multiwing attractors are generated by increasing the number of non-hyperbolic equilibrium points, which are different from the traditional methods of realising multiwing attractors by adding the index-2 saddle-focus equilibrium points in double-wing chaotic systems. The basic dynamical properties of the new system, such as dissipativity, phase portraits, the stability of the equilibria, the time-domain waveform, power spectrum, bifurcation diagram, Lyapunov exponents, and so on, are investigated by theoretical analysis and numerical simulations. Furthermore, the corresponding electronic circuit is designed and simulated on the Multisim platform. The Multisim simulation results and the hardware experimental results are in good agreement with the numerical simulations of the same system on Matlab platform, which verify the feasibility of this new grid multiwing chaotic system.

A joint numerical and experimental study of the jet of an aircraft engine installation with advanced techniques

NASA Astrophysics Data System (ADS)

Brunet, V.; Molton, P.; Bézard, H.; Deck, S.; Jacquin, L.

2012-01-01

This paper describes the results obtained during the European Union JEDI (JEt Development Investigations) project carried out in cooperation between ONERA and Airbus. The aim of these studies was first to acquire a complete database of a modern-type engine jet installation set under a wall-to-wall swept wing in various transonic flow conditions. Interactions between the engine jet, the pylon, and the wing were studied thanks to ¤advanced¥ measurement techniques. In parallel, accurate Reynolds-averaged Navier Stokes (RANS) simulations were carried out from simple ones with the Spalart Allmaras model to more complex ones like the DRSM-SSG (Differential Reynolds Stress Modef of Speziale Sarkar Gatski) turbulence model. In the end, Zonal-Detached Eddy Simulations (Z-DES) were also performed to compare different simulation techniques. All numerical results are accurately validated thanks to the experimental database acquired in parallel. This complete and complex study of modern civil aircraft engine installation allowed many upgrades in understanding and simulation methods to be obtained. Furthermore, a setup for engine jet installation studies has been validated for possible future works in the S3Ch transonic research wind-tunnel. The main conclusions are summed up in this paper.

Patient-specific 3D printing simulation to guide complex coronary intervention.

PubMed

Oliveira-Santos, Manuel; Oliveira Santos, Eduardo; Marinho, Ana Vera; Leite, Luís; Guardado, Jorge; Matos, Vítor; Pego, Guilherme Mariano; Marques, João Silva

2018-05-07

The field of three-dimensional printing applied to patient-specific simulation is evolving as a tool to enhance intervention results. We report the first case of a fully simulated percutaneous coronary intervention in a three-dimensional patient-specific model to guide treatment. An 85-year-old female presented with symptomatic in-stent restenosis in the ostial circumflex and was scheduled for percutaneous coronary intervention. Considering the complexity of the anatomy, patient setting and intervention technique, we elected to replicate the coronary anatomy using a three-dimensional model. In this way, we simulated the intervention procedure beforehand in the catheterization laboratory using standard materials. The procedure was guided by optical coherence tomography, with pre-dilatation of the lesion, implantation of a single drug-eluting stent in the ostial circumflex and kissing balloon inflation to the left anterior descending artery and circumflex. Procedural steps were replicated in the real patient's treatment, with remarkable parallelism in angiographic outcome and luminal gain at intracoronary imaging. In this proof-of-concept report, we show that patient-specific simulation is feasible to guide the treatment strategy of complex coronary artery disease. It enables the surgical team to plan and practice the procedure beforehand, and possibly predict complications and gain confidence. Copyright © 2018 Sociedade Portuguesa de Cardiologia. Publicado por Elsevier España, S.L.U. All rights reserved.

Fluid-structure interaction simulation of floating structures interacting with complex, large-scale ocean waves and atmospheric turbulence with application to floating offshore wind turbines

NASA Astrophysics Data System (ADS)

Calderer, Antoni; Guo, Xin; Shen, Lian; Sotiropoulos, Fotis

2018-02-01

We develop a numerical method for simulating coupled interactions of complex floating structures with large-scale ocean waves and atmospheric turbulence. We employ an efficient large-scale model to develop offshore wind and wave environmental conditions, which are then incorporated into a high resolution two-phase flow solver with fluid-structure interaction (FSI). The large-scale wind-wave interaction model is based on a two-fluid dynamically-coupled approach that employs a high-order spectral method for simulating the water motion and a viscous solver with undulatory boundaries for the air motion. The two-phase flow FSI solver is based on the level set method and is capable of simulating the coupled dynamic interaction of arbitrarily complex bodies with airflow and waves. The large-scale wave field solver is coupled with the near-field FSI solver with a one-way coupling approach by feeding into the latter waves via a pressure-forcing method combined with the level set method. We validate the model for both simple wave trains and three-dimensional directional waves and compare the results with experimental and theoretical solutions. Finally, we demonstrate the capabilities of the new computational framework by carrying out large-eddy simulation of a floating offshore wind turbine interacting with realistic ocean wind and waves.

Grand canonical ensemble Monte Carlo simulation of the dCpG/proflavine crystal hydrate.

PubMed Central

Resat, H; Mezei, M

1996-01-01

The grand canonical ensemble Monte Carlo molecular simulation method is used to investigate hydration patterns in the crystal hydrate structure of the dCpG/proflavine intercalated complex. The objective of this study is to show by example that the recently advocated grand canonical ensemble simulation is a computationally efficient method for determining the positions of the hydrating water molecules in protein and nucleic acid structures. A detailed molecular simulation convergence analysis and an analogous comparison of the theoretical results with experiments clearly show that the grand ensemble simulations can be far more advantageous than the comparable canonical ensemble simulations. Images FIGURE 5 FIGURE 7 PMID:8873992

Minimum MD simulation length required to achieve reliable results in free energy perturbation calculations: case study of relative binding free energies of fructose-1,6-bisphosphatase inhibitors.

PubMed

Rathore, R S; Aparoy, P; Reddanna, P; Kondapi, A K; Reddy, M Rami

2011-07-30

In an attempt to establish the criteria for the length of simulation to achieve the desired convergence of free energy calculations, two studies were carried out on chosen complexes of FBPase-AMP mimics. Calculations were performed for varied length of simulations and for different starting configurations using both conventional- and QM/MM-FEP methods. The results demonstrate that for small perturbations, 1248 ps simulation time could be regarded a reasonable yardstick to achieve convergence of the results. As the simulation time is extended, the errors associated with free energy calculations also gradually tapers off. Moreover, when starting the simulation from different initial configurations of the systems, the results are not changed significantly, when performed for 1248 ps. This study carried on FBPase-AMP mimics corroborates well with our previous successful demonstration of requirement of simulation time for solvation studies, both by conventional and ab initio FEP. The establishment of aforementioned criteria of simulation length serves a useful benchmark in drug design efforts using FEP methodologies, to draw a meaningful and unequivocal conclusion. Copyright © 2011 Wiley Periodicals, Inc.

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

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.; Wong, Jay Ming

2014-01-01

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

A Discrete Event Simulation Model for Evaluating the Performances of an M/G/C/C State Dependent Queuing System

PubMed Central

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

2013-01-01

M/G/C/C state dependent queuing networks consider service rates as a function of the number of residing entities (e.g., pedestrians, vehicles, and products). However, modeling such dynamic rates is not supported in modern Discrete Simulation System (DES) software. We designed an approach to cater this limitation and used it to construct the M/G/C/C state-dependent queuing model in Arena software. Using the model, we have evaluated and analyzed the impacts of various arrival rates to the throughput, the blocking probability, the expected service time and the expected number of entities in a complex network topology. Results indicated that there is a range of arrival rates for each network where the simulation results fluctuate drastically across replications and this causes the simulation results and analytical results exhibit discrepancies. Detail results that show how tally the simulation results and the analytical results in both abstract and graphical forms and some scientific justifications for these have been documented and discussed. PMID:23560037

Simulating complex intracellular processes using object-oriented computational modelling.

PubMed

Johnson, Colin G; Goldman, Jacki P; Gullick, William J

2004-11-01

The aim of this paper is to give an overview of computer modelling and simulation in cellular biology, in particular as applied to complex biochemical processes within the cell. This is illustrated by the use of the techniques of object-oriented modelling, where the computer is used to construct abstractions of objects in the domain being modelled, and these objects then interact within the computer to simulate the system and allow emergent properties to be observed. The paper also discusses the role of computer simulation in understanding complexity in biological systems, and the kinds of information which can be obtained about biology via simulation.

Automating Embedded Analysis Capabilities and Managing Software Complexity in Multiphysics Simulation, Part I: Template-Based Generic Programming

DOE PAGES

Pawlowski, Roger P.; Phipps, Eric T.; Salinger, Andrew G.

2012-01-01

An approach for incorporating embedded simulation and analysis capabilities in complex simulation codes through template-based generic programming is presented. This approach relies on templating and operator overloading within the C++ language to transform a given calculation into one that can compute a variety of additional quantities that are necessary for many state-of-the-art simulation and analysis algorithms. An approach for incorporating these ideas into complex simulation codes through general graph-based assembly is also presented. These ideas have been implemented within a set of packages in the Trilinos framework and are demonstrated on a simple problem from chemical engineering.

A laboratory investigation of the variability of cloud reflected radiance fields

NASA Technical Reports Server (NTRS)

Mckee, T. B.; Cox, S. K.

1986-01-01

A method to determine the radiative properties of complex cloud fields was developed. A Cloud field optical simulator (CFOS) was constructed to simulate the interaction of cloud fields with visible radiation. The CFOS was verified by comparing experimental results from it with calculations performed with a Monte Carlo radiative transfer model. A software library was developed to process, reduce, and display CFOS data. The CFSOS was utilized to study the reflected radiane patterns from simulated cloud fields.

Application of the TEMPEST computer code for simulating hydrogen distribution in model containment structures. [PWR; BWR

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

Trent, D.S.; Eyler, L.L.

In this study several aspects of simulating hydrogen distribution in geometric configurations relevant to reactor containment structures were investigated using the TEMPEST computer code. Of particular interest was the performance of the TEMPEST turbulence model in a density-stratified environment. Computed results illustrated that the TEMPEST numerical procedures predicted the measured phenomena with good accuracy under a variety of conditions and that the turbulence model used is a viable approach in complex turbulent flow simulation.

Complex disruption effect of natural polyphenols on Bcl-2-Bax: molecular dynamics simulation and essential dynamics study.

PubMed

Verma, Sharad; Singh, Amit; Mishra, Abha

2015-01-01

Apoptosis (programmed cell death) is a process by which cells died after completing physiological function or after a severe genetic damage. Apoptosis is mainly regulated by the Bcl-2 family of proteins. Anti apoptotic protein Bcl-2 prevents the Bax activation/oligomerization to form heterodimer which is responsible for release of the cytochrome c from mitochondria to the cytosol in response to death signal. Quercetin and taxifolin (natural polyphenols) efficiently bound to hydrophobic groove of Bcl-2 and altered the structure by inducing conformational changes. Taxifolin was found more efficient when compared to quercetin in terms of interaction energy and collapse of hydrophobic groove. Taxifolin and quercetin were found to dissociate the Bcl-2-Bax complex during 12 ns MD simulation. The effect of taxifolin and quercetin was, further validated by the MD simulation of ligand-unbound Bcl-2-Bax which showed stability during the simulation. Obatoclax (an inhibitor of Bcl-2) had no significant dissociation effect on Bcl-2-Bax during simulation which favored the previous experimental results and disruption effect of taxifolin and quercetin.

Quantifying uncertainty and computational complexity for pore-scale simulations

NASA Astrophysics Data System (ADS)

Chen, C.; Yuan, Z.; Wang, P.; Yang, X.; Zhenyan, L.

2016-12-01

Pore-scale simulation is an essential tool to understand the complex physical process in many environmental problems, from multi-phase flow in the subsurface to fuel cells. However, in practice, factors such as sample heterogeneity, data sparsity and in general, our insufficient knowledge of the underlying process, render many simulation parameters and hence the prediction results uncertain. Meanwhile, most pore-scale simulations (in particular, direct numerical simulation) incur high computational cost due to finely-resolved spatio-temporal scales, which further limits our data/samples collection. To address those challenges, we propose a novel framework based on the general polynomial chaos (gPC) and build a surrogate model representing the essential features of the underlying system. To be specific, we apply the novel framework to analyze the uncertainties of the system behavior based on a series of pore-scale numerical experiments, such as flow and reactive transport in 2D heterogeneous porous media and 3D packed beds. Comparing with recent pore-scale uncertainty quantification studies using Monte Carlo techniques, our new framework requires fewer number of realizations and hence considerably reduce the overall computational cost, while maintaining the desired accuracy.

Research on simulation technology of full-path infrared tail flame tracking of photoelectric theodolite in complicated environment

NASA Astrophysics Data System (ADS)

Wu, Hai-ying; Zhang, San-xi; Liu, Biao; Yue, Peng; Weng, Ying-hui

2018-02-01

The photoelectric theodolite is an important scheme to realize the tracking, detection, quantitative measurement and performance evaluation of weapon systems in ordnance test range. With the improvement of stability requirements for target tracking in complex environment, infrared scene simulation with high sense of reality and complex interference has become an indispensable technical way to evaluate the track performance of photoelectric theodolite. And the tail flame is the most important infrared radiation source of the weapon system. The dynamic tail flame with high reality is a key element for the photoelectric theodolite infrared scene simulation and imaging tracking test. In this paper, an infrared simulation method for the full-path tracking of tail flame by photoelectric theodolite is proposed aiming at the faint boundary, irregular, multi-regulated points. In this work, real tail images are employed. Simultaneously, infrared texture conversion technology is used to generate DDS texture for a particle system map. Thus, dynamic real-time tail flame simulation results with high fidelity from the theodolite perspective can be gained in the tracking process.

Active Learning for Directed Exploration of Complex Systems

NASA Technical Reports Server (NTRS)

Burl, Michael C.; Wang, Esther

2009-01-01

Physics-based simulation codes are widely used in science and engineering to model complex systems that would be infeasible to study otherwise. Such codes provide the highest-fidelity representation of system behavior, but are often so slow to run that insight into the system is limited. For example, conducting an exhaustive sweep over a d-dimensional input parameter space with k-steps along each dimension requires k(sup d) simulation trials (translating into k(sup d) CPU-days for one of our current simulations). An alternative is directed exploration in which the next simulation trials are cleverly chosen at each step. Given the results of previous trials, supervised learning techniques (SVM, KDE, GP) are applied to build up simplified predictive models of system behavior. These models are then used within an active learning framework to identify the most valuable trials to run next. Several active learning strategies are examined including a recently-proposed information-theoretic approach. Performance is evaluated on a set of thirteen synthetic oracles, which serve as surrogates for the more expensive simulations and enable the experiments to be replicated by other researchers.

Experimental and Computational Study of Sonic and Supersonic Jet Plumes

NASA Technical Reports Server (NTRS)

Venkatapathy, E.; Naughton, J. W.; Fletcher, D. G.; Edwards, Thomas A. (Technical Monitor)

1994-01-01

Study of sonic and supersonic jet plumes are relevant to understanding such phenomenon as jet-noise, plume signatures, and rocket base-heating and radiation. Jet plumes are simple to simulate and yet, have complex flow structures such as Mach disks, triple points, shear-layers, barrel shocks, shock-shear-layer interaction, etc. Experimental and computational simulation of sonic and supersonic jet plumes have been performed for under- and over-expanded, axisymmetric plume conditions. The computational simulation compare very well with the experimental observations of schlieren pictures. Experimental data such as temperature measurements with hot-wire probes are yet to be measured and will be compared with computed values. Extensive analysis of the computational simulations presents a clear picture of how the complex flow structure develops and the conditions under which self-similar flow structures evolve. From the computations, the plume structure can be further classified into many sub-groups. In the proposed paper, detail results from the experimental and computational simulations for single, axisymmetric, under- and over-expanded, sonic and supersonic plumes will be compared and the fluid dynamic aspects of flow structures will be discussed.

Sonic and Supersonic Jet Plumes

NASA Technical Reports Server (NTRS)

Venkatapathy, E.; Naughton, J. W.; Flethcher, D. G.; Edwards, Thomas A. (Technical Monitor)

1994-01-01

Study of sonic and supersonic jet plumes are relevant to understanding such phenomenon as jet-noise, plume signatures, and rocket base-heating and radiation. Jet plumes are simple to simulate and yet, have complex flow structures such as Mach disks, triple points, shear-layers, barrel shocks, shock- shear- layer interaction, etc. Experimental and computational simulation of sonic and supersonic jet plumes have been performed for under- and over-expanded, axisymmetric plume conditions. The computational simulation compare very well with the experimental observations of schlieren pictures. Experimental data such as temperature measurements with hot-wire probes are yet to be measured and will be compared with computed values. Extensive analysis of the computational simulations presents a clear picture of how the complex flow structure develops and the conditions under which self-similar flow structures evolve. From the computations, the plume structure can be further classified into many sub-groups. In the proposed paper, detail results from the experimental and computational simulations for single, axisymmetric, under- and over-expanded, sonic and supersonic plumes will be compared and the fluid dynamic aspects of flow structures will be discussed.

Beneficiation of Stillwater Complex Rock for the Production of Lunar Simulants

NASA Technical Reports Server (NTRS)

Rickman, D. L.; Young, C.; Stoeser, D.; Edmunson, J.

2014-01-01

The availability of pure, high calcium plagioclase would be a significant asset in any attempt to manufacture high-quality lunar simulants. A suitable plagioclase product can be obtained from materials obtained from the Stillwater Complex of Montana. The access, geology, petrology, and mineralogy of the relevant rocks and the mill tailings are described here. This study demonstrates successful plagioclase recovery from mill tailings produced by the Stillwater Mine Company. Hydrogen peroxide was used to remove carboxymethyl cellulose from the tailing. The characteristics of the plagioclase products are shown and locked grains are identified as a limit to achievable purity. Based on the experimental results, flowsheets were developed showing how these resources could be processed and made into 'separates' of (1) high calcium plagioclase and (2) orthopyroxene/clinopyroxene with the thought that they would be combined later to make simulant.

Large eddy simulation of a boundary layer with concave streamwise curvature

NASA Technical Reports Server (NTRS)

Lund, Thomas S.

1993-01-01

One of the most exciting recent developments in the field of large eddy simulation (LES) is the dynamic subgrid-scale model. The dynamic model concept is a general procedure for evaluating model constants by sampling a band of the smallest scales actually resolved in the simulation. To date, the procedure has been used primarily in conjunction with the Smagorinsky model. The dynamic procedure has the advantage that the value of the model constant need not be specified a priori, but rather is calculated as a function of space and time as the simulation progresses. This feature makes the dynamic model especially attractive for flows in complex geometries where it is difficult or impossible to calibrate model constants. The dynamic model was highly successful in benchmark tests involving homogeneous and channel flows. Having demonstrated the potential of the dynamic model in these simple flows, the overall direction of the LES effort at CTR shifted toward an evaluation of the model in more complex situations. The current test cases are basic engineering-type flows for which Reynolds averaged approaches were unable to model the turbulence to within engineering accuracy. Flows currently under investigation include a backward-facing step, wake behind a circular cylinder, airfoil at high angles of attack, separated flow in a diffuser, and boundary layer over a concave surface. Preliminary results from the backward-facing step and cylinder wake simulations are encouraging. Progress on the LES of a boundary layer on a concave surface is discussed. Although the geometry of a concave wall is not very complex, the boundary layer that develops on its surface is difficult to model due to the presence of streamwise Taylor-Gortler vortices. These vortices arise as a result of a centrifugal instability associated with the convex curvature.

Improved estimation of ligand macromolecule binding affinities by linear response approach using a combination of multi-mode MD simulation and QM/MM methods

NASA Astrophysics Data System (ADS)

Khandelwal, Akash; Balaz, Stefan

2007-01-01

Structure-based predictions of binding affinities of ligands binding to proteins by coordination bonds with transition metals, covalent bonds, and bonds involving charge re-distributions are hindered by the absence of proper force fields. This shortcoming affects all methods which use force-field-based molecular simulation data on complex formation for affinity predictions. One of the most frequently used methods in this category is the Linear Response (LR) approach of Åquist, correlating binding affinities with van der Waals and electrostatic energies, as extended by Jorgensen's inclusion of solvent-accessible surface areas. All these terms represent the differences, upon binding, in the ensemble averages of pertinent quantities, obtained from molecular dynamics (MD) or Monte Carlo simulations of the complex and of single components. Here we report a modification of the LR approach by: (1) the replacement of the two energy terms through the single-point QM/MM energy of the time-averaged complex structure from an MD simulation; and (2) a rigorous consideration of multiple modes (mm) of binding. The first extension alleviates the force-field related problems, while the second extension deals with the ligands exhibiting large-scale motions in the course of an MD simulation. The second modification results in the correlation equation that is nonlinear in optimized coefficients, but does not lead to an increase in the number of optimized coefficients. The application of the resulting mm QM/MM LR approach to the inhibition of zinc-dependent gelatinase B (matrix metalloproteinase 9) by 28 hydroxamate ligands indicates a significant improvement of descriptive and predictive abilities.

Payload training methodology study

NASA Technical Reports Server (NTRS)

1990-01-01

The results of the Payload Training Methodology Study (PTMS) are documented. Methods and procedures are defined for the development of payload training programs to be conducted at the Marshall Space Flight Center Payload Training Complex (PCT) for the Space Station Freedom program. The study outlines the overall training program concept as well as the six methodologies associated with the program implementation. The program concept outlines the entire payload training program from initial identification of training requirements to the development of detailed design specifications for simulators and instructional material. The following six methodologies are defined: (1) The Training and Simulation Needs Assessment Methodology; (2) The Simulation Approach Methodology; (3) The Simulation Definition Analysis Methodology; (4) The Simulator Requirements Standardization Methodology; (5) The Simulator Development Verification Methodology; and (6) The Simulator Validation Methodology.

