Explaining the heterogeneity of functional connectivity findings in multiple sclerosis: An empirically informed modeling study.

PubMed

Tewarie, Prejaas; Steenwijk, Martijn D; Brookes, Matthew J; Uitdehaag, Bernard M J; Geurts, Jeroen J G; Stam, Cornelis J; Schoonheim, Menno M

2018-06-01

To understand the heterogeneity of functional connectivity results reported in the literature, we analyzed the separate effects of grey and white matter damage on functional connectivity and networks in multiple sclerosis. For this, we employed a biophysical thalamo-cortical model consisting of interconnected cortical and thalamic neuronal populations, informed and amended by empirical diffusion MRI tractography data, to simulate functional data that mimic neurophysiological signals. Grey matter degeneration was simulated by decreasing within population connections and white matter degeneration by lowering between population connections, based on lesion predilection sites in multiple sclerosis. For all simulations, functional connectivity and functional network organization are quantified by phase synchronization and network integration, respectively. Modeling results showed that both cortical and thalamic grey matter damage induced a global increase in functional connectivity, whereas white matter damage induced an initially increased connectivity followed by a global decrease. Both white and especially grey matter damage, however, induced a decrease in network integration. These empirically informed simulations show that specific topology and timing of structural damage are nontrivial aspects in explaining functional abnormalities in MS. Insufficient attention to these aspects likely explains contradictory findings in multiple sclerosis functional imaging studies so far. © 2018 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.

Parallel-distributed mobile robot simulator

NASA Astrophysics Data System (ADS)

Okada, Hiroyuki; Sekiguchi, Minoru; Watanabe, Nobuo

1996-06-01

The aim of this project is to achieve an autonomous learning and growth function based on active interaction with the real world. It should also be able to autonomically acquire knowledge about the context in which jobs take place, and how the jobs are executed. This article describes a parallel distributed movable robot system simulator with an autonomous learning and growth function. The autonomous learning and growth function which we are proposing is characterized by its ability to learn and grow through interaction with the real world. When the movable robot interacts with the real world, the system compares the virtual environment simulation with the interaction result in the real world. The system then improves the virtual environment to match the real-world result more closely. This the system learns and grows. It is very important that such a simulation is time- realistic. The parallel distributed movable robot simulator was developed to simulate the space of a movable robot system with an autonomous learning and growth function. The simulator constructs a virtual space faithful to the real world and also integrates the interfaces between the user, the actual movable robot and the virtual movable robot. Using an ultrafast CG (computer graphics) system (FUJITSU AG series), time-realistic 3D CG is displayed.

Accounting for uncertainty in pedotransfer functions in vulnerability assessments of pesticide leaching to groundwater.

PubMed

Stenemo, Fredrik; Jarvis, Nicholas

2007-09-01

A simulation tool for site-specific vulnerability assessments of pesticide leaching to groundwater was developed, based on the pesticide fate and transport model MACRO, parameterized using pedotransfer functions and reasonable worst-case parameter values. The effects of uncertainty in the pedotransfer functions on simulation results were examined for 48 combinations of soils, pesticides and application timings, by sampling pedotransfer function regression errors and propagating them through the simulation model in a Monte Carlo analysis. An uncertainty factor, f(u), was derived, defined as the ratio between the concentration simulated with no errors, c(sim), and the 80th percentile concentration for the scenario. The pedotransfer function errors caused a large variation in simulation results, with f(u) ranging from 1.14 to 1440, with a median of 2.8. A non-linear relationship was found between f(u) and c(sim), which can be used to account for parameter uncertainty by correcting the simulated concentration, c(sim), to an estimated 80th percentile value. For fine-textured soils, the predictions were most sensitive to errors in the pedotransfer functions for two parameters regulating macropore flow (the saturated matrix hydraulic conductivity, K(b), and the effective diffusion pathlength, d) and two water retention function parameters (van Genuchten's N and alpha parameters). For coarse-textured soils, the model was also sensitive to errors in the exponent in the degradation water response function and the dispersivity, in addition to K(b), but showed little sensitivity to d. To reduce uncertainty in model predictions, improved pedotransfer functions for K(b), d, N and alpha would therefore be most useful. 2007 Society of Chemical Industry

NLC Luminosity as a Function of Beam Parameters

NASA Astrophysics Data System (ADS)

Nosochkov, Y.

2002-06-01

Realistic calculation of NLC luminosity has been performed using particle tracking in DIMAD and beam-beam simulations in GUINEA-PIG code for various values of beam emittance, energy and beta functions at the Interaction Point (IP). Results of the simulations are compared with analytic luminosity calculations. The optimum range of IP beta functions for high luminosity was identified.

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

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

AmapSim: A Structural Whole-plant Simulator Based on Botanical Knowledge and Designed to Host External Functional Models

PubMed Central

Barczi, Jean-François; Rey, Hervé; Caraglio, Yves; de Reffye, Philippe; Barthélémy, Daniel; Dong, Qiao Xue; Fourcaud, Thierry

2008-01-01

Background and Aims AmapSim is a tool that implements a structural plant growth model based on a botanical theory and simulates plant morphogenesis to produce accurate, complex and detailed plant architectures. This software is the result of more than a decade of research and development devoted to plant architecture. New advances in the software development have yielded plug-in external functions that open up the simulator to functional processes. Methods The simulation of plant topology is based on the growth of a set of virtual buds whose activity is modelled using stochastic processes. The geometry of the resulting axes is modelled by simple descriptive functions. The potential growth of each bud is represented by means of a numerical value called physiological age, which controls the value for each parameter in the model. The set of possible values for physiological ages is called the reference axis. In order to mimic morphological and architectural metamorphosis, the value allocated for the physiological age of buds evolves along this reference axis according to an oriented finite state automaton whose occupation and transition law follows a semi-Markovian function. Key Results Simulations were performed on tomato plants to demostrate how the AmapSim simulator can interface external modules, e.g. a GREENLAB growth model and a radiosity model. Conclusions The algorithmic ability provided by AmapSim, e.g. the reference axis, enables unified control to be exercised over plant development parameter values, depending on the biological process target: how to affect the local pertinent process, i.e. the pertinent parameter(s), while keeping the rest unchanged. This opening up to external functions also offers a broadened field of applications and thus allows feedback between plant growth and the physical environment. PMID:17766310

Transmission of ˜ 10 keV electron beams through thin ceramic foils: Measurements and Monte Carlo simulations of electron energy distribution functions

NASA Astrophysics Data System (ADS)

Morozov, A.; Heindl, T.; Skrobol, C.; Wieser, J.; Krücken, R.; Ulrich, A.

2008-07-01

Electron beams with particle energy of ~10 keV were sent through 300 nm thick ceramic (Si3N4 + SiO2) foils and the resulting electron energy distribution functions were recorded using a retarding grid technique. The results are compared with Monte Carlo simulations performed with two publicly available packages, Geant4 and Casino v2.42. It is demonstrated that Geant4, unlike Casino, provides electron energy distribution functions very similar to the experimental distributions. Both simulation packages provide a quite precise average energy of transmitted electrons: we demonstrate that the maximum uncertainty of the calculated values of the average energy is 6% for Geant4 and 8% for Casino, taking into account all systematic uncertainties and the discrepancies in the experimental and simulated data.

A new optimal sliding mode controller design using scalar sign function.

PubMed

Singla, Mithun; Shieh, Leang-San; Song, Gangbing; Xie, Linbo; Zhang, Yongpeng

2014-03-01

This paper presents a new optimal sliding mode controller using the scalar sign function method. A smooth, continuous-time scalar sign function is used to replace the discontinuous switching function in the design of a sliding mode controller. The proposed sliding mode controller is designed using an optimal Linear Quadratic Regulator (LQR) approach. The sliding surface of the system is designed using stable eigenvectors and the scalar sign function. Controller simulations are compared with another existing optimal sliding mode controller. To test the effectiveness of the proposed controller, the controller is implemented on an aluminum beam with piezoceramic sensor and actuator for vibration control. This paper includes the control design and stability analysis of the new optimal sliding mode controller, followed by simulation and experimental results. The simulation and experimental results show that the proposed approach is very effective. © 2013 ISA. Published by Elsevier Ltd. All rights reserved.

Cosmic reionization on computers: The faint end of the galaxy luminosity function

DOE PAGES

Gnedin, Nickolay Y.

2016-07-01

Using numerical cosmological simulations completed under the “Cosmic Reionization On Computers” project, I explore theoretical predictions for the faint end of the galaxy UV luminosity functions atmore » $$z\\gtrsim 6$$. A commonly used Schechter function approximation with the magnitude cut at $${M}_{{\\rm{cut}}}\\sim -13$$ provides a reasonable fit to the actual luminosity function of simulated galaxies. When the Schechter functional form is forced on the luminosity functions from the simulations, the magnitude cut $${M}_{{\\rm{cut}}}$$ is found to vary between -12 and -14 with a mild redshift dependence. Here, an analytical model of reionization from Madau et al., as used by Robertson et al., provides a good description of the simulated results, which can be improved even further by adding two physically motivated modifications to the original Madau et al. equation.« less

Cosmic reionization on computers: The faint end of the galaxy luminosity function

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

Gnedin, Nickolay Y.

Using numerical cosmological simulations completed under the “Cosmic Reionization On Computers” project, I explore theoretical predictions for the faint end of the galaxy UV luminosity functions atmore » $$z\\gtrsim 6$$. A commonly used Schechter function approximation with the magnitude cut at $${M}_{{\\rm{cut}}}\\sim -13$$ provides a reasonable fit to the actual luminosity function of simulated galaxies. When the Schechter functional form is forced on the luminosity functions from the simulations, the magnitude cut $${M}_{{\\rm{cut}}}$$ is found to vary between -12 and -14 with a mild redshift dependence. Here, an analytical model of reionization from Madau et al., as used by Robertson et al., provides a good description of the simulated results, which can be improved even further by adding two physically motivated modifications to the original Madau et al. equation.« less

An empirical analysis of the distribution of overshoots in a stationary Gaussian stochastic process

NASA Technical Reports Server (NTRS)

Carter, M. C.; Madison, M. W.

1973-01-01

The frequency distribution of overshoots in a stationary Gaussian stochastic process is analyzed. The primary processes involved in this analysis are computer simulation and statistical estimation. Computer simulation is used to simulate stationary Gaussian stochastic processes that have selected autocorrelation functions. An analysis of the simulation results reveals a frequency distribution for overshoots with a functional dependence on the mean and variance of the process. Statistical estimation is then used to estimate the mean and variance of a process. It is shown that for an autocorrelation function, the mean and the variance for the number of overshoots, a frequency distribution for overshoots can be estimated.

Application of trilinear softening functions based on a cohesive crack approach to the simulation of the fracture behaviour of fibre reinforced cementitious materials.

NASA Astrophysics Data System (ADS)

Enfedaque, A.; Alberti, M. G.; Gálvez, J. C.

2017-09-01

The relevance of fibre reinforced cementitious materials (FRC) has increased due to the appearance of regulations that establish the requirements needed to take into account the contribution of the fibres in the structural design. However, in order to exploit the properties of such materials it is a key aspect being able to simulate their behaviour under fracture conditions. Considering a cohesive crack approach, several authors have studied the suitability of using several softening functions. However, none of these functions can be directly applied to FRC. The present contribution analyses the suitability of multilinear softening functions in order to obtain simulation results of fracture tests of a wide variety of FRC. The implementation of multilinear softening functions has been successfully performed by means of a material user subroutine in a commercial finite element code obtaining accurate results in a wide variety of FRC. Such softening functions were capable of simulating a ductile unloading behaviour as well as a rapid unloading followed by a reloading and afterwards a slow unloading. Moreover, the implementation performed has been proven as versatile, robust and efficient from a numerical point of view.

Operation and performance of the Ciba-Corning 512 coagulation monitor during parabolic flight

NASA Technical Reports Server (NTRS)

Gocke, Robyn; Lloyd, Charles W.; Greenthaner, Nancy K.

1991-01-01

The goal was to assess the functionality and evaluate the procedures and operations required to operate the Ciba-Corning 512 Coagulation Monitor during parabolic flight. This monitor determines the clotting characteristics of blood. The analyzer operates by laser detection of the cessation of blood flow in a capillary channel within a test cartridge. Test simulator results were excellent for both pre-and post-flight. In-flight results were not obtained due to the warm-up time required for the simulator. Since this is an electronic function only, the expected results on the simulator would be the same in zero-g.

Modeling of Semiconductor Optical Amplifier Gain Characteristics for Amplification and Switching

NASA Astrophysics Data System (ADS)

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

2011-05-01

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

Detailed validation of the bidirectional effect in various Case I and Case II waters.

PubMed

Gleason, Arthur C R; Voss, Kenneth J; Gordon, Howard R; Twardowski, Michael; Sullivan, James; Trees, Charles; Weidemann, Alan; Berthon, Jean-François; Clark, Dennis; Lee, Zhong-Ping

2012-03-26

Simulated bidirectional reflectance distribution functions (BRDF) were compared with measurements made just beneath the water's surface. In Case I water, the set of simulations that varied the particle scattering phase function depending on chlorophyll concentration agreed more closely with the data than other models. In Case II water, however, the simulations using fixed phase functions agreed well with the data and were nearly indistinguishable from each other, on average. The results suggest that BRDF corrections in Case II water are feasible using single, average, particle scattering phase functions, but that the existing approach using variable particle scattering phase functions is still warranted in Case I water.

Positive Wigner functions render classical simulation of quantum computation efficient.

PubMed

Mari, A; Eisert, J

2012-12-07

We show that quantum circuits where the initial state and all the following quantum operations can be represented by positive Wigner functions can be classically efficiently simulated. This is true both for continuous-variable as well as discrete variable systems in odd prime dimensions, two cases which will be treated on entirely the same footing. Noting the fact that Clifford and Gaussian operations preserve the positivity of the Wigner function, our result generalizes the Gottesman-Knill theorem. Our algorithm provides a way of sampling from the output distribution of a computation or a simulation, including the efficient sampling from an approximate output distribution in the case of sampling imperfections for initial states, gates, or measurements. In this sense, this work highlights the role of the positive Wigner function as separating classically efficiently simulable systems from those that are potentially universal for quantum computing and simulation, and it emphasizes the role of negativity of the Wigner function as a computational resource.

Hamiltonian adaptive resolution molecular dynamics simulation of infrared dielectric functions of liquids

NASA Astrophysics Data System (ADS)

Wang, C. C.; Tan, J. Y.; Liu, L. H.

2018-05-01

Hamiltonian adaptive resolution scheme (H-AdResS), which allows to simulate materials by treating different domains of the system at different levels of resolution, is a recently proposed atomistic/coarse-grained multiscale model. In this work, a scheme to calculate the dielectric functions of liquids on account of H-AdResS is presented. In the proposed H-AdResS dielectric-function calculation scheme (DielectFunctCalS), the corrected molecular dipole moments are calculated by multiplying molecular dipole moment by the weighting fraction of the molecular mapping point. As the widths of all-atom and hybrid regions show different degrees of influence on the dielectric functions, a prefactor is multiplied to eliminate the effects of all-atom and hybrid region widths. Since one goal of using the H-AdResS method is to reduce computational costs, widths of the all-atom region and the hybrid region can be reduced considering that the coarse-grained simulation is much more timesaving compared to atomistic simulation. Liquid water and ethanol are taken as test cases to validate the DielectFunctCalS. The H-AdResS DielectFunctCalS results are in good agreement with all-atom molecular dynamics simulations. The accuracy of the H-AdResS results, together with all-atom molecular dynamics results, depends heavily on the choice of the force field and force field parameters. The H-AdResS DielectFunctCalS allows us to calculate the dielectric functions of macromolecule systems with high efficiency and makes the dielectric function calculations of large biomolecular systems possible.

Glass Formation of n-Butanol: Coarse-grained Molecular Dynamics Simulations Using Gay-Berne Potential Model

NASA Astrophysics Data System (ADS)

Xie, Gui-long; Zhang, Yong-hong; Huang, Shi-ping

2012-04-01

Using coarse-grained molecular dynamics simulations based on Gay-Berne potential model, we have simulated the cooling process of liquid n-butanol. A new set of GB parameters are obtained by fitting the results of density functional theory calculations. The simulations are carried out in the range of 290-50 K with temperature decrements of 10 K. The cooling characteristics are determined on the basis of the variations of the density, the potential energy and orientational order parameter with temperature, whose slopes all show discontinuity. Both the radial distribution function curves and the second-rank orientational correlation function curves exhibit splitting in the second peak. Using the discontinuous change of these thermodynamic and structure properties, we obtain the glass transition at an estimate of temperature Tg=120±10 K, which is in good agreement with experimental results 110±1 K.

Application of modified profile analysis to function testing of the motion/no-motion issue in an aircraft ground-handling simulation. [statistical analysis procedure for man machine systems flight simulation

NASA Technical Reports Server (NTRS)

Parrish, R. V.; Mckissick, B. T.; Steinmetz, G. G.

1979-01-01

A recent modification of the methodology of profile analysis, which allows the testing for differences between two functions as a whole with a single test, rather than point by point with multiple tests is discussed. The modification is applied to the examination of the issue of motion/no motion conditions as shown by the lateral deviation curve as a function of engine cut speed of a piloted 737-100 simulator. The results of this application are presented along with those of more conventional statistical test procedures on the same simulator data.

Simulation of thalamic prosthetic vision: reading accuracy, speed, and acuity in sighted humans.

PubMed

Vurro, Milena; Crowell, Anne Marie; Pezaris, John S

2014-01-01

The psychophysics of reading with artificial sight has received increasing attention as visual prostheses are becoming a real possibility to restore useful function to the blind through the coarse, pseudo-pixelized vision they generate. Studies to date have focused on simulating retinal and cortical prostheses; here we extend that work to report on thalamic designs. This study examined the reading performance of normally sighted human subjects using a simulation of three thalamic visual prostheses that varied in phosphene count, to help understand the level of functional ability afforded by thalamic designs in a task of daily living. Reading accuracy, reading speed, and reading acuity of 20 subjects were measured as a function of letter size, using a task based on the MNREAD chart. Results showed that fluid reading was feasible with appropriate combinations of letter size and phosphene count, and performance degraded smoothly as font size was decreased, with an approximate doubling of phosphene count resulting in an increase of 0.2 logMAR in acuity. Results here were consistent with previous results from our laboratory. Results were also consistent with those from the literature, despite using naive subjects who were not trained on the simulator, in contrast to other reports.

Terahertz spectral characteristics of two kinds of important functional oligosaccharides

NASA Astrophysics Data System (ADS)

Li, Ge; Liu, Wei; Wang, Wenai

2018-01-01

The absorption spectra of two kinds of important functional oligosaccharides were firstly acquired based on Fourier transform infrared spectroscopy in the range of 0.15-10THz. The simulation results of their infrared spectra were given based on Gaussian software, which were in good agreement with the experiment results. The rotation spectra and some perssad vibration spectra of these molecules were analyzed, and their absorption peaks were exactly identified. The components information was obtained by comparing the simulation results of different molecules.

Studies on unsaturated flow in dual-scale fiber fabrics

NASA Astrophysics Data System (ADS)

Yan, Fei; Yan, Shilin; Li, Yongjing

2018-03-01

Fiber fabrics in liquid composite molding (LCM) can be recognized as a dual-scale structure. As sink theory developed, this unsaturated flow behavior has already been simulated successfully; however, most of simulated results based on a unit cell under ideal status, thus making results were not agreement with experiment. In this study, an experimental method to establish sink function was proposed. After compared the simulation results by this sink function, it shows high accuracy with the experimental data. Subsequently, the key influencing factors for unsaturated flow have been further investigated; results show that the filling time for unsaturated flow was much longer than saturated flow. In addition, the injection pressure and permeability were the key factors lead to unsaturated flow.

Non-Black-Box Simulation from One-Way Functions and Applications to Resettable Security

DTIC Science & Technology

2012-11-05

from 2001, Barak (FOCS’01) introduced a novel non-black-box simulation technique. This technique enabled the construc- tion of new cryptographic...primitives, such as resettably-sound zero-knowledge arguments, that cannot be proven secure using just black-box simulation techniques. The work of Barak ... Barak requires the existence of collision-resistant hash functions, and a very recent result by Bitansky and Paneth (FOCS’12) instead requires the

A precise mass function in the excursion set approach

NASA Astrophysics Data System (ADS)

Del Popolo, Antonino

2017-04-01

In the present paper, using previous results from Del Popolo papers, we show how the mass function evolution can be obtained in the framework of a spherical collapse model, which has been modified to take account of dynamical friction, the cosmological constant, and angular momentum which proto-structures acquire through tidal interaction with neighbouring ones. We found an improved barrier which is in excellent agreement with simulations. The quoted barrier is used to calculated the mass function. In the case of the ΛCDM paradigm, our mass function is in good agreement (within some %) with the mass function of Klypin's Bolshoi simulation for the virial mass range 5 × 109 - 5 × 1014h-1M⊙, and 0 ≾ z ≿ 10. Similar agreement is obtained with Tinker's mass function, and Castorina's simulations.

Evaluation of automated decisionmaking methodologies and development of an integrated robotic system simulation, volume 2, part 1. Appendix A: Software documentation

NASA Technical Reports Server (NTRS)

Lowrie, J. W.; Fermelia, A. J.; Haley, D. C.; Gremban, K. D.; Vanbaalen, J.; Walsh, R. W.

1982-01-01

Documentation of the preliminary software developed as a framework for a generalized integrated robotic system simulation is presented. The program structure is composed of three major functions controlled by a program executive. The three major functions are: system definition, analysis tools, and post processing. The system definition function handles user input of system parameters and definition of the manipulator configuration. The analysis tools function handles the computational requirements of the program. The post processing function allows for more detailed study of the results of analysis tool function executions. Also documented is the manipulator joint model software to be used as the basis of the manipulator simulation which will be part of the analysis tools capability.

Studies of aggregated nanoparticles steering during magnetic-guided drug delivery in the blood vessels

NASA Astrophysics Data System (ADS)

Hoshiar, Ali Kafash; Le, Tuan-Anh; Amin, Faiz Ul; Kim, Myeong Ok; Yoon, Jungwon

2017-04-01

Magnetic-guided targeted drug delivery (TDD) systems can enhance the treatment of diverse diseases. Despite the potential and promising results of nanoparticles, aggregation prevents precise particle guidance in the vasculature. In this study, we developed a simulation platform to investigate aggregation during steering of nanoparticles using a magnetic field function. The magnetic field function (MFF) comprises a positive and negative pulsed magnetic field generated by electromagnetic coils, which prevents adherence of particles to the vessel wall during magnetic guidance. A commonly used Y-shaped vessel was simulated and the performance of the MFF analyzed; the experimental data were in agreement with the simulation results. Moreover, the effects of various parameters on magnetic guidance were evaluated and the most influential identified. The simulation results presented herein will facilitate more precise guidance of nanoparticles in vivo.

Online model checking approach based parameter estimation to a neuronal fate decision simulation model in Caenorhabditis elegans with hybrid functional Petri net with extension.

PubMed

Li, Chen; Nagasaki, Masao; Koh, Chuan Hock; Miyano, Satoru

2011-05-01

Mathematical modeling and simulation studies are playing an increasingly important role in helping researchers elucidate how living organisms function in cells. In systems biology, researchers typically tune many parameters manually to achieve simulation results that are consistent with biological knowledge. This severely limits the size and complexity of simulation models built. In order to break this limitation, we propose a computational framework to automatically estimate kinetic parameters for a given network structure. We utilized an online (on-the-fly) model checking technique (which saves resources compared to the offline approach), with a quantitative modeling and simulation architecture named hybrid functional Petri net with extension (HFPNe). We demonstrate the applicability of this framework by the analysis of the underlying model for the neuronal cell fate decision model (ASE fate model) in Caenorhabditis elegans. First, we built a quantitative ASE fate model containing 3327 components emulating nine genetic conditions. Then, using our developed efficient online model checker, MIRACH 1.0, together with parameter estimation, we ran 20-million simulation runs, and were able to locate 57 parameter sets for 23 parameters in the model that are consistent with 45 biological rules extracted from published biological articles without much manual intervention. To evaluate the robustness of these 57 parameter sets, we run another 20 million simulation runs using different magnitudes of noise. Our simulation results concluded that among these models, one model is the most reasonable and robust simulation model owing to the high stability against these stochastic noises. Our simulation results provide interesting biological findings which could be used for future wet-lab experiments.

Ray tracing the Wigner distribution function for optical simulations

NASA Astrophysics Data System (ADS)

Mout, Marco; Wick, Michael; Bociort, Florian; Petschulat, Joerg; Urbach, Paul

2018-01-01

We study a simulation method that uses the Wigner distribution function to incorporate wave optical effects in an established framework based on geometrical optics, i.e., a ray tracing engine. We use the method to calculate point spread functions and show that it is accurate for paraxial systems but produces unphysical results in the presence of aberrations. The cause of these anomalies is explained using an analytical model.

Tests of potential functional barriers for laminated multilayer food packages. Part I: Low molecular weight permeants.

PubMed

Simal-Gándara, J; Sarria-Vidal, M; Koorevaar, A; Rijk, R

2000-08-01

The advent of the functional barrier concept in food packaging has brought with it a requirement for fast tests of permeation through potential barrier materials. In such tests it would be convenient for both foodstuffs and materials below the functional barrier (sub-barrier materials) to be represented by standard simulants. By means of inverse gas chromatography, liquid paraffin spiked with appropriate permeants was considered as a potential simulant of sub-barrier materials based on polypropylene (PP) or similar polyolefins. Experiments were performed to characterize the kinetics of the permeation of low molecular weight model permeants (octene, toluene and isopropanol) from liquid paraffin, through a surrogate potential functional barrier (25 microns-thick oriented PP) into the food stimulants olive oil and 3% (w/v) acetic acid. These permeation results were interpreted in terms of three permeation kinetic models regarding the solubility of a particular model permeant in the post-barrier medium (i.e. the food simulant). The results obtained justify the development and evaluation of liquid sub-barrier simulants that would allow flexible yet rigorous testing of new laminated multilayer packaging materials.

Comparative analysis of numerical simulation techniques for incoherent imaging of extended objects through atmospheric turbulence

NASA Astrophysics Data System (ADS)

Lachinova, Svetlana L.; Vorontsov, Mikhail A.; Filimonov, Grigory A.; LeMaster, Daniel A.; Trippel, Matthew E.

2017-07-01

Computational efficiency and accuracy of wave-optics-based Monte-Carlo and brightness function numerical simulation techniques for incoherent imaging of extended objects through atmospheric turbulence are evaluated. Simulation results are compared with theoretical estimates based on known analytical solutions for the modulation transfer function of an imaging system and the long-exposure image of a Gaussian-shaped incoherent light source. It is shown that the accuracy of both techniques is comparable over the wide range of path lengths and atmospheric turbulence conditions, whereas the brightness function technique is advantageous in terms of the computational speed.

Full cycle trigonometric function on Intel Quartus II Verilog

NASA Astrophysics Data System (ADS)

Mustapha, Muhazam; Zulkarnain, Nur Antasha

2018-02-01

This paper discusses about an improvement of a previous research on hardware based trigonometric calculations. Tangent function will also be implemented to get a complete set. The functions have been simulated using Quartus II where the result will be compared to the previous work. The number of bits has also been extended for each trigonometric function. The design is based on RTL due to its resource efficient nature. At earlier stage, a technology independent test bench simulation was conducted on ModelSim due to its convenience in capturing simulation data so that accuracy information can be obtained. On second stage, Intel/Altera Quartus II will be used to simulate on technology dependent platform, particularly on the one belonging to Intel/Altera itself. Real data on no. logic elements used and propagation delay have also been obtained.

Functional connectivity change as shared signal dynamics

PubMed Central

Cole, Michael W.; Yang, Genevieve J.; Murray, John D.; Repovš, Grega; Anticevic, Alan

2015-01-01

Background An increasing number of neuroscientific studies gain insights by focusing on differences in functional connectivity – between groups, individuals, temporal windows, or task conditions. We found using simulations that additional insights into such differences can be gained by forgoing variance normalization, a procedure used by most functional connectivity measures. Simulations indicated that these functional connectivity measures are sensitive to increases in independent fluctuations (unshared signal) in time series, consistently reducing functional connectivity estimates (e.g., correlations) even though such changes are unrelated to corresponding fluctuations (shared signal) between those time series. This is inconsistent with the common notion of functional connectivity as the amount of inter-region interaction. New Method Simulations revealed that a version of correlation without variance normalization – covariance – was able to isolate differences in shared signal, increasing interpretability of observed functional connectivity change. Simulations also revealed cases problematic for non-normalized methods, leading to a “covariance conjunction” method combining the benefits of both normalized and non-normalized approaches. Results We found that covariance and covariance conjunction methods can detect functional connectivity changes across a variety of tasks and rest in both clinical and non-clinical functional MRI datasets. Comparison with Existing Method(s) We verified using a variety of tasks and rest in both clinical and non-clinical functional MRI datasets that it matters in practice whether correlation, covariance, or covariance conjunction methods are used. Conclusions These results demonstrate the practical and theoretical utility of isolating changes in shared signal, improving the ability to interpret observed functional connectivity change. PMID:26642966

Sensitivity of estimated muscle force in forward simulation of normal walking

PubMed Central

Xiao, Ming; Higginson, Jill

2009-01-01

Generic muscle parameters are often used in muscle-driven simulations of human movement estimate individual muscle forces and function. The results may not be valid since muscle properties vary from subject to subject. This study investigated the effect of using generic parameters in a muscle-driven forward simulation on muscle force estimation. We generated a normal walking simulation in OpenSim and examined the sensitivity of individual muscle to perturbations in muscle parameters, including the number of muscles, maximum isometric force, optimal fiber length and tendon slack length. We found that when changing the number muscles included in the model, only magnitude of the estimated muscle forces was affected. Our results also suggest it is especially important to use accurate values of tendon slack length and optimal fiber length for ankle plantarflexors and knee extensors. Changes in force production one muscle were typically compensated for by changes in force production by muscles in the same functional muscle group, or the antagonistic muscle group. Conclusions regarding muscle function based on simulations with generic musculoskeletal parameters should be interpreted with caution. PMID:20498485

Result of Monte-Carlo simulation of electron-photon cascades in lead and layers of lead-scintillator

NASA Technical Reports Server (NTRS)

Wasilewski, A.; Krys, E.

1985-01-01

Results of Monte-Carlo simulation of electromagnetic cascade development in lead and lead-scintillator sandwiches are analyzed. It is demonstrated that the structure function for core approximation is not applicable in the case in which the primary energy is higher than 100 GeV. The simulation data has shown that introducing an inhomogeneous chamber structure results in subsequent reduction of secondary particles.

SU-F-19A-05: Experimental and Monte Carlo Characterization of the 1 Cm CivaString 103Pd Brachytherapy Source

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

Reed, J; Micka, J; Culberson, W

Purpose: To determine the in-air azimuthal anisotropy and in-water dose distribution for the 1 cm length of the CivaString {sup 103}Pd brachytherapy source through measurements and Monte Carlo (MC) simulations. American Association of Physicists in Medicine Task Group No. 43 (TG-43) dosimetry parameters were also determined for this source. Methods: The in-air azimuthal anisotropy of the source was measured with a NaI scintillation detector and simulated with the MCNP5 radiation transport code. Measured and simulated results were normalized to their respective mean values and compared. The TG-43 dose-rate constant, line-source radial dose function, and 2D anisotropy function for this sourcemore » were determined from LiF:Mg,Ti thermoluminescent dosimeter (TLD) measurements and MC simulations. The impact of {sup 103}Pd well-loading variability on the in-water dose distribution was investigated using MC simulations by comparing the dose distribution for a source model with four wells of equal strength to that for a source model with strengths increased by 1% for two of the four wells. Results: NaI scintillation detector measurements and MC simulations of the in-air azimuthal anisotropy showed that ≥95% of the normalized data were within 1.2% of the mean value. TLD measurements and MC simulations of the TG-43 dose-rate constant, line-source radial dose function, and 2D anisotropy function agreed to within the experimental TLD uncertainties (k=2). MC simulations showed that a 1% variability in {sup 103}Pd well-loading resulted in changes of <0.1%, <0.1%, and <0.3% in the TG-43 dose-rate constant, radial dose distribution, and polar dose distribution, respectively. Conclusion: The CivaString source has a high degree of azimuthal symmetry as indicated by the NaI scintillation detector measurements and MC simulations of the in-air azimuthal anisotropy. TG-43 dosimetry parameters for this source were determined from TLD measurements and MC simulations. {sup 103}Pd well-loading variability results in minimal variations in the in-water dose distribution according to MC simulations. This work was partially supported by CivaTech Oncology, Inc. through an educational grant for Joshua Reed, John Micka, Wesley Culberson, and Larry DeWerd and through research support for Mark Rivard.« less

Probing the triplet correlation function in liquid water by experiments and molecular simulations.

PubMed

Dhabal, Debdas; Wikfeldt, Kjartan Thor; Skinner, Lawrie B; Chakravarty, Charusita; Kashyap, Hemant K

2017-01-25

Despite very significant developments in scattering experiments like X-ray and neutron diffraction, it has been challenging to elucidate the nature of tetrahedral molecular configurations in liquid water. A key question is whether the pair correlation functions, which can be obtained from scattering experiments, are sufficient to describe the tetrahedral ordering of water molecules. In our previous study (Dhabal et al., J. Chem. Phys., 2014, 141, 174504), using data-sets generated from reverse Monte Carlo and molecular dynamics simulations, we showed that the triplet correlation functions contain important information on the tetrahedrality of water in the liquid state. In the present study, X-ray scattering experiments and molecular dynamics (MD) simulations are used to link the isothermal pressure derivative of the structure factor with the triplet correlation functions for water. Triplet functions are determined for water up to 3.3 kbar at 298 K to display the effect of pressure on the water structure. The results suggest that triplet functions (H[combining tilde](q)) obtained using a rigid-body TIP4P/2005 water model are consistent with the experimental results. The triplet functions obtained in experiment as well as in simulations evince that in the case of tetrahedral liquids, exertion of higher pressure leads to a better agreement with the Kirkwood superposition approximation (KSA). We further validate this observation using the triplet correlation functions (g (3) (r,s,t)) calculated directly from simulation trajectory, revealing that both H[combining tilde](q) in q-space and g (3) (r,s,t) in real-space contain similar information on the tetrahedrality of liquids. This study demonstrates that the structure factor, even though it has only pair correlation information of the liquid structure, can shed light on three-body correlations in liquid water through its isothermal pressure derivative term.

AmapSim: a structural whole-plant simulator based on botanical knowledge and designed to host external functional models.

PubMed

Barczi, Jean-François; Rey, Hervé; Caraglio, Yves; de Reffye, Philippe; Barthélémy, Daniel; Dong, Qiao Xue; Fourcaud, Thierry

2008-05-01

AmapSim is a tool that implements a structural plant growth model based on a botanical theory and simulates plant morphogenesis to produce accurate, complex and detailed plant architectures. This software is the result of more than a decade of research and development devoted to plant architecture. New advances in the software development have yielded plug-in external functions that open up the simulator to functional processes. The simulation of plant topology is based on the growth of a set of virtual buds whose activity is modelled using stochastic processes. The geometry of the resulting axes is modelled by simple descriptive functions. The potential growth of each bud is represented by means of a numerical value called physiological age, which controls the value for each parameter in the model. The set of possible values for physiological ages is called the reference axis. In order to mimic morphological and architectural metamorphosis, the value allocated for the physiological age of buds evolves along this reference axis according to an oriented finite state automaton whose occupation and transition law follows a semi-Markovian function. Simulations were performed on tomato plants to demonstrate how the AmapSim simulator can interface external modules, e.g. a GREENLAB growth model and a radiosity model. The algorithmic ability provided by AmapSim, e.g. the reference axis, enables unified control to be exercised over plant development parameter values, depending on the biological process target: how to affect the local pertinent process, i.e. the pertinent parameter(s), while keeping the rest unchanged. This opening up to external functions also offers a broadened field of applications and thus allows feedback between plant growth and the physical environment.

PIC simulations of a three component plasma described by Kappa distribution functions as observed in Saturn's magnetosphere

NASA Astrophysics Data System (ADS)

Barbosa, Marcos; Alves, Maria Virginia; Simões Junior, Fernando

2016-04-01

In plasmas out of thermodynamic equilibrium the particle velocity distribution can be described by the so called Kappa distribution. These velocity distribution functions are a generalization of the Maxwellian distribution. Since 1960, Kappa velocity distributions were observed in several regions of interplanetary space and astrophysical plasmas. Using KEMPO1 particle simulation code, modified to introduce Kappa distribution functions as initial conditions for particle velocities, the normal modes of propagation were analyzed in a plasma containing two species of electrons with different temperatures and densities and ions as a third specie.This type of plasma is usually found in magnetospheres such as in Saturn. Numerical solutions for the dispersion relation for such a plasma predict the presence of an electron-acoustic mode, besides the Langmuir and ion-acoustic modes. In the presence of an ambient magnetic field, the perpendicular propagation (Bernstein mode) also changes, as compared to a Maxwellian plasma, due to the Kappa distribution function. Here results for simulations with and without external magnetic field are presented. The parameters for the initial conditions in the simulations were obtained from the Cassini spacecraft data. Simulation results are compared with numerical solutions of the dispersion relation obtained in the literature and they are in good agreement.