Practical Unitary Simulator for Non-Markovian Complex Processes

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

Nationwide Buildings Energy Research enabled through an integrated Data Intensive Scientific Workflow and Advanced Analysis Environment

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

Kleese van Dam, Kerstin; Lansing, Carina S.; Elsethagen, Todd O.

2014-01-28

Modern workflow systems enable scientists to run ensemble simulations at unprecedented scales and levels of complexity, allowing them to study system sizes previously impossible to achieve, due to the inherent resource requirements needed for the modeling work. However as a result of these new capabilities the science teams suddenly also face unprecedented data volumes that they are unable to analyze with their existing tools and methodologies in a timely fashion. In this paper we will describe the ongoing development work to create an integrated data intensive scientific workflow and analysis environment that offers researchers the ability to easily create andmore » execute complex simulation studies and provides them with different scalable methods to analyze the resulting data volumes. The integration of simulation and analysis environments is hereby not only a question of ease of use, but supports fundamental functions in the correlated analysis of simulation input, execution details and derived results for multi-variant, complex studies. To this end the team extended and integrated the existing capabilities of the Velo data management and analysis infrastructure, the MeDICi data intensive workflow system and RHIPE the R for Hadoop version of the well-known statistics package, as well as developing a new visual analytics interface for the result exploitation by multi-domain users. The capabilities of the new environment are demonstrated on a use case that focusses on the Pacific Northwest National Laboratory (PNNL) building energy team, showing how they were able to take their previously local scale simulations to a nationwide level by utilizing data intensive computing techniques not only for their modeling work, but also for the subsequent analysis of their modeling results. As part of the PNNL research initiative PRIMA (Platform for Regional Integrated Modeling and Analysis) the team performed an initial 3 year study of building energy demands for the US Eastern Interconnect domain, which they are now planning to extend to predict the demand for the complete century. The initial study raised their data demands from a few GBs to 400GB for the 3year study and expected tens of TBs for the full century.« less

Phase-field simulations of GaN growth by selective area epitaxy on complex mask geometries

DOE PAGES

Aagesen, Larry K.; Coltrin, Michael Elliott; Han, Jung; ...

2015-05-15

Three-dimensional phase-field simulations of GaN growth by selective area epitaxy were performed. Furthermore, this model includes a crystallographic-orientation-dependent deposition rate and arbitrarily complex mask geometries. The orientation-dependent deposition rate can be determined from experimental measurements of the relative growth rates of low-index crystallographic facets. Growth on various complex mask geometries was simulated on both c-plane and a-plane template layers. Agreement was observed between simulations and experiment, including complex phenomena occurring at the intersections between facets. The sources of the discrepancies between simulated and experimental morphologies were also investigated. We found that the model provides a route to optimize masks andmore » processing conditions during materials synthesis for solar cells, light-emitting diodes, and other electronic and opto-electronic applications.« less

Dependability analysis of parallel systems using a simulation-based approach. M.S. Thesis

NASA Technical Reports Server (NTRS)

Sawyer, Darren Charles

1994-01-01

The analysis of dependability in large, complex, parallel systems executing real applications or workloads is examined in this thesis. To effectively demonstrate the wide range of dependability problems that can be analyzed through simulation, the analysis of three case studies is presented. For each case, the organization of the simulation model used is outlined, and the results from simulated fault injection experiments are explained, showing the usefulness of this method in dependability modeling of large parallel systems. The simulation models are constructed using DEPEND and C++. Where possible, methods to increase dependability are derived from the experimental results. Another interesting facet of all three cases is the presence of some kind of workload of application executing in the simulation while faults are injected. This provides a completely new dimension to this type of study, not possible to model accurately with analytical approaches.

Epp: A C++ EGSnrc user code for x-ray imaging and scattering simulations

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

Lippuner, Jonas; Elbakri, Idris A.; Cui Congwu

2011-03-15

Purpose: Easy particle propagation (Epp) is a user code for the EGSnrc code package based on the C++ class library egspp. A main feature of egspp (and Epp) is the ability to use analytical objects to construct simulation geometries. The authors developed Epp to facilitate the simulation of x-ray imaging geometries, especially in the case of scatter studies. While direct use of egspp requires knowledge of C++, Epp requires no programming experience. Methods: Epp's features include calculation of dose deposited in a voxelized phantom and photon propagation to a user-defined imaging plane. Projection images of primary, single Rayleigh scattered, singlemore » Compton scattered, and multiple scattered photons may be generated. Epp input files can be nested, allowing for the construction of complex simulation geometries from more basic components. To demonstrate the imaging features of Epp, the authors simulate 38 keV x rays from a point source propagating through a water cylinder 12 cm in diameter, using both analytical and voxelized representations of the cylinder. The simulation generates projection images of primary and scattered photons at a user-defined imaging plane. The authors also simulate dose scoring in the voxelized version of the phantom in both Epp and DOSXYZnrc and examine the accuracy of Epp using the Kawrakow-Fippel test. Results: The results of the imaging simulations with Epp using voxelized and analytical descriptions of the water cylinder agree within 1%. The results of the Kawrakow-Fippel test suggest good agreement between Epp and DOSXYZnrc. Conclusions: Epp provides the user with useful features, including the ability to build complex geometries from simpler ones and the ability to generate images of scattered and primary photons. There is no inherent computational time saving arising from Epp, except for those arising from egspp's ability to use analytical representations of simulation geometries. Epp agrees with DOSXYZnrc in dose calculation, since they are both based on the well-validated standard EGSnrc radiation transport physics model.« less

Emittance study of a 28 GHz electron cyclotron resonance ion source for the Rare Isotope Science Project superconducting linear accelerator.

PubMed

Park, Bum-Sik; Hong, In-Seok; Jang, Ji-Ho; Jin, Hyunchang; Choi, Sukjin; Kim, Yonghwan

2016-02-01

A 28 GHz electron cyclotron resonance (ECR) ion source is being developed for use as an injector for the superconducting linear accelerator of the Rare Isotope Science Project. Beam extraction from the ECR ion source has been simulated using the KOBRA3-INP software. The simulation software can calculate charged particle trajectories in three dimensional complex magnetic field structures, which in this case are formed by the arrangement of five superconducting magnets. In this study, the beam emittance is simulated to understand the effects of plasma potential, mass-to-charge ratio, and spatial distribution. The results of these simulations and their comparison to experimental results are presented in this paper.

Interleaved concatenated codes: New perspectives on approaching the Shannon limit

PubMed Central

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

1997-01-01

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

Structural basis for binding of aurora-AG198N- INCENP complex: MD simulations and free energy calculations.

PubMed

Tanneeru, Karunakar; Guruprasad, Lalitha

2013-11-01

Aurora-A, B and C are non-receptor serine/threonine kinases in Homo sapiens. In spite of high similarity in their sequences, they possess distinct binding partners. These kinases play an important role in cell division and overexpressed in certain cancers. It has been demonstrated that Gly198 in Aurora-A kinase is responsible for its basal kinase activity, the mutation G198N transforms Aurora-A to Aurora-B like function and localization by binding to Inner centromere protein (INCENP). The molecular mechanisms, structural determinants and the binding energetics of the Aurora-A - INCENP complex owing to a single amino acid G198N mutation are not studied. Therefore, we have docked INCENP into human Aurora-A kinase, mutated Gly198 to Asn, Leu and Ala. The wild type and mutant Aurora-A - INCENP complexes were subjected to 40 ns molecular dynamics (MD) simulations. The Asn198 is located in the amphipathic cavity comprising Leu869(IN), Glu868(IN), Thr872(IN), Tyr197(AurA) and Tyr199(AurA) and the interactions mediated via hydrogen bonds are important to stabilize the Aurora-A(G198N) - INCENP complex. The fluctuations in the secondary structural elements and the solvent accessible surface area of all the four complexes during the MD simulations were studied. We calculated the binding free energy upon mutation in the three mutant complexes. The Aurora-A(G198N) - INCENP complex with hydrophilic amino acid mutation has the negative free energy of solvation indicating favorable interactions with INCENP. Our results provide the structural basis and energetics of the human Aurora-A(G198N) - INCENP complex.

A Computational Approach for Modeling Neutron Scattering Data from Lipid Bilayers

DOE PAGES

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

2017-01-12

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

The effect of distributed virtual reality simulation training on cognitive load during subsequent dissection training.

PubMed

Andersen, Steven Arild Wuyts; Konge, Lars; Sørensen, Mads Sølvsten

2018-05-07

Complex tasks such as surgical procedures can induce excessive cognitive load (CL), which can have a negative effect on learning, especially for novices. To investigate if repeated and distributed virtual reality (VR) simulation practice induces a lower CL and higher performance in subsequent cadaveric dissection training. In a prospective, controlled cohort study, 37 residents in otorhinolaryngology received VR simulation training either as additional distributed practice prior to course participation (intervention) (9 participants) or as standard practice during the course (control) (28 participants). Cognitive load was estimated as the relative change in secondary-task reaction time during VR simulation and cadaveric procedures. Structured distributed VR simulation practice resulted in lower mean reaction times (32% vs. 47% for the intervention and control group, respectively, p < 0.01) as well as a superior final-product performance during subsequent cadaveric dissection training. Repeated and distributed VR simulation causes a lower CL to be induced when the learning situation is increased in complexity. A suggested mechanism is the formation of mental schemas and reduction of the intrinsic CL. This has potential implications for surgical skills training and suggests that structured, distributed training be systematically implemented in surgical training curricula.

Characterizing time series via complexity-entropy curves

NASA Astrophysics Data System (ADS)

Ribeiro, Haroldo V.; Jauregui, Max; Zunino, Luciano; Lenzi, Ervin K.

2017-06-01

The search for patterns in time series is a very common task when dealing with complex systems. This is usually accomplished by employing a complexity measure such as entropies and fractal dimensions. However, such measures usually only capture a single aspect of the system dynamics. Here, we propose a family of complexity measures for time series based on a generalization of the complexity-entropy causality plane. By replacing the Shannon entropy by a monoparametric entropy (Tsallis q entropy) and after considering the proper generalization of the statistical complexity (q complexity), we build up a parametric curve (the q -complexity-entropy curve) that is used for characterizing and classifying time series. Based on simple exact results and numerical simulations of stochastic processes, we show that these curves can distinguish among different long-range, short-range, and oscillating correlated behaviors. Also, we verify that simulated chaotic and stochastic time series can be distinguished based on whether these curves are open or closed. We further test this technique in experimental scenarios related to chaotic laser intensity, stock price, sunspot, and geomagnetic dynamics, confirming its usefulness. Finally, we prove that these curves enhance the automatic classification of time series with long-range correlations and interbeat intervals of healthy subjects and patients with heart disease.

Propensity of a single-walled carbon nanotube-peptide to mimic a KK10 peptide in an HLA-TCR complex

NASA Astrophysics Data System (ADS)

Feng, Mei; Bell, David R.; Zhou, Ruhong

2017-12-01

The application of nanotechnology to improve disease diagnosis, treatment, monitoring, and prevention is the goal of nanomedicine. We report here a theoretical study of a functionalized single-walled carbon nanotube (CNT) mimic binding to a human leukocyte antigen-T cell receptor (HLA-TCR) immune complex as a first attempt of a potential nanomedicine for human immunodeficiency virus (HIV) vaccine development. The carbon nanotube was coated with three arginine residues to imitate the HIV type 1 immunodominant viral peptide KK10 (gag 263-272: KRWIILGLNK), named CNT-peptide hereafter. Through molecular dynamics simulations, we explore the CNT-peptide and KK10 binding to an important HLA-TCR complex. Our results suggest that the CNT-peptide and KK10 bind comparably to the HLA-TCR complex, but the CNT-peptide forms stronger interactions with the TCR. Desorption simulations highlight the innate flexibility of KK10 over the CNT-peptide, resulting in a slightly higher desorption energy required for KK10 over the CNT-peptide. Our findings indicate that the designed CNT-peptide mimic has favorable propensity to activate TCR pathways and should be further explored to understand therapeutic potential.

Genetic Simulation Tools for Post-Genome Wide Association Studies of Complex Diseases

PubMed Central

Amos, Christopher I.; Bafna, Vineet; Hauser, Elizabeth R.; Hernandez, Ryan D.; Li, Chun; Liberles, David A.; McAllister, Kimberly; Moore, Jason H.; Paltoo, Dina N.; Papanicolaou, George J.; Peng, Bo; Ritchie, Marylyn D.; Rosenfeld, Gabriel; Witte, John S.

2014-01-01

Genetic simulation programs are used to model data under specified assumptions to facilitate the understanding and study of complex genetic systems. Standardized data sets generated using genetic simulation are essential for the development and application of novel analytical tools in genetic epidemiology studies. With continuing advances in high-throughput genomic technologies and generation and analysis of larger, more complex data sets, there is a need for updating current approaches in genetic simulation modeling. To provide a forum to address current and emerging challenges in this area, the National Cancer Institute (NCI) sponsored a workshop, entitled “Genetic Simulation Tools for Post-Genome Wide Association Studies of Complex Diseases” at the National Institutes of Health (NIH) in Bethesda, Maryland on March 11-12, 2014. The goals of the workshop were to: (i) identify opportunities, challenges and resource needs for the development and application of genetic simulation models; (ii) improve the integration of tools for modeling and analysis of simulated data; and (iii) foster collaborations to facilitate development and applications of genetic simulation. During the course of the meeting the group identified challenges and opportunities for the science of simulation, software and methods development, and collaboration. This paper summarizes key discussions at the meeting, and highlights important challenges and opportunities to advance the field of genetic simulation. PMID:25371374

In-flight simulation of high agility through active control: Taming complexity by design

NASA Technical Reports Server (NTRS)

Padfield, Gareth D.; Bradley, Roy

1993-01-01

The motivation for research into helicopter agility stems from the realization that marked improvements relative to current operational types are possible, yet there is a dearth of useful criteria for flying qualities at high performance levels. Several research laboratories are currently investing resources in developing second generation airborne rotorcraft simulators. The UK's focus has been the exploitation of agility through active control technology (ACT); this paper reviews the results of studies conducted to date. The conflict between safety and performance in flight research is highlighted and the various forms of safety net to protect against system failures are described. The role of the safety pilot, and the use of actuator and flight envelope limiting are discussed. It is argued that the deep complexity of a research ACT system can only be tamed through a requirement specification assembled using design principles and cast in an operational simulation form. Work along these lines conducted at DRA is described, including the use of the Jackson System Development method and associated Ada simulation.

MOLNs: A CLOUD PLATFORM FOR INTERACTIVE, REPRODUCIBLE, AND SCALABLE SPATIAL STOCHASTIC COMPUTATIONAL EXPERIMENTS IN SYSTEMS BIOLOGY USING PyURDME

PubMed Central

Drawert, Brian; Trogdon, Michael; Toor, Salman; Petzold, Linda; Hellander, Andreas

2017-01-01

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools and a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments. PMID:28190948

A Novel DEM Approach to Simulate Block Propagation on Forested Slopes

NASA Astrophysics Data System (ADS)

Toe, David; Bourrier, Franck; Dorren, Luuk; Berger, Frédéric

2018-03-01

In order to model rockfall on forested slopes, we developed a trajectory rockfall model based on the discrete element method (DEM). This model is able to take the complex mechanical processes at work during an impact into account (large deformations, complex contact conditions) and can explicitly simulate block/soil, block/tree contacts as well as contacts between neighbouring trees. In this paper, we describe the DEM model developed and we use it to assess the protective effect of different types of forest. In addition, we compared it with a more classical rockfall simulation model. The results highlight that forests can significantly reduce rockfall hazard and that the spatial structure of coppice forests has to be taken into account in rockfall simulations in order to avoid overestimating the protective role of these forest structures against rockfall hazard. In addition, the protective role of the forests is mainly influenced by the basal area. Finally, the advantages and limitations of the DEM model were compared with classical rockfall modelling approaches.

Wind power forecasting for a real onshore wind farm on complex terrain using WRF high resolution simulations.

NASA Astrophysics Data System (ADS)

Ángel Prósper Fernández, Miguel; Casal, Carlos Otero; Canoura Fernández, Felipe; Miguez-Macho, Gonzalo

2017-04-01

Regional meteorological models are becoming a generalized tool for forecasting wind resource, due to their capacity to simulate local flow dynamics impacting wind farm production. This study focuses on the production forecast and validation of a real onshore wind farm using high horizontal and vertical resolution WRF (Weather Research and Forecasting) model simulations. The wind farm is located in Galicia, in the northwest of Spain, in a complex terrain region with high wind resource. Utilizing the Fitch scheme, specific for wind farms, a period of one year is simulated with a daily operational forecasting set-up. Power and wind predictions are obtained and compared with real data provided by the management company. Results show that WRF is able to yield good wind power operational predictions for this kind of wind farms, due to a good representation of the planetary boundary layer behaviour of the region and the good performance of the Fitch scheme under these conditions.

Optimized Materials From First Principles Simulations: Are We There Yet?

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

Galli, G; Gygi, F

2005-07-26

In the past thirty years, the use of scientific computing has become pervasive in all disciplines: collection and interpretation of most experimental data is carried out using computers, and physical models in computable form, with various degrees of complexity and sophistication, are utilized in all fields of science. However, full prediction of physical and chemical phenomena based on the basic laws of Nature, using computer simulations, is a revolution still in the making, and it involves some formidable theoretical and computational challenges. We illustrate the progress and successes obtained in recent years in predicting fundamental properties of materials in condensedmore » phases and at the nanoscale, using ab-initio, quantum simulations. We also discuss open issues related to the validation of the approximate, first principles theories used in large scale simulations, and the resulting complex interplay between computation and experiment. Finally, we describe some applications, with focus on nanostructures and liquids, both at ambient and under extreme conditions.« less

Numerical simulation of radiation fog in complex terrain

NASA Astrophysics Data System (ADS)

Zhang, X.; Musson-Genon, L.; Carissimo, B.; Dupont, E.

2009-09-01

The interest for micro-scale modeling of the atmosphere is growing for environmental applications related, for example, to energy production, transport and urban development. The turbulence in the stable layers where pollutant dispersion is low and can lead to strong pollution events. This could be further complicated by the presence of clouds or fog and is specifically difficult in urban or industrial area due to the presence of buildings. In this context, radiation fog formation and dissipation over complex terrain were therefore investigated with a state-of-the-art model. This study is divided into two phases. The first phase is a pilot stage, which consist of employing a database from the ParisFog campaign which took place in the south of Paris during winter 2006-07 to assess the ability of the cloud model to reproduce the detailed structure of radiation fog. The second phase use the validated model for the study of influence of complex terrain on fog evolution. Special attention is given to the detailed and complete simulations and validation technique used is to compare the simulated results using the 3D cloud model of computational fluid dynamical software Code_Saturne with one of the best collected in situ data during the ParisFog campaign. Several dynamical, microphysical parameterizations and simulation conditions have been described. The resulting 3D cloud model runs at a horizontal resolution of 30 m and a vertical resolution comparable to the 1D model. First results look very promising and are able to reproduce the spatial distribution of fog. The analysis of the behavior of the different parameterized physical processes suggests that the subtle balance between the various processes is achieved.

Simulation of anaerobic digestion processes using stochastic algorithm.

PubMed

Palanichamy, Jegathambal; Palani, Sundarambal

2014-01-01

The Anaerobic Digestion (AD) processes involve numerous complex biological and chemical reactions occurring simultaneously. Appropriate and efficient models are to be developed for simulation of anaerobic digestion systems. Although several models have been developed, mostly they suffer from lack of knowledge on constants, complexity and weak generalization. The basis of the deterministic approach for modelling the physico and bio-chemical reactions occurring in the AD system is the law of mass action, which gives the simple relationship between the reaction rates and the species concentrations. The assumptions made in the deterministic models are not hold true for the reactions involving chemical species of low concentration. The stochastic behaviour of the physicochemical processes can be modeled at mesoscopic level by application of the stochastic algorithms. In this paper a stochastic algorithm (Gillespie Tau Leap Method) developed in MATLAB was applied to predict the concentration of glucose, acids and methane formation at different time intervals. By this the performance of the digester system can be controlled. The processes given by ADM1 (Anaerobic Digestion Model 1) were taken for verification of the model. The proposed model was verified by comparing the results of Gillespie's algorithms with the deterministic solution for conversion of glucose into methane through degraders. At higher value of 'τ' (timestep), the computational time required for reaching the steady state is more since the number of chosen reactions is less. When the simulation time step is reduced, the results are similar to ODE solver. It was concluded that the stochastic algorithm is a suitable approach for the simulation of complex anaerobic digestion processes. The accuracy of the results depends on the optimum selection of tau value.

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

NASA Astrophysics Data System (ADS)

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

2018-07-01

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

An Integrated Software Package to Enable Predictive Simulation Capabilities

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

Chen, Yousu; Fitzhenry, Erin B.; Jin, Shuangshuang

The power grid is increasing in complexity due to the deployment of smart grid technologies. Such technologies vastly increase the size and complexity of power grid systems for simulation and modeling. This increasing complexity necessitates not only the use of high-performance-computing (HPC) techniques, but a smooth, well-integrated interplay between HPC applications. This paper presents a new integrated software package that integrates HPC applications and a web-based visualization tool based on a middleware framework. This framework can support the data communication between different applications. Case studies with a large power system demonstrate the predictive capability brought by the integrated software package,more » as well as the better situational awareness provided by the web-based visualization tool in a live mode. Test results validate the effectiveness and usability of the integrated software package.« less

Time-spatial model on the dynamics of the proliferation of Aedes aegypti

NASA Astrophysics Data System (ADS)

Gouvêa, Maury Meirelles, Jr.

2017-03-01

Some complex physical systems, such as cellular regulation, ecosystems, and societies, can be represented by local interactions between agents. Then, complex behaviors may emerge. A cellular automaton is a discrete dynamic system with these features. Among the several complex systems, epidemic diseases are given special attention by researchers with respect to their dynamics. Understanding the behavior of an epidemic may well benefit a society. For instance, different proliferation scenarios may be produced and a prevention policy set. This paper presents a new simulation method of the time-spatial spread of the Dengue mosquito with a cellular automaton. Thus, it will be possible to create different dissemination scenarios and preventive policies for these in several regions. Simulations were performed with different initial conditions and parameters as a result of which the behavior of the proposed method was characterized.

Inviscid and viscous flow modelling of complex aircraft configurations using the CFD simulation system sauna

NASA Astrophysics Data System (ADS)

Peace, Andrew J.; May, Nicholas E.; Pocock, Mark F.; Shaw, Jonathon A.

1994-04-01

This paper is concerned with the flow modelling capabilities of an advanced CFD simulation system known by the acronym SAUNA. This system is aimed primarily at complex aircraft configurations and possesses a unique grid generation strategy in its use of block-structured, unstructured or hybrid grids, depending on the geometric complexity of the addressed configuration. The main focus of the paper is in demonstrating the recently developed multi-grid, block-structured grid, viscous flow capability of SAUNA, through its evaluation on a number of configurations. Inviscid predictions are also presented, both as a means of interpreting the viscous results and with a view to showing more completely the capabilities of SAUNA. It is shown that accuracy and flexibility are combined in an efficient manner, thus demonstrating the value of SAUNA in aerodynamic design.

A Fast Method for Embattling Optimization of Ground-Based Radar Surveillance Network

NASA Astrophysics Data System (ADS)

Jiang, H.; Cheng, H.; Zhang, Y.; Liu, J.

A growing number of space activities have created an orbital debris environment that poses increasing impact risks to existing space systems and human space flight. For the safety of in-orbit spacecraft, a lot of observation facilities are needed to catalog space objects, especially in low earth orbit. Surveillance of Low earth orbit objects are mainly rely on ground-based radar, due to the ability limitation of exist radar facilities, a large number of ground-based radar need to build in the next few years in order to meet the current space surveillance demands. How to optimize the embattling of ground-based radar surveillance network is a problem to need to be solved. The traditional method for embattling optimization of ground-based radar surveillance network is mainly through to the detection simulation of all possible stations with cataloged data, and makes a comprehensive comparative analysis of various simulation results with the combinational method, and then selects an optimal result as station layout scheme. This method is time consuming for single simulation and high computational complexity for the combinational analysis, when the number of stations increases, the complexity of optimization problem will be increased exponentially, and cannot be solved with traditional method. There is no better way to solve this problem till now. In this paper, target detection procedure was simplified. Firstly, the space coverage of ground-based radar was simplified, a space coverage projection model of radar facilities in different orbit altitudes was built; then a simplified objects cross the radar coverage model was established according to the characteristics of space objects orbit motion; after two steps simplification, the computational complexity of the target detection was greatly simplified, and simulation results shown the correctness of the simplified results. In addition, the detection areas of ground-based radar network can be easily computed with the simplified model, and then optimized the embattling of ground-based radar surveillance network with the artificial intelligent algorithm, which can greatly simplifies the computational complexities. Comparing with the traditional method, the proposed method greatly improved the computational efficiency.

Simulation training tools for nonlethal weapons using gaming environments

NASA Astrophysics Data System (ADS)

Donne, Alexsana; Eagan, Justin; Tse, Gabriel; Vanderslice, Tom; Woods, Jerry

2006-05-01

Modern simulation techniques have a growing role for evaluating new technologies and for developing cost-effective training programs. A mission simulator facilitates the productive exchange of ideas by demonstration of concepts through compellingly realistic computer simulation. Revolutionary advances in 3D simulation technology have made it possible for desktop computers to process strikingly realistic and complex interactions with results depicted in real-time. Computer games now allow for multiple real human players and "artificially intelligent" (AI) simulated robots to play together. Advances in computer processing power have compensated for the inherent intensive calculations required for complex simulation scenarios. The main components of the leading game-engines have been released for user modifications, enabling game enthusiasts and amateur programmers to advance the state-of-the-art in AI and computer simulation technologies. It is now possible to simulate sophisticated and realistic conflict situations in order to evaluate the impact of non-lethal devices as well as conflict resolution procedures using such devices. Simulations can reduce training costs as end users: learn what a device does and doesn't do prior to use, understand responses to the device prior to deployment, determine if the device is appropriate for their situational responses, and train with new devices and techniques before purchasing hardware. This paper will present the status of SARA's mission simulation development activities, based on the Half-Life gameengine, for the purpose of evaluating the latest non-lethal weapon devices, and for developing training tools for such devices.

Uranyl extraction by N,N-dialkylamide ligands studied using static and dynamic DFT simulations.

PubMed

Sieffert, Nicolas; Wipff, Georges

2015-02-14

We report DFT static and dynamic studies on uranyl complexes [UO(2)(NO(3))x(H(2)O)(y)L(z)](2-x) involved in the uranyl extraction from water to an "oil" phase (hexane) by an amide ligand L (N,N-dimethylacetamide). Static DFT results "in solution" (continuum SMD models for water and hexane) predict that the stepwise formation of [UO(2)(NO(3))(2)L(2)] from the UO(2)(H(2)O)(5)(2+) species is energetically favourable, and allow us to compare cis/trans isomers of penta- and hexa-coordinated complexes and key intermediates in the two solvents. DFT-MD simulations of [UO(2)(NO(3))(2)L(2)], [UO(2)(NO(3))(2)(H(2)O)L(2)], and [UO(2)(NO(3))(H(2)O)L(2)](+) species in explicit solvent environments (water, hexane, or the water/hexane interface) represented at the MM or full-DFT level reveal a versatile solvent dependent binding mode of nitrates, also evidenced by metadynamics simulations. In water and at the interface, the latter exchange from bi- to monodentate, via in plane rotational motions in some cases. Remarkably, structures of complexes at the interface are more "water-like" than gas phase- or hexane-like. Thus, the order of U-O(NO(3))/U-O(L) bond distances observed in the gas phase (U-O(nit) < U-OL) is inverted at the interface and in water. Overall, the results are consistent with the experimental observation of uranyl extraction from nitric acid solutions by amide analogues (bearing "fatty" substituents), and allow us to propose possible extraction mechanisms, involving complexation of L "right at the interface". They also point to the importance of the solvent environment and the dynamics on the structure and stability of the complexes.

Aortic dissection simulation models for clinical support: fluid-structure interaction vs. rigid wall models.

PubMed

Alimohammadi, Mona; Sherwood, Joseph M; Karimpour, Morad; Agu, Obiekezie; Balabani, Stavroula; Díaz-Zuccarini, Vanessa

2015-04-15

The management and prognosis of aortic dissection (AD) is often challenging and the use of personalised computational models is being explored as a tool to improve clinical outcome. Including vessel wall motion in such simulations can provide more realistic and potentially accurate results, but requires significant additional computational resources, as well as expertise. With clinical translation as the final aim, trade-offs between complexity, speed and accuracy are inevitable. The present study explores whether modelling wall motion is worth the additional expense in the case of AD, by carrying out fluid-structure interaction (FSI) simulations based on a sample patient case. Patient-specific anatomical details were extracted from computed tomography images to provide the fluid domain, from which the vessel wall was extrapolated. Two-way fluid-structure interaction simulations were performed, with coupled Windkessel boundary conditions and hyperelastic wall properties. The blood was modelled using the Carreau-Yasuda viscosity model and turbulence was accounted for via a shear stress transport model. A simulation without wall motion (rigid wall) was carried out for comparison purposes. The displacement of the vessel wall was comparable to reports from imaging studies in terms of intimal flap motion and contraction of the true lumen. Analysis of the haemodynamics around the proximal and distal false lumen in the FSI model showed complex flow structures caused by the expansion and contraction of the vessel wall. These flow patterns led to significantly different predictions of wall shear stress, particularly its oscillatory component, which were not captured by the rigid wall model. Through comparison with imaging data, the results of the present study indicate that the fluid-structure interaction methodology employed herein is appropriate for simulations of aortic dissection. Regions of high wall shear stress were not significantly altered by the wall motion, however, certain collocated regions of low and oscillatory wall shear stress which may be critical for disease progression were only identified in the FSI simulation. We conclude that, if patient-tailored simulations of aortic dissection are to be used as an interventional planning tool, then the additional complexity, expertise and computational expense required to model wall motion is indeed justified.

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Modeling hydraulic regenerative hybrid vehicles using AMESim and Matlab/Simulink

NASA Astrophysics Data System (ADS)

Lynn, Alfred; Smid, Edzko; Eshraghi, Moji; Caldwell, Niall; Woody, Dan

2005-05-01

This paper presents the overview of the simulation modeling of a hydraulic system with regenerative braking used to improve vehicle emissions and fuel economy. Two simulation software packages were used together to enhance the simulation capability for fuel economy results and development of vehicle and hybrid control strategy. AMESim, a hydraulic simulation software package modeled the complex hydraulic circuit and component hardware and was interlinked with a Matlab/Simulink model of the vehicle, engine and the control strategy required to operate the vehicle and the hydraulic hybrid system through various North American and European drive cycles.

Energetic and flexibility properties captured by long molecular dynamics simulations of a membrane-embedded pMHCII-TCR complex.

PubMed

Bello, Martiniano; Correa-Basurto, José

2016-04-01

Although crystallographic data have provided important molecular insight into the interactions in the pMHC-TCR complex, the inherent features of this structural approach cause it to only provide a static picture of the interactions. While unbiased molecular dynamics simulations (UMDSs) have provided important information about the dynamic structural behavior of the pMHC-TCR complex, most of them have modeled the pMHC-TCR complex as soluble, when in physiological conditions, this complex is membrane bound; therefore, following this latter UMDS protocol might hamper important dynamic results. In this contribution, we performed three independent 300 ns-long UMDSs of the pMHCII-TCR complex anchored in two opposing membranes to explore the structural and energetic properties of the recognition of pMHCII by the TCR. The conformational ensemble generated through UMDSs was subjected to clustering and Cartesian principal component analyses (cPCA) to explore the dynamical behavior of the pMHCII-TCR association. Furthermore, based on the conformational population sampled through UMDSs, the effective binding free energy, per-residue free energy decomposition, and alanine scanning mutations were explored for the native pMHCII-TCR complex, as well as for 12 mutations (p1-p12MHCII-TCR) introduced in the native peptide. Clustering analyses and cPCA provide insight into the rocking motion of the TCR onto pMHCII, together with the presence of new electrostatic interactions not observed through crystallographic methods. Energetic results provide evidence of the main contributors to the pMHC-TCR complex formation as well as the key residues involved in this molecular recognition process.

Aeroelastic-Acoustics Simulation of Flight Systems

NASA Technical Reports Server (NTRS)

Gupta, kajal K.; Choi, S.; Ibrahim, A.

2009-01-01

This paper describes the details of a numerical finite element (FE) based analysis procedure and a resulting code for the simulation of the acoustics phenomenon arising from aeroelastic interactions. Both CFD and structural simulations are based on FE discretization employing unstructured grids. The sound pressure level (SPL) on structural surfaces is calculated from the root mean square (RMS) of the unsteady pressure and the acoustic wave frequencies are computed from a fast Fourier transform (FFT) of the unsteady pressure distribution as a function of time. The resulting tool proves to be unique as it is designed to analyze complex practical problems, involving large scale computations, in a routine fashion.

Wind energy system time-domain (WEST) analyzers

NASA Technical Reports Server (NTRS)

Dreier, M. E.; Hoffman, J. A.

1981-01-01

A portable analyzer which simulates in real time the complex nonlinear dynamics of horizontal axis wind energy systems was constructed. Math models for an aeroelastic rotor featuring nonlinear aerodynamic and inertial terms were implemented with high speed digital controllers and analog calculation. This model was combined with other math models of elastic supports, control systems, a power train and gimballed rotor kinematics. A stroboscopic display system graphically depicting distributed blade loads, motion, and other aerodynamic functions on a cathode ray tube is included. Limited correlation efforts showed good comparison between the results of this analyzer and other sophisticated digital simulations. The digital simulation results were successfully correlated with test data.

Hierarchical Model for the Analysis of Scattering Data of Complex Materials

DOE PAGES

Oyedele, Akinola; Mcnutt, Nicholas W.; Rios, Orlando; ...

2016-05-16

Interpreting the results of scattering data for complex materials with a hierarchical structure in which at least one phase is amorphous presents a significant challenge. Often the interpretation relies on the use of large-scale molecular dynamics (MD) simulations, in which a structure is hypothesized and from which a radial distribution function (RDF) can be extracted and directly compared against an experimental RDF. This computationally intensive approach presents a bottleneck in the efficient characterization of the atomic structure of new materials. Here, we propose and demonstrate an approach for a hierarchical decomposition of the RDF in which MD simulations are replacedmore » by a combination of tractable models and theory at the atomic scale and the mesoscale, which when combined yield the RDF. We apply the procedure to a carbon composite, in which graphitic nanocrystallites are distributed in an amorphous domain. We compare the model with the RDF from both MD simulation and neutron scattering data. Ultimately, this procedure is applicable for understanding the fundamental processing-structure-property relationships in complex magnetic materials.« less

Modeling the Interaction Between Hydraulic and Natural Fractures Using Dual-Lattice Discrete Element Method

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

Zhou, Jing; Huang, Hai; Deo, Milind

The interaction between hydraulic fractures (HF) and natural fractures (NF) will lead to complex fracture networks due to the branching and merging of natural and hydraulic fractures in unconventional reservoirs. In this paper, a newly developed hydraulic fracturing simulator based on discrete element method is used to predict the generation of complex fracture network in the presence of pre-existing natural fractures. By coupling geomechanics and reservoir flow within a dual lattice system, this simulator can effectively capture the poro-elastic effects and fluid leakoff into the formation. When HFs are intercepting single or multiple NFs, complex mechanisms such as direct crossing,more » arresting, dilating and branching can be simulated. Based on the model, the effects of injected fluid rate and viscosity, the orientation and permeability of NFs and stress anisotropy on the HF-NF interaction process are investigated. Combined impacts from multiple parameters are also examined in the paper. The numerical results show that large values of stress anisotropy, intercepting angle, injection rate and viscosity will impede the opening of NFs.« less

Applying Pose Clustering and MD Simulations To Eliminate False Positives in Molecular Docking.

PubMed

Makeneni, Spandana; Thieker, David F; Woods, Robert J

2018-03-26

In this work, we developed a computational protocol that employs multiple molecular docking experiments, followed by pose clustering, molecular dynamic simulations (10 ns), and energy rescoring to produce reliable 3D models of antibody-carbohydrate complexes. The protocol was applied to 10 antibody-carbohydrate co-complexes and three unliganded (apo) antibodies. Pose clustering significantly reduced the number of potential poses. For each system, 15 or fewer clusters out of 100 initial poses were generated and chosen for further analysis. Molecular dynamics (MD) simulations allowed the docked poses to either converge or disperse, and rescoring increased the likelihood that the best-ranked pose was an acceptable pose. This approach is amenable to automation and can be a valuable aid in determining the structure of antibody-carbohydrate complexes provided there is no major side chain rearrangement or backbone conformational change in the H3 loop of the CDR regions. Further, the basic protocol of docking a small ligand to a known binding site, clustering the results, and performing MD with a suitable force field is applicable to any protein ligand system.

A 1.26 μW Cytomimetic IC Emulating Complex Nonlinear Mammalian Cell Cycle Dynamics: Synthesis, Simulation and Proof-of-Concept Measured Results.

PubMed

Houssein, Alexandros; Papadimitriou, Konstantinos I; Drakakis, Emmanuel M

2015-08-01

Cytomimetic circuits represent a novel, ultra low-power, continuous-time, continuous-value class of circuits, capable of mapping on silicon cellular and molecular dynamics modelled by means of nonlinear ordinary differential equations (ODEs). Such monolithic circuits are in principle able to emulate on chip, single or multiple cell operations in a highly parallel fashion. Cytomimetic topologies can be synthesized by adopting the Nonlinear Bernoulli Cell Formalism (NBCF), a mathematical framework that exploits the striking similarities between the equations describing weakly-inverted Metal-Oxide Semiconductor (MOS) devices and coupled nonlinear ODEs, typically appearing in models of naturally encountered biochemical systems. The NBCF maps biological state variables onto strictly positive subthreshold MOS circuit currents. This paper presents the synthesis, the simulation and proof-of-concept chip results corresponding to the emulation of a complex cellular network mechanism, the skeleton model for the network of Cyclin-dependent Kinases (CdKs) driving the mammalian cell cycle. This five variable nonlinear biological model, when appropriate model parameter values are assigned, can exhibit multiple oscillatory behaviors, varying from simple periodic oscillations, to complex oscillations such as quasi-periodicity and chaos. The validity of our approach is verified by simulated results with realistic process parameters from the commercially available AMS 0.35 μm technology and by chip measurements. The fabricated chip occupies an area of 2.27 mm2 and consumes a power of 1.26 μW from a power supply of 3 V. The presented cytomimetic topology follows closely the behavior of its biological counterpart, exhibiting similar time-dependent solutions of the Cdk complexes, the transcription factors and the proteins.

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

Mohanty, Subhasish; Majumdar, Saurindranath

Irradiation creep plays a major role in the structural integrity of the graphite components in high temperature gas cooled reactors. Finite element procedures combined with a suitable irradiation creep model can be used to simulate the time-integrated structural integrity of complex shapes, such as the reactor core graphite reflector and fuel bricks. In the present work a comparative study was undertaken to understand the effect of linear and nonlinear irradiation creep on results of finite element based stress analysis. Numerical results were generated through finite element simulations of a typical graphite reflector.

Definitions of Complexity are Notoriously Difficult

NASA Astrophysics Data System (ADS)

Schuster, Peter

Definitions of complexity are notoriously difficult if not impossible at all. A good working hypothesis might be: Everything is complex that is not simple. This is precisely the way in which we define nonlinear behavior. Things appear complex for different reasons: i) Complexity may result from lack of insight, ii) complexity may result from lack of methods, and (iii) complexity may be inherent to the system. The best known example for i) is celestial mechanics: The highly complex Pythagorean epicycles become obsolete by the introduction of Newton's law of universal gravitation. To give an example for ii), pattern formation and deterministic chaos became not really understandable before extensive computer simulations became possible. Cellular metabolism may serve as an example for iii) and is caused by the enormous complexity of biochemical reaction networks with up to one hundred individual reaction fluxes. Nevertheless, only few fluxes are dominant in the sense that using Pareto optimal values for them provides near optimal values for all the others...

High-resolution dust modelling over complex terrains in West Asia

NASA Astrophysics Data System (ADS)

Basart, S.; Vendrell, L.; Baldasano, J. M.

2016-12-01

The present work demonstrates the impact of model resolution in dust propagation in a complex terrain region such as West Asia. For this purpose, two simulations using the NMMB/BSC-Dust model are performed and analysed, one with a high horizontal resolution (at 0.03° × 0.03°) and one with a lower horizontal resolution (at 0.33° × 0.33°). Both model experiments cover two intense dust storms that occurred on 17-20 March 2012 as a consequence of strong northwesterly Shamal winds that spanned over thousands of kilometres in West Asia. The comparison with ground-based (surface weather stations and sunphotometers) and satellite aerosol observations (Aqua/MODIS and MSG/SEVIRI) shows that despite differences in the magnitude of the simulated dust concentrations, the model is able to reproduce these two dust outbreaks. Differences between both simulations on the dust spread rise on regional dust transport areas in south-western Saudi Arabia, Yemen and Oman. The complex orography in south-western Saudi Arabia, Yemen and Oman (with peaks higher than 3000 m) has an impact on the transported dust concentration fields over mountain regions. Differences between both model configurations are mainly associated to the channelization of the dust flow through valleys and the differences in the modelled altitude of the mountains that alters the meteorology and blocks the dust fronts limiting the dust transport. These results demonstrate how the dust prediction in the vicinity of complex terrains improves using high-horizontal resolution simulations.

The importance of ligand speciation in environmental research: a case study.

PubMed

Sillanpää, M; Orama, M; Rämö, J; Oikari, A

2001-02-21

The speciations of EDTA and DTPA in process, waste and river waters are modelled and simulated, specifically to the mode of occurrence in the pulp and paper mill effluents and subsequently in receiving waters. Due to relatively short residence times in bleaching process and waste water treatment and slow exchange kinetics, it is expected that the thermodynamic equilibrium is not necessarily reached. Therefore, the initial speciation plays a key role. As such, the simulations have been extended to the process waters of the pulp and paper industry taking into account estimated average conditions. The results reveal that the main species are; Mn and Ca complexes of EDTA and DTPA in pulp mill process waters; Fe(III) and Mn complexes of EDTA and DTPA in waste waters; Fe(III) and Zn complexes of EDTA and DTPA in receiving waters. It is also shown how the increasing concentration of complexing agents effects the speciation. Alkaline earth metal chelation plays a significant role in the speciation of EDTA and DTPA when there is a noticeable molar excess of complexing agents compared with transition metals.