Short- and long-time diffusion and dynamic scaling in suspensions of charged colloidal particles

NASA Astrophysics Data System (ADS)

Banchio, Adolfo J.; Heinen, Marco; Holmqvist, Peter; Nägele, Gerhard

2018-04-01

We report on a comprehensive theory-simulation-experimental study of collective and self-diffusion in concentrated suspensions of charge-stabilized colloidal spheres. In theory and simulation, the spheres are assumed to interact directly by a hard-core plus screened Coulomb effective pair potential. The intermediate scattering function, fc(q, t), is calculated by elaborate accelerated Stokesian dynamics (ASD) simulations for Brownian systems where many-particle hydrodynamic interactions (HIs) are fully accounted for, using a novel extrapolation scheme to a macroscopically large system size valid for all correlation times. The study spans the correlation time range from the colloidal short-time to the long-time regime. Additionally, Brownian Dynamics (BD) simulation and mode-coupling theory (MCT) results of fc(q, t) are generated where HIs are neglected. Using these results, the influence of HIs on collective and self-diffusion and the accuracy of the MCT method are quantified. It is shown that HIs enhance collective and self-diffusion at intermediate and long times. At short times self-diffusion, and for wavenumbers outside the structure factor peak region also collective diffusion, are slowed down by HIs. MCT significantly overestimates the slowing influence of dynamic particle caging. The dynamic scattering functions obtained in the ASD simulations are in overall good agreement with our dynamic light scattering (DLS) results for a concentration series of charged silica spheres in an organic solvent mixture, in the experimental time window and wavenumber range. From the simulation data for the time derivative of the width function associated with fc(q, t), there is indication of long-time exponential decay of fc(q, t), for wavenumbers around the location of the static structure factor principal peak. The experimental scattering functions in the probed time range are consistent with a time-wavenumber factorization scaling behavior of fc(q, t) that was first reported by Segrè and Pusey [Phys. Rev. Lett. 77, 771 (1996)] for suspensions of hard spheres. Our BD simulation and MCT results predict a significant violation of exact factorization scaling which, however, is approximately restored according to the ASD results when HIs are accounted for, consistent with the experimental findings for fc(q, t). Our study of collective diffusion is amended by simulation and theoretical results for the self-intermediate scattering function, fs(q, t), and its non-Gaussian parameter α2(t) and for the particle mean squared displacement W(t) and its time derivative. Since self-diffusion properties are not assessed in standard DLS measurements, a method to deduce W(t) approximately from fc(q, t) is theoretically validated.

Computer Simulation for Calculating the Second-Order Correlation Function of Classical and Quantum Light

ERIC Educational Resources Information Center

Facao, M.; Lopes, A.; Silva, A. L.; Silva, P.

2011-01-01

We propose an undergraduate numerical project for simulating the results of the second-order correlation function as obtained by an intensity interference experiment for two kinds of light, namely bunched light with Gaussian or Lorentzian power density spectrum and antibunched light obtained from single-photon sources. While the algorithm for…

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.

Molecular Dynamics Simulations of Voltage-Gated Cation Channels: Insights on Voltage-Sensor Domain Function and Modulation

PubMed Central

Delemotte, Lucie; Klein, Michael L.; Tarek, Mounir

2012-01-01

Since their discovery in the 1950s, the structure and function of voltage-gated cation channels (VGCC) has been largely understood thanks to results stemming from electrophysiology, pharmacology, spectroscopy, and structural biology. Over the past decade, computational methods such as molecular dynamics (MD) simulations have also contributed, providing molecular level information that can be tested against experimental results, thereby allowing the validation of the models and protocols. Importantly, MD can shed light on elements of VGCC function that cannot be easily accessed through “classical” experiments. Here, we review the results of recent MD simulations addressing key questions that pertain to the function and modulation of the VGCC’s voltage-sensor domain (VSD) highlighting: (1) the movement of the S4-helix basic residues during channel activation, articulating how the electrical driving force acts upon them; (2) the nature of the VSD intermediate states on transitioning between open and closed states of the VGCC; and (3) the molecular level effects on the VSD arising from mutations of specific S4 positively charged residues involved in certain genetic diseases. PMID:22654756

Cognitive deficits are associated with poorer simulated driving in older adults with heart failure

PubMed Central

2013-01-01

Background Cognitive impairment is prevalent in older adults with heart failure (HF) and associated with reduced functional independence. HF patients appear at risk for reduced driving ability, as past work in other medical samples has shown cognitive dysfunction to be an important contributor to driving performance. The current study examined whether cognitive dysfunction was independently associated with reduced driving simulation performance in a sample of HF patients. Methods 18 persons with HF (67.72; SD = 8.56 year) completed echocardiogram and a brief neuropsychological test battery assessing global cognitive function, attention/executive function, memory and motor function. All participants then completed the Kent Multidimensional Assessment Driving Simulation (K-MADS), a driving simulator scenario with good psychometric properties. Results The sample exhibited an average Mini Mental State Examination (MMSE) score of 27.83 (SD = 2.09). Independent sample t-tests showed that HF patients performed worse than healthy adults on the driving simulation scenario. Finally, partial correlations showed worse attention/executive and motor function were independently associated with poorer driving simulation performance across several indices reflective of driving ability (i.e., centerline crossings, number of collisions, % of time over the speed limit, among others). Conclusion The current findings showed that reduced cognitive function was associated with poor simulated driving performance in older adults with HF. If replicated using behind-the-wheel testing, HF patients may be at elevated risk for unsafe driving and routine driving evaluations in this population may be warranted. PMID:24499466

Scanning tunneling microscopy image simulation of the rutile (110) TiO2 surface with hybrid functionals and the localized basis set approach

NASA Astrophysics Data System (ADS)

Di Valentin, Cristiana

2007-10-01

In this work we present a simplified procedure to use hybrid functionals and localized atomic basis sets to simulate scanning tunneling microscopy (STM) images of stoichiometric, reduced and hydroxylated rutile (110) TiO2 surface. For the two defective systems it is necessary to introduce some exact Hartree-Fock exchange in the exchange functional in order to correctly describe the details of the electronic structure. Results are compared to the standard density functional theory and planewave basis set approach. Both methods have advantages and drawbacks that are analyzed in detail. In particular, for the localized basis set approach, it is necessary to introduce a number of Gaussian function in the vacuum region above the surface in order to correctly describe the exponential decay of the integrated local density of states from the surface. In the planewave periodic approach, a thick vacuum region is required to achieve correct results. Simulated STM images are obtained for both the reduced and hydroxylated surface which nicely compare with experimental findings. A direct comparison of the two defects as displayed in the simulated STM images indicates that the OH groups should appear brighter than oxygen vacancies in perfect agreement with the experimental STM data.

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

NASA Astrophysics Data System (ADS)

Savitri, D.

2018-01-01

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

Analysis of drift correction in different simulated weighing schemes

NASA Astrophysics Data System (ADS)

Beatrici, A.; Rebelo, A.; Quintão, D.; Cacais, F. L.; Loayza, V. M.

2015-10-01

In the calibration of high accuracy mass standards some weighing schemes are used to reduce or eliminate the zero drift effects in mass comparators. There are different sources for the drift and different methods for its treatment. By using numerical methods, drift functions were simulated and a random term was included in each function. The comparison between the results obtained from ABABAB and ABBA weighing series was carried out. The results show a better efficacy of ABABAB method for drift with smooth variation and small randomness.

Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions.

PubMed

Wells, Stephen A; van der Kamp, Marc W; McGeagh, John D; Mulholland, Adrian J

2015-01-01

Large-scale conformational change is a common feature in the catalytic cycles of enzymes. Many enzymes function as homodimers with active sites that contain elements from both chains. Symmetric and anti-symmetric cooperative motions in homodimers can potentially lead to correlated active site opening and/or closure, likely to be important for ligand binding and release. Here, we examine such motions in two different domain-swapped homodimeric enzymes: the DcpS scavenger decapping enzyme and citrate synthase. We use and compare two types of all-atom simulations: conventional molecular dynamics simulations to identify physically meaningful conformational ensembles, and rapid geometric simulations of flexible motion, biased along normal mode directions, to identify relevant motions encoded in the protein structure. The results indicate that the opening/closure motions are intrinsic features of both unliganded enzymes. In DcpS, conformational change is dominated by an anti-symmetric cooperative motion, causing one active site to close as the other opens; however a symmetric motion is also significant. In CS, we identify that both symmetric (suggested by crystallography) and asymmetric motions are features of the protein structure, and as a result the behaviour in solution is largely non-cooperative. The agreement between two modelling approaches using very different levels of theory indicates that the behaviours are indeed intrinsic to the protein structures. Geometric simulations correctly identify and explore large amplitudes of motion, while molecular dynamics simulations indicate the ranges of motion that are energetically feasible. Together, the simulation approaches are able to reveal unexpected functionally relevant motions, and highlight differences between enzymes.

Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions

PubMed Central

McGeagh, John D.; Mulholland, Adrian J.

2015-01-01

Large-scale conformational change is a common feature in the catalytic cycles of enzymes. Many enzymes function as homodimers with active sites that contain elements from both chains. Symmetric and anti-symmetric cooperative motions in homodimers can potentially lead to correlated active site opening and/or closure, likely to be important for ligand binding and release. Here, we examine such motions in two different domain-swapped homodimeric enzymes: the DcpS scavenger decapping enzyme and citrate synthase. We use and compare two types of all-atom simulations: conventional molecular dynamics simulations to identify physically meaningful conformational ensembles, and rapid geometric simulations of flexible motion, biased along normal mode directions, to identify relevant motions encoded in the protein structure. The results indicate that the opening/closure motions are intrinsic features of both unliganded enzymes. In DcpS, conformational change is dominated by an anti-symmetric cooperative motion, causing one active site to close as the other opens; however a symmetric motion is also significant. In CS, we identify that both symmetric (suggested by crystallography) and asymmetric motions are features of the protein structure, and as a result the behaviour in solution is largely non-cooperative. The agreement between two modelling approaches using very different levels of theory indicates that the behaviours are indeed intrinsic to the protein structures. Geometric simulations correctly identify and explore large amplitudes of motion, while molecular dynamics simulations indicate the ranges of motion that are energetically feasible. Together, the simulation approaches are able to reveal unexpected functionally relevant motions, and highlight differences between enzymes. PMID:26241964

Magnetic Dissipation in Asymmetric Strong Guide 3D Simulations: Examples of Magnetic Diffusion and Reconnection

NASA Astrophysics Data System (ADS)

Scudder, J. D.; Karimabadi, H.; Daughton, W. S.

2013-12-01

Interpretations of 2D simulations of magnetic reconnection are greatly simplified by using the flux function, usually the out of plane component of the vector potential. This theoretical device is no longer available when simulations are analyzed in 3-D. We illustrate the results of determining the locale rates of flux slippage in simulations by a technique based on Maxwell's equations. The technique recovers the usual results obtained for the flux function in 2D simulations, but remains viable in 3D simulations where there is no flux function. The method has also been successfully tested for full PIC simulations where reconnection is geometrically forbiddden. While such layers possess measurable flux slippages (diffusion) their level is not as strong as recorded in known 2D PIC reconnection sites using the same methodology. This approach will be used to explore the spatial incidence and strength of flux slippages across a 3D, asymmetric, strong guide field run discussed previously in the literature. Regions of diffusive behavior are illustrated where LHDI has been previously identified out on the separatrices, while much stronger flux slippages, typical of the X-regions of 2D simulations, are shown to occur elsewhere throughout the simulation. These results suggest that reconnection requires sufficiently vigorous flux slippage to be self sustaining, while non-zero flux slippage can and does occur without being at the reconnection site. A cross check of this approach is provided by the mixing ratio of tagged simulation particles of known spatial origin discussed by Daughton et al., 2013 (this meeting); they provide an integral measure of flux slippage up to the present point in the simulation. We will discuss the correlations between our Maxwell based flux slippage rates and the inferred rates of change of this mixing ratio (as recorded in the local fluid frame).

Tools and Equipment Modeling for Automobile Interactive Assembling Operating Simulation

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

Wu Dianliang; Zhu Hongmin; Shanghai Key Laboratory of Advance Manufacturing Environment

Tools and equipment play an important role in the simulation of virtual assembly, especially in the assembly process simulation and plan. Because of variety in function and complexity in structure and manipulation, the simulation of tools and equipments remains to be a challenge for interactive assembly operation. Based on analysis of details and characteristics of interactive operations for automobile assembly, the functional requirement for tools and equipments of automobile assembly is given. Then, a unified modeling method for information expression and function realization of general tools and equipments is represented, and the handling methods of manual, semi-automatic, automatic tools andmore » equipments are discussed. Finally, the application in assembly simulation of rear suspension and front suspension of Roewe 750 automobile is given. The result shows that the modeling and handling methods are applicable in the interactive simulation of various tools and equipments, and can also be used for supporting assembly process planning in virtual environment.« less

High performance hybrid functional Petri net simulations of biological pathway models on CUDA.

PubMed

Chalkidis, Georgios; Nagasaki, Masao; Miyano, Satoru

2011-01-01

Hybrid functional Petri nets are a wide-spread tool for representing and simulating biological models. Due to their potential of providing virtual drug testing environments, biological simulations have a growing impact on pharmaceutical research. Continuous research advancements in biology and medicine lead to exponentially increasing simulation times, thus raising the demand for performance accelerations by efficient and inexpensive parallel computation solutions. Recent developments in the field of general-purpose computation on graphics processing units (GPGPU) enabled the scientific community to port a variety of compute intensive algorithms onto the graphics processing unit (GPU). This work presents the first scheme for mapping biological hybrid functional Petri net models, which can handle both discrete and continuous entities, onto compute unified device architecture (CUDA) enabled GPUs. GPU accelerated simulations are observed to run up to 18 times faster than sequential implementations. Simulating the cell boundary formation by Delta-Notch signaling on a CUDA enabled GPU results in a speedup of approximately 7x for a model containing 1,600 cells.

Functionality limit of classical simulated annealing

NASA Astrophysics Data System (ADS)

Hasegawa, M.

2015-09-01

By analyzing the system dynamics in the landscape paradigm, optimization function of classical simulated annealing is reviewed on the random traveling salesman problems. The properly functioning region of the algorithm is experimentally determined in the size-time plane and the influence of its boundary on the scalability test is examined in the standard framework of this method. From both results, an empirical choice of temperature length is plausibly explained as a minimum requirement that the algorithm maintains its scalability within its functionality limit. The study exemplifies the applicability of computational physics analysis to the optimization algorithm research.

Linear and nonlinear properties of the ULF waves driven by ring-beam distribution functions

NASA Technical Reports Server (NTRS)

Killen, K.; Omidi, N.; Krauss-Varban, D.; Karimabadi, H.

1995-01-01

The problem of the exitation of obliquely propagating magnetosonic waves which can steepen up (also known as shocklets) is considered. Shocklets have been observed upstream of the Earth's bow shock and at comets Giacobini-Zinner and Grigg-Skjellerup. Linear theory as well as two-dimensional (2-D) hybrid (fluid electrons, particle ions) simulations are used to determine the properties of waves generated by ring-beam velocity distributions in great detail. The effects of both proton and oxygen ring-beams are considered. The study of instabilities excited by a proton ring-beam is relevant to the region upstream of the Earth's bow shock, whereas the oxygen ring-beam corresponds to cometary ions picked up by the solar wind. Linear theory has shown that for a ring-beam, four instabilities are found, one on the nonresonant mode, one on the Alfven mode, and two along the magnetosonic/whistler branch. The relative growth rate of these instabilities is a sensitive function of parameters. Although one of the magnetosonic instabilities has maximum growth along the magnetic field, the other has maximum growth in oblique directions. We have studied the competition of these instabilities in the nonlinear regime using 2-D simulations. As in the linear limit, the nonlinear results are a function of beam density and distribution function. By performing the simulations as both initial value and driven systems, we have found that the outcome of the simulations can vary, suggesting that the latter type simulations is needed to address the observations. A general conclusion of the simulation results is that field-aligned beams do not result in the formation of shocklets, whereas ring-beam distributions can.

What do Simulations Predict for the Galaxy Stellar Mass Function and its Evolution in Different Environments?

NASA Astrophysics Data System (ADS)

Vulcani, Benedetta; De Lucia, Gabriella; Poggianti, Bianca M.; Bundy, Kevin; More, Surhud; Calvi, Rosa

2014-06-01

We present a comparison between the observed galaxy stellar mass function and the one predicted from the De Lucia & Blaizot semi-analytic model applied to the Millennium Simulation, for cluster satellites and galaxies in the field (meant as a wide portion of the sky, including all environments), in the local universe (z ~ 0.06), and at intermediate redshift (z ~ 0.6), with the aim to shed light on the processes which regulate the mass distribution in different environments. While the mass functions in the field and in its finer environments (groups, binary, and single systems) are well matched in the local universe down to the completeness limit of the observational sample, the model overpredicts the number of low-mass galaxies in the field at z ~ 0.6 and in clusters at both redshifts. Above M * = 1010.25 M ⊙, it reproduces the observed similarity of the cluster and field mass functions but not the observed evolution. Our results point out two shortcomings of the model: an incorrect treatment of cluster-specific environmental effects and an overefficient galaxy formation at early times (as already found by, e.g., Weinmann et al.). Next, we consider only simulations. Also using the Guo et al. model, we find that the high-mass end of the mass functions depends on halo mass: only very massive halos host massive galaxies, with the result that their mass function is flatter. Above M * = 109.4 M ⊙, simulations show an evolution in the number of the most massive galaxies in all environments. Mass functions obtained from the two prescriptions are different, however, results are qualitatively similar, indicating that the adopted methods to model the evolution of central and satellite galaxies still have to be better implemented in semi-analytic models.

NOTE: Implementation of angular response function modeling in SPECT simulations with GATE

NASA Astrophysics Data System (ADS)

Descourt, P.; Carlier, T.; Du, Y.; Song, X.; Buvat, I.; Frey, E. C.; Bardies, M.; Tsui, B. M. W.; Visvikis, D.

2010-05-01

Among Monte Carlo simulation codes in medical imaging, the GATE simulation platform is widely used today given its flexibility and accuracy, despite long run times, which in SPECT simulations are mostly spent in tracking photons through the collimators. In this work, a tabulated model of the collimator/detector response was implemented within the GATE framework to significantly reduce the simulation times in SPECT. This implementation uses the angular response function (ARF) model. The performance of the implemented ARF approach has been compared to standard SPECT GATE simulations in terms of the ARF tables' accuracy, overall SPECT system performance and run times. Considering the simulation of the Siemens Symbia T SPECT system using high-energy collimators, differences of less than 1% were measured between the ARF-based and the standard GATE-based simulations, while considering the same noise level in the projections, acceleration factors of up to 180 were obtained when simulating a planar 364 keV source seen with the same SPECT system. The ARF-based and the standard GATE simulation results also agreed very well when considering a four-head SPECT simulation of a realistic Jaszczak phantom filled with iodine-131, with a resulting acceleration factor of 100. In conclusion, the implementation of an ARF-based model of collimator/detector response for SPECT simulations within GATE significantly reduces the simulation run times without compromising accuracy.

Construction of multi-functional open modulized Matlab simulation toolbox for imaging ladar system

NASA Astrophysics Data System (ADS)

Wu, Long; Zhao, Yuan; Tang, Meng; He, Jiang; Zhang, Yong

2011-06-01

Ladar system simulation is to simulate the ladar models using computer simulation technology in order to predict the performance of the ladar system. This paper presents the developments of laser imaging radar simulation for domestic and overseas studies and the studies of computer simulation on ladar system with different application requests. The LadarSim and FOI-LadarSIM simulation facilities of Utah State University and Swedish Defence Research Agency are introduced in details. This paper presents the low level of simulation scale, un-unified design and applications of domestic researches in imaging ladar system simulation, which are mostly to achieve simple function simulation based on ranging equations for ladar systems. Design of laser imaging radar simulation with open and modularized structure is proposed to design unified modules for ladar system, laser emitter, atmosphere models, target models, signal receiver, parameters setting and system controller. Unified Matlab toolbox and standard control modules have been built with regulated input and output of the functions, and the communication protocols between hardware modules. A simulation based on ICCD gain-modulated imaging ladar system for a space shuttle is made based on the toolbox. The simulation result shows that the models and parameter settings of the Matlab toolbox are able to simulate the actual detection process precisely. The unified control module and pre-defined parameter settings simplify the simulation of imaging ladar detection. Its open structures enable the toolbox to be modified for specialized requests. The modulization gives simulations flexibility.

Discrete event simulation and the resultant data storage system response in the operational mission environment of Jupiter-Saturn /Voyager/ spacecraft

NASA Technical Reports Server (NTRS)

Mukhopadhyay, A. K.

1978-01-01

The Data Storage Subsystem Simulator (DSSSIM) simulating (by ground software) occurrence of discrete events in the Voyager mission is described. Functional requirements for Data Storage Subsystems (DSS) simulation are discussed, and discrete event simulation/DSSSIM processing is covered. Four types of outputs associated with a typical DSSSIM run are presented, and DSSSIM limitations and constraints are outlined.

Thermalized Drude Oscillators with the LAMMPS Molecular Dynamics Simulator.

PubMed

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

2016-01-25

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

Default network connectivity decodes brain states with simulated microgravity.

PubMed

Zeng, Ling-Li; Liao, Yang; Zhou, Zongtan; Shen, Hui; Liu, Yadong; Liu, Xufeng; Hu, Dewen

2016-04-01

With great progress of space navigation technology, it becomes possible to travel beyond Earth's gravity. So far, it remains unclear whether the human brain can function normally within an environment of microgravity and confinement. Particularly, it is a challenge to figure out some neuroimaging-based markers for rapid screening diagnosis of disrupted brain function in microgravity environment. In this study, a 7-day -6° head down tilt bed rest experiment was used to simulate the microgravity, and twenty healthy male participants underwent resting-state functional magnetic resonance imaging scans at baseline and after the simulated microgravity experiment. We used a multivariate pattern analysis approach to distinguish the brain states with simulated microgravity from normal gravity based on the functional connectivity within the default network, resulting in an accuracy of no less than 85 % via cross-validation. Moreover, most discriminative functional connections were mainly located between the limbic system and cortical areas and were enhanced after simulated microgravity, implying a self-adaption or compensatory enhancement to fulfill the need of complex demand in spatial navigation and motor control functions in microgravity environment. Overall, the findings suggest that the brain states in microgravity are likely different from those in normal gravity and that brain connectome could act as a biomarker to indicate the brain state in microgravity.

Structure of Poly(dialkylsiloxane) Melts:  Comparisons of Wide-Angle X-ray Scattering, Molecular Dynamics Simulations, and Integral Equation Theory

DOE PAGES

Habenschuss, Anton; Tsige, Mesfin; Curro, John G.; ...

2007-08-21

Here, wide-angle X-ray scattering, molecular dynamics (MD) simulations, and integral equation theory are used to study the structure of poly(diethylsiloxane) (PDES), poly(ethylmethylsiloxane) (PEMS), and poly(dimethylsiloxane) (PDMS) melts. The structure functions of PDES, PEMS, and PDMS are similar, but systematic trends in the intermolecular packing are observed. The local intramolecular structure is extracted from the experimental structure functions. The bond distances and bond angles obtained, including the large Si-O-Si angle, are in good agreement with the explicit atom (EA) and united atom (UA) potentials used in the simulations and theory and from other sources. Very good agreement is found between themore » MD simulations using the EA potentials and the experimental scattering results. Good agreement is also found between the polymer reference interaction site model (PRISM theory) and the UA MD simulations. The intermolecular structure is examined experimentally using an appropriately weighted radial distribution function and with theory and simulation using intermolecular site/site pair correlation functions. Finally, experiment, simulation, and theory show systematic increases in the chain/chain packing distances in the siloxanes as the number of sites in the pendant side chains is increased.« less

Search for function coefficient distribution in traditional Chinese medicine network

NASA Astrophysics Data System (ADS)

He, Yue; Zhang, Peipei; Sun, Anzheng; Su, Beibei; He, Da-Ren

2004-03-01

We suggest a model for a simulation on development of traditional Chinese medicine system. Suppose there are a certain number of Chinese medicines. Each of them is given randomly a "function coefficient", which has a value between 0 and 1. The larger it is the stronger is its function for solving one healthy problem and serving as an "emperor" in a prescription formulation. The smaller it is the stronger is its function for harmonizing and/or accessorizing a prescription formulation. In every step of time a new medicine is discovered. With a probability, P(m), which is determined according to our statistical investigation results, it can produce a new prescription formulation with other m-1 medicines. We assume that the probability for choosing the function coefficients of these m medicines follow a distribution function, which is everywhere smooth. A program has been set up to perform a search for this function form so that the simulation results show a best agreement to our statistical data. We believe the result function form will be helpful for an understanding on real development of traditional Chinese medicine system.

Acceleration of discrete stochastic biochemical simulation using GPGPU.

PubMed

Sumiyoshi, Kei; Hirata, Kazuki; Hiroi, Noriko; Funahashi, Akira

2015-01-01

For systems made up of a small number of molecules, such as a biochemical network in a single cell, a simulation requires a stochastic approach, instead of a deterministic approach. The stochastic simulation algorithm (SSA) simulates the stochastic behavior of a spatially homogeneous system. Since stochastic approaches produce different results each time they are used, multiple runs are required in order to obtain statistical results; this results in a large computational cost. We have implemented a parallel method for using SSA to simulate a stochastic model; the method uses a graphics processing unit (GPU), which enables multiple realizations at the same time, and thus reduces the computational time and cost. During the simulation, for the purpose of analysis, each time course is recorded at each time step. A straightforward implementation of this method on a GPU is about 16 times faster than a sequential simulation on a CPU with hybrid parallelization; each of the multiple simulations is run simultaneously, and the computational tasks within each simulation are parallelized. We also implemented an improvement to the memory access and reduced the memory footprint, in order to optimize the computations on the GPU. We also implemented an asynchronous data transfer scheme to accelerate the time course recording function. To analyze the acceleration of our implementation on various sizes of model, we performed SSA simulations on different model sizes and compared these computation times to those for sequential simulations with a CPU. When used with the improved time course recording function, our method was shown to accelerate the SSA simulation by a factor of up to 130.

Acceleration of discrete stochastic biochemical simulation using GPGPU

PubMed Central

Sumiyoshi, Kei; Hirata, Kazuki; Hiroi, Noriko; Funahashi, Akira

2015-01-01

For systems made up of a small number of molecules, such as a biochemical network in a single cell, a simulation requires a stochastic approach, instead of a deterministic approach. The stochastic simulation algorithm (SSA) simulates the stochastic behavior of a spatially homogeneous system. Since stochastic approaches produce different results each time they are used, multiple runs are required in order to obtain statistical results; this results in a large computational cost. We have implemented a parallel method for using SSA to simulate a stochastic model; the method uses a graphics processing unit (GPU), which enables multiple realizations at the same time, and thus reduces the computational time and cost. During the simulation, for the purpose of analysis, each time course is recorded at each time step. A straightforward implementation of this method on a GPU is about 16 times faster than a sequential simulation on a CPU with hybrid parallelization; each of the multiple simulations is run simultaneously, and the computational tasks within each simulation are parallelized. We also implemented an improvement to the memory access and reduced the memory footprint, in order to optimize the computations on the GPU. We also implemented an asynchronous data transfer scheme to accelerate the time course recording function. To analyze the acceleration of our implementation on various sizes of model, we performed SSA simulations on different model sizes and compared these computation times to those for sequential simulations with a CPU. When used with the improved time course recording function, our method was shown to accelerate the SSA simulation by a factor of up to 130. PMID:25762936

Marvel-ous Dwarfs: Results from Four Heroically Large Simulated Volumes of Dwarf Galaxies

NASA Astrophysics Data System (ADS)

Munshi, Ferah; Brooks, Alyson; Weisz, Daniel; Bellovary, Jillian; Christensen, Charlotte

2018-01-01

We present results from high resolution, fully cosmological simulations of cosmic sheets that contain many dwarf galaxies. Together, they create the largest collection of simulated dwarf galaxies to date, with z=0 stellar masses comparable to the LMC or smaller. In total, we have simulated almost 100 luminous dwarf galaxies, forming a sample of simulated dwarfs which span a wide range of physical (stellar and halo mass) and evolutionary properties (merger history). We show how they can be calibrated against a wealth of observations of nearby galaxies including star formation histories, HI masses and kinematics, as well as stellar metallicities. We present preliminary results answering the following key questions: What is the slope of the stellar mass function at extremely low masses? Do halos with HI and no stars exist? What is the scatter in the stellar to halo mass relationship as a function of dwarf mass? What drives the scatter? With this large suite, we are beginning to statistically characterize dwarf galaxies and identify the types and numbers of outliers to expect.

DoSSiER: Database of scientific simulation and experimental results

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

Wenzel, Hans; Yarba, Julia; Genser, Krzystof

The Geant4, GeantV and GENIE collaborations regularly perform validation and regression tests for simulation results. DoSSiER (Database of Scientific Simulation and Experimental Results) is being developed as a central repository to store the simulation results as well as the experimental data used for validation. DoSSiER can be easily accessed via a web application. In addition, a web service allows for programmatic access to the repository to extract records in json or xml exchange formats. In this paper, we describe the functionality and the current status of various components of DoSSiER as well as the technology choices we made.

DoSSiER: Database of scientific simulation and experimental results

DOE PAGES

Wenzel, Hans; Yarba, Julia; Genser, Krzystof; ...

2016-08-01

The Geant4, GeantV and GENIE collaborations regularly perform validation and regression tests for simulation results. DoSSiER (Database of Scientific Simulation and Experimental Results) is being developed as a central repository to store the simulation results as well as the experimental data used for validation. DoSSiER can be easily accessed via a web application. In addition, a web service allows for programmatic access to the repository to extract records in json or xml exchange formats. In this paper, we describe the functionality and the current status of various components of DoSSiER as well as the technology choices we made.

Digital simulation of scalar optical diffraction: revisiting chirp function sampling criteria and consequences.

PubMed

Voelz, David G; Roggemann, Michael C

2009-11-10

Accurate simulation of scalar optical diffraction requires consideration of the sampling requirement for the phase chirp function that appears in the Fresnel diffraction expression. We describe three sampling regimes for FFT-based propagation approaches: ideally sampled, oversampled, and undersampled. Ideal sampling, where the chirp and its FFT both have values that match analytic chirp expressions, usually provides the most accurate results but can be difficult to realize in practical simulations. Under- or oversampling leads to a reduction in the available source plane support size, the available source bandwidth, or the available observation support size, depending on the approach and simulation scenario. We discuss three Fresnel propagation approaches: the impulse response/transfer function (angular spectrum) method, the single FFT (direct) method, and the two-step method. With illustrations and simulation examples we show the form of the sampled chirp functions and their discrete transforms, common relationships between the three methods under ideal sampling conditions, and define conditions and consequences to be considered when using nonideal sampling. The analysis is extended to describe the sampling limitations for the more exact Rayleigh-Sommerfeld diffraction solution.

Method for simulating discontinuous physical systems

DOEpatents

Baty, Roy S.; Vaughn, Mark R.

2001-01-01

The mathematical foundations of conventional numerical simulation of physical systems provide no consistent description of the behavior of such systems when subjected to discontinuous physical influences. As a result, the numerical simulation of such problems requires ad hoc encoding of specific experimental results in order to address the behavior of such discontinuous physical systems. In the present invention, these foundations are replaced by a new combination of generalized function theory and nonstandard analysis. The result is a class of new approaches to the numerical simulation of physical systems which allows the accurate and well-behaved simulation of discontinuous and other difficult physical systems, as well as simpler physical systems. Applications of this new class of numerical simulation techniques to process control, robotics, and apparatus design are outlined.

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

PubMed Central

2013-01-01

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

Aircraft Flight Modeling During the Optimization of Gas Turbine Engine Working Process

NASA Astrophysics Data System (ADS)

Tkachenko, A. Yu; Kuz'michev, V. S.; Krupenich, I. N.

2018-01-01

The article describes a method for simulating the flight of the aircraft along a predetermined path, establishing a functional connection between the parameters of the working process of gas turbine engine and the efficiency criteria of the aircraft. This connection is necessary for solving the optimization tasks of the conceptual design stage of the engine according to the systems approach. Engine thrust level, in turn, influences the operation of aircraft, thus making accurate simulation of the aircraft behavior during flight necessary for obtaining the correct solution. The described mathematical model of aircraft flight provides the functional connection between the airframe characteristics, working process of gas turbine engines (propulsion system), ambient and flight conditions and flight profile features. This model provides accurate results of flight simulation and the resulting aircraft efficiency criteria, required for optimization of working process and control function of a gas turbine engine.

Accurate lithography simulation model based on convolutional neural networks

NASA Astrophysics Data System (ADS)

Watanabe, Yuki; Kimura, Taiki; Matsunawa, Tetsuaki; Nojima, Shigeki

2017-07-01

Lithography simulation is an essential technique for today's semiconductor manufacturing process. In order to calculate an entire chip in realistic time, compact resist model is commonly used. The model is established for faster calculation. To have accurate compact resist model, it is necessary to fix a complicated non-linear model function. However, it is difficult to decide an appropriate function manually because there are many options. This paper proposes a new compact resist model using CNN (Convolutional Neural Networks) which is one of deep learning techniques. CNN model makes it possible to determine an appropriate model function and achieve accurate simulation. Experimental results show CNN model can reduce CD prediction errors by 70% compared with the conventional model.

Climate-suitable planting as a strategy for maintaining forest productivity and functional diversity.

PubMed

Duveneck, Matthew J; Scheller, Robert M

2015-09-01

Within the time frame of the longevity of tree species, climate change will change faster than the ability of natural tree migration. Migration lags may result in reduced productivity and reduced diversity in forests under current management and climate change. We evaluated the efficacy of planting climate-suitable tree species (CSP), those tree species with current or historic distributions immediately south of a focal landscape, to maintain or increase aboveground biomass productivity, and species and functional diversity. We modeled forest change with the LANDIS-II forest simulation model for 100 years (2000-2100) at a 2-ha cell resolution and five-year time steps within two landscapes in the Great Lakes region (northeastern Minnesota and northern lower Michigan, USA). We compared current climate to low- and high-emission futures. We simulated a low-emission climate future with the Intergovernmental Panel on Climate Change (IPCC) 2007 B1 emission scenario and the Parallel Climate Model Global Circulation Model (GCM). We simulated a high-emission climate future with the IPCC A1FI emission scenario and the Geophysical Fluid Dynamics Laboratory (GFDL) GCM. We compared current forest management practices (business-as-usual) to CSP management. In the CSP scenario, we simulated a target planting of 5.28% and 4.97% of forested area per five-year time step in the Minnesota and Michigan landscapes, respectively. We found that simulated CSP species successfully established in both landscapes under all climate scenarios. The presence of CSP species generally increased simulated aboveground biomass. Species diversity increased due to CSP; however, the effect on functional diversity was variable. Because the planted species were functionally similar to many native species, CSP did not result in a consistent increase nor decrease in functional diversity. These results provide an assessment of the potential efficacy and limitations of CSP management. These results have management implications for sites where diversity and productivity are expected to decline. Future efforts to restore a specific species or forest type may not be possible, but CSP may sustain a more general ecosystem service (e.g., aboveground biomass).

Short- and long-time diffusion and dynamic scaling in suspensions of charged colloidal particles.

PubMed

Banchio, Adolfo J; Heinen, Marco; Holmqvist, Peter; Nägele, Gerhard

2018-04-07

We report on a comprehensive theory-simulation-experimental study of collective and self-diffusion in concentrated suspensions of charge-stabilized colloidal spheres. In theory and simulation, the spheres are assumed to interact directly by a hard-core plus screened Coulomb effective pair potential. The intermediate scattering function, f c (q, t), is calculated by elaborate accelerated Stokesian dynamics (ASD) simulations for Brownian systems where many-particle hydrodynamic interactions (HIs) are fully accounted for, using a novel extrapolation scheme to a macroscopically large system size valid for all correlation times. The study spans the correlation time range from the colloidal short-time to the long-time regime. Additionally, Brownian Dynamics (BD) simulation and mode-coupling theory (MCT) results of f c (q, t) are generated where HIs are neglected. Using these results, the influence of HIs on collective and self-diffusion and the accuracy of the MCT method are quantified. It is shown that HIs enhance collective and self-diffusion at intermediate and long times. At short times self-diffusion, and for wavenumbers outside the structure factor peak region also collective diffusion, are slowed down by HIs. MCT significantly overestimates the slowing influence of dynamic particle caging. The dynamic scattering functions obtained in the ASD simulations are in overall good agreement with our dynamic light scattering (DLS) results for a concentration series of charged silica spheres in an organic solvent mixture, in the experimental time window and wavenumber range. From the simulation data for the time derivative of the width function associated with f c (q, t), there is indication of long-time exponential decay of f c (q, t), for wavenumbers around the location of the static structure factor principal peak. The experimental scattering functions in the probed time range are consistent with a time-wavenumber factorization scaling behavior of f c (q, t) that was first reported by Segrè and Pusey [Phys. Rev. Lett. 77, 771 (1996)] for suspensions of hard spheres. Our BD simulation and MCT results predict a significant violation of exact factorization scaling which, however, is approximately restored according to the ASD results when HIs are accounted for, consistent with the experimental findings for f c (q, t). Our study of collective diffusion is amended by simulation and theoretical results for the self-intermediate scattering function, f s (q, t), and its non-Gaussian parameter α 2 (t) and for the particle mean squared displacement W(t) and its time derivative. Since self-diffusion properties are not assessed in standard DLS measurements, a method to deduce W(t) approximately from f c (q, t) is theoretically validated.

Use case driven approach to develop simulation model for PCS of APR1400 simulator

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

Dong Wook, Kim; Hong Soo, Kim; Hyeon Tae, Kang

2006-07-01

The full-scope simulator is being developed to evaluate specific design feature and to support the iterative design and validation in the Man-Machine Interface System (MMIS) design of Advanced Power Reactor (APR) 1400. The simulator consists of process model, control logic model, and MMI for the APR1400 as well as the Power Control System (PCS). In this paper, a use case driven approach is proposed to develop a simulation model for PCS. In this approach, a system is considered from the point of view of its users. User's view of the system is based on interactions with the system and themore » resultant responses. In use case driven approach, we initially consider the system as a black box and look at its interactions with the users. From these interactions, use cases of the system are identified. Then the system is modeled using these use cases as functions. Lower levels expand the functionalities of each of these use cases. Hence, starting from the topmost level view of the system, we proceeded down to the lowest level (the internal view of the system). The model of the system thus developed is use case driven. This paper will introduce the functionality of the PCS simulation model, including a requirement analysis based on use case and the validation result of development of PCS model. The PCS simulation model using use case will be first used during the full-scope simulator development for nuclear power plant and will be supplied to Shin-Kori 3 and 4 plant. The use case based simulation model development can be useful for the design and implementation of simulation models. (authors)« less

[Effects of marijuana and amphetamine (and its derivatives on driving performance based on the driving simulator studies].

PubMed

Drabek, Marcin; Andysz, Aleksandra

2011-01-01

This article presents the results of the driving simulator studies of the effects of marijuana and amphetamines on driving performance. The majority of these studies have been focused on identifying the impact of the tested substances on cognitive and psychomotor functions. Most of the findings on marijuana reveal its modest effect on driving ability that increases with the increasing frequency of its use and when used in conjuction with other drugs and alcohol. Similarly, small doses of amphetamines can cause a positive stimulating effect, improving certain cognitive functions, such as vigilance, but it decreases when they are overused and combined with alcohol. The results of the research on drivers' behavior under the influence of amphetamines also indicate deficits in their cognitive functions and tendency to recklessness on the road. The authors also discuss strong and weak points of simulation studies of the effects of psychoactive substances on the driving ability. An attempt was also made to clarify certain ambiguities, which occur in this field of research. A central role of the ethical and methodological limitations of simulation studies were discussed as well.

A regularized vortex-particle mesh method for large eddy simulation

NASA Astrophysics Data System (ADS)

Spietz, H. J.; Walther, J. H.; Hejlesen, M. M.

2017-11-01

We present recent developments of the remeshed vortex particle-mesh method for simulating incompressible fluid flow. The presented method relies on a parallel higher-order FFT based solver for the Poisson equation. Arbitrary high order is achieved through regularization of singular Green's function solutions to the Poisson equation and recently we have derived novel high order solutions for a mixture of open and periodic domains. With this approach the simulated variables may formally be viewed as the approximate solution to the filtered Navier Stokes equations, hence we use the method for Large Eddy Simulation by including a dynamic subfilter-scale model based on test-filters compatible with the aforementioned regularization functions. Further the subfilter-scale model uses Lagrangian averaging, which is a natural candidate in light of the Lagrangian nature of vortex particle methods. A multiresolution variation of the method is applied to simulate the benchmark problem of the flow past a square cylinder at Re = 22000 and the obtained results are compared to results from the literature.

Simulation study of entropy production in the one-dimensional Vlasov system

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

Dai, Zongliang, E-mail: liangliang1223@gmail.com; Wang, Shaojie

2016-07-15

The coarse-grain averaged distribution function of the one-dimensional Vlasov system is obtained by numerical simulation. The entropy productions in cases of the random field, the linear Landau damping, and the bump-on-tail instability are computed with the coarse-grain averaged distribution function. The computed entropy production is converged with increasing length of coarse-grain average. When the distribution function differs slightly from a Maxwellian distribution, the converged value agrees with the result computed by using the definition of thermodynamic entropy. The length of the coarse-grain average to compute the coarse-grain averaged distribution function is discussed.

A verification library for multibody simulation software

NASA Technical Reports Server (NTRS)

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

1989-01-01

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

Angular resolution and range of dipole-dipole correlations in water

NASA Astrophysics Data System (ADS)

Mathias, Gerald; Tavan, Paul

2004-03-01

We investigate the dipolar correlations in liquid water at angular resolution by molecular-dynamics simulations of a large periodic simulation system containing about 40 000 molecules. Because we are particularly interested in the long-range ordering, we use a simple three-point model for these molecules. The electrostatics is treated both by Ewald summation and by minimum image truncation combined with a reaction field approach. To gain insight into the angular dependence of the simulated dipolar ordering we introduce a suitable expansion of the molecular pair distribution function into a set of two-dimensional correlation functions. We show that these functions enable detailed insights into the shell structure of the dipolar ordering around a given water molecule. For these functions we derive analytical expressions in the particular case in which liquid water is conceived as a dielectric continuum. Comparisons of these continuum models with the correlation functions derived from the simulations yield the key result that liquid water behaves like a continuum dielectric beyond distances of about 15 Å from a given water molecule. We argue that this should be a generic property of water independent of our modeling. By comparison of the results of the two different electrostatics treatments with the continuum description we show that the boundary artifacts occurring in both methods are isotropically distributed and are locally small in the respective boundary regions.

Numerical simulations of clinical focused ultrasound functional neurosurgery

NASA Astrophysics Data System (ADS)

Pulkkinen, Aki; Werner, Beat; Martin, Ernst; Hynynen, Kullervo

2014-04-01

A computational model utilizing grid and finite difference methods were developed to simulate focused ultrasound functional neurosurgery interventions. The model couples the propagation of ultrasound in fluids (soft tissues) and solids (skull) with acoustic and visco-elastic wave equations. The computational model was applied to simulate clinical focused ultrasound functional neurosurgery treatments performed in patients suffering from therapy resistant chronic neuropathic pain. Datasets of five patients were used to derive the treatment geometry. Eight sonications performed in the treatments were then simulated with the developed model. Computations were performed by driving the simulated phased array ultrasound transducer with the acoustic parameters used in the treatments. Resulting focal temperatures and size of the thermal foci were compared quantitatively, in addition to qualitative inspection of the simulated pressure and temperature fields. This study found that the computational model and the simulation parameters predicted an average of 24 ± 13% lower focal temperature elevations than observed in the treatments. The size of the simulated thermal focus was found to be 40 ± 13% smaller in the anterior-posterior direction and 22 ± 14% smaller in the inferior-superior direction than in the treatments. The location of the simulated thermal focus was off from the prescribed target by 0.3 ± 0.1 mm, while the peak focal temperature elevation observed in the measurements was off by 1.6 ± 0.6 mm. Although the results of the simulations suggest that there could be some inaccuracies in either the tissue parameters used, or in the simulation methods, the simulations were able to predict the focal spot locations and temperature elevations adequately for initial treatment planning performed to assess, for example, the feasibility of sonication. The accuracy of the simulations could be improved if more precise ultrasound tissue properties (especially of the skull bone) could be obtained.

UK audit of analysis of quantitative parameters from renography data generated using a physical phantom.

PubMed

Nijran, Kuldip S; Houston, Alex S; Fleming, John S; Jarritt, Peter H; Heikkinen, Jari O; Skrypniuk, John V

2014-07-01

In this second UK audit of quantitative parameters obtained from renography, phantom simulations were used in cases in which the 'true' values could be estimated, allowing the accuracy of the parameters measured to be assessed. A renal physical phantom was used to generate a set of three phantom simulations (six kidney functions) acquired on three different gamma camera systems. A total of nine phantom simulations and three real patient studies were distributed to UK hospitals participating in the audit. Centres were asked to provide results for the following parameters: relative function and time-to-peak (whole kidney and cortical region). As with previous audits, a questionnaire collated information on methodology. Errors were assessed as the root mean square deviation from the true value. Sixty-one centres responded to the audit, with some hospitals providing multiple sets of results. Twenty-one centres provided a complete set of parameter measurements. Relative function and time-to-peak showed a reasonable degree of accuracy and precision in most UK centres. The overall average root mean squared deviation of the results for (i) the time-to-peak measurement for the whole kidney and (ii) the relative function measurement from the true value was 7.7 and 4.5%, respectively. These results showed a measure of consistency in the relative function and time-to-peak that was similar to the results reported in a previous renogram audit by our group. Analysis of audit data suggests a reasonable degree of accuracy in the quantification of renography function using relative function and time-to-peak measurements. However, it is reasonable to conclude that the objectives of the audit could not be fully realized because of the limitations of the mechanical phantom in providing true values for renal parameters.

Alternative ways of using field-based estimates to calibrate ecosystem models and their implications for carbon cycle studies

USGS Publications Warehouse

He, Yujie; Zhuang, Qianlai; McGuire, David; Liu, Yaling; Chen, Min

2013-01-01

Model-data fusion is a process in which field observations are used to constrain model parameters. How observations are used to constrain parameters has a direct impact on the carbon cycle dynamics simulated by ecosystem models. In this study, we present an evaluation of several options for the use of observations in modeling regional carbon dynamics and explore the implications of those options. We calibrated the Terrestrial Ecosystem Model on a hierarchy of three vegetation classification levels for the Alaskan boreal forest: species level, plant-functional-type level (PFT level), and biome level, and we examined the differences in simulated carbon dynamics. Species-specific field-based estimates were directly used to parameterize the model for species-level simulations, while weighted averages based on species percent cover were used to generate estimates for PFT- and biome-level model parameterization. We found that calibrated key ecosystem process parameters differed substantially among species and overlapped for species that are categorized into different PFTs. Our analysis of parameter sets suggests that the PFT-level parameterizations primarily reflected the dominant species and that functional information of some species were lost from the PFT-level parameterizations. The biome-level parameterization was primarily representative of the needleleaf PFT and lost information on broadleaf species or PFT function. Our results indicate that PFT-level simulations may be potentially representative of the performance of species-level simulations while biome-level simulations may result in biased estimates. Improved theoretical and empirical justifications for grouping species into PFTs or biomes are needed to adequately represent the dynamics of ecosystem functioning and structure.

Performance of Multi-chaotic PSO on a shifted benchmark functions set

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

Pluhacek, Michal; Senkerik, Roman; Zelinka, Ivan

2015-03-10

In this paper the performance of Multi-chaotic PSO algorithm is investigated using two shifted benchmark functions. The purpose of shifted benchmark functions is to simulate the time-variant real-world problems. The results of chaotic PSO are compared with canonical version of the algorithm. It is concluded that using the multi-chaotic approach can lead to better results in optimization of shifted functions.

Evaluation of Glyceraldehyde Under Simulated Prebiotic Conditions

NASA Astrophysics Data System (ADS)

Aguilar-Ovando, E.; Buhse, T.; Negrón-Mendoza, A.

2017-07-01

The aim of this work is to compare the behavior under irradiation of solid and aqueous DL-glyceraldehyde simulating prebiotic conditions. The results show the formation of sugar-like products of prebiotic significance as function of irradiation dose.

Energy deposition evaluation for ultra-low energy electron beam irradiation systems using calibrated thin radiochromic film and Monte Carlo simulations

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

Matsui, S., E-mail: smatsui@gpi.ac.jp; Mori, Y.; Nonaka, T.

2016-05-15

For evaluation of on-site dosimetry and process design in industrial use of ultra-low energy electron beam (ULEB) processes, we evaluate the energy deposition using a thin radiochromic film and a Monte Carlo simulation. The response of film dosimeter was calibrated using a high energy electron beam with an acceleration voltage of 2 MV and alanine dosimeters with uncertainty of 11% at coverage factor 2. Using this response function, the results of absorbed dose measurements for ULEB were evaluated from 10 kGy to 100 kGy as a relative dose. The deviation between the responses of deposit energy on the films andmore » Monte Carlo simulations was within 15%. As far as this limitation, relative dose estimation using thin film dosimeters with response function obtained by high energy electron irradiation and simulation results is effective for ULEB irradiation processes management.« less

Flow Channel Influence of a Collision-Based Piezoelectric Jetting Dispenser on Jet Performance

PubMed Central

Deng, Guiling; Li, Junhui; Duan, Ji’an

2018-01-01

To improve the jet performance of a bi-piezoelectric jet dispenser, mathematical and simulation models were established according to the operating principle. In order to improve the accuracy and reliability of the simulation calculation, a viscosity model of the fluid was fitted to a fifth-order function with shear rate based on rheological test data, and the needle displacement model was fitted to a nine-order function with time based on real-time displacement test data. The results show that jet performance is related to the diameter of the nozzle outlet and the cone angle of the nozzle, and the impacts of the flow channel structure were confirmed. The approach of numerical simulation is confirmed by the testing results of droplet volume. It will provide a reliable simulation platform for mechanical collision-based jet dispensing and a theoretical basis for micro jet valve design and improvement. PMID:29677140

Energy deposition evaluation for ultra-low energy electron beam irradiation systems using calibrated thin radiochromic film and Monte Carlo simulations.

PubMed

Matsui, S; Mori, Y; Nonaka, T; Hattori, T; Kasamatsu, Y; Haraguchi, D; Watanabe, Y; Uchiyama, K; Ishikawa, M

2016-05-01

For evaluation of on-site dosimetry and process design in industrial use of ultra-low energy electron beam (ULEB) processes, we evaluate the energy deposition using a thin radiochromic film and a Monte Carlo simulation. The response of film dosimeter was calibrated using a high energy electron beam with an acceleration voltage of 2 MV and alanine dosimeters with uncertainty of 11% at coverage factor 2. Using this response function, the results of absorbed dose measurements for ULEB were evaluated from 10 kGy to 100 kGy as a relative dose. The deviation between the responses of deposit energy on the films and Monte Carlo simulations was within 15%. As far as this limitation, relative dose estimation using thin film dosimeters with response function obtained by high energy electron irradiation and simulation results is effective for ULEB irradiation processes management.

TOPMODEL simulations of streamflow and depth to water table in Fishing Brook Watershed, New York, 2007-09

USGS Publications Warehouse

Nystrom, Elizabeth A.; Burns, Douglas A.

2011-01-01

TOPMODEL uses a topographic wetness index computed from surface-elevation data to simulate streamflow and subsurface-saturation state, represented by the saturation deficit. Depth to water table was computed from simulated saturation-deficit values using computed soil properties. In the Fishing Brook Watershed, TOPMODEL was calibrated to the natural logarithm of streamflow at the study area outlet and depth to water table at Sixmile Wetland using a combined multiple-objective function. Runoff and depth to water table responded differently to some of the model parameters, and the combined multiple-objective function balanced the goodness-of-fit of the model realizations with respect to these parameters. Results show that TOPMODEL reasonably simulated runoff and depth to water table during the study period. The simulated runoff had a Nash-Sutcliffe efficiency of 0.738, but the model underpredicted total runoff by 14 percent. Depth to water table computed from simulated saturation-deficit values matched observed water-table depth moderately well; the root mean squared error of absolute depth to water table was 91 millimeters (mm), compared to the mean observed depth to water table of 205 mm. The correlation coefficient for temporal depth-to-water-table fluctuations was 0.624. The variability of the TOPMODEL simulations was assessed using prediction intervals grouped using the combined multiple-objective function. The calibrated TOPMODEL results for the entire study area were applied to several subwatersheds within the study area using computed hydrogeomorphic properties of the subwatersheds.

[Research on Time-frequency Characteristics of Magneto-acoustic Signal of Different Thickness Medium Based on Wave Summing Method].

PubMed

Zhang, Shunqi; Yin, Tao; Ma, Ren; Liu, Zhipeng

2015-08-01

Functional imaging method of biological electrical characteristics based on magneto-acoustic effect gives valuable information of tissue in early tumor diagnosis, therein time and frequency characteristics analysis of magneto-acoustic signal is important in image reconstruction. This paper proposes wave summing method based on Green function solution for acoustic source of magneto-acoustic effect. Simulations and analysis under quasi 1D transmission condition are carried out to time and frequency characteristics of magneto-acoustic signal of models with different thickness. Simulation results of magneto-acoustic signal were verified through experiments. Results of the simulation with different thickness showed that time-frequency characteristics of magneto-acoustic signal reflected thickness of sample. Thin sample, which is less than one wavelength of pulse, and thick sample, which is larger than one wavelength, showed different summed waveform and frequency characteristics, due to difference of summing thickness. Experimental results verified theoretical analysis and simulation results. This research has laid a foundation for acoustic source and conductivity reconstruction to the medium with different thickness in magneto-acoustic imaging.

Adaptive temperature-accelerated dynamics

NASA Astrophysics Data System (ADS)

Shim, Yunsic; Amar, Jacques G.

2011-02-01

We present three adaptive methods for optimizing the high temperature Thigh on-the-fly in temperature-accelerated dynamics (TAD) simulations. In all three methods, the high temperature is adjusted periodically in order to maximize the performance. While in the first two methods the adjustment depends on the number of observed events, the third method depends on the minimum activation barrier observed so far and requires an a priori knowledge of the optimal high temperature T^{opt}_{high}(E_a) as a function of the activation barrier Ea for each accepted event. In order to determine the functional form of T^{opt}_{high}(E_a), we have carried out extensive simulations of submonolayer annealing on the (100) surface for a variety of metals (Ag, Cu, Ni, Pd, and Au). While the results for all five metals are different, when they are scaled with the melting temperature Tm, we find that they all lie on a single scaling curve. Similar results have also been obtained for (111) surfaces although in this case the scaling function is slightly different. In order to test the performance of all three methods, we have also carried out adaptive TAD simulations of Ag/Ag(100) annealing and growth at T = 80 K and compared with fixed high-temperature TAD simulations for different values of Thigh. We find that the performance of all three adaptive methods is typically as good as or better than that obtained in fixed high-temperature TAD simulations carried out using the effective optimal fixed high temperature. In addition, we find that the final high temperatures obtained in our adaptive TAD simulations are very close to our results for T^{opt}_{high}(E_a). The applicability of the adaptive methods to a variety of TAD simulations is also briefly discussed.

GPU-based Green's function simulations of shear waves generated by an applied acoustic radiation force in elastic and viscoelastic models.

PubMed

Yang, Yiqun; Urban, Matthew W; McGough, Robert J

2018-05-15

Shear wave calculations induced by an acoustic radiation force are very time-consuming on desktop computers, and high-performance graphics processing units (GPUs) achieve dramatic reductions in the computation time for these simulations. The acoustic radiation force is calculated using the fast near field method and the angular spectrum approach, and then the shear waves are calculated in parallel with Green's functions on a GPU. This combination enables rapid evaluation of shear waves for push beams with different spatial samplings and for apertures with different f/#. Relative to shear wave simulations that evaluate the same algorithm on an Intel i7 desktop computer, a high performance nVidia GPU reduces the time required for these calculations by a factor of 45 and 700 when applied to elastic and viscoelastic shear wave simulation models, respectively. These GPU-accelerated simulations also compared to measurements in different viscoelastic phantoms, and the results are similar. For parametric evaluations and for comparisons with measured shear wave data, shear wave simulations with the Green's function approach are ideally suited for high-performance GPUs.

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

Flight simulator fidelity assessment in a rotorcraft lateral translation maneuver

NASA Technical Reports Server (NTRS)

Hess, R. A.; Malsbury, T.; Atencio, A., Jr.

1992-01-01

A model-based methodology for assessing flight simulator fidelity in closed-loop fashion is exercised in analyzing a rotorcraft low-altitude maneuver for which flight test and simulation results were available. The addition of a handling qualities sensitivity function to a previously developed model-based assessment criteria allows an analytical comparison of both performance and handling qualities between simulation and flight test. Model predictions regarding the existence of simulator fidelity problems are corroborated by experiment. The modeling approach is used to assess analytically the effects of modifying simulator characteristics on simulator fidelity.

Disrupted resting-state functional architecture of the brain after 45-day simulated microgravity

PubMed Central

Zhou, Yuan; Wang, Yun; Rao, Li-Lin; Liang, Zhu-Yuan; Chen, Xiao-Ping; Zheng, Dang; Tan, Cheng; Tian, Zhi-Qiang; Wang, Chun-Hui; Bai, Yan-Qiang; Chen, Shan-Guang; Li, Shu

2014-01-01

Long-term spaceflight induces both physiological and psychological changes in astronauts. To understand the neural mechanisms underlying these physiological and psychological changes, it is critical to investigate the effects of microgravity on the functional architecture of the brain. In this study, we used resting-state functional MRI (rs-fMRI) to study whether the functional architecture of the brain is altered after 45 days of −6° head-down tilt (HDT) bed rest, which is a reliable model for the simulation of microgravity. Sixteen healthy male volunteers underwent rs-fMRI scans before and after 45 days of −6° HDT bed rest. Specifically, we used a commonly employed graph-based measure of network organization, i.e., degree centrality (DC), to perform a full-brain exploration of the regions that were influenced by simulated microgravity. We subsequently examined the functional connectivities of these regions using a seed-based resting-state functional connectivity (RSFC) analysis. We found decreased DC in two regions, the left anterior insula (aINS) and the anterior part of the middle cingulate cortex (MCC; also called the dorsal anterior cingulate cortex in many studies), in the male volunteers after 45 days of −6° HDT bed rest. Furthermore, seed-based RSFC analyses revealed that a functional network anchored in the aINS and MCC was particularly influenced by simulated microgravity. These results provide evidence that simulated microgravity alters the resting-state functional architecture of the brains of males and suggest that the processing of salience information, which is primarily subserved by the aINS–MCC functional network, is particularly influenced by spaceflight. The current findings provide a new perspective for understanding the relationships between microgravity, cognitive function, autonomic neural function, and central neural activity. PMID:24926242

Interactive Design Strategy for a Multi-Functional PAMAM Dendrimer-Based Nano-Therapeutic Using Computational Models and Experimental Analysis

PubMed Central

Lee, Inhan; Williams, Christopher R.; Athey, Brian D.; Baker, James R.

2010-01-01

Molecular dynamics simulations of nano-therapeutics as a final product and of all intermediates in the process of generating a multi-functional nano-therapeutic based on a poly(amidoamine) (PAMAM) dendrimer were performed along with chemical analyses of each of them. The actual structures of the dendrimers were predicted, based on potentiometric titration, gel permeation chromatography, and NMR. The chemical analyses determined the numbers of functional molecules, based on the actual structure of the dendrimer. Molecular dynamics simulations calculated the configurations of the intermediates and the radial distributions of functional molecules, based on their numbers. This interactive process between the simulation results and the chemical analyses provided a further strategy to design the next reaction steps and to gain insight into the products at each chemical reaction step. PMID:20700476

Simulating observations with HARMONI: the integral field spectrograph for the European Extremely Large Telescope

NASA Astrophysics Data System (ADS)

Zieleniewski, Simon; Thatte, Niranjan; Kendrew, Sarah; Houghton, Ryan; Tecza, Matthias; Clarke, Fraser; Fusco, Thierry; Swinbank, Mark

2014-07-01

With the next generation of extremely large telescopes commencing construction, there is an urgent need for detailed quantitative predictions of the scientific observations that these new telescopes will enable. Most of these new telescopes will have adaptive optics fully integrated with the telescope itself, allowing unprecedented spatial resolution combined with enormous sensitivity. However, the adaptive optics point spread function will be strongly wavelength dependent, requiring detailed simulations that accurately model these variations. We have developed a simulation pipeline for the HARMONI integral field spectrograph, a first light instrument for the European Extremely Large Telescope. The simulator takes high-resolution input data-cubes of astrophysical objects and processes them with accurate atmospheric, telescope and instrumental effects, to produce mock observed cubes for chosen observing parameters. The output cubes represent the result of a perfect data reduc- tion process, enabling a detailed analysis and comparison between input and output, showcasing HARMONI's capabilities. The simulations utilise a detailed knowledge of the telescope's wavelength dependent adaptive op- tics point spread function. We discuss the simulation pipeline and present an early example of the pipeline functionality for simulating observations of high redshift galaxies.

Modelling the Constraints of Spatial Environment in Fauna Movement Simulations: Comparison of a Boundaries Accurate Function and a Cost Function

NASA Astrophysics Data System (ADS)

Jolivet, L.; Cohen, M.; Ruas, A.

2015-08-01

Landscape influences fauna movement at different levels, from habitat selection to choices of movements' direction. Our goal is to provide a development frame in order to test simulation functions for animal's movement. We describe our approach for such simulations and we compare two types of functions to calculate trajectories. To do so, we first modelled the role of landscape elements to differentiate between elements that facilitate movements and the ones being hindrances. Different influences are identified depending on landscape elements and on animal species. Knowledge were gathered from ecologists, literature and observation datasets. Second, we analysed the description of animal movement recorded with GPS at fine scale, corresponding to high temporal frequency and good location accuracy. Analysing this type of data provides information on the relation between landscape features and movements. We implemented an agent-based simulation approach to calculate potential trajectories constrained by the spatial environment and individual's behaviour. We tested two functions that consider space differently: one function takes into account the geometry and the types of landscape elements and one cost function sums up the spatial surroundings of an individual. Results highlight the fact that the cost function exaggerates the distances travelled by an individual and simplifies movement patterns. The geometry accurate function represents a good bottom-up approach for discovering interesting areas or obstacles for movements.

FRAGMENTATION AND EVOLUTION OF MOLECULAR CLOUDS. II. THE EFFECT OF DUST HEATING

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

Urban, Andrea; Evans, Neal J.; Martel, Hugo

2010-02-20

We investigate the effect of heating by luminosity sources in a simulation of clustered star formation. Our heating method involves a simplified continuum radiative transfer method that calculates the dust temperature. The gas temperature is set by the dust temperature. We present the results of four simulations; two simulations assume an isothermal equation of state and the two other simulations include dust heating. We investigate two mass regimes, i.e., 84 M{sub sun} and 671 M{sub sun}, using these two different energetics algorithms. The mass functions for the isothermal simulations and simulations that include dust heating are drastically different. In themore » isothermal simulation, we do not form any objects with masses above 1 M{sub sun}. However, the simulation with dust heating, while missing some of the low-mass objects, forms high-mass objects ({approx}20 M{sub sun}) which have a distribution similar to the Salpeter initial mass function. The envelope density profiles around the stars formed in our simulation match observed values around isolated, low-mass star-forming cores. We find the accretion rates to be highly variable and, on average, increasing with final stellar mass. By including radiative feedback from stars in a cluster-scale simulation, we have determined that it is a very important effect which drastically affects the mass function and yields important insights into the formation of massive stars.« less

Prediction of helicopter simulator sickness

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

Horn, R.D.; Birdwell, J.D.; Allgood, G.O.

1990-01-01

Machine learning methods from artificial intelligence are used to identify information in sampled accelerometer signals and associative behavioral patterns which correlates pilot simulator sickness with helicopter simulator dynamics. These simulators are used to train pilots in fundamental procedures, tactics, and response to emergency conditions. Simulator sickness induced by these systems represents a risk factor to both the pilot and manufacturer. Simulator sickness symptoms are closely aligned with those of motion sickness. Previous studies have been performed by behavioral psychologists using information gathered with surveys and motor skills performance measures; however, the results are constrained by the limited information which ismore » accessible in this manner. In this work, accelerometers were installed in the simulator cab, enabling a complete record of flight dynamics and the pilot's control response as a function of time. Given the results of performance measures administered to detect simulator sickness symptoms, the problem was then to find functions of the recorded data which could be used to help predict the simulator sickness level and susceptibility. Methods based upon inductive inference were used, which yield decision trees whose leaves indicate the degree of simulator-induced sickness. The long-term goal is to develop a gauge'' which can provide an on-line prediction of simulator sickness level, given a pilot's associative behavioral patterns (learned expectations). This will allow informed decisions to be made on when to terminate a hop and provide an effective basis for determining training and flight restrictions placed upon the pilot after simulator use. 6 refs., 6 figs.« less

A new smooth-k space filter approach to calculate halo abundances

NASA Astrophysics Data System (ADS)

Leo, Matteo; Baugh, Carlton M.; Li, Baojiu; Pascoli, Silvia

2018-04-01

We propose a new filter, a smooth-k space filter, to use in the Press-Schechter approach to model the dark matter halo mass function which overcomes shortcomings of other filters. We test this against the mass function measured in N-body simulations. We find that the commonly used sharp-k filter fails to reproduce the behaviour of the halo mass function at low masses measured from simulations of models with a sharp truncation in the linear power spectrum. We show that the predictions with our new filter agree with the simulation results over a wider range of halo masses for both damped and undamped power spectra than is the case with the sharp-k and real-space top-hat filters.

Simulation of Charged Systems in Heterogeneous Dielectric Media via a True Energy Functional

NASA Astrophysics Data System (ADS)

Jadhao, Vikram; Solis, Francisco J.; de la Cruz, Monica Olvera

2012-11-01

For charged systems in heterogeneous dielectric media, a key obstacle for molecular dynamics (MD) simulations is the need to solve the Poisson equation in the media. This obstacle can be bypassed using MD methods that treat the local polarization charge density as a dynamic variable, but such approaches require access to a true free energy functional, one that evaluates to the equilibrium electrostatic energy at its minimum. In this Letter, we derive the needed functional. As an application, we develop a Car-Parrinello MD method for the simulation of free charges present near a spherical emulsion droplet separating two immiscible liquids with different dielectric constants. Our results show the presence of nonmonotonic ionic profiles in the dielectric with a lower dielectric constant.

Generating multi-double-scroll attractors via nonautonomous approach.

PubMed

Hong, Qinghui; Xie, Qingguo; Shen, Yi; Wang, Xiaoping

2016-08-01

It is a common phenomenon that multi-scroll attractors are realized by introducing the various nonlinear functions with multiple breakpoints in double scroll chaotic systems. Differently, we present a nonautonomous approach for generating multi-double-scroll attractors (MDSA) without changing the original nonlinear functions. By using the multi-level-logic pulse excitation technique in double scroll chaotic systems, MDSA can be generated. A Chua's circuit, a Jerk circuit, and a modified Lorenz system are given as designed example and the Matlab simulation results are presented. Furthermore, the corresponding realization circuits are designed. The Pspice results are in agreement with numerical simulation results, which verify the availability and feasibility of this method.

The science of rotator cuff tears: translating animal models to clinical recommendations using simulation analysis.

PubMed

Mannava, Sandeep; Plate, Johannes F; Tuohy, Christopher J; Seyler, Thorsten M; Whitlock, Patrick W; Curl, Walton W; Smith, Thomas L; Saul, Katherine R

2013-07-01

The purpose of this article is to review basic science studies using various animal models for rotator cuff research and to describe structural, biomechanical, and functional changes to muscle following rotator cuff tears. The use of computational simulations to translate the findings from animal models to human scale is further detailed. A comprehensive review was performed of the basic science literature describing the use of animal models and simulation analysis to examine muscle function following rotator cuff injury and repair in the ageing population. The findings from various studies of rotator cuff pathology emphasize the importance of preventing permanent muscular changes with detrimental results. In vivo muscle function, electromyography, and passive muscle-tendon unit properties were studied before and after supraspinatus tenotomy in a rodent rotator cuff injury model (acute vs chronic). Then, a series of simulation experiments were conducted using a validated computational human musculoskeletal shoulder model to assess both passive and active tension of rotator cuff repairs based on surgical positioning. Outcomes of rotator cuff repair may be improved by earlier surgical intervention, with lower surgical repair tensions and fewer electromyographic neuromuscular changes. An integrated approach of animal experiments, computer simulation analyses, and clinical studies may allow us to gain a fundamental understanding of the underlying pathology and interpret the results for clinical translation.

Flow and Transport in Highly Heterogeneous Porous Formations: Numerical Experiments Performed Using the Analytic Element Method

NASA Astrophysics Data System (ADS)

Jankovic, I.

2002-05-01

Flow and transport in porous formations are analyzed using numerical simulations. Hydraulic conductivity is treated as a spatial random function characterized by a probability density function and a two-point covariance function. Simulations are performed for a multi-indicator conductivity structure developed by Gedeon Dagan (personal communication). This conductivity structure contains inhomogeneities (inclusions) of elliptical and ellipsoidal geometry that are embedded in a homogeneous background. By varying the distribution of sizes and conductivities of inclusions, any probability density function and two-point covariance may be reproduced. The multi-indicator structure is selected since it yields simple approximate transport solutions (Aldo Fiori, personal communication) and accurate numerical solutions (based on the Analytic Element Method). The dispersion is examined for two conceptual models. Both models are based on the multi-indicator conductivity structure. The first model is designed to examine dispersion in aquifers with continuously varying conductivity. The inclusions in this model cover as much area/volume of the porous formation as possible. The second model is designed for aquifers that contain clay/sand/gravel lenses embedded in otherwise homogeneous background. The dispersion in both aquifer types is simulated numerically. Simulation results are compared to those obtained using simple approximate solutions. In order to infer transport statistics that are representative of an infinite domain using the numerical experiments, the inclusions are placed in a domain that was shaped as a large ellipse (2D) and a large spheroid (3D) that were submerged in an unbounded homogeneous medium. On a large scale, the large body of inclusions behaves like a single large inhomogeneity. The analytic solution for a uniform flow past the single inhomogeneity of such geometry yields uniform velocity inside the domain. The velocity differs from that at infinity and can be used to infer the effective conductivity of the medium. As many as 100,000 inhomogeneities are placed inside the domain for 2D simulations. Simulations in 3D were limited to 50,000 inclusions. A large number of simulations was conducted on a massively parallel supercomputer cluster at the Center for Computational Research, University at Buffalo. Simulations range from mildly heterogeneous formations to highly heterogeneous formations (variance of the logarithm of conductivity equal to 10) and from sparsely populated systems to systems where inhomogeneities cover 95% of the volume. Particles are released and tracked inside the core of constant mean velocity. Following the particle tracking, various medium, flow, and transport statistics are computed. These include: spatial moments of particle positions, probability density function of hydraulic conductivity and each component of velocity, their two-point covariance function in the direction of flow and normal to it, covariance of Lagrangean velocities, and probability density function of travel times to various break-through locations. Following the analytic nature of the flow solution, all the results are presented in dimensionless forms. For example, the dispersion coefficients are made dimensionless with respect to the mean velocity and size of inhomogeneities. Detailed results will be presented and compared to well known first-order results and the results that are based on simple approximate transport solutions of Aldo Fiori.

Leadership in multiteam systems.

PubMed

DeChurch, Leslie A; Marks, Michelle A

2006-03-01

This study examined 2 leader functions likely to be instrumental in synchronizing large systems of teams (i.e., multiteam systems [MTSs]). Leader strategizing and coordinating were manipulated through training, and effects on functional leadership, interteam coordination, and MTS performance were examined. Three hundred eighty-four undergraduate students participated in a laboratory simulation modeling a 3-team MTS performing an F-22 battle simulation task (N = 64 MTSs). Results indicate that both leader training manipulations improved functional leadership and interteam coordination and that functional leader behavior was positively related to MTS-level performance. Functional leadership mediated the effects of both types of training on interteam coordination, and interteam coordination fully mediated the effect of MTS leadership on MTS performance.

MODELING FUNCTIONALLY GRADED INTERPHASE REGIONS IN CARBON NANOTUBE REINFORCED COMPOSITES

NASA Technical Reports Server (NTRS)

Seidel, G. D.; Lagoudas, D. C.; Frankland, S. J. V.; Gates, T. S.

2006-01-01

A combination of micromechanics methods and molecular dynamics simulations are used to obtain the effective properties of the carbon nanotube reinforced composites with functionally graded interphase regions. The multilayer composite cylinders method accounts for the effects of non-perfect load transfer in carbon nanotube reinforced polymer matrix composites using a piecewise functionally graded interphase. The functional form of the properties in the interphase region, as well as the interphase thickness, is derived from molecular dynamics simulations of carbon nanotubes in a polymer matrix. Results indicate that the functional form of the interphase can have a significant effect on all the effective elastic constants except for the effective axial modulus for which no noticeable effects are evident.

Terahertz Spectroscopy and Solid-State Density Functional Theory Calculations of Cyanobenzaldehyde Isomers.