Evolving Scale-Free Networks by Poisson Process: Modeling and Degree Distribution.

PubMed

Feng, Minyu; Qu, Hong; Yi, Zhang; Xie, Xiurui; Kurths, Jurgen

2016-05-01

Since the great mathematician Leonhard Euler initiated the study of graph theory, the network has been one of the most significant research subject in multidisciplinary. In recent years, the proposition of the small-world and scale-free properties of complex networks in statistical physics made the network science intriguing again for many researchers. One of the challenges of the network science is to propose rational models for complex networks. In this paper, in order to reveal the influence of the vertex generating mechanism of complex networks, we propose three novel models based on the homogeneous Poisson, nonhomogeneous Poisson and birth death process, respectively, which can be regarded as typical scale-free networks and utilized to simulate practical networks. The degree distribution and exponent are analyzed and explained in mathematics by different approaches. In the simulation, we display the modeling process, the degree distribution of empirical data by statistical methods, and reliability of proposed networks, results show our models follow the features of typical complex networks. Finally, some future challenges for complex systems are discussed.

Final Report: A Broad Research Project on the Sciences of Complexity, September 15, 1994 - November 15, 1999

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

None

2000-02-01

DOE support for a broad research program in the sciences of complexity permitted the Santa Fe Institute to initiate new collaborative research within its integrative core activities as well as to host visitors to participate in research on specific topics that serve as motivation and testing ground for the study of the general principles of complex systems. Results are presented on computational biology, biodiversity and ecosystem research, and advanced computing and simulation.

Mapping mechanical force propagation through biomolecular complexes

DOE PAGES

Schoeler, Constantin; Bernardi, Rafael C.; Malinowska, Klara H.; ...

2015-08-11

In this paper, we employ single-molecule force spectroscopy with an atomic force microscope (AFM) and steered molecular dynamics (SMD) simulations to reveal force propagation pathways through a mechanically ultrastable multidomain cellulosome protein complex. We demonstrate a new combination of network-based correlation analysis supported by AFM directional pulling experiments, which allowed us to visualize stiff paths through the protein complex along which force is transmitted. Finally, the results implicate specific force-propagation routes nonparallel to the pulling axis that are advantageous for achieving high dissociation forces.

On the robustness of complex heterogeneous gene expression networks.

PubMed

Gómez-Gardeñes, Jesús; Moreno, Yamir; Floría, Luis M

2005-04-01

We analyze a continuous gene expression model on the underlying topology of a complex heterogeneous network. Numerical simulations aimed at studying the chaotic and periodic dynamics of the model are performed. The results clearly indicate that there is a region in which the dynamical and structural complexity of the system avoid chaotic attractors. However, contrary to what has been reported for Random Boolean Networks, the chaotic phase cannot be completely suppressed, which has important bearings on network robustness and gene expression modeling.

Parameterization and Sensitivity Analysis of a Complex Simulation Model for Mosquito Population Dynamics, Dengue Transmission, and Their Control

PubMed Central

Ellis, Alicia M.; Garcia, Andres J.; Focks, Dana A.; Morrison, Amy C.; Scott, Thomas W.

2011-01-01

Models can be useful tools for understanding the dynamics and control of mosquito-borne disease. More detailed models may be more realistic and better suited for understanding local disease dynamics; however, evaluating model suitability, accuracy, and performance becomes increasingly difficult with greater model complexity. Sensitivity analysis is a technique that permits exploration of complex models by evaluating the sensitivity of the model to changes in parameters. Here, we present results of sensitivity analyses of two interrelated complex simulation models of mosquito population dynamics and dengue transmission. We found that dengue transmission may be influenced most by survival in each life stage of the mosquito, mosquito biting behavior, and duration of the infectious period in humans. The importance of these biological processes for vector-borne disease models and the overwhelming lack of knowledge about them make acquisition of relevant field data on these biological processes a top research priority. PMID:21813844

Regimes of Flow over Complex Structures of Endothelial Glycocalyx: A Molecular Dynamics Simulation Study.

PubMed

Jiang, Xi Zhuo; Feng, Muye; Ventikos, Yiannis; Luo, Kai H

2018-04-10

Flow patterns on surfaces grafted with complex structures play a pivotal role in many engineering and biomedical applications. In this research, large-scale molecular dynamics (MD) simulations are conducted to study the flow over complex surface structures of an endothelial glycocalyx layer. A detailed structure of glycocalyx has been adopted and the flow/glycocalyx system comprises about 5,800,000 atoms. Four cases involving varying external forces and modified glycocalyx configurations are constructed to reveal intricate fluid behaviour. Flow profiles including temporal evolutions and spatial distributions of velocity are illustrated. Moreover, streamline length and vorticity distributions under the four scenarios are compared and discussed to elucidate the effects of external forces and glycocalyx configurations on flow patterns. Results show that sugar chain configurations affect streamline length distributions but their impact on vorticity distributions is statistically insignificant, whilst the influence of the external forces on both streamline length and vorticity distributions are trivial. Finally, a regime diagram for flow over complex surface structures is proposed to categorise flow patterns.

Simulating Carbon cycle and phenology in complex forests using a multi-layer process based ecosystem model; evaluation and use of 3D-CMCC-Forest Ecosystem Model in a deciduous and an evergreen neighboring forests, within the area of Brasschaat (Be)

NASA Astrophysics Data System (ADS)

Marconi, S.; Collalti, A.; Santini, M.; Valentini, R.

2013-12-01

3D-CMCC-Forest Ecosystem Model is a process based model formerly developed for complex forest ecosystems to estimate growth, water and carbon cycles, phenology and competition processes on a daily/monthly time scale. The Model integrates some characteristics of the functional-structural tree models with the robustness of the light use efficiency approach. It treats different heights, ages and species as discrete classes, in competition for light (vertical structure) and space (horizontal structure). The present work evaluates the results of the recently developed daily version of 3D-CMCC-FEM for two neighboring different even aged and mono specific study cases. The former is a heterogeneous Pedunculate oak forest (Quercus robur L. ), the latter a more homogeneous Scot pine forest (Pinus sylvestris L.). The multi-layer approach has been evaluated against a series of simplified versions to determine whether the improved model complexity in canopy structure definition increases its predictive ability. Results show that a more complex structure (three height layers) should be preferable to simulate heterogeneous scenarios (Pedunculate oak stand), where heights distribution within the canopy justify the distinction in dominant, dominated and sub-dominated layers. On the contrary, it seems that using a multi-layer approach for more homogeneous stands (Scot pine stand) may be disadvantageous. Forcing the structure of an homogeneous stand to a multi-layer approach may in fact increase sources of uncertainty. On the other hand forcing complex forests to a mono layer simplified model, may cause an increase in mortality and a reduction in average DBH and Height. Compared with measured CO2 flux data, model results show good ability in estimating carbon sequestration trends, on both a monthly/seasonal and daily time scales. Moreover the model simulates quite well leaf phenology and the combined effects of the two different forest stands on CO2 fluxes.

Using numeric simulation in an online e-learning environment to teach functional physiological contexts.

PubMed

Christ, Andreas; Thews, Oliver

2016-04-01

Mathematical models are suitable to simulate complex biological processes by a set of non-linear differential equations. These simulation models can be used as an e-learning tool in medical education. However, in many cases these mathematical systems have to be treated numerically which is computationally intensive. The aim of the study was to develop a system for numerical simulation to be used in an online e-learning environment. In the software system the simulation is located on the server as a CGI application. The user (student) selects the boundary conditions for the simulation (e.g., properties of a simulated patient) on the browser. With these parameters the simulation on the server is started and the simulation result is re-transferred to the browser. With this system two examples of e-learning units were realized. The first one uses a multi-compartment model of the glucose-insulin control loop for the simulation of the plasma glucose level after a simulated meal or during diabetes (including treatment by subcutaneous insulin application). The second one simulates the ion transport leading to the resting and action potential in nerves. The student can vary parameters systematically to explore the biological behavior of the system. The described system is able to simulate complex biological processes and offers the possibility to use these models in an online e-learning environment. As far as the underlying principles can be described mathematically, this type of system can be applied to a broad spectrum of biomedical or natural scientific topics. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Chimaera simulation of complex states of flowing matter

PubMed Central

2016-01-01

We discuss a unified mesoscale framework (chimaera) for the simulation of complex states of flowing matter across scales of motion. The chimaera framework can deal with each of the three macro–meso–micro levels through suitable ‘mutations’ of the basic mesoscale formulation. The idea is illustrated through selected simulations of complex micro- and nanoscale flows. This article is part of the themed issue ‘Multiscale modelling at the physics–chemistry–biology interface’. PMID:27698031

Evaluation of a micro-scale wind model's performance over realistic building clusters using wind tunnel experiments

NASA Astrophysics Data System (ADS)

Zhang, Ning; Du, Yunsong; Miao, Shiguang; Fang, Xiaoyi

2016-08-01

The simulation performance over complex building clusters of a wind simulation model (Wind Information Field Fast Analysis model, WIFFA) in a micro-scale air pollutant dispersion model system (Urban Microscale Air Pollution dispersion Simulation model, UMAPS) is evaluated using various wind tunnel experimental data including the CEDVAL (Compilation of Experimental Data for Validation of Micro-Scale Dispersion Models) wind tunnel experiment data and the NJU-FZ experiment data (Nanjing University-Fang Zhuang neighborhood wind tunnel experiment data). The results show that the wind model can reproduce the vortexes triggered by urban buildings well, and the flow patterns in urban street canyons and building clusters can also be represented. Due to the complex shapes of buildings and their distributions, the simulation deviations/discrepancies from the measurements are usually caused by the simplification of the building shapes and the determination of the key zone sizes. The computational efficiencies of different cases are also discussed in this paper. The model has a high computational efficiency compared to traditional numerical models that solve the Navier-Stokes equations, and can produce very high-resolution (1-5 m) wind fields of a complex neighborhood scale urban building canopy (~ 1 km ×1 km) in less than 3 min when run on a personal computer.

Modeling the Land Use/Cover Change in an Arid Region Oasis City Constrained by Water Resource and Environmental Policy Change using Cellular Automata Model

NASA Astrophysics Data System (ADS)

Hu, X.; Li, X.; Lu, L.

2017-12-01

Land use/cover change (LUCC) is an important subject in the research of global environmental change and sustainable development, while spatial simulation on land use/cover change is one of the key content of LUCC and is also difficult due to the complexity of the system. The cellular automata (CA) model had an irreplaceable role in simulating of land use/cover change process due to the powerful spatial computing power. However, the majority of current CA land use/cover models were binary-state model that could not provide more general information about the overall spatial pattern of land use/cover change. Here, a multi-state logistic-regression-based Markov cellular automata (MLRMCA) model and a multi-state artificial-neural-network-based Markov cellular automata (MANNMCA) model were developed and were used to simulate complex land use/cover evolutionary process in an arid region oasis city constrained by water resource and environmental policy change, the Zhangye city during the period of 1990-2010. The results indicated that the MANNMCA model was superior to MLRMCA model in simulated accuracy. These indicated that by combining the artificial neural network with CA could more effectively capture the complex relationships between the land use/cover change and a set of spatial variables. Although the MLRMCA model were also some advantages, the MANNMCA model was more appropriate for simulating complex land use/cover dynamics. The two proposed models were effective and reliable, and could reflect the spatial evolution of regional land use/cover changes. These have also potential implications for the impact assessment of water resources, ecological restoration, and the sustainable urban development in arid areas.

Large eddy simulation for predicting turbulent heat transfer in gas turbines.

PubMed

Tafti, Danesh K; He, Long; Nagendra, K

2014-08-13

Blade cooling technology will play a critical role in the next generation of propulsion and power generation gas turbines. Accurate prediction of blade metal temperature can avoid the use of excessive compressed bypass air and allow higher turbine inlet temperature, increasing fuel efficiency and decreasing emissions. Large eddy simulation (LES) has been established to predict heat transfer coefficients with good accuracy under various non-canonical flows, but is still limited to relatively simple geometries and low Reynolds numbers. It is envisioned that the projected increase in computational power combined with a drop in price-to-performance ratio will make system-level simulations using LES in complex blade geometries at engine conditions accessible to the design process in the coming one to two decades. In making this possible, two key challenges are addressed in this paper: working with complex intricate blade geometries and simulating high-Reynolds-number (Re) flows. It is proposed to use the immersed boundary method (IBM) combined with LES wall functions. A ribbed duct at Re=20 000 is simulated using the IBM, and a two-pass ribbed duct is simulated at Re=100 000 with and without rotation (rotation number Ro=0.2) using LES with wall functions. The results validate that the IBM is a viable alternative to body-conforming grids and that LES with wall functions reproduces experimental results at a much lower computational cost. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Enabling Co-Design of Multi-Layer Exascale Storage Architectures

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

Carothers, Christopher

Growing demands for computing power in applications such as energy production, climate analysis, computational chemistry, and bioinformatics have propelled computing systems toward the exascale: systems with 10 18 floating-point operations per second. These systems, to be designed and constructed over the next decade, will create unprecedented challenges in component counts, power consumption, resource limitations, and system complexity. Data storage and access are an increasingly important and complex component in extreme-scale computing systems, and significant design work is needed to develop successful storage hardware and software architectures at exascale. Co-design of these systems will be necessary to find the best possiblemore » design points for exascale systems. The goal of this work has been to enable the exploration and co-design of exascale storage systems by providing a detailed, accurate, and highly parallel simulation of exascale storage and the surrounding environment. Specifically, this simulation has (1) portrayed realistic application checkpointing and analysis workloads, (2) captured the complexity, scale, and multilayer nature of exascale storage hardware and software, and (3) executed in a timeframe that enables “what if'” exploration of design concepts. We developed models of the major hardware and software components in an exascale storage system, as well as the application I/O workloads that drive them. We used our simulation system to investigate critical questions in reliability and concurrency at exascale, helping guide the design of future exascale hardware and software architectures. Additionally, we provided this system to interested vendors and researchers so that others can explore the design space. We validated the capabilities of our simulation environment by configuring the simulation to represent the Argonne Leadership Computing Facility Blue Gene/Q system and comparing simulation results for application I/O patterns to the results of executions of these I/O kernels on the actual system.« less

Numerical Simulation of Blast Action on Civil Structures in Urban Environment

NASA Astrophysics Data System (ADS)

Valger, Svetlana A.; Fedorova, Natalya N.; Fedorov, Alexander V.

2017-10-01

Nowadays, a lot of industrial accidents accompanied by explosions are happening throughout the world. Also, increase in the number of terrorist acts committed by means of explosions is observed. For improving safety of buildings and structures it is necessary to raise their resistance to explosive effects, as well as to be able to predict degree of potential damage upon explosive loads of various intensities. One of the principal goals in designing the structure resistant to explosive effects is to determine the dynamic response of structures to the impact of the blast wave. To this end, the transient pressure loads on the walls of the civil engineering structures are to be determined. The simulation of explosion is highly complicated, involving an explosion causing the shock wave propagation in air and then interaction with a structure. The engineering-level techniques permit one to estimate an explosive shock impact only for isolated buildings. The complexity of the building, the presence of nearby structures and the surrounding environment cannot be taken into account. Advanced computer aid engineering (CAE) software techniques combined with the latest methods of discrete three-dimensional city modelling permits one to simulate and analyse the effects of explosions in urban areas with a precision which previously was not possible. In the paper, the simulation results are presented of shock wave forming due to a spherical explosive charge and its propagation in the vicinity of geometrical configuration imitating an urban environment. The numerical simulation of a flow in the vicinity of prisms of different cross-sections and heights located on a flat plate was performed. The calculations are carried out in a three-dimensional non-viscous formulation using ANSYS software. On a basis of simulation results, a complex wave structures were analysed, and all the peculiarities of flows and pressure history records on building walls were described and explained. The possibility of a correct description of the non-stationary wave flow in the vicinity of the complex of obstacles is demonstrated. The results are compared with the experimental data on the pressure distribution in gauges located on the prism walls. The estimation of shock wave exposure intensity was performed to different objects.

Experimentally modeling stochastic processes with less memory by the use of a quantum processor

PubMed Central

Palsson, Matthew S.; Gu, Mile; Ho, Joseph; Wiseman, Howard M.; Pryde, Geoff J.

2017-01-01

Computer simulation of observable phenomena is an indispensable tool for engineering new technology, understanding the natural world, and studying human society. However, the most interesting systems are often so complex that simulating their future behavior demands storing immense amounts of information regarding how they have behaved in the past. For increasingly complex systems, simulation becomes increasingly difficult and is ultimately constrained by resources such as computer memory. Recent theoretical work shows that quantum theory can reduce this memory requirement beyond ultimate classical limits, as measured by a process’ statistical complexity, C. We experimentally demonstrate this quantum advantage in simulating stochastic processes. Our quantum implementation observes a memory requirement of Cq = 0.05 ± 0.01, far below the ultimate classical limit of C = 1. Scaling up this technique would substantially reduce the memory required in simulations of more complex systems. PMID:28168218

A Tool for Parameter-space Explorations

NASA Astrophysics Data System (ADS)

Murase, Yohsuke; Uchitane, Takeshi; Ito, Nobuyasu

A software for managing simulation jobs and results, named "OACIS", is presented. It controls a large number of simulation jobs executed in various remote servers, keeps these results in an organized way, and manages the analyses on these results. The software has a web browser front end, and users can submit various jobs to appropriate remote hosts from a web browser easily. After these jobs are finished, all the result files are automatically downloaded from the computational hosts and stored in a traceable way together with the logs of the date, host, and elapsed time of the jobs. Some visualization functions are also provided so that users can easily grasp the overview of the results distributed in a high-dimensional parameter space. Thus, OACIS is especially beneficial for the complex simulation models having many parameters for which a lot of parameter searches are required. By using API of OACIS, it is easy to write a code that automates parameter selection depending on the previous simulation results. A few examples of the automated parameter selection are also demonstrated.

Probing 1D superlattices at the LaAlO3 / SrTiO3 interface

NASA Astrophysics Data System (ADS)

Briggeman, M.; Huang, M.; Tylan-Tyler, A.; Irvin, P.; Levy, J.; Lee, J.-W.; Lee, H.; Eom, C.-B.

Complex oxides and other quantum systems exhibit behavior that is currently too complex to be understood using analytic or computational methods. One approach is to use a configurable quantum system whose Hamiltonian can be mapped onto the system of interest. This approach, known as quantum simulation, requires a rich physical system whose quanta and interactions can be controlled precisely, at the level of single electrons and other degrees of freedom. Here we describe steps toward developing a quantum simulation platform, using the complex oxide heterostructure LaAlO3 / SrTiO3 , by creating quantum systems with features comparable to the mean spacing between electrons. This interface has strong, sign changing, gate-tunable electron-electron interactions that can strongly influence the quantum ground state. We explore the magnetotransport properties of 1D superlattices, where periodic modulation produces reproducible dispersive features not seen in control structures. The results of these experiments can be compared with effective 1D model Hamiltonians to bridge experiment and theory and enable quantum simulation of more complex systems. We gratefully acknowledge financial support from AFOSR (FA9550-12-1- 0057 (JL) and FA9550-12-1-0342 (CBE)), ONR N00014-15-1-2847 (JL), and NSF DMR-1234096 (CBE).

Queueing Network Models for Parallel Processing of Task Systems: an Operational Approach

NASA Technical Reports Server (NTRS)

Mak, Victor W. K.

1986-01-01

Computer performance modeling of possibly complex computations running on highly concurrent systems is considered. Earlier works in this area either dealt with a very simple program structure or resulted in methods with exponential complexity. An efficient procedure is developed to compute the performance measures for series-parallel-reducible task systems using queueing network models. The procedure is based on the concept of hierarchical decomposition and a new operational approach. Numerical results for three test cases are presented and compared to those of simulations.

Simulation assisted characterization of kaolinite-methanol intercalation complexes synthesized using cost-efficient homogenization method

NASA Astrophysics Data System (ADS)

Makó, Éva; Kovács, András; Ható, Zoltán; Kristóf, Tamás

2015-12-01

Recent experimental and simulation findings with kaolinite-methanol intercalation complexes raised the question of the existence of more stable structures in wet and dry state, which has not been fully cleared up yet. Experimental and molecular simulation analyses were used to investigate different types of kaolinite-methanol complexes, revealing their real structures. Cost-efficient homogenization methods were applied to synthesize the kaolinite-dimethyl sulfoxide and kaolinite-urea pre-intercalation complexes of the kaolinite-methanol ones. The tested homogenization method required an order of magnitude lower amount of reagents than the generally applied solution method. The influence of the type of pre-intercalated molecules and of the wetting or drying (at room temperature and at 150 °C) procedure on the intercalation was characterized experimentally by X-ray diffraction and thermal analysis. Consistent with the suggestion from the present simulations, 1.12-nm and 0.83-nm stable kaolinite-methanol complexes were identified. For these complexes, our molecular simulations predict either single-layered structures of mobile methanol/water molecules or non-intercalated structures of methoxy-functionalized kaolinite. We found that the methoxy-modified kaolinite can easily be intercalated by liquid methanol.

Surface speciation of yttrium and neodymium sorbed on rutile: Interpretations using the charge distribution model

NASA Astrophysics Data System (ADS)

Ridley, Moira K.; Hiemstra, Tjisse; Machesky, Michael L.; Wesolowski, David J.; van Riemsdijk, Willem H.