PubMed

Dash, Jyotirmayee; Ray, Shaumik; Nallappan, Kathirvel; Kaware, Vaibhav; Basutkar, Nitin; Gonnade, Rajesh G; Ambade, Ashootosh V; Joshi, Kavita; Pesala, Bala

2015-07-23

Spectral signatures in the terahertz (THz) frequency region are mainly due to bulk vibrations of the molecules. These resonances are highly sensitive to the relative position of atoms in a molecule as well as the crystal packing arrangement. To understand the variation of THz resonances, THz spectra (2-10 THz) of three structural isomers: 2-, 3-, and 4-cyanobenzaldehyde have been studied. THz spectra obtained from Fourier transform infrared (FTIR) spectrometry of these isomers show that the resonances are distinctly different especially below 5 THz. For understanding the intermolecular interactions due to hydrogen bonds, four molecule cluster simulations of each of the isomers have been carried out using the B3LYP density functional with the 6-31G(d,p) basis set in Gaussian09 software and the compliance constants are obtained. However, to understand the exact reason behind the observed resonances, simulation of each isomer considering the full crystal structure is essential. The crystal structure of each isomer has been determined using X-ray diffraction (XRD) analysis for carrying out crystal structure simulations. Density functional theory (DFT) simulations using CRYSTAL14 software, utilizing the hybrid density functional B3LYP, have been carried out to understand the vibrational modes. The bond lengths and bond angles from the optimized structures are compared with the XRD results in terms of root-mean-square-deviation (RMSD) values. Very low RMSD values confirm the overall accuracy of the results. The simulations are able to predict most of the spectral features exhibited by the isomers. The results show that low frequency modes (<3 THz) are mediated through hydrogen bonds and are dominated by intermolecular vibrations.

Abnormal pituitary-gonadal axis may be responsible for rat decreased testicular function under simulated microgravity

NASA Astrophysics Data System (ADS)

Zhou, Yi; Tan, Xin; Zhu, Bao-an; Qi, Meng-di; Ding, Su-ling

Space flight and simulated microgravity lead to suppression of mammalian spermatogenesis and decreased plasma testosterone level. In order to explain the mechanism behind the depression, we used rat tail-suspended model to simulate weightless conditions. To prevent cryptorchidism caused by tail-suspension, some experimental animals received inguinal canal ligation. The results showed that mass of testis decreased significantly and seminiferous tubules became atrophied in rats after tail-suspension. The levels of plasma testosterone (T), luteinizing hormone (LH), and follicle-stimulating hormone (FSH) in tail-suspended rats with or without inguinal canal ligation decreased significantly compared with controls, and an increased level of plasma estradiol (E) was revealed in tail-suspended rats. The results indicate that besides the direct influence of fluid shift upon testis under short-term simulated microgravity, the pituitary function is also disturbed as a result of either immobilization stress or weight loss during tail-suspension treatment, which is responsible to some extent for the decreased testosterone secretion level and the atrophia of testis. The conversion of testosterone into E under simulated microgravity is another possible cause for the decline of plasma testosterone.

Quark fragmentation functions in NJL-jet model

NASA Astrophysics Data System (ADS)

Bentz, Wolfgang; Matevosyan, Hrayr; Thomas, Anthony

2014-09-01

We report on our studies of quark fragmentation functions in the Nambu-Jona-Lasinio (NJL) - jet model. The results of Monte-Carlo simulations for the fragmentation functions to mesons and nucleons, as well as to pion and kaon pairs (dihadron fragmentation functions) are presented. The important role of intermediate vector meson resonances for those semi-inclusive deep inelastic production processes is emphasized. Our studies are very relevant for the extraction of transverse momentum dependent quark distribution functions from measured scattering cross sections. We report on our studies of quark fragmentation functions in the Nambu-Jona-Lasinio (NJL) - jet model. The results of Monte-Carlo simulations for the fragmentation functions to mesons and nucleons, as well as to pion and kaon pairs (dihadron fragmentation functions) are presented. The important role of intermediate vector meson resonances for those semi-inclusive deep inelastic production processes is emphasized. Our studies are very relevant for the extraction of transverse momentum dependent quark distribution functions from measured scattering cross sections. Supported by Grant in Aid for Scientific Research, Japanese Ministry of Education, Culture, Sports, Science and Technology, Project No. 20168769.

The heavy ion diffusion region in magnetic reconnection in the Earth's magnetotail

NASA Astrophysics Data System (ADS)

Liu, Y. H.; Mouikis, C. G.; Kistler, L. M.; Wang, S.; Roytershteyn, V.; Karimabadi, H.

2015-05-01

While the plasma in the Earth's magnetotail predominantly consists of protons and electrons, there are times when a significant amount of oxygen is present. When magnetic reconnection occurs, the behavior of these heavy ions can be significantly different from that of the protons, due to their larger gyroradius. In this study, we investigate the heavy ion distribution functions in the reconnection ion diffusion region from a 2.5D three-species particle-in-cell numerical simulation and compare those with Cluster observations from the near-Earth magnetotail. From the simulation results, we find that the heavy ions are demagnetized and accelerated in a larger diffusion region, the heavy ion diffusion region. The ion velocity distribution functions show that, inside the heavy ion diffusion region, heavy ions appear as counterstreaming beams along z in the GSM x-z plane, while drifting in y, carrying cross-tail current. We compare this result with Cluster observations in the vicinity of reconnection regions in the near-Earth magnetotail and find that the simulation predictions are consistent with the observed ion distribution functions in the ion diffusion region, as well as the inflow, exhaust, and separatrix regions. Based on the simulation and observation results, the presence of a multiscale diffusion region model, for O+ abundant reconnection events in the Earth's magnetotail, is demonstrated. A test particle simulation shows that in the diffusion region, the H+ gains energy mainly through Ex, while the O+ energy gain comes equally from Ex and Ey.

Validating density-functional theory simulations at high energy-density conditions with liquid krypton shock experiments to 850 GPa on Sandia's Z machine

DOE PAGES

Mattsson, Thomas R.; Root, Seth; Mattsson, Ann E.; ...

2014-11-11

We use Sandia's Z machine and magnetically accelerated flyer plates to shock compress liquid krypton to 850 GPa and compare with results from density-functional theory (DFT) based simulations using the AM05 functional. We also employ quantum Monte Carlo calculations to motivate the choice of AM05. We conclude that the DFT results are sensitive to the quality of the pseudopotential in terms of scattering properties at high energy/temperature. A new Kr projector augmented wave potential was constructed with improved scattering properties which resulted in excellent agreement with the experimental results to 850 GPa and temperatures above 10 eV (110 kK). Inmore » conclusion, we present comparisons of our data from the Z experiments and DFT calculations to current equation of state models of krypton to determine the best model for high energy-density applications.« less

Generalized nonequilibrium vertex correction method in coherent medium theory for quantum transport simulation of disordered nanoelectronics

NASA Astrophysics Data System (ADS)

Yan, Jiawei; Ke, Youqi

2016-07-01

Electron transport properties of nanoelectronics can be significantly influenced by the inevitable and randomly distributed impurities/defects. For theoretical simulation of disordered nanoscale electronics, one is interested in both the configurationally averaged transport property and its statistical fluctuation that tells device-to-device variability induced by disorder. However, due to the lack of an effective method to do disorder averaging under the nonequilibrium condition, the important effects of disorders on electron transport remain largely unexplored or poorly understood. In this work, we report a general formalism of Green's function based nonequilibrium effective medium theory to calculate the disordered nanoelectronics. In this method, based on a generalized coherent potential approximation for the Keldysh nonequilibrium Green's function, we developed a generalized nonequilibrium vertex correction method to calculate the average of a two-Keldysh-Green's-function correlator. We obtain nine nonequilibrium vertex correction terms, as a complete family, to express the average of any two-Green's-function correlator and find they can be solved by a set of linear equations. As an important result, the averaged nonequilibrium density matrix, averaged current, disorder-induced current fluctuation, and averaged shot noise, which involve different two-Green's-function correlators, can all be derived and computed in an effective and unified way. To test the general applicability of this method, we applied it to compute the transmission coefficient and its fluctuation with a square-lattice tight-binding model and compared with the exact results and other previously proposed approximations. Our results show very good agreement with the exact results for a wide range of disorder concentrations and energies. In addition, to incorporate with density functional theory to realize first-principles quantum transport simulation, we have also derived a general form of conditionally averaged nonequilibrium Green's function for multicomponent disorders.

Mass functions from the excursion set model

NASA Astrophysics Data System (ADS)

Hiotelis, Nicos; Del Popolo, Antonino

2017-11-01

Aims: We aim to study the stochastic evolution of the smoothed overdensity δ at scale S of the form δ(S) = ∫0S K(S,u)dW(u), where K is a kernel and dW is the usual Wiener process. Methods: For a Gaussian density field, smoothed by the top-hat filter, in real space, we used a simple kernel that gives the correct correlation between scales. A Monte Carlo procedure was used to construct random walks and to calculate first crossing distributions and consequently mass functions for a constant barrier. Results: We show that the evolution considered here improves the agreement with the results of N-body simulations relative to analytical approximations which have been proposed from the same problem by other authors. In fact, we show that an evolution which is fully consistent with the ideas of the excursion set model, describes accurately the mass function of dark matter haloes for values of ν ≤ 1 and underestimates the number of larger haloes. Finally, we show that a constant threshold of collapse, lower than it is usually used, it is able to produce a mass function which approximates the results of N-body simulations for a variety of redshifts and for a wide range of masses. Conclusions: A mass function in good agreement with N-body simulations can be obtained analytically using a lower than usual constant collapse threshold.

Optimization of the Monte Carlo code for modeling of photon migration in tissue.

PubMed

Zołek, Norbert S; Liebert, Adam; Maniewski, Roman

2006-10-01

The Monte Carlo method is frequently used to simulate light transport in turbid media because of its simplicity and flexibility, allowing to analyze complicated geometrical structures. Monte Carlo simulations are, however, time consuming because of the necessity to track the paths of individual photons. The time consuming computation is mainly associated with the calculation of the logarithmic and trigonometric functions as well as the generation of pseudo-random numbers. In this paper, the Monte Carlo algorithm was developed and optimized, by approximation of the logarithmic and trigonometric functions. The approximations were based on polynomial and rational functions, and the errors of these approximations are less than 1% of the values of the original functions. The proposed algorithm was verified by simulations of the time-resolved reflectance at several source-detector separations. The results of the calculation using the approximated algorithm were compared with those of the Monte Carlo simulations obtained with an exact computation of the logarithm and trigonometric functions as well as with the solution of the diffusion equation. The errors of the moments of the simulated distributions of times of flight of photons (total number of photons, mean time of flight and variance) are less than 2% for a range of optical properties, typical of living tissues. The proposed approximated algorithm allows to speed up the Monte Carlo simulations by a factor of 4. The developed code can be used on parallel machines, allowing for further acceleration.

Metabolic flux estimation using particle swarm optimization with penalty function.

PubMed

Long, Hai-Xia; Xu, Wen-Bo; Sun, Jun

2009-01-01

Metabolic flux estimation through 13C trace experiment is crucial for quantifying the intracellular metabolic fluxes. In fact, it corresponds to a constrained optimization problem that minimizes a weighted distance between measured and simulated results. In this paper, we propose particle swarm optimization (PSO) with penalty function to solve 13C-based metabolic flux estimation problem. The stoichiometric constraints are transformed to an unconstrained one, by penalizing the constraints and building a single objective function, which in turn is minimized using PSO algorithm for flux quantification. The proposed algorithm is applied to estimate the central metabolic fluxes of Corynebacterium glutamicum. From simulation results, it is shown that the proposed algorithm has superior performance and fast convergence ability when compared to other existing algorithms.

Simulations and experiments on RITA-2 at PSI

NASA Astrophysics Data System (ADS)

Klausen, S. N.; Lefmann, K.; McMorrow, D. F.; Altorfer, F.; Janssen, S.; Lüthy, M.

The cold-neutron triple-axis spectrometer RITA-2 designed and built at Riso National Laboratory was installed at the neutron source SINQ at Paul Scherrer Institute in April/May 2001. In connection with the installation of RITA-2, computer simulations were performed using the neutron ray-tracing package McStas. The simulation results are compared to real experimental results obtained with a powder sample. Especially, the flux at the sample position and the resolution function of the spectrometer are investigated.

Research on an expert system for database operation of simulation-emulation math models. Volume 2, Phase 1: Results

NASA Technical Reports Server (NTRS)

Kawamura, K.; Beale, G. O.; Schaffer, J. D.; Hsieh, B. J.; Padalkar, S.; Rodriguez-Moscoso, J. J.

1985-01-01

A reference manual is provided for NESS, a simulation expert system. This manual gives user information regarding starting and operating NASA expert simulation system (NESS). This expert system provides an intelligent interface to a generic simulation program for spacecraft attitude control problems. A menu of the functions the system can perform is provided. Control repeated returns to this menu after executing each user request.

Comparison of effects of copropagated and precomputed atmosphere profiles on Monte Carlo trajectory simulation

NASA Technical Reports Server (NTRS)

Queen, Eric M.; Omara, Thomas M.

1990-01-01

A realization of a stochastic atmosphere model for use in simulations is presented. The model provides pressure, density, temperature, and wind velocity as a function of latitude, longitude, and altitude, and is implemented in a three degree of freedom simulation package. This implementation is used in the Monte Carlo simulation of an aeroassisted orbital transfer maneuver and results are compared to those of a more traditional approach.

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

Borowik, Piotr, E-mail: pborow@poczta.onet.pl; Thobel, Jean-Luc, E-mail: jean-luc.thobel@iemn.univ-lille1.fr; Adamowicz, Leszek, E-mail: adamo@if.pw.edu.pl

Standard computational methods used to take account of the Pauli Exclusion Principle into Monte Carlo (MC) simulations of electron transport in semiconductors may give unphysical results in low field regime, where obtained electron distribution function takes values exceeding unity. Modified algorithms were already proposed and allow to correctly account for electron scattering on phonons or impurities. Present paper extends this approach and proposes improved simulation scheme allowing including Pauli exclusion principle for electron–electron (e–e) scattering into MC simulations. Simulations with significantly reduced computational cost recreate correct values of the electron distribution function. Proposed algorithm is applied to study transport propertiesmore » of degenerate electrons in graphene with e–e interactions. This required adapting the treatment of e–e scattering in the case of linear band dispersion relation. Hence, this part of the simulation algorithm is described in details.« less

The Application of High Energy Resolution Green's Functions to Threat Scenario Simulation

NASA Astrophysics Data System (ADS)

Thoreson, Gregory G.; Schneider, Erich A.

2012-04-01

Radiation detectors installed at key interdiction points provide defense against nuclear smuggling attempts by scanning vehicles and traffic for illicit nuclear material. These hypothetical threat scenarios may be modeled using radiation transport simulations. However, high-fidelity models are computationally intensive. Furthermore, the range of smuggler attributes and detector technologies create a large problem space not easily overcome by brute-force methods. Previous research has demonstrated that decomposing the scenario into independently simulated components using Green's functions can simulate photon detector signals with coarse energy resolution. This paper extends this methodology by presenting physics enhancements and numerical treatments which allow for an arbitrary level of energy resolution for photon transport. As a result, spectroscopic detector signals produced from full forward transport simulations can be replicated while requiring multiple orders of magnitude less computation time.

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.

Research on modeling and conduction disturbance simulation of secondary power system in a device

NASA Astrophysics Data System (ADS)

Ding, Xu; Yu, Zhi-Yong; Jin, Rui

2017-06-01

To find electromagnetic interference (EMI) and other problems in the secondary power supply system design quickly and effectively, simulations are carried out under the Saber simulation software platform. The DC/DC converter model with complete performance and electromagnetic characteristics is established by combining parametric modeling with Mast language. By using the method of macro modeling, the hall current sensor and power supply filter model are established respectively based on the function, schematic diagram of the components. Also the simulation of the component model and the whole secondary power supply system are carried out. The simulation results show that the proposed model satisfies the functional requirements of the system and has high accuracy. At the same time, due to the ripple characteristics in the DC/DC converter modeling, it can be used as a conducted interference model to simulate the power bus conducted emission CE102 project under the condition that the simulated load is full, which provides a useful reference for the electromagnetic interference suppression of the system.

Effects of optimized root water uptake parameterization schemes on water and heat flux simulation in a maize agroecosystem

NASA Astrophysics Data System (ADS)

Cai, Fu; Ming, Huiqing; Mi, Na; Xie, Yanbing; Zhang, Yushu; Li, Rongping

2017-04-01

As root water uptake (RWU) is an important link in the water and heat exchange between plants and ambient air, improving its parameterization is key to enhancing the performance of land surface model simulations. Although different types of RWU functions have been adopted in land surface models, there is no evidence as to which scheme most applicable to maize farmland ecosystems. Based on the 2007-09 data collected at the farmland ecosystem field station in Jinzhou, the RWU function in the Common Land Model (CoLM) was optimized with scheme options in light of factors determining whether roots absorb water from a certain soil layer ( W x ) and whether the baseline cumulative root efficiency required for maximum plant transpiration ( W c ) is reached. The sensibility of the parameters of the optimization scheme was investigated, and then the effects of the optimized RWU function on water and heat flux simulation were evaluated. The results indicate that the model simulation was not sensitive to W x but was significantly impacted by W c . With the original model, soil humidity was somewhat underestimated for precipitation-free days; soil temperature was simulated with obvious interannual and seasonal differences and remarkable underestimations for the maize late-growth stage; and sensible and latent heat fluxes were overestimated and underestimated, respectively, for years with relatively less precipitation, and both were simulated with high accuracy for years with relatively more precipitation. The optimized RWU process resulted in a significant improvement of CoLM's performance in simulating soil humidity, temperature, sensible heat, and latent heat, for dry years. In conclusion, the optimized RWU scheme available for the CoLM model is applicable to the simulation of water and heat flux for maize farmland ecosystems in arid areas.

Compaction-Based Deformable Terrain Model as an Interface for Real-Time Vehicle Dynamics Simulations

DTIC Science & Technology

2013-04-16

to vehicular loads, and the resulting visco-elastic-plastic stress/strain on the affected soil volume. Pedo transfer functions allow for the...resulting visco-elastic-plastic stress/strain on the affected soil volume. Pedo transfer functions allow for the calculation of the soil mechanics model

Chemical Computer Man: Chemical Agent Response Simulation (CARS). Technical report, January 1983-September 1985

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

Davis, E.G.; Mioduszewski, R.J.

The Chemical Computer Man: Chemical Agent Response Simulation (CARS) is a computer model and simulation program for estimating the dynamic changes in human physiological dysfunction resulting from exposures to chemical-threat nerve agents. The newly developed CARS methodology simulates agent exposure effects on the following five indices of human physiological function: mental, vision, cardio-respiratory, visceral, and limbs. Mathematical models and the application of basic pharmacokinetic principles were incorporated into the simulation so that for each chemical exposure, the relationship between exposure dosage, absorbed dosage (agent blood plasma concentration), and level of physiological response are computed as a function of time. CARS,more » as a simulation tool, is designed for the users with little or no computer-related experience. The model combines maximum flexibility with a comprehensive user-friendly interactive menu-driven system. Users define an exposure problem and obtain immediate results displayed in tabular, graphical, and image formats. CARS has broad scientific and engineering applications, not only in technology for the soldier in the area of Chemical Defense, but also in minimizing animal testing in biomedical and toxicological research and the development of a modeling system for human exposure to hazardous-waste chemicals.« less

Kinetic Monte Carlo simulation of self-organized pattern formation induced by ion beam sputtering using crater functions

NASA Astrophysics Data System (ADS)

Yang, Zhangcan; Lively, Michael A.; Allain, Jean Paul

2015-02-01

The production of self-organized nanostructures by ion beam sputtering has been of keen interest to researchers for many decades. Despite numerous experimental and theoretical efforts to understand ion-induced nanostructures, there are still many basic questions open to discussion, such as the role of erosion or curvature-dependent sputtering. In this work, a hybrid MD/kMC (molecular dynamics/kinetic Monte Carlo) multiscale atomistic model is developed to investigate these knowledge gaps, and its predictive ability is validated across the experimental parameter space. This model uses crater functions, which were obtained from MD simulations, to model the prompt mass redistribution due to single-ion impacts. Defect migration, which is missing from previous models that use crater functions, is treated by a kMC Arrhenius method. Using this model, a systematic study was performed for silicon bombarded by Ar+ ions of various energies (100 eV, 250 eV, 500 eV, 700 eV, and 1000 eV) at incidence angles of 0∘ to 80∘. The simulation results were compared with experimental findings, showing good agreement in many aspects of surface evolution, such as the phase diagram. The underestimation of the ripple wavelength by the simulations suggests that surface diffusion is not the main smoothening mechanism for ion-induced pattern formation. Furthermore, the simulated results were compared with moment-description continuum theory and found to give better results, as the simulation did not suffer from the same mathematical inconsistencies as the continuum model. The key finding was that redistributive effects are dominant in the formation of flat surfaces and parallel-mode ripples, but erosive effects are dominant at high angles when perpendicular-mode ripples are formed. Ion irradiation with simultaneous sample rotation was also simulated, resulting in arrays of square-ordered dots. The patterns obtained from sample rotation were strongly correlated to the rotation speed and to the pattern types formed without sample rotation, and a critical value of about 5 rpm was found between disordered ripples and square-ordered dots. Finally, simulations of dual-beam sputtering were performed, with the resulting patterns determined by the flux ratio of the two beams and the pattern types resulting from single-beam sputtering under the same conditions.

Three-Dimensional Finite-Element Simulation for a Thermoelectric Generator Module

NASA Astrophysics Data System (ADS)

Hu, Xiaokai; Takazawa, Hiroyuki; Nagase, Kazuo; Ohta, Michihiro; Yamamoto, Atsushi

2015-10-01

A three-dimensional closed-circuit numerical model of a thermoelectric generator (TEG) module has been constructed with COMSOL® Multiphysics to verify a module test system. The Seebeck, Peltier, and Thomson effects and Joule heating are included in the thermoelectric conversion model. The TEG model is employed to simulate the operation of a 16-leg TEG module based on bismuth telluride with temperature-dependent material properties. The module is mounted on a test platform, and simulated by combining the heat conduction process and thermoelectric conversion process. Simulation results are obtained for the terminal voltage, output power, heat flow, and efficiency as functions of the electric current; the results are compared with measurement data. The Joule and Thomson heats in all the thermoelectric legs, as functions of the electric current, are calculated by finite-element volume integration over the entire legs. The Peltier heat being pumped at the hot side and released at the cold side of the module are also presented in relation to the electric current. The energy balance relations between heat and electricity are verified to support the simulation.

Effects of channel tap spacing on delay-lock tracking

NASA Astrophysics Data System (ADS)

Dana, Roger A.; Milner, Brian R.; Bogusch, Robert L.

1995-12-01

High fidelity simulations of communication links operating through frequency selective fading channels require both accurate channel models and faithful reproduction of the received signal. In modern radio receivers, processing beyond the analog-to-digital converter (A/D) is done digitally, so a high fidelity simulation is actually an emulation of this digital signal processing. The 'simulation' occurs in constructing the output of the A/D. One approach to constructing the A/D output is to convolve the channel impulse response function with the combined impulse response of the transmitted modulation and the A/D. For both link simulations and hardware channel simulators, the channel impulse response function is then generated with a finite number of samples per chip, and the convolution is implemented in a tapped delay line. In this paper we discuss the effects of the channel model tap spacing on the performance of delay locked loops (DLLs) in both direct sequence and frequency hopped spread spectrum systems. A frequency selective fading channel is considered, and the channel impulse response function is constructed with an integer number of taps per modulation symbol or chip. The tracking loop time delay is computed theoretically for this tapped delay line channel model and is compared to the results of high fidelity simulations of actual DLLs. A surprising result is obtained. The performance of the DLL depends strongly on the number of taps per chip. As this number increases the DLL delay approaches the theoretical limit.

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.

Modeling Water Redistribution in a Near-Surface Arid Soil

NASA Astrophysics Data System (ADS)

Luo, Y.; Ghezzehei, T. A.; Berli, M.; Dijkema, J.; Koonce, J.

2017-12-01

Desert soils cover about one third of the Earth's land surface and play an important role in the ecology and hydrology of arid environments. Despite their large extend, relatively little is known about their near-surface (top centimeters to meter) water dynamics. Recent studies by Koonce (2016) and Dijkema et al. (2017) shed light on the water dynamics of near-surface arid soil but also revealed some of the challenges to simulate the water redistribution in arid soils. The goal of this study was to improve water redistribution simulations in near-surface arid soils by employing more advanced hydraulic conductivity functions. Expanding on the work by Dijkema et al. (2017), we used a HYDRUS-1D model with different hydraulic conductivity functions to simulate water redistribution within the soil as a function of precipitation, evaporation and drainage. Model calculations were compared with measured data from the SEPHAS weighing lysimeters in Boulder City, NV. Preliminary results indicate that water redistribution simulations of near-surface arid soils can be improved by using hydraulic conductivity functions that can capture capillary, film and vapor flow, like for example the Peter-Durner-Iden (PDI) model.

Velocity statistics of the Nagel-Schreckenberg model

NASA Astrophysics Data System (ADS)

Bain, Nicolas; Emig, Thorsten; Ulm, Franz-Josef; Schreckenberg, Michael

2016-02-01

The statistics of velocities in the cellular automaton model of Nagel and Schreckenberg for traffic are studied. From numerical simulations, we obtain the probability distribution function (PDF) for vehicle velocities and the velocity-velocity (vv) covariance function. We identify the probability to find a standing vehicle as a potential order parameter that signals nicely the transition between free congested flow for a sufficiently large number of velocity states. Our results for the vv covariance function resemble features of a second-order phase transition. We develop a 3-body approximation that allows us to relate the PDFs for velocities and headways. Using this relation, an approximation to the velocity PDF is obtained from the headway PDF observed in simulations. We find a remarkable agreement between this approximation and the velocity PDF obtained from simulations.

Velocity statistics of the Nagel-Schreckenberg model.

PubMed

Bain, Nicolas; Emig, Thorsten; Ulm, Franz-Josef; Schreckenberg, Michael

2016-02-01

The statistics of velocities in the cellular automaton model of Nagel and Schreckenberg for traffic are studied. From numerical simulations, we obtain the probability distribution function (PDF) for vehicle velocities and the velocity-velocity (vv) covariance function. We identify the probability to find a standing vehicle as a potential order parameter that signals nicely the transition between free congested flow for a sufficiently large number of velocity states. Our results for the vv covariance function resemble features of a second-order phase transition. We develop a 3-body approximation that allows us to relate the PDFs for velocities and headways. Using this relation, an approximation to the velocity PDF is obtained from the headway PDF observed in simulations. We find a remarkable agreement between this approximation and the velocity PDF obtained from simulations.

Polymer density functional theory approach based on scaling second-order direct correlation function.

PubMed

Zhou, Shiqi

2006-06-01

A second-order direct correlation function (DCF) from solving the polymer-RISM integral equation is scaled up or down by an equation of state for bulk polymer, the resultant scaling second-order DCF is in better agreement with corresponding simulation results than the un-scaling second-order DCF. When the scaling second-order DCF is imported into a recently proposed LTDFA-based polymer DFT approach, an originally associated adjustable but mathematically meaningless parameter now becomes mathematically meaningful, i.e., the numerical value lies now between 0 and 1. When the adjustable parameter-free version of the LTDFA is used instead of the LTDFA, i.e., the adjustable parameter is fixed at 0.5, the resultant parameter-free version of the scaling LTDFA-based polymer DFT is also in good agreement with the corresponding simulation data for density profiles. The parameter-free version of the scaling LTDFA-based polymer DFT is employed to investigate the density profiles of a freely jointed tangent hard sphere chain near a variable sized central hard sphere, again the predictions reproduce accurately the simulational results. Importance of the present adjustable parameter-free version lies in its combination with a recently proposed universal theoretical way, in the resultant formalism, the contact theorem is still met by the adjustable parameter associated with the theoretical way.

Computer Simulation Results for the Two-Point Probability Function of Composite Media

NASA Astrophysics Data System (ADS)

Smith, P.; Torquato, S.

1988-05-01

Computer simulation results are reported for the two-point matrix probability function S2 of two-phase random media composed of disks distributed with an arbitrary degree of impenetrability λ. The novel technique employed to sample S2( r) (which gives the probability of finding the endpoints of a line segment of length r in the matrix) is very accurate and has a fast execution time. Results for the limiting cases λ = 0 (fully penetrable disks) and λ = 1 (hard disks), respectively, compare very favorably with theoretical predictions made by Torquato and Beasley and by Torquato and Lado. Results are also reported for several values of λ. that lie between these two extremes: cases which heretofore have not been examined.

GPU-based Green’s function simulations of shear waves generated by an applied acoustic radiation force in elastic and viscoelastic models

NASA Astrophysics Data System (ADS)

Yang, Yiqun; Urban, Matthew W.; McGough, Robert J.

2018-05-01

Shear wave calculations induced by an acoustic radiation force are very time-consuming on desktop computers, and high-performance graphics processing units (GPUs) achieve dramatic reductions in the computation time for these simulations. The acoustic radiation force is calculated using the fast near field method and the angular spectrum approach, and then the shear waves are calculated in parallel with Green’s functions on a GPU. This combination enables rapid evaluation of shear waves for push beams with different spatial samplings and for apertures with different f/#. Relative to shear wave simulations that evaluate the same algorithm on an Intel i7 desktop computer, a high performance nVidia GPU reduces the time required for these calculations by a factor of 45 and 700 when applied to elastic and viscoelastic shear wave simulation models, respectively. These GPU-accelerated simulations also compared to measurements in different viscoelastic phantoms, and the results are similar. For parametric evaluations and for comparisons with measured shear wave data, shear wave simulations with the Green’s function approach are ideally suited for high-performance GPUs.

Statistics of voids in hierarchical universes

NASA Technical Reports Server (NTRS)

Fry, J. N.

1986-01-01

As one alternative to the N-point galaxy correlation function statistics, the distribution of holes or the probability that a volume of given size and shape be empty of galaxies can be considered. The probability of voids resulting from a variety of hierarchical patterns of clustering is considered, and these are compared with the results of numerical simulations and with observations. A scaling relation required by the hierarchical pattern of higher order correlation functions is seen to be obeyed in the simulations, and the numerical results show a clear difference between neutrino models and cold-particle models; voids are more likely in neutrino universes. Observational data do not yet distinguish but are close to being able to distinguish between models.

Generating multi-double-scroll attractors via nonautonomous approach

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

Hong, Qinghui; Xie, Qingguo, E-mail: qgxie@mail.hust.edu.cn; Shen, Yi

It is a common phenomenon that multi-scroll attractors are realized by introducing the various nonlinear functions with multiple breakpoints in double scroll chaotic systems. Differently, we present a nonautonomous approach for generating multi-double-scroll attractors (MDSA) without changing the original nonlinear functions. By using the multi-level-logic pulse excitation technique in double scroll chaotic systems, MDSA can be generated. A Chua's circuit, a Jerk circuit, and a modified Lorenz system are given as designed example and the Matlab simulation results are presented. Furthermore, the corresponding realization circuits are designed. The Pspice results are in agreement with numerical simulation results, which verify themore » availability and feasibility of this method.« less

Estimation of discontinuous coefficients in parabolic systems: Applications to reservoir simulation

NASA Technical Reports Server (NTRS)

Lamm, P. D.

1984-01-01

Spline based techniques for estimating spatially varying parameters that appear in parabolic distributed systems (typical of those found in reservoir simulation problems) are presented. The problem of determining discontinuous coefficients, estimating both the functional shape and points of discontinuity for such parameters is discussed. Convergence results and a summary of numerical performance of the resulting algorithms are given.

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

PubMed

Marsalek, Ondrej; Markland, Thomas E

2016-02-07

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

Evolution of surface characteristics in material removal simulation with subaperture tools

NASA Astrophysics Data System (ADS)

Kim, Sug-Whan; Jee, Myung-Kook

2002-02-01

Over the last decade, we have witnessed that the fabrication of 200 - 2000 mm scale have received relatively little attention from the fabrication technology development, compared to those of smaller than 200 mm and of larger than 2000 mm in diameter. As a result, the optical surfaces of these scales are still predominantly completed by small optics shops where opticians apply the traditional technique for polishing. Lack of tools in aiding opticians for planning, executing and analyzing their polishing work is a root cause for long and, sometimes, unpredictable delivery and high manufacturing cost for such optical surfaces. We present the on-going development of a software simulation environment called Surface Analysis and Fabrication Environment (SAFE). It is primarily intended to increase the throughput of polishing and testing cycles by allowing opticians to simulate the resulting surface form and roughness with input polishing variables. A brief review of current polishing techniques and their target optics clarifies the need for such simulation tool. This is followed by the development targets and a preliminary simulation plan using the developmental version of SAFE. Among many polishing variables, two removal assumptions and three different types of removal functions we used for the polishing simulation presented. The simulations show that the Gaussian removal function with the proportional removal assumption resulted in the fastest, though marginal, convergence to a super-polished surface of 0.56 micron Peat- to-Valley in form accuracy and of 0.02 nanometer in surface roughness Ra. Other meaningful results and their implications are also presented.

Dynamic Modulation of Human Motor Activity When Observing Actions

PubMed Central

Press, Clare; Cook, Jennifer; Blakemore, Sarah-Jayne; Kilner, James

2012-01-01

Previous studies have demonstrated that when we observe somebody else executing an action many areas of our own motor systems are active. It has been argued that these motor activations are evidence that we motorically simulate observed actions; this motoric simulation may support various functions such as imitation and action understanding. However, whether motoric simulation is indeed the function of motor activations during action observation is controversial, due to inconsistency in findings. Previous studies have demonstrated dynamic modulations in motor activity when we execute actions. Therefore, if we do motorically simulate observed actions, our motor systems should also be modulated dynamically, and in a corresponding fashion, during action observation. Using magnetoencephalography, we recorded the cortical activity of human participants while they observed actions performed by another person. Here, we show that activity in the human motor system is indeed modulated dynamically during action observation. The finding that activity in the motor system is modulated dynamically when observing actions can explain why studies of action observation using functional magnetic resonance imaging have reported conflicting results, and is consistent with the hypothesis that we motorically simulate observed actions. PMID:21414901

2-D Modeling of Nanoscale MOSFETs: Non-Equilibrium Green's Function Approach

NASA Technical Reports Server (NTRS)

Svizhenko, Alexei; Anantram, M. P.; Govindan, T. R.; Biegel, Bryan

2001-01-01

We have developed physical approximations and computer code capable of realistically simulating 2-D nanoscale transistors, using the non-equilibrium Green's function (NEGF) method. This is the most accurate full quantum model yet applied to 2-D device simulation. Open boundary conditions and oxide tunneling are treated on an equal footing. Electrons in the ellipsoids of the conduction band are treated within the anisotropic effective mass approximation. Electron-electron interaction is treated within Hartree approximation by solving NEGF and Poisson equations self-consistently. For the calculations presented here, parallelization is performed by distributing the solution of NEGF equations to various processors, energy wise. We present simulation of the "benchmark" MIT 25nm and 90nm MOSFETs and compare our results to those from the drift-diffusion simulator and the quantum-corrected results available. In the 25nm MOSFET, the channel length is less than ten times the electron wavelength, and the electron scattering time is comparable to its transit time. Our main results are: (1) Simulated drain subthreshold current characteristics are shown, where the potential profiles are calculated self-consistently by the corresponding simulation methods. The current predicted by our quantum simulation has smaller subthreshold slope of the Vg dependence which results in higher threshold voltage. (2) When gate oxide thickness is less than 2 nm, gate oxide leakage is a primary factor which determines off-current of a MOSFET (3) Using our 2-D NEGF simulator, we found several ways to drastically decrease oxide leakage current without compromising drive current. (4) Quantum mechanically calculated electron density is much smaller than the background doping density in the poly silicon gate region near oxide interface. This creates an additional effective gate voltage. Different ways to. include this effect approximately will be discussed.

Acoustic-based proton range verification in heterogeneous tissue: simulation studies

NASA Astrophysics Data System (ADS)

Jones, Kevin C.; Nie, Wei; Chu, James C. H.; Turian, Julius V.; Kassaee, Alireza; Sehgal, Chandra M.; Avery, Stephen

2018-01-01

Acoustic-based proton range verification (protoacoustics) is a potential in vivo technique for determining the Bragg peak position. Previous measurements and simulations have been restricted to homogeneous water tanks. Here, a CT-based simulation method is proposed and applied to a liver and prostate case to model the effects of tissue heterogeneity on the protoacoustic amplitude and time-of-flight range verification accuracy. For the liver case, posterior irradiation with a single proton pencil beam was simulated for detectors placed on the skin. In the prostate case, a transrectal probe measured the protoacoustic pressure generated by irradiation with five separate anterior proton beams. After calculating the proton beam dose deposition, each CT voxel’s material properties were mapped based on Hounsfield Unit values, and thermoacoustically-generated acoustic wave propagation was simulated with the k-Wave MATLAB toolbox. By comparing the simulation results for the original liver CT to homogenized variants, the effects of heterogeneity were assessed. For the liver case, 1.4 cGy of dose at the Bragg peak generated 50 mPa of pressure (13 cm distal), a 2×  lower amplitude than simulated in a homogeneous water tank. Protoacoustic triangulation of the Bragg peak based on multiple detector measurements resulted in 0.4 mm accuracy for a δ-function proton pulse irradiation of the liver. For the prostate case, higher amplitudes are simulated (92-1004 mPa) for closer detectors (<8 cm). For four of the prostate beams, the protoacoustic range triangulation was accurate to  ⩽1.6 mm (δ-function proton pulse). Based on the results, application of protoacoustic range verification to heterogeneous tissue will result in decreased signal amplitudes relative to homogeneous water tank measurements, but accurate range verification is still expected to be possible.

System Simulation of Nuclear Power Plant by Coupling RELAP5 and Matlab/Simulink

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

Meng Lin; Dong Hou; Zhihong Xu

2006-07-01

Since RELAP5 code has general and advanced features in thermal-hydraulic computation, it has been widely used in transient and accident safety analysis, experiment planning analysis, and system simulation, etc. So we wish to design, analyze, verify a new Instrumentation And Control (I and C) system of Nuclear Power Plant (NPP) based on the best-estimated code, and even develop our engineering simulator. But because of limited function of simulating control and protection system in RELAP5, it is necessary to expand the function for high efficient, accurate, flexible design and simulation of I and C system. Matlab/Simulink, a scientific computation software, justmore » can compensate the limitation, which is a powerful tool in research and simulation of plant process control. The software is selected as I and C part to be coupled with RELAP5 code to realize system simulation of NPPs. There are two key techniques to be solved. One is the dynamic data exchange, by which Matlab/Simulink receives plant parameters and returns control results. Database is used to communicate the two codes. Accordingly, Dynamic Link Library (DLL) is applied to link database in RELAP5, while DLL and S-Function is applied in Matlab/Simulink. The other problem is synchronization between the two codes for ensuring consistency in global simulation time. Because Matlab/Simulink always computes faster than RELAP5, the simulation time is sent by RELAP5 and received by Matlab/Simulink. A time control subroutine is added into the simulation procedure of Matlab/Simulink to control its simulation advancement. Through these ways, Matlab/Simulink is dynamically coupled with RELAP5. Thus, in Matlab/Simulink, we can freely design control and protection logic of NPPs and test it with best-estimated plant model feedback. A test will be shown to illuminate that results of coupling calculation are nearly the same with one of single RELAP5 with control logic. In practice, a real Pressurized Water Reactor (PWR) is modeled by RELAP5 code, and its main control and protection system is duplicated by Matlab/Simulink. Some steady states and transients are calculated under control of these I and C systems, and the results are compared with the plant test curves. The application showed that it can do exact system simulation of NPPs by coupling RELAP5 and Matlab/Simulink. This paper will mainly focus on the coupling method, plant thermal-hydraulic model, main control logics, test and application results. (authors)« less

Combined effects of simulated acid rain and lanthanum chloride on chloroplast structure and functional elements in rice.

PubMed

Hu, Huiqing; Wang, Lihong; Zhou, Qing; Huang, Xiaohua

2016-05-01

Acid rain and rare earth element (REE) pollution exist simultaneously in many agricultural regions. However, how REE pollution and acid rain affect plant growth in combination remains largely unknown. In this study, the combined effects of simulated acid rain and lanthanum chloride (LaCl3) on chloroplast morphology, chloroplast ultrastructure, functional element contents, chlorophyll content, and the net photosynthetic rate (P n) in rice (Oryza sativa) were investigated by simulating acid rain and rare earth pollution. Under the combined treatment of simulated acid rain at pH 4.5 and 0.08 mM LaCl3, the chloroplast membrane was smooth, proteins on this membrane were uniform, chloroplast structure was integrated, and the thylakoids were orderly arranged, and simulated acid rain and LaCl3 exhibited a mild antagonistic effect; the Mg, Ca, Mn contents, the chlorophyll content, and the P n increased under this combined treatment, with a synergistic effect of simulated acid rain and LaCl3. Under other combined treatments of simulated acid rain and LaCl3, the chloroplast membrane surface was uneven, a clear "hole" was observed on the surface of chloroplasts, and the thylakoids were dissolved and loose; and the P n and contents of functional elements (P, Mg, K, Ca, Mn, Fe, Ni, Cu, Zn and Mo) and chlorophyll decreased. Under these combined treatments, simulated acid rain and LaCl3 exhibited a synergistic effect. Based on the above results, a model of the combined effects of simulated acid rain and LaCl3 on plant photosynthesis was established in order to reveal the combined effects on plant photosynthesis, especially on the photosynthetic organelle-chloroplast. Our results would provide some references for further understanding the mechanism of the combined effects of simulated acid rain and LaCl3 on plant photosynthesis.

Computer simulation of the metastatic progression.

PubMed

Wedemann, Gero; Bethge, Anja; Haustein, Volker; Schumacher, Udo

2014-01-01

A novel computer model based on a discrete event simulation procedure describes quantitatively the processes underlying the metastatic cascade. Analytical functions describe the size of the primary tumor and the metastases, while a rate function models the intravasation events of the primary tumor and metastases. Events describe the behavior of the malignant cells until the formation of new metastases. The results of the computer simulations are in quantitative agreement with clinical data determined from a patient with hepatocellular carcinoma in the liver. The model provides a more detailed view on the process than a conventional mathematical model. In particular, the implications of interventions on metastasis formation can be calculated.

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

NASA Astrophysics Data System (ADS)

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

2014-07-01

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

Minerva exoplanet detection sensitivity from simulated observations

NASA Astrophysics Data System (ADS)

McCrady, Nate; Nava, C.

2014-01-01

Small rocky planets induce radial velocity signals that are difficult to detect in the presence of stellar noise sources of comparable or larger amplitude. Minerva is a dedicated, robotic observatory that will attain 1 meter per second precision to detect these rocky planets in the habitable zone around nearby stars. We present results of an ongoing project investigating Minerva’s planet detection sensitivity as a function of observational cadence, planet mass, and orbital parameters (period, eccentricity, and argument of periastron). Radial velocity data is simulated with realistic observing cadence, accounting for weather patterns at Mt. Hopkins, Arizona. Instrumental and stellar noise are added to the simulated observations, including effects of oscillation, jitter, starspots and rotation. We extract orbital parameters from the simulated RV data using the RVLIN code. A Monte Carlo analysis is used to explore the parameter space and evaluate planet detection completeness. Our results will inform the Minerva observing strategy by providing a quantitative measure of planet detection sensitivity as a function of orbital parameters and cadence.

Ca-Pri a Cellular Automata Phenomenological Research Investigation: Simulation Results

NASA Astrophysics Data System (ADS)

Iannone, G.; Troisi, A.

2013-05-01

Following the introduction of a phenomenological cellular automata (CA) model capable to reproduce city growth and urban sprawl, we develop a toy model simulation considering a realistic framework. The main characteristic of our approach is an evolution algorithm based on inhabitants preferences. The control of grown cells is obtained by means of suitable functions which depend on the initial condition of the simulation. New born urban settlements are achieved by means of a logistic evolution of the urban pattern while urban sprawl is controlled by means of the population evolution function. In order to compare model results with a realistic urban framework we have considered, as the area of study, the island of Capri (Italy) in the Mediterranean Sea. Two different phases of the urban evolution on the island have been taken into account: a new born initial growth as induced by geographic suitability and the simulation of urban spread after 1943 induced by the population evolution after this date.

On the zero-crossing of the three-gluon Green's function from lattice simulations

NASA Astrophysics Data System (ADS)

Athenodorou, Andreas; Boucaud, Philippe; de Soto, Feliciano; Rodríguez-Quintero, José; Zafeiropoulos, Savvas

2018-03-01

We report on some efforts recently made in order to gain a better understanding of some IR properties of the 3-point gluon Green's function by exploiting results from large-volume quenched lattice simulations. These lattice results have been obtained by using both tree-level Symanzik and the standard Wilson action, in the aim of assessing the possible impact of effects presumably resulting from a particular choice for the discretization of the action. The main resulting feature is the existence of a negative log-aritmic divergence at zero-momentum, which pulls the 3-gluon form factors down at low momenta and, consequently, yields a zero-crossing at a given deep IR momentum. The results can be correctly explained by analyzing the relevant Dyson-Schwinger equations and appropriate truncation schemes.

Charge transport in nanostructured materials: Implementation and verification of constrained density functional theory

DOE PAGES

Goldey, Matthew B.; Brawand, Nicholas P.; Voros, Marton; ...

2017-04-20

The in silico design of novel complex materials for energy conversion requires accurate, ab initio simulation of charge transport. In this work, we present an implementation of constrained density functional theory (CDFT) for the calculation of parameters for charge transport in the hopping regime. We verify our implementation against literature results for molecular systems, and we discuss the dependence of results on numerical parameters and the choice of localization potentials. In addition, we compare CDFT results with those of other commonly used methods for simulating charge transport between nanoscale building blocks. As a result, we show that some of thesemore » methods give unphysical results for thermally disordered configurations, while CDFT proves to be a viable and robust approach.« less

Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical

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

Genova, Alessandro, E-mail: alessandro.genova@rutgers.edu; Pavanello, Michele, E-mail: m.pavanello@rutgers.edu; Ceresoli, Davide, E-mail: davide.ceresoli@cnr.it

2016-06-21

In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange–correlation potentials that aremore » linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH{sup •} radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH{sup •} radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.« less

Shear flow simulations of biaxial nematic liquid crystals

NASA Astrophysics Data System (ADS)

Sarman, Sten

1997-08-01

We have calculated the viscosities of a biaxial nematic liquid crystal phase of a variant of the Gay-Berne fluid [J. G. Gay and B. J. Berne, J. Chem. Phys. 74, 3316 (1981)] by performing molecular dynamics simulations. The equations of motion have been augmented by a director constraint torque that fixes the orientation of the directors. This makes it possible to fix them at different angles relative to the stream lines in shear flow simulations. In equilibrium simulations the constraints generate a new ensemble. One finds that the Green-Kubo relations for the viscosities become linear combinations of time correlation function integrals in this ensemble whereas they are complicated rational functions in the conventional canonical ensemble. We have evaluated these Green-Kubo relations for all the shear viscosities and all the twist viscosities. We have also calculated the alignment angles, which are functions of the viscosity coefficients. We find that there are three real alignment angles but a linear stability analysis shows that only one of them corresponds to a stable director orientation. The Green-Kubo results have been cross checked by nonequilibrium shear flow simulations. The results from the different methods agree very well. Finally, we have evaluated the Miesowicz viscosities [D. Baalss, Z. Naturforsch. Teil A 45, 7 (1990)]. They vary by more than 2 orders of magnitude. The viscosity is consequently highly orientation dependent.

Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical.

PubMed

Genova, Alessandro; Ceresoli, Davide; Pavanello, Michele

2016-06-21

In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange-correlation potentials that are linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH(•) radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH(•) radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.

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.

Turbulence simulation mechanization for Space Shuttle Orbiter dynamics and control studies

NASA Technical Reports Server (NTRS)

Tatom, F. B.; King, R. L.

1977-01-01

The current version of the NASA turbulent simulation model in the form of a digital computer program, TBMOD, is described. The logic of the program is discussed and all inputs and outputs are defined. An alternate method of shear simulation suitable for incorporation into the model is presented. The simulation is based on a von Karman spectrum and the assumption of isotropy. The resulting spectral density functions for the shear model are included.

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.

Solute-solvent cavity and bridge functions. I. Varying size of the solute

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

Vyalov, I., E-mail: ivan.vyalov@iit.it; Chuev, G., E-mail: genchuev@rambler.ru; Georgi, N., E-mail: georgi@mis.mpg.de

2014-08-21

In this work we present the results of the extensive molecular simulations of solute-solvent cavity and bridge functions. The mixtures of Lennard-Jones solvent with Lennard-Jones solute at infinite dilution are considered for different solute-solvent size ratios—up to 4:1. The Percus-Yevick and hypernetted chain closures deviate substantially from simulation results in the investigated temperature and density ranges. We also find that the behavior of the indirect and cavity correlation functions is non-monotonous within the hard-core region, but the latter can be successfully approximated by mean-field theory if the solute-solvent interaction energy is divided into repulsive and attractive contribution, according to Weeks-Chandler-Andersenmore » theory. Furthermore, in spite of the non-monotonous behavior of logarithm of the cavity function and the indirect correlation function, their difference, i.e., the bridge function remains constant within the hard-core region. Such behavior of the bridge and indirect correlation functions at small distances and for small values of indirect correlation function is well known from the Duh-Haymet plots, where the non-unique relationship results in loops of the bridge function vs. indirect correlation function graphs. We show that the same pathological behavior appears also when distance is small and indirect correlation function is large. We further show that the unique functional behavior of the bridge function can be established when bridge is represented as a function of the renormalized, repulsive indirect correlation function.« less

Molecular dynamics simulation of polyacrylamides in potassium montmorillonite clay hydrates

NASA Astrophysics Data System (ADS)

Zhang, Junfang; Rivero, Mayela; Choi, S. K.

2007-02-01

We present molecular dynamics simulation results for polyacrylamide in potassium montmorillonite clay-aqueous systems. Interlayer molecular structure and dynamics properties are investigated. The number density profile, radial distribution function, root-mean-square deviation (RMSD), mean-square displacement (MSD) and diffusion coefficient are reported. The calculations are conducted in constant NVT ensembles, at T = 300 K and with layer spacing of 40 Å. Our simulation results showed that polyacrylamides had little impact on the structure of interlayer water. Density profiles and radial distribution function indicated that hydration shells were formed. In the presence of polyacrylamides more potassium counterions move close to the clay surface while water molecules move away, indicating that potassium counterions are hydrated to a lesser extent than the system in which no polyacrylamides were added. The diffusion coefficients for potassium and water decreased when polyacrylamides were added.

Deorbitalization strategies for meta-generalized-gradient-approximation exchange-correlation functionals

NASA Astrophysics Data System (ADS)

Mejia-Rodriguez, Daniel; Trickey, S. B.

2017-11-01

We explore the simplification of widely used meta-generalized-gradient approximation (mGGA) exchange-correlation functionals to the Laplacian level of refinement by use of approximate kinetic-energy density functionals (KEDFs). Such deorbitalization is motivated by the prospect of reducing computational cost while recovering a strictly Kohn-Sham local potential framework (rather than the usual generalized Kohn-Sham treatment of mGGAs). A KEDF that has been rather successful in solid simulations proves to be inadequate for deorbitalization, but we produce other forms which, with parametrization to Kohn-Sham results (not experimental data) on a small training set, yield rather good results on standard molecular test sets when used to deorbitalize the meta-GGA made very simple, Tao-Perdew-Staroverov-Scuseria, and strongly constrained and appropriately normed functionals. We also study the difference between high-fidelity and best-performing deorbitalizations and discuss possible implications for use in ab initio molecular dynamics simulations of complicated condensed phase systems.

An arc tangent function demodulation method of fiber-optic Fabry-Perot high-temperature pressure sensor

NASA Astrophysics Data System (ADS)

Ren, Qianyu; Li, Junhong; Hong, Yingping; Jia, Pinggang; Xiong, Jijun

2017-09-01

A new demodulation algorithm of the fiber-optic Fabry-Perot cavity length based on the phase generated carrier (PGC) is proposed in this paper, which can be applied in the high-temperature pressure sensor. This new algorithm based on arc tangent function outputs two orthogonal signals by utilizing an optical system, which is designed based on the field-programmable gate array (FPGA) to overcome the range limit of the original PGC arc tangent function demodulation algorithm. The simulation and analysis are also carried on. According to the analysis of demodulation speed and precision, the simulation of different numbers of sampling points, and measurement results of the pressure sensor, the arc tangent function demodulation method has good demodulation results: 1 MHz processing speed of single data and less than 1% error showing practical feasibility in the fiber-optic Fabry-Perot cavity length demodulation of the Fabry-Perot high-temperature pressure sensor.

Magnified gradient function with deterministic weight modification in adaptive learning.

PubMed

Ng, Sin-Chun; Cheung, Chi-Chung; Leung, Shu-Hung

2004-11-01

This paper presents two novel approaches, backpropagation (BP) with magnified gradient function (MGFPROP) and deterministic weight modification (DWM), to speed up the convergence rate and improve the global convergence capability of the standard BP learning algorithm. The purpose of MGFPROP is to increase the convergence rate by magnifying the gradient function of the activation function, while the main objective of DWM is to reduce the system error by changing the weights of a multilayered feedforward neural network in a deterministic way. Simulation results show that the performance of the above two approaches is better than BP and other modified BP algorithms for a number of learning problems. Moreover, the integration of the above two approaches forming a new algorithm called MDPROP, can further improve the performance of MGFPROP and DWM. From our simulation results, the MDPROP algorithm always outperforms BP and other modified BP algorithms in terms of convergence rate and global convergence capability.

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

PubMed

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

2015-05-12

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

Velocity Gradient Power Functional for Brownian Dynamics.

PubMed

de Las Heras, Daniel; Schmidt, Matthias

2018-01-12

We present an explicit and simple approximation for the superadiabatic excess (over ideal gas) free power functional, admitting the study of the nonequilibrium dynamics of overdamped Brownian many-body systems. The functional depends on the local velocity gradient and is systematically obtained from treating the microscopic stress distribution as a conjugate field. The resulting superadiabatic forces are beyond dynamical density functional theory and are of a viscous nature. Their high accuracy is demonstrated by comparison to simulation results.

Velocity Gradient Power Functional for Brownian Dynamics

NASA Astrophysics Data System (ADS)

de las Heras, Daniel; Schmidt, Matthias

2018-01-01

We present an explicit and simple approximation for the superadiabatic excess (over ideal gas) free power functional, admitting the study of the nonequilibrium dynamics of overdamped Brownian many-body systems. The functional depends on the local velocity gradient and is systematically obtained from treating the microscopic stress distribution as a conjugate field. The resulting superadiabatic forces are beyond dynamical density functional theory and are of a viscous nature. Their high accuracy is demonstrated by comparison to simulation results.

TU-EF-204-07: Add Tube Current Modulation to a Low Dose Simulation Tool for CT Systems

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

Ding, Y.; Department of Physics, University of Arizona, Tucson, AZ; Wen, G.

2015-06-15

Purpose: We extended the capabilities of a low dose simulation tool to model Tube-Current Modulation (TCM). TCM is widely used in clinical practice to reduce radiation dose in CT scans. We expect the tool to be valuable for various clinical applications (e.g., optimize protocols, compare reconstruction techniques and evaluate TCM methods). Methods: The tube current is input as a function of z location, instead of a fixed value. Starting from the line integrals of a scan, a new Poisson noise realization at a lower dose is generated for each view. To validate the new functionality, we compared simulated scans withmore » real scans in image space. Results: First we assessed noise in the difference between the low-dose simulations and the original high-dose scan. When the simulated tube current is a step function of z location, the noise at each segment matches the noise of 3 separate constant-tube-current-simulations. Secondly, with a phantom that forces TCM, we compared a low-dose simulation with an equivalent real low-dose scan. The mean CT number of the simulated scan and the real low-dose scan were 137.7±0.6 and 137.8±0.5 respectively. Furthermore, with 240 ROIs, the noise of the simulated scan and the real low-dose scan were 24.03±0.45 and 23.99±0.43 respectively, and they were not statistically different (2-sample t-test, p-value=0.28). The facts that the noise reflected the trend of the TCM curve, and that the absolute noise measurements were not statistically different validated the TCM function. Conclusion: We successfully added tube-current modulation functionality in an existing low dose simulation tool. We demonstrated that the noise reflected an input tube-current modulation curve. In addition, we verified that the noise and mean CT number of our simulation agreed with a real low dose scan. The authors are all employees of Philips. Yijun Ding is also supported by NIBIB P41EB002035 and NIBIB R01EB000803.« less

A reduced basis method for molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Vincent-Finley, Rachel Elisabeth

In this dissertation, we develop a method for molecular simulation based on principal component analysis (PCA) of a molecular dynamics trajectory and least squares approximation of a potential energy function. Molecular dynamics (MD) simulation is a computational tool used to study molecular systems as they evolve through time. With respect to protein dynamics, local motions, such as bond stretching, occur within femtoseconds, while rigid body and large-scale motions, occur within a range of nanoseconds to seconds. To capture motion at all levels, time steps on the order of a femtosecond are employed when solving the equations of motion and simulations must continue long enough to capture the desired large-scale motion. To date, simulations of solvated proteins on the order of nanoseconds have been reported. It is typically the case that simulations of a few nanoseconds do not provide adequate information for the study of large-scale motions. Thus, the development of techniques that allow longer simulation times can advance the study of protein function and dynamics. In this dissertation we use principal component analysis (PCA) to identify the dominant characteristics of an MD trajectory and to represent the coordinates with respect to these characteristics. We augment PCA with an updating scheme based on a reduced representation of a molecule and consider equations of motion with respect to the reduced representation. We apply our method to butane and BPTI and compare the results to standard MD simulations of these molecules. Our results indicate that the molecular activity with respect to our simulation method is analogous to that observed in the standard MD simulation with simulations on the order of picoseconds.

Initial mass function of planetesimals formed by the streaming instability

NASA Astrophysics Data System (ADS)

Schäfer, Urs; Yang, Chao-Chin; Johansen, Anders

2017-01-01

The streaming instability is a mechanism to concentrate solid particles into overdense filaments that undergo gravitational collapse and form planetesimals. However, it remains unclear how the initial mass function of these planetesimals depends on the box dimensions of numerical simulations. To resolve this, we perform simulations of planetesimal formation with the largest box dimensions to date, allowing planetesimals to form simultaneously in multiple filaments that can only emerge within such large simulation boxes. In our simulations, planetesimals with sizes between 80 km and several hundred kilometers form. We find that a power law with a rather shallow exponential cutoff at the high-mass end represents the cumulative birth mass function better than an integrated power law. The steepness of the exponential cutoff is largely independent of box dimensions and resolution, while the exponent of the power law is not constrained at the resolutions we employ. Moreover, we find that the characteristic mass scale of the exponential cutoff correlates with the mass budget in each filament. Together with previous studies of high-resolution simulations with small box domains, our results therefore imply that the cumulative birth mass function of planetesimals is consistent with an exponentially tapered power law with a power-law exponent of approximately -1.6 and a steepness of the exponential cutoff in the range of 0.3-0.4.

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

DOE PAGES

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

2015-04-08

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

Modified Monte Carlo method for study of electron transport in degenerate electron gas in the presence of electron-electron interactions, application to graphene

NASA Astrophysics Data System (ADS)

Borowik, Piotr; Thobel, Jean-Luc; Adamowicz, Leszek

2017-07-01

Standard computational methods used to take account of the Pauli Exclusion Principle into Monte Carlo (MC) simulations of electron transport in semiconductors may give unphysical results in low field regime, where obtained electron distribution function takes values exceeding unity. Modified algorithms were already proposed and allow to correctly account for electron scattering on phonons or impurities. Present paper extends this approach and proposes improved simulation scheme allowing including Pauli exclusion principle for electron-electron (e-e) scattering into MC simulations. Simulations with significantly reduced computational cost recreate correct values of the electron distribution function. Proposed algorithm is applied to study transport properties of degenerate electrons in graphene with e-e interactions. This required adapting the treatment of e-e scattering in the case of linear band dispersion relation. Hence, this part of the simulation algorithm is described in details.

Mesoscale Thermodynamic Analysis of Atomic-Scale Dislocation-Obstacle Interactions Simulated by Molecular Dynamics

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

Monet, Giath; Bacon, David J; Osetskiy, Yury N

2010-01-01

Given the time and length scales in molecular dynamics (MD) simulations of dislocation-defect interactions, quantitative MD results cannot be used directly in larger scale simulations or compared directly with experiment. A method to extract fundamental quantities from MD simulations is proposed here. The first quantity is a critical stress defined to characterise the obstacle resistance. This mesoscopic parameter, rather than the obstacle 'strength' designed for a point obstacle, is to be used for an obstacle of finite size. At finite temperature, our analyses of MD simulations allow the activation energy to be determined as a function of temperature. The resultsmore » confirm the proportionality between activation energy and temperature that is frequently observed by experiment. By coupling the data for the activation energy and the critical stress as functions of temperature, we show how the activation energy can be deduced at a given value of the critical stress.« less

Simulations of Turbulent Momentum and Scalar Transport in Non-Reacting Confined Swirling Coaxial Jets

NASA Technical Reports Server (NTRS)

Shih, Tsan-Hsing; Liu, Nan-Suey; Moder, Jeffrey P.

2015-01-01

This paper presents the numerical simulations of confined three-dimensional coaxial water jets. The objectives are to validate the newly proposed nonlinear turbulence models of momentum and scalar transport, and to evaluate the newly introduced scalar APDF and DWFDF equation along with its Eulerian implementation in the National Combustion Code (NCC). Simulations conducted include the steady RANS, the unsteady RANS (URANS), and the time-filtered Navier-Stokes (TFNS); both without and with invoking the APDF or DWFDF equation. When the APDF (ensemble averaged probability density function) or DWFDF (density weighted filtered density function) equation is invoked, the simulations are of a hybrid nature, i.e., the transport equations of energy and species are replaced by the APDF or DWFDF equation. Results of simulations are compared with the available experimental data. Some positive impacts of the nonlinear turbulence models and the Eulerian scalar APDF and DWFDF approach are observed.

Biopathways representation and simulation on hybrid functional petri net.

PubMed

Matsuno, Hiroshi; Tanaka, Yukiko; Aoshima, Hitoshi; Doi, Atsushi; Matsui, Mika; Miyano, Satoru

2011-01-01

The following two matters should be resolved in order for biosimulation tools to be accepted by users in biology/medicine: (1) remove issues which are irrelevant to biological importance, and (2) allow users to represent biopathways intuitively and understand/manage easily the details of representation and simulation mechanism. From these criteria, we firstly define a novel notion of Petri net called Hybrid Functional Petri Net (HFPN). Then, we introduce a software tool, Genomic Object Net, for representing and simulating biopathways, which we have developed by employing the architecture of HFPN. In order to show the usefulness of Genomic Object Net for representing and simulating biopathways, we show two HFPN representations of gene regulation mechanisms of Drosophila melanogaster (fruit fly) circadian rhythm and apoptosis induced by Fas ligand. The simulation results of these biopathways are also correlated with biological observations. The software is available to academic users from http://www.GenomicObject.Net/.

Urban nonpoint source pollution buildup and washoff models for simulating storm runoff quality in the Los Angeles County.

PubMed

Wang, Long; Wei, Jiahua; Huang, Yuefei; Wang, Guangqian; Maqsood, Imran

2011-07-01

Many urban nonpoint source pollution models utilize pollutant buildup and washoff functions to simulate storm runoff quality of urban catchments. In this paper, two urban pollutant washoff load models are derived using pollutant buildup and washoff functions. The first model assumes that there is no residual pollutant after a storm event while the second one assumes that there is always residual pollutant after each storm event. The developed models are calibrated and verified with observed data from an urban catchment in the Los Angeles County. The application results show that the developed model with consideration of residual pollutant is more capable of simulating nonpoint source pollution from urban storm runoff than that without consideration of residual pollutant. For the study area, residual pollutant should be considered in pollutant buildup and washoff functions for simulating urban nonpoint source pollution when the total runoff volume is less than 30 mm. Copyright © 2011 Elsevier Ltd. All rights reserved.

Security Analysis of Selected AMI Failure Scenarios Using Agent Based Game Theoretic Simulation

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

Abercrombie, Robert K; Schlicher, Bob G; Sheldon, Frederick T

Information security analysis can be performed using game theory implemented in dynamic Agent Based Game Theoretic (ABGT) simulations. Such simulations can be verified with the results from game theory analysis and further used to explore larger scale, real world scenarios involving multiple attackers, defenders, and information assets. We concentrated our analysis on the Advanced Metering Infrastructure (AMI) functional domain which the National Electric Sector Cyber security Organization Resource (NESCOR) working group has currently documented 29 failure scenarios. The strategy for the game was developed by analyzing five electric sector representative failure scenarios contained in the AMI functional domain. From thesemore » five selected scenarios, we characterize them into three specific threat categories affecting confidentiality, integrity and availability (CIA). The analysis using our ABGT simulation demonstrates how to model the AMI functional domain using a set of rationalized game theoretic rules decomposed from the failure scenarios in terms of how those scenarios might impact the AMI network with respect to CIA.« less

Free-energy simulations reveal molecular mechanism for functional switch of a DNA helicase

PubMed Central

Ma, Wen; Whitley, Kevin D; Schulten, Klaus

2018-01-01

Helicases play key roles in genome maintenance, yet it remains elusive how these enzymes change conformations and how transitions between different conformational states regulate nucleic acid reshaping. Here, we developed a computational technique combining structural bioinformatics approaches and atomic-level free-energy simulations to characterize how the Escherichia coli DNA repair enzyme UvrD changes its conformation at the fork junction to switch its function from unwinding to rezipping DNA. The lowest free-energy path shows that UvrD opens the interface between two domains, allowing the bound ssDNA to escape. The simulation results predict a key metastable 'tilted' state during ssDNA strand switching. By simulating FRET distributions with fluorophores attached to UvrD, we show that the new state is supported quantitatively by single-molecule measurements. The present study deciphers key elements for the 'hyper-helicase' behavior of a mutant and provides an effective framework to characterize directly structure-function relationships in molecular machines. PMID:29664402

Free-energy simulations reveal molecular mechanism for functional switch of a DNA helicase.

PubMed

Ma, Wen; Whitley, Kevin D; Chemla, Yann R; Luthey-Schulten, Zaida; Schulten, Klaus

2018-04-17

Helicases play key roles in genome maintenance, yet it remains elusive how these enzymes change conformations and how transitions between different conformational states regulate nucleic acid reshaping. Here, we developed a computational technique combining structural bioinformatics approaches and atomic-level free-energy simulations to characterize how the Escherichia coli DNA repair enzyme UvrD changes its conformation at the fork junction to switch its function from unwinding to rezipping DNA. The lowest free-energy path shows that UvrD opens the interface between two domains, allowing the bound ssDNA to escape. The simulation results predict a key metastable 'tilted' state during ssDNA strand switching. By simulating FRET distributions with fluorophores attached to UvrD, we show that the new state is supported quantitatively by single-molecule measurements. The present study deciphers key elements for the 'hyper-helicase' behavior of a mutant and provides an effective framework to characterize directly structure-function relationships in molecular machines. © 2018, Ma et al.

Simulation of Near-Edge X-ray Absorption Fine Structure with Time-Dependent Equation-of-Motion Coupled-Cluster Theory.

PubMed

Nascimento, Daniel R; DePrince, A Eugene

2017-07-06

An explicitly time-dependent (TD) approach to equation-of-motion (EOM) coupled-cluster theory with single and double excitations (CCSD) is implemented for simulating near-edge X-ray absorption fine structure in molecular systems. The TD-EOM-CCSD absorption line shape function is given by the Fourier transform of the CCSD dipole autocorrelation function. We represent this transform by its Padé approximant, which provides converged spectra in much shorter simulation times than are required by the Fourier form. The result is a powerful framework for the blackbox simulation of broadband absorption spectra. K-edge X-ray absorption spectra for carbon, nitrogen, and oxygen in several small molecules are obtained from the real part of the absorption line shape function and are compared with experiment. The computed and experimentally obtained spectra are in good agreement; the mean unsigned error in the predicted peak positions is only 1.2 eV. We also explore the spectral signatures of protonation in these molecules.

Ground Simulation of an Autonomous Satellite Rendezvous and Tracking System Using Dual Robotic Systems

NASA Technical Reports Server (NTRS)

Trube, Matthew J.; Hyslop, Andrew M.; Carignan, Craig R.; Easley, Joseph W.

2012-01-01

A hardware-in-the-loop ground system was developed for simulating a robotic servicer spacecraft tracking a target satellite at short range. A relative navigation sensor package "Argon" is mounted on the end-effector of a Fanuc 430 manipulator, which functions as the base platform of the robotic spacecraft servicer. Machine vision algorithms estimate the pose of the target spacecraft, mounted on a Rotopod R-2000 platform, relay the solution to a simulation of the servicer spacecraft running in "Freespace", which performs guidance, navigation and control functions, integrates dynamics, and issues motion commands to a Fanuc platform controller so that it tracks the simulated servicer spacecraft. Results will be reviewed for several satellite motion scenarios at different ranges. Key words: robotics, satellite, servicing, guidance, navigation, tracking, control, docking.

The galaxy luminosity function around groups

NASA Astrophysics Data System (ADS)

González, R. E.; Padilla, N. D.; Galaz, G.; Infante, L.

2005-11-01

We present a study on the variations of the luminosity function of galaxies around clusters in a numerical simulation with semi-analytic galaxies, attempting to detect these variations in the 2dF Galaxy Redshift Survey. We subdivide the simulation box into equal-density regions around clusters, which we assume can be achieved by selecting objects at a given normalized distance (r/rrms, where rrms is an estimate of the halo radius) from the group centre. The semi-analytic model predicts important variations in the luminosity function out to r/rrms~= 5. In brief, variations in the mass function of haloes around clusters (large dark matter haloes with M > 1012h-1Msolar) lead to cluster central regions that present a high abundance of bright galaxies (high M* values) as well as low-luminosity galaxies (high α) at r/rrms~= 3 there is a lack of bright galaxies, which shows the depletion of galaxies in the regions surrounding clusters (minimum in M* and α), and a tendency to constant luminosity function parameters at larger cluster-centric distances. We take into account the observational biases present in the real data by reproducing the peculiar velocity effect on the redshifts of galaxies in the simulation box, and also by producing mock catalogues. We find that excluding from the analysis galaxies which in projection are close to the centres of the groups provides results that are qualitatively consistent with the full simulation box results. When we apply this method to mock catalogues of the 2dF Galaxy Redshift Survey (2dFGRS) and the 2PIGG catalogue of groups, we find that the variations in the luminosity function are almost completely erased by the Finger of God effect; only a lack of bright galaxies at r/rrms~= 3 can be marginally detected in the mock catalogues. The results from the real 2dFGRS data show a clearer detection of a dip in M* and α for r/rrms= 3, consistent with the semi-analytic predictions.

Road load simulator tests of the Gould phase 1 functional model silicon controlled rectifier ac motor controller for electric vehicles

NASA Astrophysics Data System (ADS)

Gourash, F.

1984-02-01

The test results for a functional model ac motor controller for electric vehicles and a three-phase induction motor which were dynamically tested on the Lewis Research Center road load simulator are presented. Results show that the controller has the capability to meet the SAE-J227a D cycle test schedule and to accelerate a 1576-kg (3456-lb) simulated vehicle to a cruise speed of 88.5 km/hr (55 mph). Combined motor controller efficiency is 72 percent and the power inverter efficiency alone is 89 percent for the cruise region of the D cycle. Steady state test results for motoring, regeneration, and thermal data obtained by operating the simulator as a conventional dynamometer are in agreement with the contractor's previously reported data. The regeneration test results indicate that a reduction in energy requirements for urban driving cycles is attainable with regenerative braking. Test results and data in this report serve as a data base for further development of ac motor controllers and propulsion systems for electric vehicles. The controller uses state-of-the-art silicon controlled rectifier (SCR) power semiconductors and microprocessor-based logic and control circuitry. The controller was developed by Gould Laboratories under a Lewis contract for the Department of Energy's Electric and Hybrid Vehicle program.

Road load simulator tests of the Gould phase 1 functional model silicon controlled rectifier ac motor controller for electric vehicles

NASA Technical Reports Server (NTRS)

Gourash, F.

1984-01-01

The test results for a functional model ac motor controller for electric vehicles and a three-phase induction motor which were dynamically tested on the Lewis Research Center road load simulator are presented. Results show that the controller has the capability to meet the SAE-J227a D cycle test schedule and to accelerate a 1576-kg (3456-lb) simulated vehicle to a cruise speed of 88.5 km/hr (55 mph). Combined motor controller efficiency is 72 percent and the power inverter efficiency alone is 89 percent for the cruise region of the D cycle. Steady state test results for motoring, regeneration, and thermal data obtained by operating the simulator as a conventional dynamometer are in agreement with the contractor's previously reported data. The regeneration test results indicate that a reduction in energy requirements for urban driving cycles is attainable with regenerative braking. Test results and data in this report serve as a data base for further development of ac motor controllers and propulsion systems for electric vehicles. The controller uses state-of-the-art silicon controlled rectifier (SCR) power semiconductors and microprocessor-based logic and control circuitry. The controller was developed by Gould Laboratories under a Lewis contract for the Department of Energy's Electric and Hybrid Vehicle program.

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.

Molecular dynamics simulation of unsaturated lipid bilayers at low hydration: parameterization and comparison with diffraction studies.