2012-10-01

The adsorption of Y3+ and Nd3+ onto rutile has been evaluated over a wide range of pH (3-11) and surface loading conditions, as well as at two ionic strengths (0.03 and 0.3 m), and temperatures (25 and 50 °C). The experimental results reveal the same adsorption behavior for the two trivalent ions onto the rutile surface, with Nd3+ first adsorbing at slightly lower pH values. The adsorption of both Y3+ and Nd3+ commences at pH values below the pHznpc of rutile. The experimental results were evaluated using a charge distribution (CD) and multisite complexation (MUSIC) model, and Basic Stern layer description of the electric double layer (EDL). The coordination geometry of possible surface complexes were constrained by molecular-level information obtained from X-ray standing wave measurements and molecular dynamic (MD) simulation studies. X-ray standing wave measurements showed an inner-sphere tetradentate complex for Y3+ adsorption onto the (1 1 0) rutile surface (Zhang et al., 2004b). The MD simulation studies suggest additional bidentate complexes may form. The CD values for all surface species were calculated based on a bond valence interpretation of the surface complexes identified by X-ray and MD. The calculated CD values were corrected for the effect of dipole orientation of interfacial water. At low pH, the tetradentate complex provided excellent fits to the Y3+ and Nd3+ experimental data. The experimental and surface complexation modeling results show a strong pH dependence, and suggest that the tetradentate surface species hydrolyze with increasing pH. Furthermore, with increased surface loading of Y3+ on rutile the tetradentate binding mode was augmented by a hydrolyzed-bidentate Y3+ surface complex. Collectively, the experimental and surface complexation modeling results demonstrate that solution chemistry and surface loading impacts Y3+ surface speciation. The approach taken of incorporating molecular-scale information into surface complexation models (SCMs) should aid in elucidating a fundamental understating of ion-adsorption reactions.

Accounting for Parameter Uncertainty in Complex Atmospheric Models, With an Application to Greenhouse Gas Emissions Evaluation

NASA Astrophysics Data System (ADS)

Swallow, B.; Rigby, M. L.; Rougier, J.; Manning, A.; Thomson, D.; Webster, H. N.; Lunt, M. F.; O'Doherty, S.

2016-12-01

In order to understand underlying processes governing environmental and physical phenomena, a complex mathematical model is usually required. However, there is an inherent uncertainty related to the parameterisation of unresolved processes in these simulators. Here, we focus on the specific problem of accounting for uncertainty in parameter values in an atmospheric chemical transport model. Systematic errors introduced by failing to account for these uncertainties have the potential to have a large effect on resulting estimates in unknown quantities of interest. One approach that is being increasingly used to address this issue is known as emulation, in which a large number of forward runs of the simulator are carried out, in order to approximate the response of the output to changes in parameters. However, due to the complexity of some models, it is often unfeasible to run large numbers of training runs that is usually required for full statistical emulators of the environmental processes. We therefore present a simplified model reduction method for approximating uncertainties in complex environmental simulators without the need for very large numbers of training runs. We illustrate the method through an application to the Met Office's atmospheric transport model NAME. We show how our parameter estimation framework can be incorporated into a hierarchical Bayesian inversion, and demonstrate the impact on estimates of UK methane emissions, using atmospheric mole fraction data. We conclude that accounting for uncertainties in the parameterisation of complex atmospheric models is vital if systematic errors are to be minimized and all relevant uncertainties accounted for. We also note that investigations of this nature can prove extremely useful in highlighting deficiencies in the simulator that might otherwise be missed.

Stereoscopy for visual simulation of materials of complex appearance

NASA Astrophysics Data System (ADS)

da Graça, Fernando; Paljic, Alexis; Lafon-Pham, Dominique; Callet, Patrick

2014-03-01

The present work studies the role of stereoscopy on perceived surface aspect of computer generated complex materials. The objective is to investigate if, and how, the additional information conveyed by the binocular vision affects the observer judgment on the evaluation of flake density in an effect paint simulation. We have set up a heuristic flake model with a Voronoi: modelization of flakes. The model was implemented in our rendering engine using global illumination, ray tracing, with an off axis-frustum method for the calculation of stereo images. We conducted a user study based on a flake density discrimination task to determine perception thresholds (JNDs). Results show that stereoscopy slightly improves density perception. We propose an analysis methodology based on granulometry. This allows for a discussion of the results on the basis of scales of observation.

Design of Improved Arithmetic Logic Unit in Quantum-Dot Cellular Automata

NASA Astrophysics Data System (ADS)

Heikalabad, Saeed Rasouli; Gadim, Mahya Rahimpour

2018-06-01

The quantum-dot cellular automata (QCA) can be replaced to overcome the limitation of CMOS technology. An arithmetic logic unit (ALU) is a basic structure of any computer devices. In this paper, design of improved single-bit arithmetic logic unit in quantum dot cellular automata is presented. The proposed structure for ALU has AND, OR, XOR and ADD operations. A unique 2:1 multiplexer, an ultra-efficient two-input XOR and a low complexity full adder are used in the proposed structure. Also, an extended design of this structure is provided for two-bit ALU in this paper. The proposed structure of ALU is simulated by QCADesigner and simulation result is evaluated. Evaluation results show that the proposed design has best performance in terms of area, complexity and delay compared to the previous designs.

Design of Improved Arithmetic Logic Unit in Quantum-Dot Cellular Automata

NASA Astrophysics Data System (ADS)

Heikalabad, Saeed Rasouli; Gadim, Mahya Rahimpour

2018-03-01

The quantum-dot cellular automata (QCA) can be replaced to overcome the limitation of CMOS technology. An arithmetic logic unit (ALU) is a basic structure of any computer devices. In this paper, design of improved single-bit arithmetic logic unit in quantum dot cellular automata is presented. The proposed structure for ALU has AND, OR, XOR and ADD operations. A unique 2:1 multiplexer, an ultra-efficient two-input XOR and a low complexity full adder are used in the proposed structure. Also, an extended design of this structure is provided for two-bit ALU in this paper. The proposed structure of ALU is simulated by QCADesigner and simulation result is evaluated. Evaluation results show that the proposed design has best performance in terms of area, complexity and delay compared to the previous designs.

Power estimation using simulations for air pollution time-series studies

PubMed Central

2012-01-01

Background Estimation of power to assess associations of interest can be challenging for time-series studies of the acute health effects of air pollution because there are two dimensions of sample size (time-series length and daily outcome counts), and because these studies often use generalized linear models to control for complex patterns of covariation between pollutants and time trends, meteorology and possibly other pollutants. In general, statistical software packages for power estimation rely on simplifying assumptions that may not adequately capture this complexity. Here we examine the impact of various factors affecting power using simulations, with comparison of power estimates obtained from simulations with those obtained using statistical software. Methods Power was estimated for various analyses within a time-series study of air pollution and emergency department visits using simulations for specified scenarios. Mean daily emergency department visit counts, model parameter value estimates and daily values for air pollution and meteorological variables from actual data (8/1/98 to 7/31/99 in Atlanta) were used to generate simulated daily outcome counts with specified temporal associations with air pollutants and randomly generated error based on a Poisson distribution. Power was estimated by conducting analyses of the association between simulated daily outcome counts and air pollution in 2000 data sets for each scenario. Power estimates from simulations and statistical software (G*Power and PASS) were compared. Results In the simulation results, increasing time-series length and average daily outcome counts both increased power to a similar extent. Our results also illustrate the low power that can result from using outcomes with low daily counts or short time series, and the reduction in power that can accompany use of multipollutant models. Power estimates obtained using standard statistical software were very similar to those from the simulations when properly implemented; implementation, however, was not straightforward. Conclusions These analyses demonstrate the similar impact on power of increasing time-series length versus increasing daily outcome counts, which has not previously been reported. Implementation of power software for these studies is discussed and guidance is provided. PMID:22995599

Research on Multi Hydrological Models Applicability and Modelling Data Uncertainty Analysis for Flash Flood Simulation in Hilly Area

NASA Astrophysics Data System (ADS)

Ye, L.; Wu, J.; Wang, L.; Song, T.; Ji, R.

2017-12-01

Flooding in small-scale watershed in hilly area is characterized by short time periods and rapid rise and recession due to the complex underlying surfaces, various climate type and strong effect of human activities. It is almost impossible for a single hydrological model to describe the variation of flooding in both time and space accurately for all the catchments in hilly area because the hydrological characteristics can vary significantly among different catchments. In this study, we compare the performance of 5 hydrological models with varying degrees of complexity for simulation of flash flood for 14 small-scale watershed in China in order to find the relationship between the applicability of the hydrological models and the catchments characteristics. Meanwhile, given the fact that the hydrological data is sparse in hilly area, the effect of precipitation data, DEM resolution and their interference on the uncertainty of flood simulation is also illustrated. In general, the results showed that the distributed hydrological model (HEC-HMS in this study) performed better than the lumped hydrological models. Xinajiang and API models had good simulation for the humid catchments when long-term and continuous rainfall data is provided. Dahuofang model can simulate the flood peak well while the runoff generation module is relatively poor. In addition, the effect of diverse modelling data on the simulations is not simply superposed, and there is a complex interaction effect among different modelling data. Overall, both the catchment hydrological characteristics and modelling data situation should be taken into consideration in order to choose the suitable hydrological model for flood simulation for small-scale catchment in hilly area.

Activity and stability of a complex bacterial soil community under simulated Martian conditions

NASA Astrophysics Data System (ADS)

Hansen, Aviaja Anna; Merrison, Jonathan; Nørnberg, Per; Aagaard Lomstein, Bente; Finster, Kai

2005-04-01

A simulation experiment with a complex bacterial soil community in a Mars simulation chamber was performed to determine the effect of Martian conditions on community activity, stability and survival. At three different depths in the soil core short-term effects of Martian conditions with and without ultraviolet (UV) exposure corresponding to 8 Martian Sol were compared. Community metabolic activities and functional diversity, measured as glucose respiration and versatility in substrate utilization, respectively, decreased after UV exposure, whereas they remained unaffected by Martian conditions without UV exposure. In contrast, the numbers of culturable bacteria and the genetic diversity were unaffected by the simulated Martian conditions both with and without UV exposure. The genetic diversity of the soil community and of the colonies grown on agar plates were evaluated by denaturant gradient gel electrophoresis (DGGE) on DNA extracts. Desiccation of the soil prior to experimentation affected the functional diversity by decreasing the versatility in substrate utilization. The natural dominance of endospores and Gram-positive bacteria in the investigated Mars-analogue soil may explain the limited effect of the Mars incubations on the survival and community structure. Our results suggest that UV radiation and desiccation are major selecting factors on bacterial functional diversity in terrestrial bacterial communities incubated under simulated Martian conditions. Furthermore, these results suggest that forward contamination of Mars is a matter of great concern in future space missions.

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

PubMed

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

2016-10-21

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

i3Drive, a 3D interactive driving simulator.

PubMed

Ambroz, Miha; Prebil, Ivan

2010-01-01

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

Modeling protein-small molecule interactions: structure and thermodynamics of noble gases binding in a cavity in mutant phage T4 lysozyme L99A.

PubMed

Mann, G; Hermans, J

2000-09-29

The complexes of phage T4 lysozyme L99A with noble gases have been studied by molecular dynamics simulation. In a long simulation of the complex with one Xe atom, the structure was found to undergo global conformation change involving a reversible opening and closing of the entrance to the substrate-binding site, during which the conformations of the N and C-terminal domains varied little. The distributions of Xe positions sampled in dynamics simulations were refined in terms of anisotropic Gaussian distributions via least-squares minimization of the difference between Fourier transforms. In addition, molecular transformation simulations have been applied in order to calculate the binding free energies of Xe, Kr and Ar relative to a standard state at a pressure of 1 bar. A single bound Xe is found to assume an equilibrium distribution over three adjacent preferred sites, while in a two-Xe complex, the two Xe atoms preferentially occupy two of these. The positions of the three sites agree closely with the positions of bound Xe determined in the refined crystal structure of a complex formed at a pressure of 8 bar Xe, and the calculated affinities agree well with the observed partial occupancies. At a pressure of 8 bar, a mixture of one-Xe and two-Xe complexes is present, and similarly for complexes with Kr and Ar, with single occupancy relatively more prevalent with Kr and Ar. (Binding of a third Xe atom is found to be quite unfavorable.) A comparison with simulation results for the binding of benzene to the same site leads to the conclusion that binding of Xe within cavities in proteins is common because of several favorable factors: (1) Xe has a large atomic polarizability; (2) Xe can be applied at a relatively high pressure, i.e. high chemical potential; (3) an unfavorable entropic term related to the need to orient the ligand in the binding site is absent. Finally, it is found that the model's binding energy of a water molecule in the cavity is insufficient to overcome the unfavorable binding entropy. Copyright 2000 Academic Press.

An Example-Based Brain MRI Simulation Framework.

PubMed

He, Qing; Roy, Snehashis; Jog, Amod; Pham, Dzung L

2015-02-21

The simulation of magnetic resonance (MR) images plays an important role in the validation of image analysis algorithms such as image segmentation, due to lack of sufficient ground truth in real MR images. Previous work on MRI simulation has focused on explicitly modeling the MR image formation process. However, because of the overwhelming complexity of MR acquisition these simulations must involve simplifications and approximations that can result in visually unrealistic simulated images. In this work, we describe an example-based simulation framework, which uses an "atlas" consisting of an MR image and its anatomical models derived from the hard segmentation. The relationships between the MR image intensities and its anatomical models are learned using a patch-based regression that implicitly models the physics of the MR image formation. Given the anatomical models of a new brain, a new MR image can be simulated using the learned regression. This approach has been extended to also simulate intensity inhomogeneity artifacts based on the statistical model of training data. Results show that the example based MRI simulation method is capable of simulating different image contrasts and is robust to different choices of atlas. The simulated images resemble real MR images more than simulations produced by a physics-based model.

Numerical simulation of complex part manufactured by selective laser melting process

NASA Astrophysics Data System (ADS)

Van Belle, Laurent

2017-10-01

Selective Laser Melting (SLM) process belonging to the family of the Additive Manufacturing (AM) technologies, enable to build parts layer by layer, from metallic powder and a CAD model. Physical phenomena that occur in the process have the same issues as conventional welding. Thermal gradients generate significant residual stresses and distortions in the parts. Moreover, the large and complex parts to manufacturing, accentuate the undesirable effects. Therefore, it is essential for manufacturers to offer a better understanding of the process and to ensure production reliability of parts with high added value. This paper focuses on the simulation of manufacturing turbine by SLM process in order to calculate residual stresses and distortions. Numerical results will be presented.

Design and simulation of the direct drive servo system

NASA Astrophysics Data System (ADS)

Ren, Changzhi; Liu, Zhao; Song, Libin; Yi, Qiang; Chen, Ken; Zhang, Zhenchao

2010-07-01

As direct drive technology is finding their way into telescope drive designs for its many advantages, it would push to more reliable and cheaper solutions for future telescope complex motion system. However, the telescope drive system based on the direct drive technology is one high integrated electromechanical system, which one complex electromechanical design method is adopted to improve the efficiency, reliability and quality of the system during the design and manufacture circle. The telescope is one ultra-exact, ultra-speed, high precision and huge inertial instrument, which the direct torque motor adopted by the telescope drive system is different from traditional motor. This paper explores the design process and some simulation results are discussed.

A systems-based approach for integrated design of materials, products and design process chains

NASA Astrophysics Data System (ADS)

Panchal, Jitesh H.; Choi, Hae-Jin; Allen, Janet K.; McDowell, David L.; Mistree, Farrokh

2007-12-01

The concurrent design of materials and products provides designers with flexibility to achieve design objectives that were not previously accessible. However, the improved flexibility comes at a cost of increased complexity of the design process chains and the materials simulation models used for executing the design chains. Efforts to reduce the complexity generally result in increased uncertainty. We contend that a systems based approach is essential for managing both the complexity and the uncertainty in design process chains and simulation models in concurrent material and product design. Our approach is based on simplifying the design process chains systematically such that the resulting uncertainty does not significantly affect the overall system performance. Similarly, instead of striving for accurate models for multiscale systems (that are inherently complex), we rely on making design decisions that are robust to uncertainties in the models. Accordingly, we pursue hierarchical modeling in the context of design of multiscale systems. In this paper our focus is on design process chains. We present a systems based approach, premised on the assumption that complex systems can be designed efficiently by managing the complexity of design process chains. The approach relies on (a) the use of reusable interaction patterns to model design process chains, and (b) consideration of design process decisions using value-of-information based metrics. The approach is illustrated using a Multifunctional Energetic Structural Material (MESM) design example. Energetic materials store considerable energy which can be released through shock-induced detonation; conventionally, they are not engineered for strength properties. The design objectives for the MESM in this paper include both sufficient strength and energy release characteristics. The design is carried out by using models at different length and time scales that simulate different aspects of the system. Finally, by applying the method to the MESM design problem, we show that the integrated design of materials and products can be carried out more efficiently by explicitly accounting for design process decisions with the hierarchy of models.

Synchronization of fractional-order complex-valued neural networks with time delay.

PubMed

Bao, Haibo; Park, Ju H; Cao, Jinde

2016-09-01

This paper deals with the problem of synchronization of fractional-order complex-valued neural networks with time delays. By means of linear delay feedback control and a fractional-order inequality, sufficient conditions are obtained to guarantee the synchronization of the drive-response systems. Numerical simulations are provided to show the effectiveness of the obtained results. Copyright © 2016 Elsevier Ltd. All rights reserved.

Chimaera simulation of complex states of flowing matter.

PubMed

Succi, S

2016-11-13

We discuss a unified mesoscale framework (chimaera) for the simulation of complex states of flowing matter across scales of motion. The chimaera framework can deal with each of the three macro-meso-micro levels through suitable 'mutations' of the basic mesoscale formulation. The idea is illustrated through selected simulations of complex micro- and nanoscale flows.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'. © 2016 The Author(s).

Potent New Small-Molecule Inhibitor of Botulinum Neurotoxin Serotype A Endopeptidase Developed by Synthesis-Based Computer-Aided Molecular Design

DTIC Science & Technology

2009-11-01

dynamics of the complex predicted by multiple molecular dynamics simulations , and discuss further structural optimization to achieve better in vivo efficacy...complex with BoNTAe and the dynamics of the complex predicted by multiple molecular dynamics simulations (MMDSs). On the basis of the 3D model, we discuss...is unlimited whereas AHP exhibited 54% inhibition under the same conditions (Table 1). Computer Simulation Twenty different molecular dynamics

The Influence of Model Complexity on the Impact Response of a Shuttle Leading-Edge Panel Finite Element Simulation

NASA Technical Reports Server (NTRS)

Jones, Lisa E. (Technical Monitor); Stockwell, Alan E.

2005-01-01

LS-DYNA simulations were conducted to study the influence of model complexity on the response of a typical Reinforced Carbon-Carbon (RCC) panel to a foam impact at a location approximately midway between the ribs. A structural model comprised of Panels 10, 11, and TSeal 11 was chosen as the baseline model for the study. A simulation was conducted with foam striking Panel 10 at Location 4 at an alpha angle of 10 degrees, with an impact velocity of 1000 ft/sec. A second simulation was conducted after removing Panel 11 from the model, and a third simulation was conducted after removing both Panel 11 and T-Seal 11. All three simulations showed approximately the same response for Panel 10, and the simplified simulation model containing only Panel 10 was shown to be significantly less expensive to execute than the other two more complex models.

High Fidelity Simulations of Plume Impingement to the International Space Station

NASA Technical Reports Server (NTRS)

Lumpkin, Forrest E., III; Marichalar, Jeremiah; Stewart, Benedicte D.

2012-01-01

With the retirement of the Space Shuttle, the United States now depends on recently developed commercial spacecraft to supply the International Space Station (ISS) with cargo. These new vehicles supplement ones from international partners including the Russian Progress, the European Autonomous Transfer Vehicle (ATV), and the Japanese H-II Transfer Vehicle (HTV). Furthermore, to carry crew to the ISS and supplement the capability currently provided exclusively by the Russian Soyuz, new designs and a refinement to a cargo vehicle design are in work. Many of these designs include features such as nozzle scarfing or simultaneous firing of multiple thrusters resulting in complex plumes. This results in a wide variety of complex plumes impinging upon the ISS. Therefore, to ensure safe "proximity operations" near the ISS, the need for accurate and efficient high fidelity simulation of plume impingement to the ISS is as high as ever. A capability combining computational fluid dynamics (CFD) and the Direct Simulation Monte Carlo (DSMC) techniques has been developed to properly model the large density variations encountered as the plume expands from the high pressure in the combustion chamber to the near vacuum conditions at the orbiting altitude of the ISS. Details of the computational tools employed by this method, including recent software enhancements and the best practices needed to achieve accurate simulations, are discussed. Several recent examples of the application of this high fidelity capability are presented. These examples highlight many of the real world, complex features of plume impingement that occur when "visiting vehicles" operate in the vicinity of the ISS.

A Simplified Finite Element Simulation for Straightening Process of Thin-Walled Tube

NASA Astrophysics Data System (ADS)

Zhang, Ziqian; Yang, Huilin

2017-12-01

The finite element simulation is an effective way for the study of thin-walled tube in the two cross rolls straightening process. To determine the accurate radius of curvature of the roll profile more efficiently, a simplified finite element model based on the technical parameters of an actual two cross roll straightening machine, was developed to simulate the complex straightening process. Then a dynamic simulation was carried out using ANSYS LS-DYNA program. The result implied that the simplified finite element model was reasonable for simulate the two cross rolls straightening process, and can be obtained the radius of curvature of the roll profile with the tube’s straightness 2 mm/m.