PubMed Central

Feller, S E; Yin, D; Pastor, R W; MacKerell, A D

1997-01-01

A potential energy function for unsaturated hydrocarbons is proposed and is shown to agree well with experiment, using molecular dynamics simulations of a water/octene interface and a dioleoyl phosphatidylcholine (DOPC) bilayer. The simulation results verify most of the assumptions used in interpreting the DOPC experiments, but suggest a few that should be reconsidered. Comparisons with recent results of a simulation of a dipalmitoyl phosphatidylcholine (DPPC) lipid bilayer show that disorder is comparable, even though the temperature, hydration level, and surface area/lipid for DOPC are lower. These observations highlight the dramatic effects of unsaturation on bilayer structure. Images FIGURE 3 PMID:9370424

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

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

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

2013-12-01

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

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

Crystalline lens MTF measurement during simulated accommodation

NASA Astrophysics Data System (ADS)

Borja, David; Takeuchi, Gaku; Ziebarth, Noel; Acosta, Ana C.; Manns, Fabrice; Parel, Jean-Marie

2005-04-01

Purpose: To design and test an optical system to measure the optical quality of post mortem lenses during simulated accommodation. Methods: An optical bench top system was designed to measure the point spread function and calculate the modulation transfer function (MTF) of monkey and human ex-vivo crystalline lenses. The system consists of a super luminescent diode emitting at 850nm, collimated into a 3mm beam which is focused by the ex-vivo lens under test. The intensity distribution at the focus (point spread function) is re-imaged and magnified onto a beam profiler CCD camera. The optical quality in terms of spatial frequency response (modulation transfer function) is calculated by Fourier transform of the point spread function. The system was used on ex-vivo lenses with attached zonules, ciliary body and sclera. The sclera was glued to 8 separate PMMA segments and stretched radial by 5mm on an accommodation simulating lens stretching device. The point spread function was measured for each lens in the relaxed and stretched state for 5 human (ages 38-86 years) and 5 cynomolgus monkey (ages 53 - 67 months) fresh post mortem crystalline lenses. Results: Stretching induced measurable changes in the MTF. The cutoff frequency increased from 54.4+/-13.6 lp/mm unstretched to 59.5+/-21.4 lp/mm stretched in the post-presbyopic human and from 51.9+/-24.7 lp/mm unstretched to 57.7+/-18.5 lp/mm stretched cynomolgus monkey lenses. Conclusion: The results demonstrate the feasibility of measuring the optical quality of ex-vivo human and cynomolgus monkey lenses during simulated accommodation. Additional experiments are underway to quantify changes in optical quality induced by stretching.

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.

Curvilinear grids for WENO methods in astrophysical simulations

NASA Astrophysics Data System (ADS)

Grimm-Strele, H.; Kupka, F.; Muthsam, H. J.

2014-03-01

We investigate the applicability of curvilinear grids in the context of astrophysical simulations and WENO schemes. With the non-smooth mapping functions from Calhoun et al. (2008), we can tackle many astrophysical problems which were out of scope with the standard grids in numerical astrophysics. We describe the difficulties occurring when implementing curvilinear coordinates into our WENO code, and how we overcome them. We illustrate the theoretical results with numerical data. The WENO finite difference scheme works only for high Mach number flows and smooth mapping functions, whereas the finite volume scheme gives accurate results even for low Mach number flows and on non-smooth grids.

Effects of a simulated microgravity model on cell structure and function in rat testis and epididymis

NASA Technical Reports Server (NTRS)

Hadley, Jill A.; Hall, Joseph C.; O'Brien, Ami; Ball, Richard

1992-01-01

The effect of simulated microgravity on the structure and function of the testis and epididymis cells was investigated in rats subjected to 7 days of tail suspension. Results of a histological examination revealed presence of disorganized seminiferous tubules and accumulation of large multinucleated cells and spermatids in the lumen of the epididymis. In addition, decreases in the content of testis protein and in testosterone levels in the testis, the interstitial fluid, and the epididymis were observed.

Domain of validity of the perturbative approach to femtosecond optical spectroscopy

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

Gelin, Maxim F.; Rao, B. Jayachander; Nest, Mathias

2013-12-14

We have performed numerical nonperturbative simulations of transient absorption pump-probe responses for a series of molecular model systems. The resulting signals as a function of the laser field strength and the pump-probe delay time are compared with those obtained in the perturbative response function formalism. The simulations and their theoretical analysis indicate that the perturbative description remains valid up to moderately strong laser pulses, corresponding to a rather substantial depopulation (population) of the initial (final) electronic states.

Quadruplex digital flight control system assessment

NASA Technical Reports Server (NTRS)

Mulcare, D. B.; Downing, L. E.; Smith, M. K.

1988-01-01

Described are the development and validation of a double fail-operational digital flight control system architecture for critical pitch axis functions. Architectural tradeoffs are assessed, system simulator modifications are described, and demonstration testing results are critiqued. Assessment tools and their application are also illustrated. Ultimately, the vital role of system simulation, tailored to digital mechanization attributes, is shown to be essential to validating the airworthiness of full-time critical functions such as augmented fly-by-wire systems for relaxed static stability airplanes.

Density functional theory calculation of refractive indices of liquid-forming silicon oil compounds

NASA Astrophysics Data System (ADS)

Lee, Sanghun; Park, Sung Soo; Hagelberg, Frank

2012-02-01

A combination of quantum chemical calculation and molecular dynamics simulation is applied to compute refractive indices of liquid-forming silicon oils. The densities of these species are obtained from molecular dynamics simulations based on the NPT ensemble while the molecular polarizabilities are evaluated by density functional theory. This procedure is shown to yield results well compatible with available experimental data, suggesting that it represents a robust and economic route for determining the refractive indices of liquid-forming organic complexes containing silicon.

A simple scaling law for the equation of state and the radial distribution functions calculated by density-functional theory molecular dynamics

NASA Astrophysics Data System (ADS)

Danel, J.-F.; Kazandjian, L.

2018-06-01

It is shown that the equation of state (EOS) and the radial distribution functions obtained by density-functional theory molecular dynamics (DFT-MD) obey a simple scaling law. At given temperature, the thermodynamic properties and the radial distribution functions given by a DFT-MD simulation remain unchanged if the mole fractions of nuclei of given charge and the average volume per atom remain unchanged. A practical interest of this scaling law is to obtain an EOS table for a fluid from that already obtained for another fluid if it has the right characteristics. Another practical interest of this result is that an asymmetric mixture made up of light and heavy atoms requiring very different time steps can be replaced by a mixture of atoms of equal mass, which facilitates the exploration of the configuration space in a DFT-MD simulation. The scaling law is illustrated by numerical results.

Comparison of particle swarm optimization and simulated annealing for locating additional boreholes considering combined variance minimization

NASA Astrophysics Data System (ADS)

Soltani-Mohammadi, Saeed; Safa, Mohammad; Mokhtari, Hadi

2016-10-01

One of the most important stages in complementary exploration is optimal designing the additional drilling pattern or defining the optimum number and location of additional boreholes. Quite a lot research has been carried out in this regard in which for most of the proposed algorithms, kriging variance minimization as a criterion for uncertainty assessment is defined as objective function and the problem could be solved through optimization methods. Although kriging variance implementation is known to have many advantages in objective function definition, it is not sensitive to local variability. As a result, the only factors evaluated for locating the additional boreholes are initial data configuration and variogram model parameters and the effects of local variability are omitted. In this paper, with the goal of considering the local variability in boundaries uncertainty assessment, the application of combined variance is investigated to define the objective function. Thus in order to verify the applicability of the proposed objective function, it is used to locate the additional boreholes in Esfordi phosphate mine through the implementation of metaheuristic optimization methods such as simulated annealing and particle swarm optimization. Comparison of results from the proposed objective function and conventional methods indicates that the new changes imposed on the objective function has caused the algorithm output to be sensitive to the variations of grade, domain's boundaries and the thickness of mineralization domain. The comparison between the results of different optimization algorithms proved that for the presented case the application of particle swarm optimization is more appropriate than simulated annealing.

Simulation of FRET dyes allows quantitative comparison against experimental data

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

A simplified computational memory model from information processing.

PubMed

Zhang, Lanhua; Zhang, Dongsheng; Deng, Yuqin; Ding, Xiaoqian; Wang, Yan; Tang, Yiyuan; Sun, Baoliang

2016-11-23

This paper is intended to propose a computational model for memory from the view of information processing. The model, called simplified memory information retrieval network (SMIRN), is a bi-modular hierarchical functional memory network by abstracting memory function and simulating memory information processing. At first meta-memory is defined to express the neuron or brain cortices based on the biology and graph theories, and we develop an intra-modular network with the modeling algorithm by mapping the node and edge, and then the bi-modular network is delineated with intra-modular and inter-modular. At last a polynomial retrieval algorithm is introduced. In this paper we simulate the memory phenomena and functions of memorization and strengthening by information processing algorithms. The theoretical analysis and the simulation results show that the model is in accordance with the memory phenomena from information processing view.

Directed translocation of a flexible polymer through a cone-shaped nano-channel

NASA Astrophysics Data System (ADS)

Nikoofard, Narges; Khalilian, Hamidreza; Fazli, Hossein

2013-08-01

Translocation of a flexible polymer through a cone-shaped channel is studied, theoretically and using computer simulations. Our simulations show that the shape of the channel causes the polymer translocation to be a driven process. The effective driving force of entropic origin acting on the polymer is calculated as a function of the length and the apex-angle of the channel, theoretically. It is found that the translocation time is a non-monotonic function of the apex-angle of the channel. By increasing the apex-angle from zero, the translocation time shows a minimum and then a maximum. Also, it is found that regardless of the value of the apex-angle, the translocation time is a uniformly decreasing function of the channel length. The results of the theory and the simulation are in good qualitative agreement.

Proximity functions for electrons up to 10 keV

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

Chmelevsky, D.; Kellerer, A.M.; Terrissol, M.

1980-11-01

Proximity functions for electrons up to 10 keV in water are computed from simulated particle tracks. Numerical results are given for the differential functions t(x) and the integral functions T(x). Basic characteristics of these functions and their connections to other microdosimetric quantities are considered. As an example of the applicability of the proximity functions, the quantity y/sub D/ for spheres is derived from t(x).

Simulation of synthetic discriminant function optical implementation

NASA Astrophysics Data System (ADS)

Riggins, J.; Butler, S.

1984-12-01

The optical implementation of geometrical shape and synthetic discriminant function matched filters is computer modeled. The filter implementation utilizes the Allebach-Keegan computer-generated hologram algorithm. Signal-to-noise and efficiency measurements were made on the resultant correlation planes.

RFI in hybrid loops - Simulation and experimental results.

NASA Technical Reports Server (NTRS)

Ziemer, R. E.; Nelson, D. R.; Raghavan, H. R.

1972-01-01

A digital simulation of an imperfect second-order hybrid phase-locked loop (HPLL) operating in radio frequency interference (RFI) is described. Its performance is characterized in terms of phase error variance and phase error probability density function (PDF). Monte-Carlo simulation is used to show that the HPLL can be superior to the conventional phase-locked loops in RFI backgrounds when minimum phase error variance is the goodness criterion. Similar experimentally obtained data are given in support of the simulation data.

The Simulation of Daily Temperature Time Series from GCM Output. Part II: Sensitivity Analysis of an Empirical Transfer Function Methodology.

NASA Astrophysics Data System (ADS)

Winkler, Julie A.; Palutikof, Jean P.; Andresen, Jeffrey A.; Goodess, Clare M.

1997-10-01

Empirical transfer functions have been proposed as a means for `downscaling' simulations from general circulation models (GCMs) to the local scale. However, subjective decisions made during the development of these functions may influence the ensuing climate scenarios. This research evaluated the sensitivity of a selected empirical transfer function methodology to 1) the definition of the seasons for which separate specification equations are derived, 2) adjustments for known departures of the GCM simulations of the predictor variables from observations, 3) the length of the calibration period, 4) the choice of function form, and 5) the choice of predictor variables. A modified version of the Climatological Projection by Model Statistics method was employed to generate control (1 × CO2) and perturbed (2 × CO2) scenarios of daily maximum and minimum temperature for two locations with diverse climates (Alcantarilla, Spain, and Eau Claire, Michigan). The GCM simulations used in the scenario development were from the Canadian Climate Centre second-generation model (CCC GCMII).Variations in the downscaling methodology were found to have a statistically significant impact on the 2 × CO2 climate scenarios, even though the 1 × CO2 scenarios for the different transfer function approaches were often similar. The daily temperature scenarios for Alcantarilla and Eau Claire were most sensitive to the decision to adjust for deficiencies in the GCM simulations, the choice of predictor variables, and the seasonal definitions used to derive the functions (i.e., fixed seasons, floating seasons, or no seasons). The scenarios were less sensitive to the choice of function form (i.e., linear versus nonlinear) and to an increase in the length of the calibration period.The results of Part I, which identified significant departures of the CCC GCMII simulations of two candidate predictor variables from observations, together with those presented here in Part II, 1) illustrate the importance of detailed comparisons of observed and GCM 1 × CO2 series of candidate predictor variables as an initial step in impact analysis, 2) demonstrate that decisions made when developing the transfer functions can have a substantial influence on the 2 × CO2 scenarios and their interpretation, 3) highlight the uncertainty in the appropriate criteria for evaluating transfer function approaches, and 4) suggest that automation of empirical transfer function methodologies is inappropriate because of differences in the performance of transfer functions between sites and because of spatial differences in the GCM's ability to adequately simulate the predictor variables used in the functions.

Soft materials design via self assembly of functionalized icosahedral particles

NASA Astrophysics Data System (ADS)

Muthukumar, Vidyalakshmi Chockalingam

In this work we simulate self assembly of icosahedral building blocks using a coarse grained model of the icosahedral capsid of virus 1m1c. With significant advancements in site-directed functionalization of these macromolecules [1], we propose possible application of such self-assembled materials for drug delivery. While there have been some reports on organization of viral particles in solution through functionalization, exploiting this behaviour for obtaining well-ordered stoichiometric structures has not yet been explored. Our work is in well agreement with the earlier simulation studies of icosahedral gold nanocrystals, giving chain like patterns [5] and also broadly in agreement with the wet lab works of Finn, M.G. et al., who have shown small predominantly chain-like aggregates with mannose-decorated Cowpea Mosaic Virus (CPMV) [22] and small two dimensional aggregates with oligonucleotide functionalization on the CPMV capsid [1]. To quantify the results of our Coarse Grained Molecular Dynamics Simulations I developed analysis routines in MATLAB using which we found the most preferable nearest neighbour distances (from the radial distribution function (RDF) calculations) for different lengths of the functional groups and under different implicit solvent conditions, and the most frequent coordination number for a virus particle (histogram plots further using the information from RDF). Visual inspection suggests that our results most likely span the low temperature limits explored in the works of Finn, M.G. et al., and show a good degree of agreement with the experimental results in [1] at an annealing temperature of 4°C. Our work also reveals the possibility of novel stoichiometric N-mer type aggregates which could be synthesized using these capsids with appropriate functionalization and solvent conditions.

Arm retraction dynamics of entangled star polymers: A forward flux sampling method study

NASA Astrophysics Data System (ADS)

Zhu, Jian; Likhtman, Alexei E.; Wang, Zuowei

2017-07-01

The study of dynamics and rheology of well-entangled branched polymers remains a challenge for computer simulations due to the exponentially growing terminal relaxation times of these polymers with increasing molecular weights. We present an efficient simulation algorithm for studying the arm retraction dynamics of entangled star polymers by combining the coarse-grained slip-spring (SS) model with the forward flux sampling (FFS) method. This algorithm is first applied to simulate symmetric star polymers in the absence of constraint release (CR). The reaction coordinate for the FFS method is determined by finding good agreement of the simulation results on the terminal relaxation times of mildly entangled stars with those obtained from direct shooting SS model simulations with the relative difference between them less than 5%. The FFS simulations are then carried out for strongly entangled stars with arm lengths up to 16 entanglements that are far beyond the accessibility of brute force simulations in the non-CR condition. Apart from the terminal relaxation times, the same method can also be applied to generate the relaxation spectra of all entanglements along the arms which are desired for the development of quantitative theories of entangled branched polymers. Furthermore, we propose a numerical route to construct the experimentally measurable relaxation correlation functions by effectively linking the data stored at each interface during the FFS runs. The obtained star arm end-to-end vector relaxation functions Φ (t ) and the stress relaxation function G(t) are found to be in reasonably good agreement with standard SS simulation results in the terminal regime. Finally, we demonstrate that this simulation method can be conveniently extended to study the arm-retraction problem in entangled star polymer melts with CR by modifying the definition of the reaction coordinate, while the computational efficiency will depend on the particular slip-spring or slip-link model employed.

Conducting Simulation Studies in the R Programming Environment.

PubMed

Hallgren, Kevin A

2013-10-12

Simulation studies allow researchers to answer specific questions about data analysis, statistical power, and best-practices for obtaining accurate results in empirical research. Despite the benefits that simulation research can provide, many researchers are unfamiliar with available tools for conducting their own simulation studies. The use of simulation studies need not be restricted to researchers with advanced skills in statistics and computer programming, and such methods can be implemented by researchers with a variety of abilities and interests. The present paper provides an introduction to methods used for running simulation studies using the R statistical programming environment and is written for individuals with minimal experience running simulation studies or using R. The paper describes the rationale and benefits of using simulations and introduces R functions relevant for many simulation studies. Three examples illustrate different applications for simulation studies, including (a) the use of simulations to answer a novel question about statistical analysis, (b) the use of simulations to estimate statistical power, and (c) the use of simulations to obtain confidence intervals of parameter estimates through bootstrapping. Results and fully annotated syntax from these examples are provided.

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

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

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

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

Importance of Vibronic Effects in the UV-Vis Spectrum of the 7,7,8,8-Tetracyanoquinodimethane Anion.

PubMed

Tapavicza, Enrico; Furche, Filipp; Sundholm, Dage

2016-10-11

We present a computational method for simulating vibronic absorption spectra in the ultraviolet-visible (UV-vis) range and apply it to the 7,7,8,8-tetracyanoquinodimethane anion (TCNQ - ), which has been used as a ligand in black absorbers. Gaussian broadening of vertical electronic excitation energies of TCNQ - from linear-response time-dependent density functional theory produces only one band, which is qualitatively incorrect. Thus, the harmonic vibrational modes of the two lowest doublet states were computed, and the vibronic UV-vis spectrum was simulated using the displaced harmonic oscillator approximation, the frequency-shifted harmonic oscillator approximation, and the full Duschinsky formalism. An efficient real-time generating function method was implemented to avoid the exponential complexity of conventional Franck-Condon approaches to vibronic spectra. The obtained UV-vis spectra for TCNQ - agree well with experiment; the Duschinsky rotation is found to have only a minor effect on the spectrum. Born-Oppenheimer molecular dynamics simulations combined with calculations of the electronic excitation energies for a large number of molecular structures were also used for simulating the UV-vis spectrum. The Born-Oppenheimer molecular dynamics simulations yield a broadening of the energetically lowest peak in the absorption spectrum, but additional vibrational bands present in the experimental and simulated quantum harmonic oscillator spectra are not observed in the molecular dynamics simulations. Our results underline the importance of vibronic effects for the UV-vis spectrum of TCNQ - , and they establish an efficient method for obtaining vibronic spectra using a combination of linear-response time-dependent density functional theory and a real-time generating function approach.

Unfolding the neutron spectrum of a NE213 scintillator using artificial neural networks.

PubMed

Sharghi Ido, A; Bonyadi, M R; Etaati, G R; Shahriari, M

2009-10-01

Artificial neural networks technology has been applied to unfold the neutron spectra from the pulse height distribution measured with NE213 liquid scintillator. Here, both the single and multi-layer perceptron neural network models have been implemented to unfold the neutron spectrum from an Am-Be neutron source. The activation function and the connectivity of the neurons have been investigated and the results have been analyzed in terms of the network's performance. The simulation results show that the neural network that utilizes the Satlins transfer function has the best performance. In addition, omitting the bias connection of the neurons improve the performance of the network. Also, the SCINFUL code is used for generating the response functions in the training phase of the process. Finally, the results of the neural network simulation have been compared with those of the FORIST unfolding code for both (241)Am-Be and (252)Cf neutron sources. The results of neural network are in good agreement with FORIST code.

On the logistic equation subject to uncertainties in the environmental carrying capacity and initial population density

NASA Astrophysics Data System (ADS)

Dorini, F. A.; Cecconello, M. S.; Dorini, L. B.

2016-04-01

It is recognized that handling uncertainty is essential to obtain more reliable results in modeling and computer simulation. This paper aims to discuss the logistic equation subject to uncertainties in two parameters: the environmental carrying capacity, K, and the initial population density, N0. We first provide the closed-form results for the first probability density function of time-population density, N(t), and its inflection point, t*. We then use the Maximum Entropy Principle to determine both K and N0 density functions, treating such parameters as independent random variables and considering fluctuations of their values for a situation that commonly occurs in practice. Finally, closed-form results for the density functions and statistical moments of N(t), for a fixed t > 0, and of t* are provided, considering the uniform distribution case. We carried out numerical experiments to validate the theoretical results and compared them against that obtained using Monte Carlo simulation.

Numerical simulation of a flow past a triangular sail-type blade of a wind generator using the ANSYS FLUENT software package

NASA Astrophysics Data System (ADS)

Kusaiynov, K.; Tanasheva, N. K.; Min'kov, L. L.; Nusupbekov, B. R.; Stepanova, Yu. O.; Rozhkova, A. V.

2016-02-01

An air flow past a single triangular sail-type blade of a wind turbine is analyzed by numerical simulation for low velocities of the incoming flow. The results of numerical simulation indicate a monotonic increase in the drag force and the lift force as functions of the incoming flow; empirical dependences of these quantities are obtained.

Predictions of Crystal Structures from First Principles

DTIC Science & Technology

2007-06-01

RDX crystal in hoped that the problem could be resolved by the molecular dynamics simulations . The fully ab initio development of density functional... Molecular Dynamics Simulations of RDX i.e., without any use of experimental results (except that Crystal the geometry of monomers was derived from X-ray...applied in molecular dynamics simulations of the RDX system, due to its size, is intractable by any high-level ab crystal. We performed isothermal

Simulating patient-specific heart shape and motion using SPECT perfusion images with the MCAT phantom

NASA Astrophysics Data System (ADS)

Faber, Tracy L.; Garcia, Ernest V.; Lalush, David S.; Segars, W. Paul; Tsui, Benjamin M.

2001-05-01

The spline-based Mathematical Cardiac Torso (MCAT) phantom is a realistic software simulation designed to simulate single photon emission computed tomographic (SPECT) data. It incorporates a heart model of known size and shape; thus, it is invaluable for measuring accuracy of acquisition, reconstruction, and post-processing routines. New functionality has been added by replacing the standard heart model with left ventricular (LV) epicaridal and endocardial surface points detected from actual patient SPECT perfusion studies. LV surfaces detected from standard post-processing quantitation programs are converted through interpolation in space and time into new B-spline models. Perfusion abnormalities are added to the model based on results of standard perfusion quantification. The new LV is translated and rotated to fit within existing atria and right ventricular models, which are scaled based on the size of the LV. Simulations were created for five different patients with myocardial infractions who had undergone SPECT perfusion imaging. Shape, size, and motion of the resulting activity map were compared visually to the original SPECT images. In all cases, size, shape and motion of simulated LVs matched well with the original images. Thus, realistic simulations with known physiologic and functional parameters can be created for evaluating efficacy of processing algorithms.

Simulations of the Formation and Evolution of X-ray Clusters

NASA Astrophysics Data System (ADS)

Bryan, G. L.; Klypin, A.; Norman, M. L.

1994-05-01

We describe results from a set of Omega = 1 Cold plus Hot Dark Matter (CHDM) and Cold Dark Matter (CDM) simulations. We examine the formation and evolution of X-ray clusters in a cosmological setting with sufficient numbers to perform statistical analysis. We find that CDM, normalized to COBE, seems to produce too many large clusters, both in terms of the luminosity (dn/dL) and temperature (dn/dT) functions. The CHDM simulation produces fewer clusters and the temperature distribution (our numerically most secure result) matches observations where they overlap. The computed cluster luminosity function drops below observations, but we are almost surely underestimating the X-ray luminosity. Because of the lower fluctuations in CHDM, there are only a small number of bright clusters in our simulation volume; however we can use the simulated clusters to fix the relation between temperature and velocity dispersion, allowing us to use collisionless N-body codes to probe larger length scales with correspondingly brighter clusters. The hydrodynamic simulations have been performed with a hybrid particle-mesh scheme for the dark matter and a high resolution grid-based piecewise parabolic method for the adiabatic gas dynamics. This combination has been implemented for massively parallel computers, allowing us to achive grids as large as 512(3) .

Refined lateral energy correction functions for the KASCADE-Grande experiment based on Geant4 simulations

NASA Astrophysics Data System (ADS)

Gherghel-Lascu, A.; Apel, W. D.; Arteaga-Velázquez, J. C.; Bekk, K.; Bertaina, M.; Blümer, J.; Bozdog, H.; Brancus, I. M.; Cantoni, E.; Chiavassa, A.; Cossavella, F.; Daumiller, K.; de Souza, V.; Di Pierro, F.; Doll, P.; Engel, R.; Engler, J.; Fuchs, B.; Fuhrmann, D.; Gils, H. J.; Glasstetter, R.; Grupen, C.; Haungs, A.; Heck, D.; Hörandel, J. R.; Huber, D.; Huege, T.; Kampert, K.-H.; Kang, D.; Klages, H. O.; Link, K.; Łuczak, P.; Mathes, H. J.; Mayer, H. J.; Milke, J.; Mitrica, B.; Morello, C.; Oehlschläger, J.; Ostapchenko, S.; Palmieri, N.; Petcu, M.; Pierog, T.; Rebel, H.; Roth, M.; Schieler, H.; Schoo, S.; Schröder, F. G.; Sima, O.; Toma, G.; Trinchero, G. C.; Ulrich, H.; Weindl, A.; Wochele, J.; Zabierowski, J.

2015-02-01

In previous studies of KASCADE-Grande data, a Monte Carlo simulation code based on the GEANT3 program has been developed to describe the energy deposited by EAS particles in the detector stations. In an attempt to decrease the simulation time and ensure compatibility with the geometry description in standard KASCADE-Grande analysis software, several structural elements have been neglected in the implementation of the Grande station geometry. To improve the agreement between experimental and simulated data, a more accurate simulation of the response of the KASCADE-Grande detector is necessary. A new simulation code has been developed based on the GEANT4 program, including a realistic geometry of the detector station with structural elements that have not been considered in previous studies. The new code is used to study the influence of a realistic detector geometry on the energy deposited in the Grande detector stations by particles from EAS events simulated by CORSIKA. Lateral Energy Correction Functions are determined and compared with previous results based on GEANT3.

Cole-Davidson dynamics of simple chain models.

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

Dotson, Taylor C.; McCoy, John Dwane; Adolf, Douglas Brian

2008-10-01

Rotational relaxation functions of the end-to-end vector of short, freely jointed and freely rotating chains were determined from molecular dynamics simulations. The associated response functions were obtained from the one-sided Fourier transform of the relaxation functions. The Cole-Davidson function was used to fit the response functions with extensive use being made of Cole-Cole plots in the fitting procedure. For the systems studied, the Cole-Davidson function provided remarkably accurate fits [as compared to the transform of the Kohlrausch-Williams-Watts (KWW) function]. The only appreciable deviations from the simulation results were in the high frequency limit and were due to ballistic or freemore » rotation effects. The accuracy of the Cole-Davidson function appears to be the result of the transition in the time domain from stretched exponential behavior at intermediate time to single exponential behavior at long time. Such a transition can be explained in terms of a distribution of relaxation times with a well-defined longest relaxation time. Since the Cole-Davidson distribution has a sharp cutoff in relaxation time (while the KWW function does not), it makes sense that the Cole-Davidson would provide a better frequency-domain description of the associated response function than the KWW function does.« less

On the zero-crossing of the three-gluon Green's function from lattice simulations

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

Athenodorou, Andreas; Boucaud, Philippe; de Soto, Feliciano

We report on some efforts recently made in order to gain a better understanding of some IR properties of the 3-point gluon Green’s function by exploiting results from large-volume quenched lattice simulations. These lattice results have been obtained by using both tree-level Symanzik and the standard Wilson action, in the aim of assessing the possible impact of effects presumably resulting from a particular choice for the discretization of the action. The main resulting feature is the existence of a negative log-aritmic divergence at zero-momentum, which pulls the 3-gluon form factors down at low momenta and, consequently, yields a zero-crossing atmore » a given deep IR momentum. The results can be correctly explained by analyzing the relevant Dyson-Schwinger equations and appropriate truncation schemes.« less

A new DG nanoscale TFET based on MOSFETs by using source gate electrode: 2D simulation and an analytical potential model

NASA Astrophysics Data System (ADS)

Ramezani, Zeinab; Orouji, Ali A.

2017-08-01

This paper suggests and investigates a double-gate (DG) MOSFET, which emulates tunnel field effect transistors (M-TFET). We have combined this novel concept into a double-gate MOSFET, which behaves as a tunneling field effect transistor by work function engineering. In the proposed structure, in addition to the main gate, we utilize another gate over the source region with zero applied voltage and a proper work function to convert the source region from N+ to P+. We check the impact obtained by varying the source gate work function and source doping on the device parameters. The simulation results of the M-TFET indicate that it is a suitable case for a switching performance. Also, we present a two-dimensional analytic potential model of the proposed structure by solving the Poisson's equation in x and y directions and by derivatives from the potential profile; thus, the electric field is achieved. To validate our present model, we use the SILVACO ATLAS device simulator. The analytical results have been compared with it.

Percolation analyses of observed and simulated galaxy clustering

NASA Astrophysics Data System (ADS)

Bhavsar, S. P.; Barrow, J. D.

1983-11-01

A percolation cluster analysis is performed on equivalent regions of the CFA redshift survey of galaxies and the 4000 body simulations of gravitational clustering made by Aarseth, Gott and Turner (1979). The observed and simulated percolation properties are compared and, unlike correlation and multiplicity function analyses, favour high density (Omega = 1) models with n = - 1 initial data. The present results show that the three-dimensional data are consistent with the degree of filamentary structure present in isothermal models of galaxy formation at the level of percolation analysis. It is also found that the percolation structure of the CFA data is a function of depth. Percolation structure does not appear to be a sensitive probe of intrinsic filamentary structure.

AB INITIO Molecular Dynamics Simulations of Water Under Static and Shock Compressed Conditions

NASA Astrophysics Data System (ADS)

Goldman, Nir; Fried, Laurence E.; Mundy, Christopher J.; Kuo, I.-F. William; Curioni, Alessandro; Reed, Evan J.

2007-12-01

We report herein a series of ab initio simulations of water under both static and shocked conditions. We have calculated the coherent x-ray scattering intensity of several phases of water under high pressure, using ab initio Density Functional Theory (DFT). We provide new atomic scattering form factors for water at extreme conditions, which take into account frequently neglected changes in ionic charge and electron delocalization. We have also simulated liquid water undergoing shock loading of velocities from 5-11 km/s using the Multi-Scale Shock Technique (MSST). We show that Density Functional Theory (DFT) molecular dynamics results compare extremely well to experiments on the water shock Hugoniot.

N-Ω Interaction from High-Energy Heavy Ion Collisions

NASA Astrophysics Data System (ADS)

Morita, Kenji; Ohnishi, Akira; Hatsuda, Tetsuo

We discuss possible observation of the N-Ω interaction from intensity correlation function in high energy heavy ion collisions. Recently a lattice QCD simulation by the HAL QCD collaboration predicts the existence of a N-Ω bound state in the 5S2 channel. We adopt the N-Ω interaction potential obtained by the lattice simulation and use it to calculate the N-Ω correlation function. We also study the variation of the correlation function with respect to the change of the binding energy and scattering parameters. Our result indicates that heavy ion collisions at RHIC and LHC may provide information on the possible existence of the N-Ω dibaryon.

AMR Studies of Star Formation: Simulations and Simulated Observations

NASA Astrophysics Data System (ADS)

Offner, Stella; McKee, C. F.; Klein, R. I.

2009-01-01

Molecular clouds are typically observed to be approximately virialized with gravitational and turbulent energy in balance, yielding a star formation rate of a few percent. The origin and characteristics of the observed supersonic turbulence are poorly understood, and without continued energy injection the turbulence is predicted to decay within a cloud dynamical time. Recent observations and analytic work have suggested a strong connection between the initial stellar mass function, the core mass function, and turbulence characteristics. The role of magnetic fields in determining core lifetimes, shapes, and kinematic properties remains hotly debated. Simulations are a formidable tool for studying the complex process of star formation and addressing these puzzles. I present my results modeling low-mass star formation using the ORION adaptive mesh refinement (AMR) code. I investigate the properties of forming cores and protostars in simulations in which the turbulence is driven to maintain virial balance and where it is allowed to decay. I will discuss simulated observations of cores in dust emission and in molecular tracers and compare to observations of local star-forming clouds. I will also present results from ORION cluster simulations including flux-limited diffusion radiative transfer and show that radiative feedback, even from low-mass stars, has a significant effect on core fragmentation, disk properties, and the IMF. Finally, I will discuss the new simulation frontier of AMR multigroup radiative transfer.

Fabrication and evaluation of novel rabbit model cardiovascular simulator with 3D printer

NASA Astrophysics Data System (ADS)

Jang, Min; Lee, Min-Woo; Seo, See-Yoon; Shin, Sang-Hoon

2017-03-01

Simulators allow researchers to study the hemodynamics of the cardiovascular system in a reproducible way without using complicated equations. Previous simulators focused on heart functions. However, a detailed model of the vessels is required to replicate the pulse wave of the arterial system. A computer simulation was used to simplify the arterial branch because producing every small artery is neither possible nor necessary. A 3D-printed zig was used to make a hand-made arterial tree. The simulator that was developed was evaluated by comparing its results to in-vivo data, in terms of the hemodynamic parameters (waveform, augmentation index, impedance, etc.) that were measured at three points: the ascending aorta, the thoracic aorta, and the brachiocephalic artery. The results from the simulator showed good agreement with the in-vivo data. Therefore, this simulator can be used as a research tool for the cardiovascular study of animal models, specifically rabbits.

Time-dependent quantum transport: An efficient method based on Liouville-von-Neumann equation for single-electron density matrix

NASA Astrophysics Data System (ADS)

Xie, Hang; Jiang, Feng; Tian, Heng; Zheng, Xiao; Kwok, Yanho; Chen, Shuguang; Yam, ChiYung; Yan, YiJing; Chen, Guanhua

2012-07-01

Basing on our hierarchical equations of motion for time-dependent quantum transport [X. Zheng, G. H. Chen, Y. Mo, S. K. Koo, H. Tian, C. Y. Yam, and Y. J. Yan, J. Chem. Phys. 133, 114101 (2010), 10.1063/1.3475566], we develop an efficient and accurate numerical algorithm to solve the Liouville-von-Neumann equation. We solve the real-time evolution of the reduced single-electron density matrix at the tight-binding level. Calculations are carried out to simulate the transient current through a linear chain of atoms, with each represented by a single orbital. The self-energy matrix is expanded in terms of multiple Lorentzian functions, and the Fermi distribution function is evaluated via the Padè spectrum decomposition. This Lorentzian-Padè decomposition scheme is employed to simulate the transient current. With sufficient Lorentzian functions used to fit the self-energy matrices, we show that the lead spectral function and the dynamics response can be treated accurately. Compared to the conventional master equation approaches, our method is much more efficient as the computational time scales cubically with the system size and linearly with the simulation time. As a result, the simulations of the transient currents through systems containing up to one hundred of atoms have been carried out. As density functional theory is also an effective one-particle theory, the Lorentzian-Padè decomposition scheme developed here can be generalized for first-principles simulation of realistic systems.

A semi-grand canonical Monte Carlo simulation model for ion binding to ionizable surfaces: proton binding of carboxylated latex particles as a case study.