Molecular dynamics simulation and TDDFT study of the structures and UV-vis absorption spectra of MCT-β-CD and its inclusion complexes.

PubMed

Lu, Huijuan; Wang, Yujiao; Xie, Xiaomei; Chen, Feifei; Li, Wei

2015-01-01

In this research, the inclusion ratios and inclusion constants of MCT-β-CD/PERM and MCT-β-CD/CYPERM inclusion complexes were measured by UV-vis and fluorescence spectroscopy. The inclusion ratios are both 1:1, and the inclusion constants are 60 and 342.5 for MCT-β-CD/PERM and MCT-β-CD/CYPERM, respectively. The stabilities of inclusion complexes were investigated by MD simulation. MD shows that VDW energy plays a vital role in the stability of inclusion complex, and the destruction of inclusion complex is due to the increasing temperature. The UV-vis absorption spectra of MCT-β-CD and its inclusion complexes were studied by time-dependent density functional theory (TDDFT) method employing BLYP-D3, B3LYP-D3 and M06-2X-D3 functionals. BLYP-D3 well reproduces the UV-vis absorption spectrum and reveals that the absorption bands of MCT-β-CD mainly arise from n→π(∗) and n→σ(∗) transition, and those of inclusion complexes mainly arise from intramolecular charge transfer (ICT). ICT results in the shift of main absorption bands of MCT-β-CD. Copyright © 2015 Elsevier B.V. All rights reserved.

Secondary task for full flight simulation incorporating tasks that commonly cause pilot error: Time estimation

NASA Technical Reports Server (NTRS)

Rosch, E.

1975-01-01

The task of time estimation, an activity occasionally performed by pilots during actual flight, was investigated with the objective of providing human factors investigators with an unobtrusive and minimally loading additional task that is sensitive to differences in flying conditions and flight instrumentation associated with the main task of piloting an aircraft simulator. Previous research indicated that the duration and consistency of time estimates is associated with the cognitive, perceptual, and motor loads imposed by concurrent simple tasks. The relationships between the length and variability of time estimates and concurrent task variables under a more complex situation involving simulated flight were clarified. The wrap-around effect with respect to baseline duration, a consequence of mode switching at intermediate levels of concurrent task distraction, should contribute substantially to estimate variability and have a complex effect on the shape of the resulting distribution of estimates.

MD simulations of papillomavirus DNA-E2 protein complexes hints at a protein structural code for DNA deformation.

PubMed

Falconi, M; Oteri, F; Eliseo, T; Cicero, D O; Desideri, A

2008-08-01

The structural dynamics of the DNA binding domains of the human papillomavirus strain 16 and the bovine papillomavirus strain 1, complexed with their DNA targets, has been investigated by modeling, molecular dynamics simulations, and nuclear magnetic resonance analysis. The simulations underline different dynamical features of the protein scaffolds and a different mechanical interaction of the two proteins with DNA. The two protein structures, although very similar, show differences in the relative mobility of secondary structure elements. Protein structural analyses, principal component analysis, and geometrical and energetic DNA analyses indicate that the two transcription factors utilize a different strategy in DNA recognition and deformation. Results show that the protein indirect DNA readout is not only addressable to the DNA molecule flexibility but it is finely tuned by the mechanical and dynamical properties of the protein scaffold involved in the interaction.

Information driving force and its application in agent-based modeling

NASA Astrophysics Data System (ADS)

Chen, Ting-Ting; Zheng, Bo; Li, Yan; Jiang, Xiong-Fei

2018-04-01

Exploring the scientific impact of online big-data has attracted much attention of researchers from different fields in recent years. Complex financial systems are typical open systems profoundly influenced by the external information. Based on the large-scale data in the public media and stock markets, we first define an information driving force, and analyze how it affects the complex financial system. The information driving force is observed to be asymmetric in the bull and bear market states. As an application, we then propose an agent-based model driven by the information driving force. Especially, all the key parameters are determined from the empirical analysis rather than from statistical fitting of the simulation results. With our model, both the stationary properties and non-stationary dynamic behaviors are simulated. Considering the mean-field effect of the external information, we also propose a few-body model to simulate the financial market in the laboratory.

Brownian Dynamics and Molecular Dynamics Study of the Association between Hydrogenase and Ferredoxin from Chlamydomonas reinhardtii

PubMed Central

Long, Hai; Chang, Christopher H.; King, Paul W.; Ghirardi, Maria L.; Kim, Kwiseon

2008-01-01

The [FeFe] hydrogenase from the green alga Chlamydomonas reinhardtii can catalyze the reduction of protons to hydrogen gas using electrons supplied from photosystem I and transferred via ferredoxin. To better understand the association of the hydrogenase and the ferredoxin, we have simulated the process over multiple timescales. A Brownian dynamics simulation method gave an initial thorough sampling of the rigid-body translational and rotational phase spaces, and the resulting trajectories were used to compute the occupancy and free-energy landscapes. Several important hydrogenase-ferredoxin encounter complexes were identified from this analysis, which were then individually simulated using atomistic molecular dynamics to provide more details of the hydrogenase and ferredoxin interaction. The ferredoxin appeared to form reasonable complexes with the hydrogenase in multiple orientations, some of which were good candidates for inclusion in a transition state ensemble of configurations for electron transfer. PMID:18621810

Linear-algebraic bath transformation for simulating complex open quantum systems

DOE PAGES

Huh, Joonsuk; Mostame, Sarah; Fujita, Takatoshi; ...

2014-12-02

In studying open quantum systems, the environment is often approximated as a collection of non-interacting harmonic oscillators, a configuration also known as the star-bath model. It is also well known that the star-bath can be transformed into a nearest-neighbor interacting chain of oscillators. The chain-bath model has been widely used in renormalization group approaches. The transformation can be obtained by recursion relations or orthogonal polynomials. Based on a simple linear algebraic approach, we propose a bath partition strategy to reduce the system-bath coupling strength. As a result, the non-interacting star-bath is transformed into a set of weakly coupled multiple parallelmore » chains. Furthermore, the transformed bath model allows complex problems to be practically implemented on quantum simulators, and it can also be employed in various numerical simulations of open quantum dynamics.« less

Numerical simulation of deformation and fracture of space protective shell structures from concrete and fiber concrete under pulse loading

NASA Astrophysics Data System (ADS)

Radchenko, P. A.; Batuev, S. P.; Radchenko, A. V.; Plevkov, V. S.

2015-11-01

This paper presents results of numerical simulation of interaction between aircraft Boeing 747-400 and protective shell of nuclear power plant. The shell is presented as complex multilayered cellular structure comprising layers of concrete and fiber concrete bonded with steel trusses. Numerical simulation was held three-dimensionally using the author's algorithm and software taking into account algorithms for building grids of complex geometric objects and parallel computations. The dynamics of stress-strain state and fracture of structure were studied. Destruction is described using two-stage model that allows taking into account anisotropy of elastic and strength properties of concrete and fiber concrete. It is shown that wave processes initiate destruction of shell cellular structure—cells start to destruct in unloading wave, originating after output of compression wave to the free surfaces of cells.

Atomic scale simulations of vapor cooled carbon clusters

NASA Astrophysics Data System (ADS)

Bogana, M. P.; Colombo, L.

2007-03-01

By means of atomistic simulations we observed the formation of many topologically non-equivalent carbon clusters formed by the condensation of liquid droplets, including: (i) standard fullerenes and onion-like structures, (ii) clusters showing extremely complex surfaces with both positive and negative curvatures and (iii) complex endohedral structures. In this work we offer a thorough structural characterization of the above systems, as well as an attempt to correlate the resulting structure to the actual protocol of growth. The IR and Raman responses of some exotic linear carbon structures have been further investigated, finding good agreement with experimental evidence of carbinoid structures in cluster-assembled films. Towards the aim of fully understanding the process of cluster-to-cluster coalescence dynamics, we further simulated an aerosol of amorphous carbon clusters at controlled temperatures. Various annealing temperatures and times have been observed, identifying different pathways for cluster ripening, ranging from simple coalescence to extensive reconstruction.

On the application of hybrid meshes in hydraulic machinery CFD simulations

NASA Astrophysics Data System (ADS)

Schlipf, M.; Tismer, A.; Riedelbauch, S.

2016-11-01

The application of two different hybrid mesh types for the simulation of a Francis runner for automated optimization processes without user input is investigated. Those mesh types are applied to simplified test cases such as flow around NACA airfoils to identify the special mesh resolution effects with reduced complexity, like rotating cascade flows, as they occur in a turbomachine runner channel. The analysis includes the application of those different meshes on the geometries by keeping defined quality criteria and exploring the influences on the simulation results. All results are compared with reference values gained by simulations with blockstructured hexahedron meshes and the same numerical scheme. This avoids additional inaccuracies caused by further numerical and experimental measurement methods. The results show that a simulation with hybrid meshes built up by a blockstructured domain with hexahedrons around the blade in combination with a tetrahedral far field in the channel is sufficient to get results which are almost as accurate as the results gained by the reference simulation. Furthermore this method is robust enough for automated processes without user input and enables comparable meshes in size, distribution and quality for different similar geometries as occurring in optimization processes.

Front panel engineering with CAD simulation tool

NASA Astrophysics Data System (ADS)

Delacour, Jacques; Ungar, Serge; Mathieu, Gilles; Hasna, Guenther; Martinez, Pascal; Roche, Jean-Christophe

1999-04-01

THe progress made recently in display technology covers many fields of application. The specification of radiance, colorimetry and lighting efficiency creates some new challenges for designers. Photometric design is limited by the capability of correctly predicting the result of a lighting system, to save on the costs and time taken to build multiple prototypes or bread board benches. The second step of the research carried out by company OPTIS is to propose an optimization method to be applied to the lighting system, developed in the software SPEOS. The main features of the tool requires include the CAD interface, to enable fast and efficient transfer between mechanical and light design software, the source modeling, the light transfer model and an optimization tool. The CAD interface is mainly a prototype of transfer, which is not the subjects here. Photometric simulation is efficiently achieved by using the measured source encoding and a simulation by the Monte Carlo method. Today, the advantages and the limitations of the Monte Carlo method are well known. The noise reduction requires a long calculation time, which increases with the complexity of the display panel. A successful optimization is difficult to achieve, due to the long calculation time required for each optimization pass including a Monte Carlo simulation. The problem was initially defined as an engineering method of study. The experience shows that good understanding and mastering of the phenomenon of light transfer is limited by the complexity of non sequential propagation. The engineer must call for the help of a simulation and optimization tool. The main point needed to be able to perform an efficient optimization is a quick method for simulating light transfer. Much work has been done in this area and some interesting results can be observed. It must be said that the Monte Carlo method wastes time calculating some results and information which are not required for the needs of the simulation. Low efficiency transfer system cost a lot of lost time. More generally, the light transfer simulation can be treated efficiently when the integrated result is composed of elementary sub results that include quick analytical calculated intersections. The first axis of research appear. The quick integration research and the quick calculation of geometric intersections. The first axis of research brings some general solutions also valid for multi-reflection systems. The second axis requires some deep thinking on the intersection calculation. An interesting way is the subdivision of space in VOXELS. This is an adapted method of 3D division of space according to the objects and their location. An experimental software has been developed to provide a validation of the method. The gain is particularly high in complex systems. An important reduction in the calculation time has been achieved.

Heat as a tracer to estimate dissolved organic carbon flux from a restored wetland

USGS Publications Warehouse

Burow, K.R.; Constantz, J.; Fujii, R.

2005-01-01

Heat was used as a natural tracer to characterize shallow ground water flow beneath a complex wetland system. Hydrogeologic data were combined with measured vertical temperature profiles to constrain a series of two-dimensional, transient simulations of ground water flow and heat transport using the model code SUTRA (Voss 1990). The measured seasonal temperature signal reached depths of 2.7 m beneath the pond. Hydraulic conductivity was varied in each of the layers in the model in a systematic manual calibration of the two-dimensional model to obtain the best fit to the measured temperature and hydraulic head. Results of a series of representative best-fit simulations represent a range in hydraulic conductivity values that had the best agreement between simulated and observed temperatures and that resulted in simulated pond seepage values within 1 order of magnitude of pond seepage estimated from the water budget. Resulting estimates of ground water discharge to an adjacent agricultural drainage ditch were used to estimate potential dissolved organic carbon (DOC) loads resulting from the restored wetland. Estimated DOC loads ranged from 45 to 1340 g C/(m2 year), which is higher than estimated DOC loads from surface water. In spite of the complexity in characterizing ground water flow in peat soils, using heat as a tracer provided a constrained estimate of subsurface flow from the pond to the agricultural drainage ditch. Copyright ?? 2005 National Ground Water Association.

Semantic Information Processing of Physical Simulation Based on Scientific Concept Vocabulary Model

NASA Astrophysics Data System (ADS)

Kino, Chiaki; Suzuki, Yoshio; Takemiya, Hiroshi

Scientific Concept Vocabulary (SCV) has been developed to actualize Cognitive methodology based Data Analysis System: CDAS which supports researchers to analyze large scale data efficiently and comprehensively. SCV is an information model for processing semantic information for physics and engineering. In the model of SCV, all semantic information is related to substantial data and algorisms. Consequently, SCV enables a data analysis system to recognize the meaning of execution results output from a numerical simulation. This method has allowed a data analysis system to extract important information from a scientific view point. Previous research has shown that SCV is able to describe simple scientific indices and scientific perceptions. However, it is difficult to describe complex scientific perceptions by currently-proposed SCV. In this paper, a new data structure for SCV has been proposed in order to describe scientific perceptions in more detail. Additionally, the prototype of the new model has been constructed and applied to actual data of numerical simulation. The result means that the new SCV is able to describe more complex scientific perceptions.

Cloud chamber experiments on the origin of ice crystal complexity in cirrus clouds

NASA Astrophysics Data System (ADS)

Schnaiter, Martin; Järvinen, Emma; Vochezer, Paul; Abdelmonem, Ahmed; Wagner, Robert; Jourdan, Olivier; Mioche, Guillaume; Shcherbakov, Valery N.; Schmitt, Carl G.; Tricoli, Ugo; Ulanowski, Zbigniew; Heymsfield, Andrew J.

2016-04-01

This study reports on the origin of small-scale ice crystal complexity and its influence on the angular light scattering properties of cirrus clouds. Cloud simulation experiments were conducted at the AIDA (Aerosol Interactions and Dynamics in the Atmosphere) cloud chamber of the Karlsruhe Institute of Technology (KIT). A new experimental procedure was applied to grow and sublimate ice particles at defined super- and subsaturated ice conditions and for temperatures in the -40 to -60 °C range. The experiments were performed for ice clouds generated via homogeneous and heterogeneous initial nucleation. Small-scale ice crystal complexity was deduced from measurements of spatially resolved single particle light scattering patterns by the latest version of the Small Ice Detector (SID-3). It was found that a high crystal complexity dominates the microphysics of the simulated clouds and the degree of this complexity is dependent on the available water vapor during the crystal growth. Indications were found that the small-scale crystal complexity is influenced by unfrozen H2SO4 / H2O residuals in the case of homogeneous initial ice nucleation. Angular light scattering functions of the simulated ice clouds were measured by the two currently available airborne polar nephelometers: the polar nephelometer (PN) probe of Laboratoire de Métérologie et Physique (LaMP) and the Particle Habit Imaging and Polar Scattering (PHIPS-HALO) probe of KIT. The measured scattering functions are featureless and flat in the side and backward scattering directions. It was found that these functions have a rather low sensitivity to the small-scale crystal complexity for ice clouds that were grown under typical atmospheric conditions. These results have implications for the microphysical properties of cirrus clouds and for the radiative transfer through these clouds.

Designing Better Scaffolding in Teaching Complex Systems with Graphical Simulations

ERIC Educational Resources Information Center

Li, Na

2013-01-01

Complex systems are an important topic in science education today, but they are usually difficult for secondary-level students to learn. Although graphic simulations have many advantages in teaching complex systems, scaffolding is a critical factor for effective learning. This dissertation study was conducted around two complementary research…

WRF simulation over complex terrain during a southern California wildfire event

NASA Astrophysics Data System (ADS)

Lu, W.; Zhong, S.; Charney, J. J.; Bian, X.; Liu, S.

2012-03-01

In October 2007, the largest wildfire-related evacuation in California's history occurred as severe wildfires broke out across southern California. Smoke from these wildfires contributed to elevated pollutant concentrations in the atmosphere, affecting air quality in a vast region of the western United States. High-resolution numerical simulations were performed using the Weather Research and Forecast (WRF) model to understand the atmospheric conditions during the wildfire episode and how the complex circulation patterns might affect smoke transport and dispersion. The simulated meteorological fields were validated using surface and upper air observations in California and Nevada. To distinguish the performance of the WRF in different geographic regions, the surface stations were grouped into coastal sites, valley and basin sites, and mountain sites, and the results for the three categories were analyzed and intercompared. For temperature and moisture, the mountain category has the best agreement with the observations, while the coastal category was the worst. For wind, the model performance for the three categories was very similar. The flow patterns over complex terrain were also analyzed under different synoptic conditions and the possible impact of the terrain on smoke and pollutant pathways is analyzed by employing a Lagrangian Particle Dispersion Model. When high mountains prevent the smoke from moving inland, the mountain passes act as active pathways for smoke transport; meanwhile, chimney effect helps inject the pollutants to higher levels, where they are transported regionally. The results highlight the role of complex topography in the assessment of the possible smoke transport patterns in the region.

Stochastic model simulation using Kronecker product analysis and Zassenhaus formula approximation.

PubMed

Caglar, Mehmet Umut; Pal, Ranadip

2013-01-01

Probabilistic Models are regularly applied in Genetic Regulatory Network modeling to capture the stochastic behavior observed in the generation of biological entities such as mRNA or proteins. Several approaches including Stochastic Master Equations and Probabilistic Boolean Networks have been proposed to model the stochastic behavior in genetic regulatory networks. It is generally accepted that Stochastic Master Equation is a fundamental model that can describe the system being investigated in fine detail, but the application of this model is computationally enormously expensive. On the other hand, Probabilistic Boolean Network captures only the coarse-scale stochastic properties of the system without modeling the detailed interactions. We propose a new approximation of the stochastic master equation model that is able to capture the finer details of the modeled system including bistabilities and oscillatory behavior, and yet has a significantly lower computational complexity. In this new method, we represent the system using tensors and derive an identity to exploit the sparse connectivity of regulatory targets for complexity reduction. The algorithm involves an approximation based on Zassenhaus formula to represent the exponential of a sum of matrices as product of matrices. We derive upper bounds on the expected error of the proposed model distribution as compared to the stochastic master equation model distribution. Simulation results of the application of the model to four different biological benchmark systems illustrate performance comparable to detailed stochastic master equation models but with considerably lower computational complexity. The results also demonstrate the reduced complexity of the new approach as compared to commonly used Stochastic Simulation Algorithm for equivalent accuracy.

Near-field diffraction from amplitude diffraction gratings: theory, simulation and results

NASA Astrophysics Data System (ADS)

Abedin, Kazi Monowar; Rahman, S. M. Mujibur

2017-08-01

We describe a computer simulation method by which the complete near-field diffract pattern of an amplitude diffraction grating can be generated. The technique uses the method of iterative Fresnel integrals to calculate and generate the diffraction images. Theoretical background as well as the techniques to perform the simulation is described. The program is written in MATLAB, and can be implemented in any ordinary PC. Examples of simulated diffraction images are presented and discussed. The generated images in the far-field where they reduce to Fraunhofer diffraction pattern are also presented for a realistic grating, and compared with the results predicted by the grating equation, which is applicable in the far-field. The method can be used as a tool to teach the complex phenomenon of diffraction in classrooms.

Complex Systems Simulation and Optimization | Computational Science | NREL

Science.gov Websites

account. Stochastic Optimization and Control: Formulation and implementation of advanced optimization and account uncertainty. Contact Wesley Jones Group Manager, Complex Systems Simulation and Optimiziation

An Extended N-Player Network Game and Simulation of Four Investment Strategies on a Complex Innovation Network

PubMed Central

Zhou, Wen; Koptyug, Nikita; Ye, Shutao; Jia, Yifan; Lu, Xiaolong

2016-01-01

As computer science and complex network theory develop, non-cooperative games and their formation and application on complex networks have been important research topics. In the inter-firm innovation network, it is a typical game behavior for firms to invest in their alliance partners. Accounting for the possibility that firms can be resource constrained, this paper analyzes a coordination game using the Nash bargaining solution as allocation rules between firms in an inter-firm innovation network. We build an extended inter-firm n-player game based on nonidealized conditions, describe four investment strategies and simulate the strategies on an inter-firm innovation network in order to compare their performance. By analyzing the results of our experiments, we find that our proposed greedy strategy is the best-performing in most situations. We hope this study provides a theoretical insight into how firms make investment decisions. PMID:26745375

Modeling and simulation for fewer-axis grinding of complex surface

NASA Astrophysics Data System (ADS)

Li, Zhengjian; Peng, Xiaoqiang; Song, Ci

2017-10-01

As the basis of fewer-axis grinding of complex surface, the grinding mathematical model is of great importance. A mathematical model of the grinding wheel was established, and then coordinate and normal vector of the wheel profile could be calculated. Through normal vector matching at the cutter contact point and the coordinate system transformation, the grinding mathematical model was established to work out the coordinate of the cutter location point. Based on the model, interference analysis was simulated to find out the right position and posture of workpiece for grinding. Then positioning errors of the workpiece including the translation positioning error and the rotation positioning error were analyzed respectively, and the main locating datum was obtained. According to the analysis results, the grinding tool path was planned and generated to grind the complex surface, and good form accuracy was obtained. The grinding mathematical model is simple, feasible and can be widely applied.