PubMed

Madurga, Sergio; Rey-Castro, Carlos; Pastor, Isabel; Vilaseca, Eudald; David, Calin; Garcés, Josep Lluís; Puy, Jaume; Mas, Francesc

2011-11-14

In this paper, we present a computer simulation study of the ion binding process at an ionizable surface using a semi-grand canonical Monte Carlo method that models the surface as a discrete distribution of charged and neutral functional groups in equilibrium with explicit ions modelled in the context of the primitive model. The parameters of the simulation model were tuned and checked by comparison with experimental titrations of carboxylated latex particles in the presence of different ionic strengths of monovalent ions. The titration of these particles was analysed by calculating the degree of dissociation of the latex functional groups vs. pH curves at different background salt concentrations. As the charge of the titrated surface changes during the simulation, a procedure to keep the electroneutrality of the system is required. Here, two approaches are used with the choice depending on the ion selected to maintain electroneutrality: counterion or coion procedures. We compare and discuss the difference between the procedures. The simulations also provided a microscopic description of the electrostatic double layer (EDL) structure as a function of pH and ionic strength. The results allow us to quantify the effect of the size of the background salt ions and of the surface functional groups on the degree of dissociation. The non-homogeneous structure of the EDL was revealed by plotting the counterion density profiles around charged and neutral surface functional groups. © 2011 American Institute of Physics

Forecasting Nonlinear Chaotic Time Series with Function Expression Method Based on an Improved Genetic-Simulated Annealing Algorithm

PubMed Central

Wang, Jun; Zhou, Bi-hua; Zhou, Shu-dao; Sheng, Zheng

2015-01-01

The paper proposes a novel function expression method to forecast chaotic time series, using an improved genetic-simulated annealing (IGSA) algorithm to establish the optimum function expression that describes the behavior of time series. In order to deal with the weakness associated with the genetic algorithm, the proposed algorithm incorporates the simulated annealing operation which has the strong local search ability into the genetic algorithm to enhance the performance of optimization; besides, the fitness function and genetic operators are also improved. Finally, the method is applied to the chaotic time series of Quadratic and Rossler maps for validation. The effect of noise in the chaotic time series is also studied numerically. The numerical results verify that the method can forecast chaotic time series with high precision and effectiveness, and the forecasting precision with certain noise is also satisfactory. It can be concluded that the IGSA algorithm is energy-efficient and superior. PMID:26000011

DES Prediction of Cavitation Erosion and Its Validation for a Ship Scale Propeller

NASA Astrophysics Data System (ADS)

Ponkratov, Dmitriy, Dr

2015-12-01

Lloyd's Register Technical Investigation Department (LR TID) have developed numerical functions for the prediction of cavitation erosion aggressiveness within Computational Fluid Dynamics (CFD) simulations. These functions were previously validated for a model scale hydrofoil and ship scale rudder [1]. For the current study the functions were applied to a cargo ship's full scale propeller, on which the severe cavitation erosion was reported. The performed Detach Eddy Simulation (DES) required a fine computational mesh (approximately 22 million cells), together with a very small time step (2.0E-4 s). As the cavitation for this type of vessel is primarily caused by a highly non-uniform wake, the hull was also included in the simulation. The applied method under predicted the cavitation extent and did not fully resolve the tip vortex; however, the areas of cavitation collapse were captured successfully. Consequently, the developed functions showed a very good prediction of erosion areas, as confirmed by comparison with underwater propeller inspection results.

All-atom molecular dynamics of the HBV capsid reveals insights into biological function and cryo-EM resolution limits

PubMed Central

Perilla, Juan R; Schlicksup, Christopher John; Venkatakrishnan, Balasubramanian; Zlotnick, Adam; Schulten, Klaus

2018-01-01

The hepatitis B virus capsid represents a promising therapeutic target. Experiments suggest the capsid must be flexible to function; however, capsid structure and dynamics have not been thoroughly characterized in the absence of icosahedral symmetry constraints. Here, all-atom molecular dynamics simulations are leveraged to investigate the capsid without symmetry bias, enabling study of capsid flexibility and its implications for biological function and cryo-EM resolution limits. Simulation results confirm flexibility and reveal a propensity for asymmetric distortion. The capsid’s influence on ionic species suggests a mechanism for modulating the display of cellular signals and implicates the capsid’s triangular pores as the location of signal exposure. A theoretical image reconstruction performed using simulated conformations indicates how capsid flexibility may limit the resolution of cryo-EM. Overall, the present work provides functional insight beyond what is accessible to experimental methods and raises important considerations regarding asymmetry in structural studies of icosahedral virus capsids. PMID:29708495

Atomistic Simulations of Hydrodynamic and Interaction Forces on Functionalized Silica Nanoparticles

NASA Astrophysics Data System (ADS)

Lane, J. Matthew D.; Ismail, Ahmed E.; Chandross, Michael; Lorenz, Christian D.; Grest, Gary S.

2009-03-01

It is often desired to prevent the flocculation and phase separation of nanoparticles in solution. This can be accomplished either by manipulating the solvent or by tailoring the surface chemistry of the nanoparticles through functionalization with a monolayer of oligomer chains. Since it is not known how these functionalized coatings affect the interactions between nanoparticles and with the surrounding solvent, we present results from a series of molecular dynamics simulations of polyethylene oxide (PEO) coated silica nanoparticles of varying size (5 to 20 nm diameter) in water. For a single nanoparticle we determined the Stokes drag on the nanoparticle as it moves through the solvent and as it approaches a wall. Due to hydrodynamic interactions there are large finite size effects which we estimate by varying the size of the simulation cell. We also determined both solvent-mediated (velocity-independent) and lubrication (velocity-dependent) forces between two nanoparticles as a function of the coverage and chain length of the PEO chains.

Forecasting nonlinear chaotic time series with function expression method based on an improved genetic-simulated annealing algorithm.

PubMed

Wang, Jun; Zhou, Bi-hua; Zhou, Shu-dao; Sheng, Zheng

2015-01-01

The paper proposes a novel function expression method to forecast chaotic time series, using an improved genetic-simulated annealing (IGSA) algorithm to establish the optimum function expression that describes the behavior of time series. In order to deal with the weakness associated with the genetic algorithm, the proposed algorithm incorporates the simulated annealing operation which has the strong local search ability into the genetic algorithm to enhance the performance of optimization; besides, the fitness function and genetic operators are also improved. Finally, the method is applied to the chaotic time series of Quadratic and Rossler maps for validation. The effect of noise in the chaotic time series is also studied numerically. The numerical results verify that the method can forecast chaotic time series with high precision and effectiveness, and the forecasting precision with certain noise is also satisfactory. It can be concluded that the IGSA algorithm is energy-efficient and superior.

Oxygen reduction on a Pt(111) catalyst in HT-PEM fuel cells by density functional theory

NASA Astrophysics Data System (ADS)

Sun, Hong; Li, Jie; Almheiri, Saif; Xiao, Jianyu

2017-08-01

The oxygen reduction reaction plays an important role in the performance of high-temperature proton exchange membrane (HT-PEM) fuel cells. In this study, a molecular dynamics model, which is based on the density functional theory and couples the system's energy, the exchange-correlation energy functional, the charge density distribution function, and the simplified Kohn-Sham equation, was developed to simulate the oxygen reduction reaction on a Pt(111) surface. Additionally, an electrochemical reaction system on the basis of a four-electron reaction mechanism was also developed for this simulation. The reaction path of the oxygen reduction reaction, the product structure of each reaction step and the system's energy were simulated. It is found that the first step reaction of the first hydrogen ion with the oxygen molecule is the controlling step of the overall reaction. Increasing the operating temperature speeds up the first step reaction rate and slightly decreases its reaction energy barrier. Our results provide insight into the working principles of HT-PEM fuel cells.

New Insights on the White Dwarf Luminosity and Mass Functions from the LSS-GAC Survey

NASA Astrophysics Data System (ADS)

Rebassa-Mansergas, Alberto; Liu, Xiaowei; Cojocaru, Ruxandra; Torres, Santiago; García–Berro, Enrique; Yuan, Haibo; Huang, Yang; Xiang, Maosheng

2015-06-01

The white dwarf (WD) population observed in magnitude-limited surveys can be used to derive the luminosity function (LF) and mass function (MF), once the corresponding volume corrections are employed. However, the WD samples from which the observational LFs and MFs are built are the result of complicated target selection algorithms. Thus, it is difficult to quantify the effects of the observational biases on the observed functions. The LAMOST (Large sky Area Multi-Object fiber Spectroscopic Telescope) spectroscopic survey of the Galactic anti-center (LSS-GAC) has well-defined selection criteria. This is a noticeable advantage over previous surveys. Here we derive the WD LF and MF of the LSS-GAC, and use a Monte Carlo code to simulate the WD population in the Galactic anti-center. We apply the well-defined LSS-GAC selection criteria to the simulated populations, taking into account all observational biases, and perform the first meaningful comparison between the simulated WD LFs and MFs and the observed ones.

First-Principles Molecular Dynamics Simulations of NaCl in Water: Performance of Advanced Exchange-Correlation Approximations in Density Functional Theory

NASA Astrophysics Data System (ADS)

Yao, Yi; Kanai, Yosuke

Our ability to correctly model the association of oppositely charged ions in water is fundamental in physical chemistry and essential to various technological and biological applications of molecular dynamics (MD) simulations. MD simulations using classical force fields often show strong clustering of NaCl in the aqueous ionic solutions as a consequence of a deep contact pair minimum in the potential of mean force (PMF) curve. First-Principles Molecular Dynamics (FPMD) based on Density functional theory (DFT) with the popular PBE exchange-correlation approximation, on the other hand, show a different result with a shallow contact pair minimum in the PMF. We employed two of most promising exchange-correlation approximations, ωB97xv by Mardiorossian and Head-Gordon and SCAN by Sun, Ruzsinszky and Perdew, to examine the PMF using FPMD simulations. ωB97xv is highly empirically and optimized in the space of range-separated hybrid functional with a dispersion correction while SCAN is the most recent meta-GGA functional that is constructed by satisfying various known conditions in well-defined physical limits. We will discuss our findings for PMF, charge transfer, water dipoles, etc.

Self-Consistent Determination of Atomic Charges of Ionic Liquid through a Combination of Molecular Dynamics Simulation and Density Functional Theory.

PubMed

Ishizuka, Ryosuke; Matubayasi, Nobuyuki

2016-02-09

A self-consistent scheme is developed to determine the atomic partial charges of ionic liquid. Molecular dynamics (MD) simulation was conducted to sample a set of ion configurations, and these configurations were subject to density functional theory (DFT) calculations to determine the partial charges. The charges were then averaged and used as inputs for the subsequent MD simulation, and MD and DFT calculations were repeated until the MD results are not altered any more. We applied this scheme to 1,3-dimethylimidazolium bis(trifluoromethylsulfonyl) imide ([C1mim][NTf2]) and investigated its structure and dynamics as a function of temperature. At convergence, the average ionic charges were ±0.84 e at 350 K due to charge transfer among ions, where e is the elementary charge, while the reduced ionic charges do not affect strongly the density of [C1mim][NTf2] and radial distribution function. Instead, major effects are found on the energetics and dynamics, with improvements of the overestimated heat of vaporization and the too slow motions of ions observed in MD simulations using commonly used force fields.

Crossflow-Vortex Breakdown on Swept Wings: Correlation of Nonlinear Physics

NASA Technical Reports Server (NTRS)

Joslin, R. D.; Streett, C. L.

1994-01-01

The spatial evolution of cross flow-vortex packets in a laminar boundary layer on a swept wing are computed by the direct numerical simulation of the incompressible Navier- Stokes equations. A wall-normal velocity distribution of steady suction and blowing at the wing surface is used to generate a strip of equally spaced and periodic disturbances along the span. Three simulations are conducted to study the effect of initial amplitude on the disturbance evolution, to determine the role of traveling cross ow modes in transition, and to devise a correlation function to guide theories of transition prediction. In each simulation, the vortex packets first enter a chordwise region of linear independent growth, then, the individual packets coalesce downstream and interact with adjacent packets, and, finally, the vortex packets nonlinearly interact to generate inflectional velocity profiles. As the initial amplitude of the disturbance is increased, the length of the evolution to breakdown decreases. For this pressure gradient, stationary modes dominate the disturbance evolution. A two-coeffcient function was devised to correlate the simulation results. The coefficients, combined with a single simulation result, provide sufficient information to generate the evolution pattern for disturbances of any initial amplitude.

Software aspects of the Geant4 validation repository

NASA Astrophysics Data System (ADS)

Dotti, Andrea; Wenzel, Hans; Elvira, Daniel; Genser, Krzysztof; Yarba, Julia; Carminati, Federico; Folger, Gunter; Konstantinov, Dmitri; Pokorski, Witold; Ribon, Alberto

2017-10-01

The Geant4, GeantV and GENIE collaborations regularly perform validation and regression tests for simulation results. DoSSiER (Database of Scientific Simulation and Experimental Results) is being developed as a central repository to store the simulation results as well as the experimental data used for validation. DoSSiER is easily accessible via a web application. In addition, a web service allows for programmatic access to the repository to extract records in JSON or XML exchange formats. In this article, we describe the functionality and the current status of various components of DoSSiER as well as the technology choices we made.

Software Aspects of the Geant4 Validation Repository

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

Dotti, Andrea; Wenzel, Hans; Elvira, Daniel

2016-01-01

The Geant4, GeantV and GENIE collaborations regularly perform validation and regression tests for simulation results. DoSSiER (Database of Scientic Simulation and Experimental Results) is being developed as a central repository to store the simulation results as well as the experimental data used for validation. DoSSiER is easily accessible via a web application. In addition, a web service allows for programmatic access to the repository to extract records in JSON or XML exchange formats. In this article, we describe the functionality and the current status of various components of DoSSiER as well as the technology choices we made.

A Wigner-based ray-tracing method for imaging simulations

NASA Astrophysics Data System (ADS)

Mout, B. M.; Wick, M.; Bociort, F.; Urbach, H. P.

2015-09-01

The Wigner Distribution Function (WDF) forms an alternative representation of the optical field. It can be a valuable tool for understanding and classifying optical systems. Furthermore, it possesses properties that make it suitable for optical simulations: both the intensity and the angular spectrum can be easily obtained from the WDF and the WDF remains constant along the paths of paraxial geometrical rays. In this study we use these properties by implementing a numerical Wigner-Based Ray-Tracing method (WBRT) to simulate diffraction effects at apertures in free-space and in imaging systems. Both paraxial and non-paraxial systems are considered and the results are compared with numerical implementations of the Rayleigh-Sommerfeld and Fresnel diffraction integrals to investigate the limits of the applicability of this approach. The results of the different methods are in good agreement when simulating free-space diffraction or calculating point spread functions (PSFs) for aberration-free imaging systems, even at numerical apertures exceeding the paraxial regime. For imaging systems with aberrations, the PSFs of WBRT diverge from the results using diffraction integrals. For larger aberrations WBRT predicts negative intensities, suggesting that this model is unable to deal with aberrations.

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

NASA Astrophysics Data System (ADS)

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

2014-02-01

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

Applications of New Surrogate Global Optimization Algorithms including Efficient Synchronous and Asynchronous Parallelism for Calibration of Expensive Nonlinear Geophysical Simulation Models.

NASA Astrophysics Data System (ADS)

Shoemaker, C. A.; Pang, M.; Akhtar, T.; Bindel, D.

2016-12-01

New parallel surrogate global optimization algorithms are developed and applied to objective functions that are expensive simulations (possibly with multiple local minima). The algorithms can be applied to most geophysical simulations, including those with nonlinear partial differential equations. The optimization does not require simulations be parallelized. Asynchronous (and synchronous) parallel execution is available in the optimization toolbox "pySOT". The parallel algorithms are modified from serial to eliminate fine grained parallelism. The optimization is computed with open source software pySOT, a Surrogate Global Optimization Toolbox that allows user to pick the type of surrogate (or ensembles), the search procedure on surrogate, and the type of parallelism (synchronous or asynchronous). pySOT also allows the user to develop new algorithms by modifying parts of the code. In the applications here, the objective function takes up to 30 minutes for one simulation, and serial optimization can take over 200 hours. Results from Yellowstone (NSF) and NCSS (Singapore) supercomputers are given for groundwater contaminant hydrology simulations with applications to model parameter estimation and decontamination management. All results are compared with alternatives. The first results are for optimization of pumping at many wells to reduce cost for decontamination of groundwater at a superfund site. The optimization runs with up to 128 processors. Superlinear speed up is obtained for up to 16 processors, and efficiency with 64 processors is over 80%. Each evaluation of the objective function requires the solution of nonlinear partial differential equations to describe the impact of spatially distributed pumping and model parameters on model predictions for the spatial and temporal distribution of groundwater contaminants. The second application uses an asynchronous parallel global optimization for groundwater quality model calibration. The time for a single objective function evaluation varies unpredictably, so efficiency is improved with asynchronous parallel calculations to improve load balancing. The third application (done at NCSS) incorporates new global surrogate multi-objective parallel search algorithms into pySOT and applies it to a large watershed calibration problem.

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

Keefer, Donald A.; Shaffer, Eric G.; Storsved, Brynne

A free software application, RVA, has been developed as a plugin to the US DOE-funded ParaView visualization package, to provide support in the visualization and analysis of complex reservoirs being managed using multi-fluid EOR techniques. RVA, for Reservoir Visualization and Analysis, was developed as an open-source plugin to the 64 bit Windows version of ParaView 3.14. RVA was developed at the University of Illinois at Urbana-Champaign, with contributions from the Illinois State Geological Survey, Department of Computer Science and National Center for Supercomputing Applications. RVA was designed to utilize and enhance the state-of-the-art visualization capabilities within ParaView, readily allowing jointmore » visualization of geologic framework and reservoir fluid simulation model results. Particular emphasis was placed on enabling visualization and analysis of simulation results highlighting multiple fluid phases, multiple properties for each fluid phase (including flow lines), multiple geologic models and multiple time steps. Additional advanced functionality was provided through the development of custom code to implement data mining capabilities. The built-in functionality of ParaView provides the capacity to process and visualize data sets ranging from small models on local desktop systems to extremely large models created and stored on remote supercomputers. The RVA plugin that we developed and the associated User Manual provide improved functionality through new software tools, and instruction in the use of ParaView-RVA, targeted to petroleum engineers and geologists in industry and research. The RVA web site (http://rva.cs.illinois.edu) provides an overview of functions, and the development web site (https://github.com/shaffer1/RVA) provides ready access to the source code, compiled binaries, user manual, and a suite of demonstration data sets. Key functionality has been included to support a range of reservoirs visualization and analysis needs, including: sophisticated connectivity analysis, cross sections through simulation results between selected wells, simplified volumetric calculations, global vertical exaggeration adjustments, ingestion of UTChem simulation results, ingestion of Isatis geostatistical framework models, interrogation of joint geologic and reservoir modeling results, joint visualization and analysis of well history files, location-targeted visualization, advanced correlation analysis, visualization of flow paths, and creation of static images and animations highlighting targeted reservoir features.« less

RVA: A Plugin for ParaView 3.14

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

2015-09-04

RVA is a plugin developed for the 64-bit Windows version of the ParaView 3.14 visualization package. RVA is designed to provide support in the visualization and analysis of complex reservoirs being managed using multi-fluid EOR techniques. RVA, for Reservoir Visualization and Analysis, was developed at the University of Illinois at Urbana-Champaign, with contributions from the Illinois State Geological Survey, Department of Computer Science and National Center for Supercomputing Applications. RVA was designed to utilize and enhance the state-of-the-art visualization capabilities within ParaView, readily allowing joint visualization of geologic framework and reservoir fluid simulation model results. Particular emphasis was placed onmore » enabling visualization and analysis of simulation results highlighting multiple fluid phases, multiple properties for each fluid phase (including flow lines), multiple geologic models and multiple time steps. Additional advanced functionality was provided through the development of custom code to implement data mining capabilities. The built-in functionality of ParaView provides the capacity to process and visualize data sets ranging from small models on local desktop systems to extremely large models created and stored on remote supercomputers. The RVA plugin that we developed and the associated User Manual provide improved functionality through new software tools, and instruction in the use of ParaView-RVA, targeted to petroleum engineers and geologists in industry and research. The RVA web site (http://rva.cs.illinois.edu) provides an overview of functions, and the development web site (https://github.com/shaffer1/RVA) provides ready access to the source code, compiled binaries, user manual, and a suite of demonstration data sets. Key functionality has been included to support a range of reservoirs visualization and analysis needs, including: sophisticated connectivity analysis, cross sections through simulation results between selected wells, simplified volumetric calculations, global vertical exaggeration adjustments, ingestion of UTChem simulation results, ingestion of Isatis geostatistical framework models, interrogation of joint geologic and reservoir modeling results, joint visualization and analysis of well history files, location-targeted visualization, advanced correlation analysis, visualization of flow paths, and creation of static images and animations highlighting targeted reservoir features.« less

Implementation of the vortex force formalism in the coupled ocean-atmosphere-wave-sediment transport (COAWST) modeling system for inner shelf and surf zone applications

USGS Publications Warehouse

Kumar, Nirnimesh; Voulgaris, George; Warner, John C.; Olabarrieta, Maitane

2012-01-01

Model results from the planar beach case show good agreement with depth-averaged analytical solutions and with theoretical flow structures. Simulation results for the DUCK' 94 experiment agree closely with measured profiles of cross-shore and longshore velocity data from and . Diagnostic simulations showed that the nonlinear processes of wave roller generation and wave-induced mixing are important for the accurate simulation of surf zone flows. It is further recommended that a more realistic approach for determining the contribution of wave rollers and breaking induced turbulent mixing can be formulated using non-dimensional parameters which are functions of local wave parameters and the beach slope. Dominant terms in the cross-shore momentum balance are found to be the quasi-static pressure gradient and breaking acceleration. In the alongshore direction, bottom stress, breaking acceleration, horizontal advection and horizontal vortex forces dominate the momentum balance. The simulation results for the bar/rip channel morphology case clearly show the ability of the modeling system to reproduce horizontal and vertical circulation patterns similar to those found in laboratory studies and to numerical simulations using the radiation stress representation. The vortex force term is found to be more important at locations where strong flow vorticity interacts with the wave-induced Stokes flow field. Outside the surf zone, the three-dimensional model simulations of wave-induced flows for non-breaking waves closely agree with flow observations from MVCO, with the vertical structure of the simulated flow varying as a function of the vertical viscosity as demonstrated by Lentz et al. (2008).

Static tool influence function for fabrication simulation of hexagonal mirror segments for extremely large telescopes.

PubMed

Kim, Dae Wook; Kim, Sug-Whan

2005-02-07

We present a novel simulation technique that offers efficient mass fabrication strategies for 2m class hexagonal mirror segments of extremely large telescopes. As the first of two studies in series, we establish the theoretical basis of the tool influence function (TIF) for precessing tool polishing simulation for non-rotating workpieces. These theoretical TIFs were then used to confirm the reproducibility of the material removal foot-prints (measured TIFs) of the bulged precessing tooling reported elsewhere. This is followed by the reverse-computation technique that traces, employing the simplex search method, the real polishing pressure from the empirical TIF. The technical details, together with the results and implications described here, provide the theoretical tool for material removal essential to the successful polishing simulation which will be reported in the second study.

Molecular Dynamics Study of Thermally Augmented Nanodroplet Motion on Chemical Energy Induced Wettability Gradient Surfaces.

PubMed

Chakraborty, Monojit; Chowdhury, Anamika; Bhusan, Richa; DasGupta, Sunando

2015-10-20

Droplet motion on a surface with chemical energy induced wettability gradient has been simulated using molecular dynamics (MD) simulation to highlight the underlying physics of molecular movement near the solid-liquid interface including the contact line friction. The simulations mimic experiments in a comprehensive manner wherein microsized droplets are propelled by the surface wettability gradient against forces opposed to motion. The liquid-wall Lennard-Jones interaction parameter and the substrate temperature are varied to explore their effects on the three-phase contact line friction coefficient. The contact line friction is observed to be a strong function of temperature at atomistic scales, confirming their experimentally observed inverse functionality. Additionally, the MD simulation results are successfully compared with those from an analytical model for self-propelled droplet motion on gradient surfaces.

Spectral solver for multi-scale plasma physics simulations with dynamically adaptive number of moments

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

Vencels, Juris; Delzanno, Gian Luca; Johnson, Alec

2015-06-01

A spectral method for kinetic plasma simulations based on the expansion of the velocity distribution function in a variable number of Hermite polynomials is presented. The method is based on a set of non-linear equations that is solved to determine the coefficients of the Hermite expansion satisfying the Vlasov and Poisson equations. In this paper, we first show that this technique combines the fluid and kinetic approaches into one framework. Second, we present an adaptive strategy to increase and decrease the number of Hermite functions dynamically during the simulation. The technique is applied to the Landau damping and two-stream instabilitymore » test problems. Performance results show 21% and 47% saving of total simulation time in the Landau and two-stream instability test cases, respectively.« less

Plasmonic resonances of nanoparticles from large-scale quantum mechanical simulations

NASA Astrophysics Data System (ADS)

Zhang, Xu; Xiang, Hongping; Zhang, Mingliang; Lu, Gang

2017-09-01

Plasmonic resonance of metallic nanoparticles results from coherent motion of its conduction electrons, driven by incident light. For the nanoparticles less than 10 nm in diameter, localized surface plasmonic resonances become sensitive to the quantum nature of the conduction electrons. Unfortunately, quantum mechanical simulations based on time-dependent Kohn-Sham density functional theory are computationally too expensive to tackle metal particles larger than 2 nm. Herein, we introduce the recently developed time-dependent orbital-free density functional theory (TD-OFDFT) approach which enables large-scale quantum mechanical simulations of plasmonic responses of metallic nanostructures. Using TD-OFDFT, we have performed quantum mechanical simulations to understand size-dependent plasmonic response of Na nanoparticles and plasmonic responses in Na nanoparticle dimers and trimers. An outlook of future development of the TD-OFDFT method is also presented.

Methodology for functional MRI of simulated driving.

PubMed

Kan, Karen; Schweizer, Tom A; Tam, Fred; Graham, Simon J

2013-01-01

The developed world faces major socioeconomic and medical challenges associated with motor vehicle accidents caused by risky driving. Functional magnetic resonance imaging (fMRI) of individuals using virtual reality driving simulators may provide an important research tool to assess driving safety, based on brain activity and behavior. A fMRI-compatible driving simulator was developed and evaluated in the context of straight driving, turning, and stopping in 16 young healthy adults. Robust maps of brain activity were obtained, including activation of the primary motor cortex, cerebellum, visual cortex, and parietal lobe, with limited head motion (<1.5 mm deviation from mean head position in the superior∕inferior direction in all subjects) and only minor correlations between head motion, steering, or braking behavior. These results are consistent with previous literature and suggest that with care, fMRI of simulated driving is a feasible undertaking.

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.

A review: Functional near infrared spectroscopy evaluation in muscle tissues using Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Halim, A. A. A.; Laili, M. H.; Salikin, M. S.; Rusop, M.

2018-05-01

Monte Carlo Simulation has advanced their quantification based on number of the photon counting to solve the propagation of light inside the tissues including the absorption, scattering coefficient and act as preliminary study for functional near infrared application. The goal of this paper is to identify the optical properties using Monte Carlo simulation for non-invasive functional near infrared spectroscopy (fNIRS) evaluation of penetration depth in human muscle. This paper will describe the NIRS principle and the basis for its proposed used in Monte Carlo simulation which focused on several important parameters include ATP, ADP and relate with blow flow and oxygen content at certain exercise intensity. This will cover the advantages and limitation of such application upon this simulation. This result may help us to prove that our human muscle is transparent to this near infrared region and could deliver a lot of information regarding to the oxygenation level in human muscle. Thus, this might be useful for non-invasive technique for detecting oxygen status in muscle from living people either athletes or working people and allowing a lots of investigation muscle physiology in future.

Parameterization of backbone flexibility in a coarse-grained force field for proteins (COFFDROP) derived from all-atom explicit-solvent molecular dynamics simulations of all possible two-residue peptides

PubMed Central

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

2015-01-01

Recently, we reported the parameterization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs, and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downwards in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multi-domain proteins connected by flexible linkers. PMID:26574429

Mathematic simulation of soil-vegetation condition and land use structure applying basin approach

NASA Astrophysics Data System (ADS)

Mishchenko, Natalia; Shirkin, Leonid; Krasnoshchekov, Alexey

2016-04-01

Ecosystems anthropogenic transformation is basically connected to the changes of land use structure and human impact on soil fertility. The Research objective is to simulate the stationary state of river basins ecosystems. Materials and Methods. Basin approach has been applied in the research. Small rivers basins of the Klyazma river have been chosen as our research objects. They are situated in the central part of the Russian plain. The analysis is carried out applying integrated characteristics of ecosystems functioning and mathematic simulation methods. To design mathematic simulator functional simulation methods and principles on the basis of regression, correlation and factor analysis have been applied in the research. Results. Mathematic simulation resulted in defining possible permanent conditions of "phytocenosis-soil" system in coordinates of phytomass, phytoproductivity, humus percentage in soil. Ecosystem productivity is determined not only by vegetation photosynthesis activity but also by the area ratio of forest and meadow phytocenosis. Local maximums attached to certain phytomass areas and humus content in soil have been defined on the basin phytoproductivity distribution diagram. We explain the local maximum by synergetic effect. It appears with the definite ratio of forest and meadow phytocenosis. In this case, utmost values of phytomass for the whole area are higher than just a sum of utmost values of phytomass for the forest and meadow phytocenosis. Efficient correlation of natural forest and meadow phytocenosis has been defined for the Klyazma river. Conclusion. Mathematic simulation methods assist in forecasting the ecosystem conditions under various changes of land use structure. Nowadays overgrowing of the abandoned agricultural lands is very actual for the Russian Federation. Simulation results demonstrate that natural ratio of forest and meadow phytocenosis for the area will restore during agricultural overgrowing.

An energy-circuit population model for great egrets (Ardea alba) at Lake Okeechobee, Florida, U.S.A

USGS Publications Warehouse

Smith, Jeff P.

1997-01-01

I simulated the annual population cycles of Great Egrets (Ardea alba) at Lake Okeechobee, Florida, to provide a framework for evaluating the local population dynamics of nesting and foraging wading birds. The external forcing functions were solar energy, minimum air temperature, water depth, surface-water drying rate, and season. Solar input controlled the production of prey at moderate to high lake stages, but water area exerted primary control during a two-year drought. Modeling prey production as a linear function of water area resulted in underestimation of prey density during the drought, suggesting that prey organisms maintained high fecundity while concentrated in submerged vegetation at the lakeward fringe of the littoral zone. Simulation confirmed that large influxes of wading birds during the drought were the combined result of a regional refuge response and the availability of concentrated prey. Modeling immigration and emigration as primarily functions of the surface-water drying rate, rather than lake stage, resulted in a closer match of observed and simulated population trends for foraging birds, suggesting that the pattern of surface-water fluctuations was a more important factor than water depth. Simulation indicated an abrupt-threshold response rather than a linear association between foraging efficiency and low temperatures, which reduce activity levels of forage fishes. Great Egret breeder recruitment is primarily a function of prey availability, climate, and hydrologic trends, but simulation confirmed the concurrent involvement of a seasonal or physiological-readiness factor. An attractor function driven by high winter lake stages was necessary to reproduce observed patterns of breeder recruitment, suggesting that Great Egrets initiate nesting based on environmental cues that lead to peak food availability when nestlings are present. Poor correspondence of reproductive effort and nest productivity suggested that the drought compromised the birds' predictive abilities. The need to model breeder recruitment as a function of a maximum rate rather than the size of the local foraging population suggested that birds may nest on the lake even though on-lake foraging conditions are poor. Simulated and observed estimates of egg and hatching production did not match, suggesting that the causes of failure during incubation were complex or more localized than could be accounted for with lakewide hydrologic and climatic data. A forced increase in prey consumption of 12% was necessary to reproduce observed, high levels of nest productivity in 1990, which corresponded to the finding that panhandled fish constituted 10–12% of the biomass fed to Great Egret nestlings that year.

Tire-rim interface pressure of a commercial vehicle wheel under radial loads: theory and experiment

NASA Astrophysics Data System (ADS)

Wan, Xiaofei; Shan, Yingchun; Liu, Xiandong; He, Tian; Wang, Jiegong

2017-11-01

The simulation of the radial fatigue test of a wheel has been a necessary tool to improve the design of the wheel and calculate its fatigue life. The simulation model, including the strong nonlinearity of the tire structure and material, may produce accurate results, but often leads to a divergence in calculation. Thus, a simplified simulation model in which the complicated tire model is replaced with a tire-wheel contact pressure model is used extensively in the industry. In this paper, a simplified tire-rim interface pressure model of a wheel under a radial load is established, and the pressure of the wheel under different radial loads is tested. The tire-rim contact behavior affected by the radial load is studied and analyzed according to the test result, and the tire-rim interface pressure extracted from the test result is used to evaluate the simplified pressure model and the traditional cosine function model. The results show that the proposed model may provide a more accurate prediction of the wheel radial fatigue life than the traditional cosine function model.

Effects of system size and cooling rate on the structure and properties of sodium borosilicate glasses from molecular dynamics simulations.

PubMed

Deng, Lu; Du, Jincheng

2018-01-14

Borosilicate glasses form an important glass forming system in both glass science and technologies. The structure and property changes of borosilicate glasses as a function of thermal history in terms of cooling rate during glass formation and simulation system sizes used in classical molecular dynamics (MD) simulation were investigated with recently developed composition dependent partial charge potentials. Short and medium range structural features such as boron coordination, Si and B Q n distributions, and ring size distributions were analyzed to elucidate the effects of cooling rate and simulation system size on these structure features and selected glass properties such as glass transition temperature, vibration density of states, and mechanical properties. Neutron structure factors, neutron broadened pair distribution functions, and vibrational density of states were calculated and compared with results from experiments as well as ab initio calculations to validate the structure models. The results clearly indicate that both cooling rate and system size play an important role on the structures of these glasses, mainly by affecting the 3 B and 4 B distributions and consequently properties of the glasses. It was also found that different structure features and properties converge at different sizes or cooling rates; thus convergence tests are needed in simulations of the borosilicate glasses depending on the targeted properties. The results also shed light on the complex thermal history dependence on structure and properties in borosilicate glasses and the protocols in MD simulations of these and other glass materials.

Effects of system size and cooling rate on the structure and properties of sodium borosilicate glasses from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Deng, Lu; Du, Jincheng

2018-01-01

Borosilicate glasses form an important glass forming system in both glass science and technologies. The structure and property changes of borosilicate glasses as a function of thermal history in terms of cooling rate during glass formation and simulation system sizes used in classical molecular dynamics (MD) simulation were investigated with recently developed composition dependent partial charge potentials. Short and medium range structural features such as boron coordination, Si and B Qn distributions, and ring size distributions were analyzed to elucidate the effects of cooling rate and simulation system size on these structure features and selected glass properties such as glass transition temperature, vibration density of states, and mechanical properties. Neutron structure factors, neutron broadened pair distribution functions, and vibrational density of states were calculated and compared with results from experiments as well as ab initio calculations to validate the structure models. The results clearly indicate that both cooling rate and system size play an important role on the structures of these glasses, mainly by affecting the 3B and 4B distributions and consequently properties of the glasses. It was also found that different structure features and properties converge at different sizes or cooling rates; thus convergence tests are needed in simulations of the borosilicate glasses depending on the targeted properties. The results also shed light on the complex thermal history dependence on structure and properties in borosilicate glasses and the protocols in MD simulations of these and other glass materials.

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.

An Integrated Study on a Novel High Temperature High Entropy Alloy

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

Yang, Shizhong

2016-12-31

This report summarizes our recent works of theoretical modeling, simulation, and experimental validation of the simulation results on the new refractory high entropy alloy (HEA) design and oxide doped refractory HEA research. The simulation of the stability and thermal dynamics simulation on potential thermal stable candidates were performed and related HEA with oxide doped samples were synthesized and characterized. The HEA ab initio density functional theory and molecular dynamics physical property simulation methods and experimental texture validation techniques development, achievements already reached, course work development, students and postdoc training, and future improvement research directions are briefly introduced.

Scaling effects in direct shear tests

USGS Publications Warehouse

Orlando, A.D.; Hanes, D.M.; Shen, H.H.

2009-01-01

Laboratory experiments of the direct shear test were performed on spherical particles of different materials and diameters. Results of the bulk friction vs. non-dimensional shear displacement are presented as a function of the non-dimensional particle diameter. Simulations of the direct shear test were performed using the Discrete Element Method (DEM). The simulation results show Considerable differences with the physical experiments. Particle level material properties, such as the coefficients of static friction, restitution and rolling friction need to be known a priori in order to guarantee that the simulation results are an accurate representation of the physical phenomenon. Furthermore, laboratory results show a clear size dependency on the results, with smaller particles having a higher bulk friction than larger ones. ?? 2009 American Institute of Physics.

New functionalized IRMOF-10 with strong affinity for methanol: A simulation study

NASA Astrophysics Data System (ADS)

Liu, Zewei; Zhang, Kai; Wu, Ying; Xi, Hongxia

2018-05-01

Grand Canonical Monte Carlo (GCMC) method simulation combined with density functional theory (DFT) calculation were used to investigate the methanol adsorption in IRMOF-10, with nitrogen and metal-doping functionalizations in order to understand the underlying performance of MOFs in methanol adsorption. New doped IRMOF-10s (M-2N-IRMOF-10, M = Be, Mg, Ca, Sr, Ba) were theoretically constructed by binding nitrogen atoms of organic linkers in N-doping IRMOF-10 (2N-IRMOF-10) with various metal atoms. 2N-IRMOF-10 shows only a little higher methanol capacity in the measured pressure range. However, M-2N-IRMOF-10s (especially Be-2N-IRMOF-10) demonstrate much higher methanol capacity due to the stronger interaction between the induced Be atoms and methanol molecules. Furthermore, the obtained results can be attributed to the new adsorption sites created by metal-doping, as revealed by the more exothermic binding energies (BEs) on Be-sites (-160.8 kJ/mol) than Zn-sites (-19.4 kJ/mol). According to the simulation results, it can be concluded that functionalized IRMOF-10 are capable of enhancing the adsorption capacity of methanol at pressure from 0 to 12 kPa at 298 K. This study provides a new functionalized method to effectively enhance methanol adsorption capacity of MOFs, which might extend the application of MOFs on methanol adsorption in the near future.