An Extended N-Player Network Game and Simulation of Four Investment Strategies on a Complex Innovation Network.

PubMed

Zhou, Wen; Koptyug, Nikita; Ye, Shutao; Jia, Yifan; Lu, Xiaolong

2016-01-01

As computer science and complex network theory develop, non-cooperative games and their formation and application on complex networks have been important research topics. In the inter-firm innovation network, it is a typical game behavior for firms to invest in their alliance partners. Accounting for the possibility that firms can be resource constrained, this paper analyzes a coordination game using the Nash bargaining solution as allocation rules between firms in an inter-firm innovation network. We build an extended inter-firm n-player game based on nonidealized conditions, describe four investment strategies and simulate the strategies on an inter-firm innovation network in order to compare their performance. By analyzing the results of our experiments, we find that our proposed greedy strategy is the best-performing in most situations. We hope this study provides a theoretical insight into how firms make investment decisions.

Deriving urban dynamic evolution rules from self-adaptive cellular automata with multi-temporal remote sensing images

NASA Astrophysics Data System (ADS)

He, Yingqing; Ai, Bin; Yao, Yao; Zhong, Fajun

2015-06-01

Cellular automata (CA) have proven to be very effective for simulating and predicting the spatio-temporal evolution of complex geographical phenomena. Traditional methods generally pose problems in determining the structure and parameters of CA for a large, complex region or a long-term simulation. This study presents a self-adaptive CA model integrated with an artificial immune system to discover dynamic transition rules automatically. The model's parameters are allowed to be self-modified with the application of multi-temporal remote sensing images: that is, the CA can adapt itself to the changed and complex environment. Therefore, urban dynamic evolution rules over time can be efficiently retrieved by using this integrated model. The proposed AIS-based CA model was then used to simulate the rural-urban land conversion of Guangzhou city, located in the core of China's Pearl River Delta. The initial urban land was directly classified from TM satellite image in the year 1990. Urban land in the years 1995, 2000, 2005, 2009 and 2012 was correspondingly used as the observed data to calibrate the model's parameters. With the quantitative index figure of merit (FoM) and pattern similarity, the comparison was further performed between the AIS-based model and a Logistic CA model. The results indicate that the AIS-based CA model can perform better and with higher precision in simulating urban evolution, and the simulated spatial pattern is closer to the actual development situation.

Current status and future challenges in T-cell receptor/peptide/MHC molecular dynamics simulations.

PubMed

Knapp, Bernhard; Demharter, Samuel; Esmaielbeiki, Reyhaneh; Deane, Charlotte M

2015-11-01

The interaction between T-cell receptors (TCRs) and major histocompatibility complex (MHC)-bound epitopes is one of the most important processes in the adaptive human immune response. Several hypotheses on TCR triggering have been proposed. Many of them involve structural and dynamical adjustments in the TCR/peptide/MHC interface. Molecular Dynamics (MD) simulations are a computational technique that is used to investigate structural dynamics at atomic resolution. Such simulations are used to improve understanding of signalling on a structural level. Here we review how MD simulations of the TCR/peptide/MHC complex have given insight into immune system reactions not achievable with current experimental methods. Firstly, we summarize methods of TCR/peptide/MHC complex modelling and TCR/peptide/MHC MD trajectory analysis methods. Then we classify recently published simulations into categories and give an overview of approaches and results. We show that current studies do not come to the same conclusions about TCR/peptide/MHC interactions. This discrepancy might be caused by too small sample sizes or intrinsic differences between each interaction process. As computational power increases future studies will be able to and should have larger sample sizes, longer runtimes and additional parts of the immunological synapse included. © The Author 2015. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Ligand Selectivity Mechanism and Conformational Changes in Guanine Riboswitch by Molecular Dynamics Simulations and Free Energy Calculations.

PubMed

Hu, Guodong; Ma, Aijing; Wang, Jihua

2017-04-24

Riboswitches regulate gene expression through direct and specific interactions with small metabolite molecules. Binding of a ligand to its RNA target is high selectivity and affinity and induces conformational changes of the RNA's secondary and tertiary structure. The structural difference of two purine riboswitches aptamers is caused by only one single mutation, where cytosine 74 in the guanine riboswitch is corresponding to a uracil 74 in adenine riboswitch. Here we employed molecular dynamics (MD) simulation, molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and thermodynamic integration computational methodologies to evaluate the energetic and conformational changes of ligands binding to purine riboswitches. The snapshots used in MM-PBSA calculation were extracted from ten 50 ns MD simulation trajectories for each complex. These free energy results are in consistent with the experimental data and rationalize the selectivity of the riboswitches for different ligands. In particular, it is found that the loss in binding free energy upon mutation is mainly electrostatic in guanine (GUA) and riboswitch complex. Furthermore, new hydrogen bonds are found in mutated complexes. To reveal the conformational properties of guanine riboswitch, we performed a total of 6 μs MD simulations in both the presence and the absence of the ligand GUA. The MD simulations suggest that the conformation of guanine riboswitch depends on the distance of two groups in the binding pocket of ligand. The conformation is in a close conformation when U51-A52 is close to C74-U75.

Real-world hydrologic assessment of a fully-distributed hydrological model in a parallel computing environment

NASA Astrophysics Data System (ADS)

Vivoni, Enrique R.; Mascaro, Giuseppe; Mniszewski, Susan; Fasel, Patricia; Springer, Everett P.; Ivanov, Valeriy Y.; Bras, Rafael L.

2011-10-01

SummaryA major challenge in the use of fully-distributed hydrologic models has been the lack of computational capabilities for high-resolution, long-term simulations in large river basins. In this study, we present the parallel model implementation and real-world hydrologic assessment of the Triangulated Irregular Network (TIN)-based Real-time Integrated Basin Simulator (tRIBS). Our parallelization approach is based on the decomposition of a complex watershed using the channel network as a directed graph. The resulting sub-basin partitioning divides effort among processors and handles hydrologic exchanges across boundaries. Through numerical experiments in a set of nested basins, we quantify parallel performance relative to serial runs for a range of processors, simulation complexities and lengths, and sub-basin partitioning methods, while accounting for inter-run variability on a parallel computing system. In contrast to serial simulations, the parallel model speed-up depends on the variability of hydrologic processes. Load balancing significantly improves parallel speed-up with proportionally faster runs as simulation complexity (domain resolution and channel network extent) increases. The best strategy for large river basins is to combine a balanced partitioning with an extended channel network, with potential savings through a lower TIN resolution. Based on these advances, a wider range of applications for fully-distributed hydrologic models are now possible. This is illustrated through a set of ensemble forecasts that account for precipitation uncertainty derived from a statistical downscaling model.

Dshell++: A Component Based, Reusable Space System Simulation Framework

NASA Technical Reports Server (NTRS)

Lim, Christopher S.; Jain, Abhinandan

2009-01-01

This paper describes the multi-mission Dshell++ simulation framework for high fidelity, physics-based simulation of spacecraft, robotic manipulation and mobility systems. Dshell++ is a C++/Python library which uses modern script driven object-oriented techniques to allow component reuse and a dynamic run-time interface for complex, high-fidelity simulation of spacecraft and robotic systems. The goal of the Dshell++ architecture is to manage the inherent complexity of physicsbased simulations while supporting component model reuse across missions. The framework provides several features that support a large degree of simulation configurability and usability.

Numerical simulations of windblown dust over complex terrain: the Fiambalá Basin episode in June 2015

NASA Astrophysics Data System (ADS)

Mingari, Leonardo A.; Collini, Estela A.; Folch, Arnau; Báez, Walter; Bustos, Emilce; Soledad Osores, María; Reckziegel, Florencia; Alexander, Peter; Viramonte, José G.

2017-06-01

On 13 June 2015, the London Volcanic Ash Advisory Centre (VAAC) warned the Buenos Aires VAAC about a possible volcanic eruption from the Nevados Ojos del Salado volcano (6879 m), located in the Andes mountain range on the border between Chile and Argentina. A volcanic ash cloud was detected by the SEVIRI instrument on board the Meteosat Second Generation (MSG) satellites from 14:00 UTC on 13 June. In this paper, we provide the first comprehensive description of this event through observations and numerical simulations. Our results support the hypothesis that the phenomenon was caused by wind remobilization of ancient pyroclastic deposits (ca. 4.5 ka Cerro Blanco eruption) from the Bolsón de Fiambalá (Fiambalá Basin) in northwestern Argentina. We have investigated the spatiotemporal distribution of aerosols and the emission process over complex terrain to gain insight into the key role played by the orography and the condition that triggered the long-range transport episode. Numerical simulations of windblown dust were performed using the ARW (Advanced Research WRF) core of the WRF (Weather Research and Forecasting) model (WRF-ARW) and FALL3D modeling system with meteorological fields downscaled to a spatial resolution of 2 km in order to resolve the complex orography of the area. Results indicate that favorable conditions to generate dust uplifting occurred in northern Fiambalá Basin, where orographic effects caused strong surface winds. According to short-range numerical simulations, dust particles were confined to near-ground layers around the emission areas. In contrast, dust aerosols were injected up to 5-6 km high in central and southern regions of the Fiambalá Basin, where intense ascending airflows are driven by horizontal convergence. Long-range transport numerical simulations were also performed to model the dust cloud spreading over northern Argentina. Results of simulated vertical particle column mass were compared with the MSG-SEVIRI retrieval product. We tested two numerical schemes: with the default configuration of the FALL3D model, we found difficulties to simulate transport through orographic barriers, whereas an alternative configuration, using a numerical scheme to more accurately compute the horizontal advection in abrupt terrains, substantially improved the model performance.

Evidence for the dissolution of molybdenum during tribocorrosion of CoCrMo hip implants in the presence of serum protein.

PubMed

Simoes, Thiago A; Bryant, Michael G; Brown, Andy P; Milne, Steven J; Ryan, Mary; Neville, Anne; Brydson, Rik

2016-11-01

We have characterized CoCrMo, Metal-on-Metal (MoM) implant, wear debris particles and their dissolution following cycling in a hip simulator, and have related the results to the tribocorrosion of synthetic wear debris produced by milling CoCrMo powders in solutions representative of environments in the human body. Importantly, we have employed a modified ICP-MS sample preparation procedure to measure the release of ions from CoCrMo alloys during wear simulation in different media; this involved use of nano-porous ultrafilters which allowed complete separation of particles from free ions and complexes in solution. As a result, we present a new perspective on the release of metal ions and formation of metal complexes from CoCrMo implants. The new methodology enables the mass balance of ions relative to complexes and particles during tribocorrosion in hip simulators to be determined. A much higher release of molybdenum ions relative to cobalt and chromium has been measured. The molybdenum dissolution was enhanced by the presence of bovine serum albumin (BSA), possibly due to the formation of metal-protein complexes. Overall, we believe that the results could have significant implications for the analysis and interpretation of metal ion levels in fluids extracted from hip arthroplasty patients; we suggest that metal levels, including molybdenum, be analysed in these fluids using the protocol described here. We have developed an important new protocol for the analysis of metal ion levels in fluids extracted from hip implant patients and also hip simulators. Using this procedure, we present a new perspective on the release of metal ions from CoCrMo alloy implants, revealing significantly lower levels of metal ion release during tribocorrosion in hip simulators than previously thought, combined with the release of much higher percentages of molybdenum ions relative to cobalt and chromium. This work is of relevance, both from the perspective of the fundamental science and study of metal-protein interactions, enabling understanding of the ongoing problem associated with the biotribocorrosion and the link to inflammation associated with Metal-on-Metal (MoM) hip implants made from CoCrMo alloys. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Ordinal optimization and its application to complex deterministic problems

NASA Astrophysics Data System (ADS)

Yang, Mike Shang-Yu

1998-10-01

We present in this thesis a new perspective to approach a general class of optimization problems characterized by large deterministic complexities. Many problems of real-world concerns today lack analyzable structures and almost always involve high level of difficulties and complexities in the evaluation process. Advances in computer technology allow us to build computer models to simulate the evaluation process through numerical means, but the burden of high complexities remains to tax the simulation with an exorbitant computing cost for each evaluation. Such a resource requirement makes local fine-tuning of a known design difficult under most circumstances, let alone global optimization. Kolmogorov equivalence of complexity and randomness in computation theory is introduced to resolve this difficulty by converting the complex deterministic model to a stochastic pseudo-model composed of a simple deterministic component and a white-noise like stochastic term. The resulting randomness is then dealt with by a noise-robust approach called Ordinal Optimization. Ordinal Optimization utilizes Goal Softening and Ordinal Comparison to achieve an efficient and quantifiable selection of designs in the initial search process. The approach is substantiated by a case study in the turbine blade manufacturing process. The problem involves the optimization of the manufacturing process of the integrally bladed rotor in the turbine engines of U.S. Air Force fighter jets. The intertwining interactions among the material, thermomechanical, and geometrical changes makes the current FEM approach prohibitively uneconomical in the optimization process. The generalized OO approach to complex deterministic problems is applied here with great success. Empirical results indicate a saving of nearly 95% in the computing cost.

Molecular Origins of Thermal Transitions in Polyelectrolyte Assemblies

NASA Astrophysics Data System (ADS)

Yildirim, Erol; Zhang, Yanpu; Antila, Hanne S.; Lutkenhaus, Jodie L.; Sammalkorpi, Maria; Aalto Team; Texas A&M Team

2015-03-01

Polyelectrolyte (PE) multilayers and complexes formed from oppositely charged polymers can exhibit extraordinary superhydrophobicity, mechanical strength and responsiveness resulting in applications ranging functional membranes, optics, sensors and drug delivery. Depending on the assembly conditions, PE assemblies may undergo a thermal transition from glassy to soft behavior under heating. Our earlier work using thermal analysis measurements shows a distinct thermal transition for PE layer-by-layer (LbL) systems assembled with added salt but no analogous transition in films assembled without added salt or dry systems. These findings raise interesting questions on the nature of the thermal transition; here, we explore its molecular origins through characterization of the PE aggregates by temperature-controlled all-atom molecular dynamics simulations. We show via molecular simulations the thermal transition results from the existence of an LCST (lower critical solution temperature) in the PE systems: the diffusion behavior, hydrogen bond formation, and bridging capacity of water molecules plasticizing the complex changes at the transition temperature. We quantify the behavior, map its chemistry specificity through comparison of strongly and weakly charged PE complexes, and connect the findings to our interrelated QCM-D experiments.

Developing a Measurement for Task Complexity in Flight.

PubMed

Zheng, Yiyuan; Lu, Yanyu; Wang, Zhen; Huang, Dan; Fu, Shan

2015-08-01

Task complexity is regarded as an essential metric that is related to a pilot's performance and workload. Normally, pilots follow Standard Operating Procedures (SOPs) during a flight. In this study, we developed a measurement named Task Complexity in Flight (TCIF) to represent the task complexity in the SOPs. The TCIF measurement combined four complexity components into one index: actions logic complexity (ALC), actions size complexity (ASC), information control exchange complexity (ICEC), and control mode complexity (CMC).To verify the measurement, we calculated 11 tasks during the takeoff and landing phases from the SOPs, and invited 10 pilots to perform the same tasks in a flight simulator. After flight, the TCIF results were compared with two workload measurements: the Bedford scale and heart rate. The results of TCIF and the 4 components of the 11 tasks were calculated. Further, the TCIF results showed a significant correlation with the Bedford scores (R=0.851) and were also consistent with the difference in heart rate (R=0.816). Therefore, with the increased TCIF results, both the Bedford scale and the difference in heart rate increased. TCIF was proposed based on the flight operating conditions. Although additional studies of TCIF are necessary, the results of this study suggest this measurement could effectively indicate task complexity in flight, and could also be used to guide pilot training and task allocation on the flight deck.

Benchmark tests for a Formula SAE Student car prototyping

NASA Astrophysics Data System (ADS)

Mariasiu, Florin

2011-12-01

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

Dry Volume Fracturing Simulation of Shale Gas Reservoir

NASA Astrophysics Data System (ADS)

Xu, Guixi; Wang, Shuzhong; Luo, Xiangrong; Jing, Zefeng

2017-11-01

Application of CO2 dry fracturing technology to shale gas reservoir development in China has advantages of no water consumption, little reservoir damage and promoting CH4 desorption. This paper uses Meyer simulation to study complex fracture network extension and the distribution characteristics of shale gas reservoirs in the CO2 dry volume fracturing process. The simulation results prove the validity of the modified CO2 dry fracturing fluid used in shale volume fracturing and provides a theoretical basis for the following study on interval optimization of the shale reservoir dry volume fracturing.

A finite-difference time-domain electromagnetic solver in a generalized coordinate system

NASA Astrophysics Data System (ADS)

Hochberg, Timothy Allen

A new, finite-difference, time-domain method for the simulation of full-wave electromagnetic wave propogation in complex structures is developed. This method is simple and flexible; it allows for the simulation of transient wave propogation in a large class of practical structures. Boundary conditions are implemented for perfect and imperfect electrically conducting boundaries, perfect magnetically conducting boundaries, and absorbing boundaries. The method is validated with the aid of several different types of test cases. Two types of coaxial cables with helical breaks are simulated and the results are discussed.

Simulation of traffic control signal systems

NASA Technical Reports Server (NTRS)

Connolly, P. J.; Concannon, P. A.; Ricci, R. C.

1974-01-01

In recent years there has been considerable interest in the development and testing of control strategies for networks of urban traffic signal systems by simulation. Simulation is an inexpensive and timely method for evaluating the effect of these traffic control strategies since traffic phenomena are too complex to be defined by analytical models and since a controlled experiment may be hazardous, expensive, and slow in producing meaningful results. This paper describes the application of an urban traffic corridor program, to evaluate the effectiveness of different traffic control strategies for the Massachusetts Avenue TOPICS Project.

Simulated studies of wear and friction in total hip prosthesis components with various ball sizes and surface finishes

NASA Technical Reports Server (NTRS)

Swikert, M. A.; Johnson, R. L.

1976-01-01

Experiments were conducted on a newly designed total hip joint simulator. The apparatus closely simulates the complex motions and loads of the human hip in normal walking. The wear and friction of presently used appliance configurations and materials were determined. A surface treatment of the metal femoral ball specimens was applied to influence wear. The results of the investigation indicate that wear can be reduced by mechanical treatment of metal femoral ball surfaces. A metallographic examination and surface roughness measurements were made.

MFIX simulation of NETL/PSRI challenge problem of circulating fluidized bed

DOE PAGES

Li, Tingwen; Dietiker, Jean-François; Shahnam, Mehrdad

2012-12-01

In this paper, numerical simulations of NETL/PSRI challenge problem of circulating fluidized bed (CFB) using the open-source code Multiphase Flow with Interphase eXchange (MFIX) are reported. Two rounds of simulation results are reported including the first-round blind test and the second-round modeling refinement. Three-dimensional high fidelity simulations are conducted to model a 12-inch diameter pilot-scale CFB riser. Detailed comparisons between numerical results and experimental data are made with respect to axial pressure gradient profile, radial profiles of solids velocity and solids mass flux along different radial directions at various elevations for operating conditions covering different fluidization regimes. Overall, the numericalmore » results show that CFD can predict the complex gas–solids flow behavior in the CFB riser reasonably well. In addition, lessons learnt from modeling this challenge problem are presented.« less

Numerical simulation for the air entrainment of aerated flow with an improved multiphase SPH model

NASA Astrophysics Data System (ADS)

Wan, Hang; Li, Ran; Pu, Xunchi; Zhang, Hongwei; Feng, Jingjie

2017-11-01

Aerated flow is a complex hydraulic phenomenon that exists widely in the field of environmental hydraulics. It is generally characterised by large deformation and violent fragmentation of the free surface. Compared to Euler methods (volume of fluid (VOF) method or rigid-lid hypothesis method), the existing single-phase Smooth Particle Hydrodynamics (SPH) method has performed well for solving particle motion. A lack of research on interphase interaction and air concentration, however, has affected the application of SPH model. In our study, an improved multiphase SPH model is presented to simulate aeration flows. A drag force was included in the momentum equation to ensure accuracy of the air particle slip velocity. Furthermore, a calculation method for air concentration is developed to analyse the air entrainment characteristics. Two studies were used to simulate the hydraulic and air entrainment characteristics. And, compared with the experimental results, the simulation results agree with the experimental results well.

A program code generator for multiphysics biological simulation using markup languages.

PubMed

Amano, Akira; Kawabata, Masanari; Yamashita, Yoshiharu; Rusty Punzalan, Florencio; Shimayoshi, Takao; Kuwabara, Hiroaki; Kunieda, Yoshitoshi

2012-01-01

To cope with the complexity of the biological function simulation models, model representation with description language is becoming popular. However, simulation software itself becomes complex in these environment, thus, it is difficult to modify the simulation conditions, target computation resources or calculation methods. In the complex biological function simulation software, there are 1) model equations, 2) boundary conditions and 3) calculation schemes. Use of description model file is useful for first point and partly second point, however, third point is difficult to handle for various calculation schemes which is required for simulation models constructed from two or more elementary models. We introduce a simulation software generation system which use description language based description of coupling calculation scheme together with cell model description file. By using this software, we can easily generate biological simulation code with variety of coupling calculation schemes. To show the efficiency of our system, example of coupling calculation scheme with three elementary models are shown.

Molecular Docking and Molecular Dynamics to Identify a Novel Human Immunodeficiency Virus Inhibitor from Alkaloids of Toddalia asiatica.

PubMed

Priya, R; Sumitha, Rajendrarao; Doss, C George Priya; Rajasekaran, C; Babu, S; Seenivasan, R; Siva, R

2015-10-01

Acquired immunodeficiency syndrome caused by human immunodeficiency virus (HIV) is an immunosuppressive disease. Over the past decades, it has plagued human health due to the grave consequences in its harness. For this reason, anti-HIV agents are imperative, and the search for the same from natural resources would assure the safety. In this investigation we have performed molecular docking, molecular property prediction, drug-likeness score, and molecular dynamics (MD) simulation to develop a novel anti-HIV drug. We have screened 12 alkaloids from a medicinal plant Toddalia asiatica for its probabilistic binding with the active site of the HIV-1-reverse transcriptase (HIV-1-RT) domain (the major contributor to the onset of the disease). The docking results were evaluated based on free energies of binding (ΔG), and the results suggested toddanol, toddanone, and toddalenone to be potent inhibitors of HIV-1-RT. In addition, the alkaloids were subjected to molecular property prediction analysis. Toddanol and toddanone with more rotatable bonds were found to have a drug-likeness score of 0.23 and 0.11, respectively. These scores were comparable with the standard anti-HIV drug zidovudine with a model score 0.28. Finally, two characteristic protein-ligand complexes were exposed to MD simulation to determine the stability of the predicted conformations. The toddanol-RT complex showed higher stability and stronger H-bonds than toddanone-RT complex. Based on these observations, we firmly believe that the alkaloid toddanol could aid in efficient HIV-1 drug discovery. In the present study, the molecular docking and MD simulations are performed to explore the possible binding mode of HIV 1 RT with 12 alkaloids of T. asiatica. Molecular docking by AutoDock4 revealed three alkaloids toddanol, toddanone, and toddalenone with highest binding affinity towards HIV 1 RT. The drug likeness model score revealed a positive score for toddanol and toddanone which is comparable to the drug likeness score of the standard anti HIV drug zidovudine. Results from simulation analysis revealed that toddanol RT complex is more stable than toddanone RT complex inferring toddanol as a potential anti HIV drug molecule. Abbreviations used: HIV: Human immunodeficiency virus, HIV 1 RT: HIV 1 reverse transcriptase, RNase H: Ribonuclease H, MD: Molecular dynamics, PDB: Protein databank, RMSD: Root mean square deviation, RMSF: Root mean square fluctuation.

Interaction and dynamics of homologous pairing protein 2 (HOP2) and DNA studied by MD simulation

NASA Astrophysics Data System (ADS)

Moktan, Hem; Pezza, Roberto; Zhou, Donghua

2015-03-01

The homologous pairing protein 2 (Hop2) plays an important role in meiosis and DNA repair. Together with protein Mnd1, Hop2 enhances the strand invasion activity of recombinase Dmc1 by over 30 times, facilitating proper synapsis of homologous chromosomes. We recently determined the NMR structure of the N-terminal domain of Hop2 and proposed a model of Protein-DNA complex based on NMR chemical shift perturbations and mutagenesis studies (Moktan, J Biol Chem 2014 10.1074/jbc.M114.548180). However structure and dynamics of the complex have not been studied at the atomic level yet. Here, we used classical MD simulations to study the interactions between the N-terminal HOP2 and DNA. The simulated results indicate that helix3 (H3) interacts with DNA in major groove and wing1 (W1) interacts mostly in minor groove mainly via direct hydrogen bonds. Also it is found that binding leads to reduced fluctuations in both protein and DNA. Several water bridge interactions have been identified. The residue-wise contributions to the interaction energy were evaluated. Also the functional motion of the protein is analyzed using principal component analysis. The results confirmed the importance of H3 and W1 for the stability of the complex, which is consistent with our previous experimental studies.

Key Structures and Interactions for Binding of Mycobacterium tuberculosis Protein Kinase B Inhibitors from Molecular Dynamics Simulation.

PubMed

Punkvang, Auradee; Kamsri, Pharit; Saparpakorn, Patchreenart; Hannongbua, Supa; Wolschann, Peter; Irle, Stephan; Pungpo, Pornpan

2015-07-01

Substituted aminopyrimidine inhibitors have recently been introduced as antituberculosis agents. These inhibitors show impressive activity against protein kinase B, a Ser/Thr protein kinase that is essential for cell growth of M. tuberculosis. However, up to now, X-ray structures of the protein kinase B enzyme complexes with the substituted aminopyrimidine inhibitors are currently unavailable. Consequently, structural details of their binding modes are questionable, prohibiting the structural-based design of more potent protein kinase B inhibitors in the future. Here, molecular dynamics simulations, in conjunction with molecular mechanics/Poisson-Boltzmann surface area binding free-energy analysis, were employed to gain insight into the complex structures of the protein kinase B inhibitors and their binding energetics. The complex structures obtained by the molecular dynamics simulations show binding free energies in good agreement with experiment. The detailed analysis of molecular dynamics results shows that Glu93, Val95, and Leu17 are key residues responsible to the binding of the protein kinase B inhibitors. The aminopyrazole group and the pyrimidine core are the crucial moieties of substituted aminopyrimidine inhibitors for interaction with the key residues. Our results provide a structural concept that can be used as a guide for the future design of protein kinase B inhibitors with highly increased antagonistic activity. © 2014 John Wiley & Sons A/S.

Design of a multi-agent hydroeconomic model to simulate a complex human-water system: Early insights from the Jordan Water Project

NASA Astrophysics Data System (ADS)

Yoon, J.; Klassert, C. J. A.; Lachaut, T.; Selby, P. D.; Knox, S.; Gorelick, S.; Rajsekhar, D.; Tilmant, A.; Avisse, N.; Harou, J. J.; Gawel, E.; Klauer, B.; Mustafa, D.; Talozi, S.; Sigel, K.

2015-12-01

Our work focuses on development of a multi-agent, hydroeconomic model for purposes of water policy evaluation in Jordan. The model adopts a modular approach, integrating biophysical modules that simulate natural and engineered phenomena with human modules that represent behavior at multiple levels of decision making. The hydrologic modules are developed using spatially-distributed groundwater and surface water models, which are translated into compact simulators for efficient integration into the multi-agent model. For the groundwater model, we adopt a response matrix method approach in which a 3-dimensional MODFLOW model of a complex regional groundwater system is converted into a linear simulator of groundwater response by pre-processing drawdown results from several hundred numerical simulation runs. Surface water models for each major surface water basin in the country are developed in SWAT and similarly translated into simple rainfall-runoff functions for integration with the multi-agent model. The approach balances physically-based, spatially-explicit representation of hydrologic systems with the efficiency required for integration into a complex multi-agent model that is computationally amenable to robust scenario analysis. For the multi-agent model, we explicitly represent human agency at multiple levels of decision making, with agents representing riparian, management, supplier, and water user groups. The agents' decision making models incorporate both rule-based heuristics as well as economic optimization. The model is programmed in Python using Pynsim, a generalizable, open-source object-oriented code framework for modeling network-based water resource systems. The Jordan model is one of the first applications of Pynsim to a real-world water management case study. Preliminary results from a tanker market scenario run through year 2050 are presented in which several salient features of the water system are investigated: competition between urban and private farmer agents, the emergence of a private tanker market, disparities in economic wellbeing to different user groups caused by unique supply conditions, and response of the complex system to various policy interventions.

An approach for modelling snowcover ablation and snowmelt runoff in cold region environments

NASA Astrophysics Data System (ADS)

Dornes, Pablo Fernando

Reliable hydrological model simulations are the result of numerous complex interactions among hydrological inputs, landscape properties, and initial conditions. Determination of the effects of these factors is one of the main challenges in hydrological modelling. This situation becomes even more difficult in cold regions due to the ungauged nature of subarctic and arctic environments. This research work is an attempt to apply a new approach for modelling snowcover ablation and snowmelt runoff in complex subarctic environments with limited data while retaining integrity in the process representations. The modelling strategy is based on the incorporation of both detailed process understanding and inputs along with information gained from observations of basin-wide streamflow phenomenon; essentially a combination of deductive and inductive approaches. The study was conducted in the Wolf Creek Research Basin, Yukon Territory, using three models, a small-scale physically based hydrological model, a land surface scheme, and a land surface hydrological model. The spatial representation was based on previous research studies and observations, and was accomplished by incorporating landscape units, defined according to topography and vegetation, as the spatial model elements. Comparisons between distributed and aggregated modelling approaches showed that simulations incorporating distributed initial snowcover and corrected solar radiation were able to properly simulate snowcover ablation and snowmelt runoff whereas the aggregated modelling approaches were unable to represent the differential snowmelt rates and complex snowmelt runoff dynamics. Similarly, the inclusion of spatially distributed information in a land surface scheme clearly improved simulations of snowcover ablation. Application of the same modelling approach at a larger scale using the same landscape based parameterisation showed satisfactory results in simulating snowcover ablation and snowmelt runoff with minimal calibration. Verification of this approach in an arctic basin illustrated that landscape based parameters are a feasible regionalisation framework for distributed and physically based models. In summary, the proposed modelling philosophy, based on the combination of an inductive and deductive reasoning, is a suitable strategy for reliable predictions of snowcover ablation and snowmelt runoff in cold regions and complex environments.

Linking MODFLOW with an agent-based land-use model to support decision making

USGS Publications Warehouse

Reeves, H.W.; Zellner, M.L.

2010-01-01

The U.S. Geological Survey numerical groundwater flow model, MODFLOW, was integrated with an agent-based land-use model to yield a simulator for environmental planning studies. Ultimately, this integrated simulator will be used as a means to organize information, illustrate potential system responses, and facilitate communication within a participatory modeling framework. Initial results show the potential system response to different zoning policy scenarios in terms of the spatial patterns of development, which is referred to as urban form, and consequent impacts on groundwater levels. These results illustrate how the integrated simulator is capable of representing the complexity of the system. From a groundwater modeling perspective, the most important aspect of the integration is that the simulator generates stresses on the groundwater system within the simulation in contrast to the traditional approach that requires the user to specify the stresses through time. Copyright ?? 2010 The Author(s). Journal compilation ?? 2010 National Ground Water Association.

A method for validation of finite element forming simulation on basis of a pointwise comparison of distance and curvature

NASA Astrophysics Data System (ADS)

Dörr, Dominik; Joppich, Tobias; Schirmaier, Fabian; Mosthaf, Tobias; Kärger, Luise; Henning, Frank

2016-10-01

Thermoforming of continuously fiber reinforced thermoplastics (CFRTP) is ideally suited to thin walled and complex shaped products. By means of forming simulation, an initial validation of the producibility of a specific geometry, an optimization of the forming process and the prediction of fiber-reorientation due to forming is possible. Nevertheless, applied methods need to be validated. Therefor a method is presented, which enables the calculation of error measures for the mismatch between simulation results and experimental tests, based on measurements with a conventional coordinate measuring device. As a quantitative measure, describing the curvature is provided, the presented method is also suitable for numerical or experimental sensitivity studies on wrinkling behavior. The applied methods for forming simulation, implemented in Abaqus explicit, are presented and applied to a generic geometry. The same geometry is tested experimentally and simulation and test results are compared by the proposed validation method.

Time-dependent broken-symmetry density functional theory simulation of the optical response of entangled paramagnetic defects: Color centers in lithium fluoride

NASA Astrophysics Data System (ADS)

Janesko, Benjamin G.

2018-02-01

Parameter-free atomistic simulations of entangled solid-state paramagnetic defects may aid in the rational design of devices for quantum information science. This work applies time-dependent density functional theory (TDDFT) embedded-cluster simulations to a prototype entangled-defect system, namely two adjacent singlet-coupled F color centers in lithium fluoride. TDDFT calculations accurately reproduce the experimental visible absorption of both isolated and coupled F centers. The most accurate results are obtained by combining spin symmetry breaking to simulate strong correlation, a large fraction of exact (Hartree-Fock-like) exchange to minimize the defect electrons' self-interaction error, and a standard semilocal approximation for dynamical correlations between the defect electrons and the surrounding ionic lattice. These results motivate application of two-reference correlated ab initio approximations to the M-center, and application of TDDFT in parameter-free simulations of more complex entangled paramagnetic defect architectures.

Guidance law simulation studies for complex approaches using the Microwave Landing System (MLS)

NASA Technical Reports Server (NTRS)

Feather, J. B.

1986-01-01

This report documents results for MLS guidance algorithm development conducted by DAC for NASA under the Advance Transport Operating Systems (ATOPS) Technology Studies program (NAS1-18028). The study consisted of evaluating guidance laws for vertical and lateral path control, as well as speed control, by simulating an MLS approach for the Washington National Airport. This work is an extension and generalization of a previous ATOPS contract (NAS1-16202) completed by DAC in 1985. The Washington river approach was simulated by six waypoints and one glideslope change and consisted of an eleven nautical mile approach path. Tracking performance was generated for 10 cases representing several different conditions, which included MLS noise, steady wind, turbulence, and windshear. Results of this simulation phase are suitable for use in future fixed-base simulator evaluations employing actual hardware (autopilot and a performance management system), as well as crew procedures and information requirements for MLS.

Predicting Protein-protein Association Rates using Coarse-grained Simulation and Machine Learning

NASA Astrophysics Data System (ADS)

Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao

2017-04-01

Protein-protein interactions dominate all major biological processes in living cells. We have developed a new Monte Carlo-based simulation algorithm to study the kinetic process of protein association. We tested our method on a previously used large benchmark set of 49 protein complexes. The predicted rate was overestimated in the benchmark test compared to the experimental results for a group of protein complexes. We hypothesized that this resulted from molecular flexibility at the interface regions of the interacting proteins. After applying a machine learning algorithm with input variables that accounted for both the conformational flexibility and the energetic factor of binding, we successfully identified most of the protein complexes with overestimated association rates and improved our final prediction by using a cross-validation test. This method was then applied to a new independent test set and resulted in a similar prediction accuracy to that obtained using the training set. It has been thought that diffusion-limited protein association is dominated by long-range interactions. Our results provide strong evidence that the conformational flexibility also plays an important role in regulating protein association. Our studies provide new insights into the mechanism of protein association and offer a computationally efficient tool for predicting its rate.

Predicting Protein–protein Association Rates using Coarse-grained Simulation and Machine Learning

PubMed Central

Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao

2017-01-01

Protein–protein interactions dominate all major biological processes in living cells. We have developed a new Monte Carlo-based simulation algorithm to study the kinetic process of protein association. We tested our method on a previously used large benchmark set of 49 protein complexes. The predicted rate was overestimated in the benchmark test compared to the experimental results for a group of protein complexes. We hypothesized that this resulted from molecular flexibility at the interface regions of the interacting proteins. After applying a machine learning algorithm with input variables that accounted for both the conformational flexibility and the energetic factor of binding, we successfully identified most of the protein complexes with overestimated association rates and improved our final prediction by using a cross-validation test. This method was then applied to a new independent test set and resulted in a similar prediction accuracy to that obtained using the training set. It has been thought that diffusion-limited protein association is dominated by long-range interactions. Our results provide strong evidence that the conformational flexibility also plays an important role in regulating protein association. Our studies provide new insights into the mechanism of protein association and offer a computationally efficient tool for predicting its rate. PMID:28418043

Predicting Protein-protein Association Rates using Coarse-grained Simulation and Machine Learning.

PubMed

Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao

2017-04-18

Protein-protein interactions dominate all major biological processes in living cells. We have developed a new Monte Carlo-based simulation algorithm to study the kinetic process of protein association. We tested our method on a previously used large benchmark set of 49 protein complexes. The predicted rate was overestimated in the benchmark test compared to the experimental results for a group of protein complexes. We hypothesized that this resulted from molecular flexibility at the interface regions of the interacting proteins. After applying a machine learning algorithm with input variables that accounted for both the conformational flexibility and the energetic factor of binding, we successfully identified most of the protein complexes with overestimated association rates and improved our final prediction by using a cross-validation test. This method was then applied to a new independent test set and resulted in a similar prediction accuracy to that obtained using the training set. It has been thought that diffusion-limited protein association is dominated by long-range interactions. Our results provide strong evidence that the conformational flexibility also plays an important role in regulating protein association. Our studies provide new insights into the mechanism of protein association and offer a computationally efficient tool for predicting its rate.

An ODE-Based Wall Model for Turbulent Flow Simulations

NASA Technical Reports Server (NTRS)

Berger, Marsha J.; Aftosmis, Michael J.

2017-01-01

Fully automated meshing for Reynolds-Averaged Navier-Stokes Simulations, Mesh generation for complex geometry continues to be the biggest bottleneck in the RANS simulation process; Fully automated Cartesian methods routinely used for inviscid simulations about arbitrarily complex geometry; These methods lack of an obvious & robust way to achieve near wall anisotropy; Goal: Extend these methods for RANS simulation without sacrificing automation, at an affordable cost; Note: Nothing here is limited to Cartesian methods, and much becomes simpler in a body-fitted setting.

Simulating wall and corner fire tests on wood products with the OSU room fire model

Treesearch

H. C. Tran

1994-01-01

This work demonstrates the complexity of modeling wall and corner fires in a compartment. The model chosen for this purpose is the Ohio State University (OSU) room fire model. This model was designed to simulate fire growth on walls in a compartment and therefore lends itself to direct comparison with standard room test results. The model input were bench-scale data...

The Self-Assembly of Particles with Multipolar Interactions

DTIC Science & Technology

2004-01-01

the LATEX template in which this thesis has been written. I also thank Kevin Van Workum and Jack Douglas for contributing simulation work and some...of the computational expense of simulating such complex self-assembly systems at the molecular level and a desire to understand the self-assembly at...Dissertation directed by: Professor Wolfgang Losert Department of Physics In this thesis , we describe results from investigations of the self-assembly of

A model for the neural control of pineal periodicity

NASA Astrophysics Data System (ADS)

de Oliveira Cruz, Frederico Alan; Soares, Marilia Amavel Gomes; Cortez, Celia Martins

2016-12-01

The aim of this work was verify if a computational model associating the synchronization dynamics of coupling oscillators to a set of synaptic transmission equations would be able to simulate the control of pineal by a complex neural pathway that connects the retina to this gland. Results from the simulations showed that the frequency and temporal firing patterns were in the range of values found in literature.

Dynamics of biomolecules, ligand binding & biological functions

NASA Astrophysics Data System (ADS)

Yi, Myunggi

Proteins are flexible and dynamic. One static structure alone does not often completely explain biological functions of the protein, and some proteins do not even have high resolution structures. In order to provide better understanding to the biological functions of nicotinic acetylcholine receptor, Diphtheria toxin repressor and M2 proton channel, the dynamics of these proteins are investigated using molecular modeling and molecular dynamics (MD) simulations. With absence of high resolution structure of alpha7 receptor, the homology models of apo and cobra toxin bound forms have been built. From the MD simulations of these model structures, we observed one subunit of apo simulation moved away from other four subunits. With local movement of flexible loop regions, the whole subunit tilted clockwise. These conformational changes occurred spontaneously, and were strongly correlated with the conformational change when the channel is activated by agonists. Unlike other computational studies, we directly compared our model of open conformation with the experimental data. However, the subunits of toxin bound form were stable, and conformational change is restricted by the bound cobra toxin. These results provide activation and inhibition mechanisms of alpha7 receptors and a possible explanation for intermediate conductance of the channel. Intramolecular complex of SH3-like domain with a proline-rich (Pr) peptide segment in Diphtheria toxin repressor (DtxR) is stabilized in inactive state. Upon activation of DtxR by transition metal binding, this intramolecular complex should be dissociated. The dynamics of this intramolecular complex is investigated using MD simulations and NMR spectroscopy. We observed spontaneous opening and closing motions of the Pr segment binding pockets in both Pr-SH3 and SH3 simulations. The MD simulation results and NMR relaxation data suggest that the Pr segment exhibits a binding ↔ unbinding equilibrium. Despite a wealth of experimental validation of Gouy-Chapman (GC) theory to charged lipid membranes, a test of GC theory by MD simulations has been elusive. Here we demonstrate that the ion distributions at different salt concentrations in anionic lipid bilayer systems agree well with GC predictions using MD simulations. Na+ ions are adsorbed to the bilayer through favorable interactions with carbonyls and hydroxyls, reducing the surface charge density by 72.5%. The interactions of amantadine, an antiinfluenza A drug, with DMPC bilayers are investigated by an MD simulation and by solid-state NMR. The MD simulation results and NMR data demonstrate that amantadine is located within the interfacial region with upward orientation and interacts with the lipid headgroup and glycerol backbone, while the adamantane group of amantadine interacts with the glycerol backbone and much of fatty acyl chain, as it wraps underneath of the drug. The lipid headgroup orientation is influenced by the drug as well. The recent prevalence of amantadine-resistant mutants makes a development of new drug urgent. The mechanism of inhibition of M2 proton channel in influenza virus A by amantadine is investigated. In the absence of high resolution structure, we model the apo and drug bound forms based on NMR structures. MD simulations demonstrate that channel pore is blocked by a primary gate formed by Trp41 helped by His37 and a secondary gate formed by Val27. The blockage by the secondary gate is extended by the drug bound just below the gate, resulting in a broken water wire throughout the simulation, suggesting a novel role of Val27 in the inhibition by amantadine. Recent X-ray structure validates the simulation results.