Effect of simulated rill erosion on overland flow connectivity in synthetically generated fields

NASA Astrophysics Data System (ADS)

Penuela Fernandez, Andres; Rocio Rodriguez Pleguezuelo, Carmen; Javaux, Mathieu; Bielders, Charles L.

2014-05-01

Preferential flow paths developed during rill erosion processes connect different parts of the soil surface that may increase the degree of connectivity and hence the hydrological response of the soil surface. However, few studies have tried to quantify the effect of rill networks on overland flow connectivity. For this purpose, simulated rill networks were generated by the RillGrow erosion model (Favis-Mortlock, 1998; Favis-Mortlock et al. 2000) on synthetically generated fields. To characterize the hydrological connectivity a functional connectivity indicator called the relative surface connection function (RSCf) (Antoine et al. 2009) was used. This indicator, which relates the area connected to the outflow boundary to the degree of filling of maximum depression storage (MDS), is fast to compute and was previously shown to be able to efficiently discriminate between contrasted connectivity scenarios. The RSCf function was calculated for different DEM obtained at different times during the development of the simulated rill networks. The evolution of overland flow connectivity was then quantified and compared at these different time steps. The results of this study showed that the changes in microtopography resulting from the simulated rill erosion have a strong impact on the hydrological connectivity as reflected in the RSCf. Furthermore, the results show that the evolution of the RSCf may allow identifying different types of erosion since the shape of the RSCf only starts to change when rill networks are visualized on the surface.

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

The construction of general basis functions in reweighting ensemble dynamics simulations: Reproduce equilibrium distribution in complex systems from multiple short simulation trajectories

NASA Astrophysics Data System (ADS)

Zhang, Chuan-Biao; Ming, Li; Xin, Zhou

2015-12-01

Ensemble simulations, which use multiple short independent trajectories from dispersive initial conformations, rather than a single long trajectory as used in traditional simulations, are expected to sample complex systems such as biomolecules much more efficiently. The re-weighted ensemble dynamics (RED) is designed to combine these short trajectories to reconstruct the global equilibrium distribution. In the RED, a number of conformational functions, named as basis functions, are applied to relate these trajectories to each other, then a detailed-balance-based linear equation is built, whose solution provides the weights of these trajectories in equilibrium distribution. Thus, the sufficient and efficient selection of basis functions is critical to the practical application of RED. Here, we review and present a few possible ways to generally construct basis functions for applying the RED in complex molecular systems. Especially, for systems with less priori knowledge, we could generally use the root mean squared deviation (RMSD) among conformations to split the whole conformational space into a set of cells, then use the RMSD-based-cell functions as basis functions. We demonstrate the application of the RED in typical systems, including a two-dimensional toy model, the lattice Potts model, and a short peptide system. The results indicate that the RED with the constructions of basis functions not only more efficiently sample the complex systems, but also provide a general way to understand the metastable structure of conformational space. Project supported by the National Natural Science Foundation of China (Grant No. 11175250).

MioLab, a rat cardiac contractile force simulator: Applications to teaching cardiac cell physiology and biophysics.

PubMed

da Silva, Robson Rodrigues; Bissaco, Marcia Aparecida Silva; Goroso, Daniel Gustavo

2015-12-01

Understanding the basic concepts of physiology and biophysics of cardiac cells can be improved by virtual experiments that illustrate the complex excitation-contraction coupling process in cardiac cells. The aim of this study is to propose a rat cardiac myocyte simulator, with which calcium dynamics in excitation-contraction coupling of an isolated cell can be observed. This model has been used in the course "Mathematical Modeling and Simulation of Biological Systems". In this paper we present the didactic utility of the simulator MioLab(®). The simulator enables virtual experiments that can help studying inhibitors and activators in the sarcoplasmic reticulum sodium-calcium exchanger, thus corroborating a better understanding of the effects of medications, which are used to treat arrhythmias, on these compartments. The graphical interfaces were developed not only to facilitate the use of the simulator, but also to promote a constructive learning on the subject, since there are animations and videos for each stage of the simulation. The effectiveness of the simulator was tested by a group of graduate students. Some examples of simulations were presented in order to describe the overall structure of the simulator. Part of these virtual experiments became an activity for Biomedical Engineering graduate students, who evaluated the simulator based on its didactic quality. As a result, students answered a questionnaire on the usability and functionality of the simulator as a teaching tool. All students performed the proposed activities and classified the simulator as an optimal or good learning tool. In their written questions, students indicated as negative characteristics some problems with visualizing graphs; as positive characteristics, they indicated the simulator's didactic function, especially tutorials and videos on the topic of this study. The results show that the simulator complements the study of the physiology and biophysics of the cardiac cell. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

A simplified computational memory model from information processing

PubMed Central

Zhang, Lanhua; Zhang, Dongsheng; Deng, Yuqin; Ding, Xiaoqian; Wang, Yan; Tang, Yiyuan; Sun, Baoliang

2016-01-01

This paper is intended to propose a computational model for memory from the view of information processing. The model, called simplified memory information retrieval network (SMIRN), is a bi-modular hierarchical functional memory network by abstracting memory function and simulating memory information processing. At first meta-memory is defined to express the neuron or brain cortices based on the biology and graph theories, and we develop an intra-modular network with the modeling algorithm by mapping the node and edge, and then the bi-modular network is delineated with intra-modular and inter-modular. At last a polynomial retrieval algorithm is introduced. In this paper we simulate the memory phenomena and functions of memorization and strengthening by information processing algorithms. The theoretical analysis and the simulation results show that the model is in accordance with the memory phenomena from information processing view. PMID:27876847

An Exospheric Temperature Model Based On CHAMP Observations and TIEGCM Simulations

NASA Astrophysics Data System (ADS)

Ruan, Haibing; Lei, Jiuhou; Dou, Xiankang; Liu, Siqing; Aa, Ercha

2018-02-01

In this work, thermospheric densities from the accelerometer measurement on board the CHAMP satellite during 2002-2009 and the simulations from the National Center for Atmospheric Research Thermosphere Ionosphere Electrodynamics General Circulation Model (NCAR-TIEGCM) are employed to develop an empirical exospheric temperature model (ETM). The two-dimensional basis functions of the ETM are first provided from the principal component analysis of the TIEGCM simulations. Based on the exospheric temperatures derived from CHAMP thermospheric densities, a global distribution of the exospheric temperatures is reconstructed. A parameterization is conducted for each basis function amplitude as a function of solar-geophysical and seasonal conditions. Thus, the ETM can be utilized to model the thermospheric temperature and mass density under a specified condition. Our results showed that the averaged standard deviation of the ETM is generally less than 10% than approximately 30% in the MSIS model. Besides, the ETM reproduces the global thermospheric evolutions including the equatorial thermosphere anomaly.

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

Sathasivam, Saratha

New activation function is examined for its ability to accelerate the performance of doing logic programming in Hopfield network. This method has a higher capacity and upgrades the neuro symbolic integration. Computer simulations are carried out to validate the effectiveness of the new activation function. Empirical results obtained support our theory.

Coarse-grained hydrodynamics from correlation functions

NASA Astrophysics Data System (ADS)

Palmer, Bruce

2018-02-01

This paper will describe a formalism for using correlation functions between different grid cells as the basis for determining coarse-grained hydrodynamic equations for modeling the behavior of mesoscopic fluid systems. Configurations from a molecular dynamics simulation or other atomistic simulation are projected onto basis functions representing grid cells in a continuum hydrodynamic simulation. Equilibrium correlation functions between different grid cells are evaluated from the molecular simulation and used to determine the evolution operator for the coarse-grained hydrodynamic system. The formalism is demonstrated on a discrete particle simulation of diffusion with a spatially dependent diffusion coefficient. Correlation functions are calculated from the particle simulation and the spatially varying diffusion coefficient is recovered using a fitting procedure.

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

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

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

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

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

DOE PAGES

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

2016-10-17

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

High resolution modelling of soil moisture patterns with TerrSysMP: A comparison with sensor network data

NASA Astrophysics Data System (ADS)

Gebler, S.; Hendricks Franssen, H.-J.; Kollet, S. J.; Qu, W.; Vereecken, H.

2017-04-01

The prediction of the spatial and temporal variability of land surface states and fluxes with land surface models at high spatial resolution is still a challenge. This study compares simulation results using TerrSysMP including a 3D variably saturated groundwater flow model (ParFlow) coupled to the Community Land Model (CLM) of a 38 ha managed grassland head-water catchment in the Eifel (Germany), with soil water content (SWC) measurements from a wireless sensor network, actual evapotranspiration recorded by lysimeters and eddy covariance stations and discharge observations. TerrSysMP was discretized with a 10 × 10 m lateral resolution, variable vertical resolution (0.025-0.575 m), and the following parameterization strategies of the subsurface soil hydraulic parameters: (i) completely homogeneous, (ii) homogeneous parameters for different soil horizons, (iii) different parameters for each soil unit and soil horizon and (iv) heterogeneous stochastic realizations. Hydraulic conductivity and Mualem-Van Genuchten parameters in these simulations were sampled from probability density functions, constructed from either (i) soil texture measurements and Rosetta pedotransfer functions (ROS), or (ii) estimated soil hydraulic parameters by 1D inverse modelling using shuffle complex evolution (SCE). The results indicate that the spatial variability of SWC at the scale of a small headwater catchment is dominated by topography and spatially heterogeneous soil hydraulic parameters. The spatial variability of the soil water content thereby increases as a function of heterogeneity of soil hydraulic parameters. For lower levels of complexity, spatial variability of the SWC was underrepresented in particular for the ROS-simulations. Whereas all model simulations were able to reproduce the seasonal evapotranspiration variability, the poor discharge simulations with high model bias are likely related to short-term ET dynamics and the lack of information about bedrock characteristics and an on-site drainage system in the uncalibrated model. In general, simulation performance was better for the SCE setups. The SCE-simulations had a higher inverse air entry parameter resulting in SWC dynamics in better correspondence with data than the ROS simulations during dry periods. This illustrates that small scale measurements of soil hydraulic parameters cannot be transferred to the larger scale and that interpolated 1D inverse parameter estimates result in an acceptable performance for the catchment.

Suppression of Biodynamic Interference by Adaptive Filtering

NASA Technical Reports Server (NTRS)

Velger, M.; Merhav, S. J.; Grunwald, A. J.

1984-01-01

Preliminary experimental results obtained in moving base simulator tests are presented. Both for pursuit and compensatory tracking tasks, a strong deterioration in tracking performance due to biodynamic interference is found. The use of adaptive filtering is shown to substantially alleviate these effects, resulting in a markedly improved tracking performance and reduction in task difficulty. The effect of simulator motion and of adaptive filtering on human operator describing functions is investigated. Adaptive filtering is found to substantially increase pilot gain and cross-over frequency, implying a more tight tracking behavior. The adaptive filter is found to be effective in particular for high-gain proportional dynamics, low display forcing function power and for pursuit tracking task configurations.

On the Effects of Artificial Feeding on Bee Colony Dynamics: A Mathematical Model

PubMed Central

Paiva, Juliana Pereira Lisboa Mohallem; Paiva, Henrique Mohallem; Esposito, Elisa; Morais, Michelle Manfrini

2016-01-01

This paper proposes a new mathematical model to evaluate the effects of artificial feeding on bee colony population dynamics. The proposed model is based on a classical framework and contains differential equations that describe the changes in the number of hive bees, forager bees, and brood cells, as a function of amounts of natural and artificial food. The model includes the following elements to characterize the artificial feeding scenario: a function to model the preference of the bees for natural food over artificial food; parameters to quantify the quality and palatability of artificial diets; a function to account for the efficiency of the foragers in gathering food under different environmental conditions; and a function to represent different approaches used by the beekeeper to feed the hive with artificial food. Simulated results are presented to illustrate the main characteristics of the model and its behavior under different scenarios. The model results are validated with experimental data from the literature involving four different artificial diets. A good match between simulated and experimental results was achieved. PMID:27875589

Comparison of image deconvolution algorithms on simulated and laboratory infrared images

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

Proctor, D.

1994-11-15

We compare Maximum Likelihood, Maximum Entropy, Accelerated Lucy-Richardson, Weighted Goodness of Fit, and Pixon reconstructions of simple scenes as a function of signal-to-noise ratio for simulated images with randomly generated noise. Reconstruction results of infrared images taken with the TAISIR (Temperature and Imaging System InfraRed) are also discussed.

Effects of Simulation to Teach Students with Disabilities Basic Finance Skills

ERIC Educational Resources Information Center

Rowe, Dawn A.; Test, David W.

2013-01-01

This study used a multiple probe design across participants to examine the effects of classroom simulation using static picture prompts to teach students to make a purchase using a debit card and track expenses by subtracting purchase amounts and adding deposits into a check register. Results demonstrated a functional relation between simulated…

SimEngine v. 1.0

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

Le, Hai D.

2017-03-02

SimEngine provides the core functionalities and components that are key to the development of discrete event simulation tools. These include events, activities, event queues, random number generators, and basic result tracking classes. SimEngine was designed for high performance, integrates seamlessly into any Microsoft .Net development environment, and provides a flexible API for simulation developers.

Full-band quantum simulation of electron devices with the pseudopotential method: Theory, implementation, and applications

NASA Astrophysics Data System (ADS)

Pala, M. G.; Esseni, D.

2018-03-01

This paper presents the theory, implementation, and application of a quantum transport modeling approach based on the nonequilibrium Green's function formalism and a full-band empirical pseudopotential Hamiltonian. We here propose to employ a hybrid real-space/plane-wave basis that results in a significant reduction of the computational complexity compared to a full plane-wave basis. To this purpose, we provide a theoretical formulation in the hybrid basis of the quantum confinement, the self-energies of the leads, and the coupling between the device and the leads. After discussing the theory and the implementation of the new simulation methodology, we report results for complete, self-consistent simulations of different electron devices, including a silicon Esaki diode, a thin-body silicon field effect transistor (FET), and a germanium tunnel FET. The simulated transistors have technologically relevant geometrical features with a semiconductor film thickness of about 4 nm and a channel length ranging from 10 to 17 nm. We believe that the newly proposed formalism may find applications also in transport models based on ab initio Hamiltonians, as those employed in density functional theory methods.

Set-free Markov state model building

NASA Astrophysics Data System (ADS)

Weber, Marcus; Fackeldey, Konstantin; Schütte, Christof

2017-03-01

Molecular dynamics (MD) simulations face challenging problems since the time scales of interest often are much longer than what is possible to simulate; and even if sufficiently long simulations are possible the complex nature of the resulting simulation data makes interpretation difficult. Markov State Models (MSMs) help to overcome these problems by making experimentally relevant time scales accessible via coarse grained representations that also allow for convenient interpretation. However, standard set-based MSMs exhibit some caveats limiting their approximation quality and statistical significance. One of the main caveats results from the fact that typical MD trajectories repeatedly re-cross the boundary between the sets used to build the MSM which causes statistical bias in estimating the transition probabilities between these sets. In this article, we present a set-free approach to MSM building utilizing smooth overlapping ansatz functions instead of sets and an adaptive refinement approach. This kind of meshless discretization helps to overcome the recrossing problem and yields an adaptive refinement procedure that allows us to improve the quality of the model while exploring state space and inserting new ansatz functions into the MSM.

Determining accurate measurements of the growth rate from the galaxy correlation function in simulations

NASA Astrophysics Data System (ADS)

Contreras, Carlos; Blake, Chris; Poole, Gregory B.; Marin, Felipe

2013-04-01

We use high-resolution N-body simulations to develop a new, flexible empirical approach for measuring the growth rate from redshift-space distortions in the 2-point galaxy correlation function. We quantify the systematic error in measuring the growth rate in a 1 h-3 Gpc3 volume over a range of redshifts, from the dark matter particle distribution and a range of halo-mass catalogues with a number density comparable to the latest large-volume galaxy surveys such as the WiggleZ Dark Energy Survey and the Baryon Oscillation Spectroscopic Survey. Our simulations allow us to span halo masses with bias factors ranging from unity (probed by emission-line galaxies) to more massive haloes hosting luminous red galaxies. We show that the measured growth rate is sensitive to the model adopted for the small-scale real-space correlation function, and in particular that the `standard' assumption of a power-law correlation function can result in a significant systematic error in the growth-rate determination. We introduce a new, empirical fitting function that produces results with a lower (5-10 per cent) amplitude of systematic error. We also introduce a new technique which permits the galaxy pairwise velocity distribution, the quantity which drives the non-linear growth of structure, to be measured as a non-parametric stepwise function. Our (model-independent) results agree well with an exponential pairwise velocity distribution, expected from theoretical considerations, and are consistent with direct measurements of halo velocity differences from the parent catalogues. In a companion paper, we present the application of our new methodology to the WiggleZ Survey data set.

A novel method for calculating relative free energy of similar molecules in two environments

NASA Astrophysics Data System (ADS)

Farhi, Asaf; Singh, Bipin

2017-03-01

Calculating relative free energies is a topic of substantial interest and has many applications including solvation and binding free energies, which are used in computational drug discovery. However, there remain the challenges of accuracy, simple implementation, robustness and efficiency, which prevent the calculations from being automated and limit their use. Here we present an exact and complete decoupling analysis in which the partition functions of the compared systems decompose into the partition functions of the common and different subsystems. This decoupling analysis is applicable to submolecules with coupled degrees of freedom such as the methyl group and to any potential function (including the typical dihedral potentials), enabling to remove less terms in the transformation which results in a more efficient calculation. Then we show mathematically, in the context of partition function decoupling, that the two compared systems can be simulated separately, eliminating the need to design a composite system. We demonstrate the decoupling analysis and the separate transformations in a relative free energy calculation using MD simulations for a general force field and compare to another calculation and to experimental results. We present a unified soft-core technique that ensures the monotonicity of the numerically integrated function (analytical proof) which is important for the selection of intermediates. We show mathematically that in this soft-core technique the numerically integrated function can be non-steep only when we transform the systems separately, which can simplify the numerical integration. Finally, we show that when the systems have rugged energy landscape they can be equilibrated without introducing another sampling dimension which can also enable to use the simulation results for other free energy calculations.

Cooling rate effects in sodium silicate glasses: Bridging the gap between molecular dynamics simulations and experiments

NASA Astrophysics Data System (ADS)

Li, Xin; Song, Weiying; Yang, Kai; Krishnan, N. M. Anoop; Wang, Bu; Smedskjaer, Morten M.; Mauro, John C.; Sant, Gaurav; Balonis, Magdalena; Bauchy, Mathieu

2017-08-01

Although molecular dynamics (MD) simulations are commonly used to predict the structure and properties of glasses, they are intrinsically limited to short time scales, necessitating the use of fast cooling rates. It is therefore challenging to compare results from MD simulations to experimental results for glasses cooled on typical laboratory time scales. Based on MD simulations of a sodium silicate glass with varying cooling rate (from 0.01 to 100 K/ps), here we show that thermal history primarily affects the medium-range order structure, while the short-range order is largely unaffected over the range of cooling rates simulated. This results in a decoupling between the enthalpy and volume relaxation functions, where the enthalpy quickly plateaus as the cooling rate decreases, whereas density exhibits a slower relaxation. Finally, we show that, using the proper extrapolation method, the outcomes of MD simulations can be meaningfully compared to experimental values when extrapolated to slower cooling rates.

Microstructure simulation of rapidly solidified ASP30 high-speed steel particles by gas atomization

NASA Astrophysics Data System (ADS)

Ma, Jie; Wang, Bo; Yang, Zhi-liang; Wu, Guang-xin; Zhang, Jie-yu; Zhao, Shun-li

2016-03-01

In this study, the microstructure evolution of rapidly solidified ASP30 high-speed steel particles was predicted using a simulation method based on the cellular automaton-finite element (CAFE) model. The dendritic growth kinetics, in view of the characteristics of ASP30 steel, were calculated and combined with macro heat transfer calculations by user-defined functions (UDFs) to simulate the microstructure of gas-atomized particles. The relationship among particle diameter, undercooling, and the convection heat transfer coefficient was also investigated to provide cooling conditions for simulations. The simulated results indicated that a columnar grain microstructure was observed in small particles, whereas an equiaxed microstructure was observed in large particles. In addition, the morphologies and microstructures of gas-atomized ASP30 steel particles were also investigated experimentally using scanning electron microscopy (SEM). The experimental results showed that four major types of microstructures were formed: dendritic, equiaxed, mixed, and multi-droplet microstructures. The simulated results and the available experimental data are in good agreement.

Improving the performance of water desalination through ultra-permeable functionalized nanoporous graphene oxide membrane

NASA Astrophysics Data System (ADS)

Hosseini, Mostafa; Azamat, Jafar; Erfan-Niya, Hamid

2018-01-01

Molecular dynamics simulations were performed to investigate the water desalination performance of nanoporous graphene oxide (NPGO) membranes. The simulated systems consist of a NPGO as a membrane with a functionalized pore in its center immersed in an aqueous ionic solution and a graphene sheet as a barrier. The considered NPGO membranes are involved four types of pore with different size and chemistry. The results indicated that the NPGO membrane has effective efficiency in salt rejection as well as high performance in water flux. For all types of pore with the radius size of 2.9-4.5 Å, the NPGO shows salt rejection of >89%. Functional groups on the surface and edge of pores have a great effect on water flux. To precisely understand the effect of functional groups on the surface of nanostructured membranes, nanoporous graphene was simulated under the same condition for comparison. Hydrophilic groups on the surface make the NPGO as an ultra-permeable membrane. As a result, the obtained water flux for NPGO was about 77% greater than graphene. Also, it was found that the water flux of NPGO is 2-5 orders of magnitude greater than other existing reverse osmosis membranes. Therefore, the investigated systems can be recommended as a model for the water desalination.

On the room-temperature phase diagram of high pressure hydrogen: an ab initio molecular dynamics perspective and a diffusion Monte Carlo study.

PubMed

Chen, Ji; Ren, Xinguo; Li, Xin-Zheng; Alfè, Dario; Wang, Enge

2014-07-14

The finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-art DMC results as benchmark, comparisons of the energy differences between structures generated from the MD and PIMD simulations, with molecular and dissociated hydrogens, respectively, in the weak molecular layers of phase IV, indicate that standard functionals in DFT tend to underestimate the dissociation barrier of the weak molecular layers in this mixed phase. Because of this underestimation, inclusion of the quantum nuclear effects (QNEs) in PIMD using electronic structures generated with these functionals leads to artificially dissociated hydrogen layers in phase IV and an error compensation between the neglect of QNEs and the deficiencies of these functionals in standard ab initio MD simulations exists. This analysis partly rationalizes why earlier ab initio MD simulations complement so well the experimental observations. The temperature and pressure dependencies for the stability of phase IV were also studied in the end and compared with earlier results.

Confined active Brownian particles: theoretical description of propulsion-induced accumulation

NASA Astrophysics Data System (ADS)

Das, Shibananda; Gompper, Gerhard; Winkler, Roland G.

2018-01-01

The stationary-state distribution function of confined active Brownian particles (ABPs) is analyzed by computer simulations and analytical calculations. We consider a radial harmonic as well as an anharmonic confinement potential. In the simulations, the ABP is propelled with a prescribed velocity along a body-fixed direction, which is changing in a diffusive manner. For the analytical approach, the Cartesian components of the propulsion velocity are assumed to change independently; active Ornstein-Uhlenbeck particle (AOUP). This results in very different velocity distribution functions. The analytical solution of the Fokker-Planck equation for an AOUP in a harmonic potential is presented and a conditional distribution function is provided for the radial particle distribution at a given magnitude of the propulsion velocity. This conditional probability distribution facilitates the description of the coupling of the spatial coordinate and propulsion, which yields activity-induced accumulation of particles. For the anharmonic potential, a probability distribution function is derived within the unified colored noise approximation. The comparison of the simulation results with theoretical predictions yields good agreement for large rotational diffusion coefficients, e.g. due to tumbling, even for large propulsion velocities (Péclet numbers). However, we find significant deviations already for moderate Péclet number, when the rotational diffusion coefficient is on the order of the thermal one.

Efficient sampling of reversible cross-linking polymers: Self-assembly of single-chain polymeric nanoparticles

NASA Astrophysics Data System (ADS)

Oyarzún, Bernardo; Mognetti, Bortolo Matteo

2018-03-01

We present a new simulation technique to study systems of polymers functionalized by reactive sites that bind/unbind forming reversible linkages. Functionalized polymers feature self-assembly and responsive properties that are unmatched by the systems lacking selective interactions. The scales at which the functional properties of these materials emerge are difficult to model, especially in the reversible regime where such properties result from many binding/unbinding events. This difficulty is related to large entropic barriers associated with the formation of intra-molecular loops. In this work, we present a simulation scheme that sidesteps configurational costs by dedicated Monte Carlo moves capable of binding/unbinding reactive sites in a single step. Cross-linking reactions are implemented by trial moves that reconstruct chain sections attempting, at the same time, a dimerization reaction between pairs of reactive sites. The model is parametrized by the reaction equilibrium constant of the reactive species free in solution. This quantity can be obtained by means of experiments or atomistic/quantum simulations. We use the proposed methodology to study the self-assembly of single-chain polymeric nanoparticles, starting from flexible precursors carrying regularly or randomly distributed reactive sites. We focus on understanding differences in the morphology of chain nanoparticles when linkages are reversible as compared to the well-studied case of irreversible reactions. Intriguingly, we find that the size of regularly functionalized chains, in good solvent conditions, is non-monotonous as a function of the degree of functionalization. We clarify how this result follows from excluded volume interactions and is peculiar of reversible linkages and regular functionalizations.

Finite Element Simulation and Experimental Verification of Internal Stress of Quenched AISI 4140 Cylinders

NASA Astrophysics Data System (ADS)

Liu, Yu; Qin, Shengwei; Hao, Qingguo; Chen, Nailu; Zuo, Xunwei; Rong, Yonghua

2017-03-01

The study of internal stress in quenched AISI 4140 medium carbon steel is of importance in engineering. In this work, the finite element simulation (FES) was employed to predict the distribution of internal stress in quenched AISI 4140 cylinders with two sizes of diameter based on exponent-modified (Ex-Modified) normalized function. The results indicate that the FES based on Ex-Modified normalized function proposed is better consistent with X-ray diffraction measurements of the stress distribution than FES based on normalized function proposed by Abrassart, Desalos and Leblond, respectively, which is attributed that Ex-Modified normalized function better describes transformation plasticity. Effect of temperature distribution on the phase formation, the origin of residual stress distribution and effect of transformation plasticity function on the residual stress distribution were further discussed.

Impact of the river nutrient load variability on the North Aegean ecosystem functioning over the last decades

NASA Astrophysics Data System (ADS)

Tsiaras, K. P.; Petihakis, G.; Kourafalou, V. H.; Triantafyllou, G.

2014-02-01

The impact of river load variability on the North Aegean ecosystem functioning over the last decades (1980-2000) was investigated by means of a coupled hydrodynamic/biogeochemical model simulation. Model results were validated against available SeaWiFS Chl-a and in situ data. The simulated food web was found dominated by small cells, in agreement with observations, with most of the carbon channelled through the microbial loop. Diatoms and dinoflagellates presented a higher relative abundance in the more productive coastal areas. The increased phosphate river loads in the early 80s resulted in nitrogen and silicate deficiency in coastal, river-influenced regions. Primary production presented a decreasing trend for most areas. During periods of increased phosphate/nitrate inputs, silicate deficiency resulted in a relative decrease of diatoms, triggering an increase of dinoflagellates. Such an increase was simulated in the late 90s in the Thermaikos Gulf, in agreement with the observed increased occurrence of Harmful Algal Blooms. Microzooplankton was found to closely follow the relative increase of dinoflagellates under higher nutrient availability, showing a faster response than mesozooplankton. Sensitivity simulations with varying nutrient river inputs revealed a linear response of net primary production and plankton biomass. A stronger effect of river inputs was simulated in the enclosed Thermaikos Gulf, in terms of productivity and plankton composition, showing a significant increase of dinoflagellates relative abundance under increased nutrient loads.

Optimal design of wind barriers using 3D computational fluid dynamics simulations

NASA Astrophysics Data System (ADS)

Fang, H.; Wu, X.; Yang, X.

2017-12-01

Desertification is a significant global environmental and ecological problem that requires human-regulated control and management. Wind barriers are commonly used to reduce wind velocity or trap drifting sand in arid or semi-arid areas. Therefore, optimal design of wind barriers becomes critical in Aeolian engineering. In the current study, we perform 3D computational fluid dynamics (CFD) simulations for flow passing through wind barriers with different structural parameters. To validate the simulation results, we first inter-compare the simulated flow field results with those from both wind-tunnel experiments and field measurements. Quantitative analyses of the shelter effect are then conducted based on a series of simulations with different structural parameters (such as wind barrier porosity, row numbers, inter-row spacing and belt schemes). The results show that wind barriers with porosity of 0.35 could provide the longest shelter distance (i.e., where the wind velocity reduction is more than 50%) thus are recommended in engineering designs. To determine the optimal row number and belt scheme, we introduce a cost function that takes both wind-velocity reduction effects and economical expense into account. The calculated cost function show that a 3-row-belt scheme with inter-row spacing of 6h (h as the height of wind barriers) and inter-belt spacing of 12h is the most effective.

The relationship between stochastic and deterministic quasi-steady state approximations.

PubMed

Kim, Jae Kyoung; Josić, Krešimir; Bennett, Matthew R

2015-11-23

The quasi steady-state approximation (QSSA) is frequently used to reduce deterministic models of biochemical networks. The resulting equations provide a simplified description of the network in terms of non-elementary reaction functions (e.g. Hill functions). Such deterministic reductions are frequently a basis for heuristic stochastic models in which non-elementary reaction functions are used to define reaction propensities. Despite their popularity, it remains unclear when such stochastic reductions are valid. It is frequently assumed that the stochastic reduction can be trusted whenever its deterministic counterpart is accurate. However, a number of recent examples show that this is not necessarily the case. Here we explain the origin of these discrepancies, and demonstrate a clear relationship between the accuracy of the deterministic and the stochastic QSSA for examples widely used in biological systems. With an analysis of a two-state promoter model, and numerical simulations for a variety of other models, we find that the stochastic QSSA is accurate whenever its deterministic counterpart provides an accurate approximation over a range of initial conditions which cover the likely fluctuations from the quasi steady-state (QSS). We conjecture that this relationship provides a simple and computationally inexpensive way to test the accuracy of reduced stochastic models using deterministic simulations. The stochastic QSSA is one of the most popular multi-scale stochastic simulation methods. While the use of QSSA, and the resulting non-elementary functions has been justified in the deterministic case, it is not clear when their stochastic counterparts are accurate. In this study, we show how the accuracy of the stochastic QSSA can be tested using their deterministic counterparts providing a concrete method to test when non-elementary rate functions can be used in stochastic simulations.

Improvement and comparison of likelihood functions for model calibration and parameter uncertainty analysis within a Markov chain Monte Carlo scheme

NASA Astrophysics Data System (ADS)

Cheng, Qin-Bo; Chen, Xi; Xu, Chong-Yu; Reinhardt-Imjela, Christian; Schulte, Achim

2014-11-01

In this study, the likelihood functions for uncertainty analysis of hydrological models are compared and improved through the following steps: (1) the equivalent relationship between the Nash-Sutcliffe Efficiency coefficient (NSE) and the likelihood function with Gaussian independent and identically distributed residuals is proved; (2) a new estimation method of the Box-Cox transformation (BC) parameter is developed to improve the effective elimination of the heteroscedasticity of model residuals; and (3) three likelihood functions-NSE, Generalized Error Distribution with BC (BC-GED) and Skew Generalized Error Distribution with BC (BC-SGED)-are applied for SWAT-WB-VSA (Soil and Water Assessment Tool - Water Balance - Variable Source Area) model calibration in the Baocun watershed, Eastern China. Performances of calibrated models are compared using the observed river discharges and groundwater levels. The result shows that the minimum variance constraint can effectively estimate the BC parameter. The form of the likelihood function significantly impacts on the calibrated parameters and the simulated results of high and low flow components. SWAT-WB-VSA with the NSE approach simulates flood well, but baseflow badly owing to the assumption of Gaussian error distribution, where the probability of the large error is low, but the small error around zero approximates equiprobability. By contrast, SWAT-WB-VSA with the BC-GED or BC-SGED approach mimics baseflow well, which is proved in the groundwater level simulation. The assumption of skewness of the error distribution may be unnecessary, because all the results of the BC-SGED approach are nearly the same as those of the BC-GED approach.

Propagation of uncertainty by Monte Carlo simulations in case of basic geodetic computations

NASA Astrophysics Data System (ADS)

Wyszkowska, Patrycja

2017-12-01

The determination of the accuracy of functions of measured or adjusted values may be a problem in geodetic computations. The general law of covariance propagation or in case of the uncorrelated observations the propagation of variance (or the Gaussian formula) are commonly used for that purpose. That approach is theoretically justified for the linear functions. In case of the non-linear functions, the first-order Taylor series expansion is usually used but that solution is affected by the expansion error. The aim of the study is to determine the applicability of the general variance propagation law in case of the non-linear functions used in basic geodetic computations. The paper presents errors which are a result of negligence of the higher-order expressions and it determines the range of such simplification. The basis of that analysis is the comparison of the results obtained by the law of propagation of variance and the probabilistic approach, namely Monte Carlo simulations. Both methods are used to determine the accuracy of the following geodetic computations: the Cartesian coordinates of unknown point in the three-point resection problem, azimuths and distances of the Cartesian coordinates, height differences in the trigonometric and the geometric levelling. These simulations and the analysis of the results confirm the possibility of applying the general law of variance propagation in basic geodetic computations even if the functions are non-linear. The only condition is the accuracy of observations, which cannot be too low. Generally, this is not a problem with using present geodetic instruments.

The Effect of Error in Item Parameter Estimates on the Test Response Function Method of Linking.

ERIC Educational Resources Information Center

Kaskowitz, Gary S.; De Ayala, R. J.

2001-01-01

Studied the effect of item parameter estimation for computation of linking coefficients for the test response function (TRF) linking/equating method. Simulation results showed that linking was more accurate when there was less error in the parameter estimates, and that 15 or 25 common items provided better results than 5 common items under both…

Generalized non-equilibrium vertex correction method in coherent medium theory for quantum transport simulation of disordered nanoelectronics

NASA Astrophysics Data System (ADS)

Yan, Jiawei; Ke, Youqi

In realistic nanoelectronics, disordered impurities/defects are inevitable and play important roles in electron transport. However, due to the lack of effective quantum transport method, the important effects of disorders remain poorly understood. Here, we report a generalized non-equilibrium vertex correction (NVC) method with coherent potential approximation to treat the disorder effects in quantum transport simulation. With this generalized NVC method, any averaged product of two single-particle Green's functions can be obtained by solving a set of simple linear equations. As a result, the averaged non-equilibrium density matrix and various important transport properties, including averaged current, disordered induced current fluctuation and the averaged shot noise, can all be efficiently computed in a unified scheme. Moreover, a generalized form of conditionally averaged non-equilibrium Green's function is derived to incorporate with density functional theory to enable first-principles simulation. We prove the non-equilibrium coherent potential equals the non-equilibrium vertex correction. Our approach provides a unified, efficient and self-consistent method for simulating non-equilibrium quantum transport through disorder nanoelectronics. Shanghaitech start-up fund.

Simulations of Spray Reacting Flows in a Single Element LDI Injector With and Without Invoking an Eulerian Scalar PDF Method

NASA Technical Reports Server (NTRS)

Shih, Tsan-Hsing; Liu, Nan-Suey

2012-01-01

This paper presents the numerical simulations of the Jet-A spray reacting flow in a single element lean direct injection (LDI) injector by using the National Combustion Code (NCC) with and without invoking the Eulerian scalar probability density function (PDF) method. The flow field is calculated by using the Reynolds averaged Navier-Stokes equations (RANS and URANS) with nonlinear turbulence models, and when the scalar PDF method is invoked, the energy and compositions or species mass fractions are calculated by solving the equation of an ensemble averaged density-weighted fine-grained probability density function that is referred to here as the averaged probability density function (APDF). A nonlinear model for closing the convection term of the scalar APDF equation is used in the presented simulations and will be briefly described. Detailed comparisons between the results and available experimental data are carried out. Some positive findings of invoking the Eulerian scalar PDF method in both improving the simulation quality and reducing the computing cost are observed.

In search of a viable reaction pathway in the chelation of a metallo-protein

NASA Astrophysics Data System (ADS)

Rose, Frisco; Hodak, Miroslav; Bernholc, Jerry

2010-03-01

Misfolded metallo-proteins are potential causal agents in the onset of neuro-degenerative diseases, such as Alzheimer's and Parkinson's Diseases (PD). Experimental results involving metal chelation have shown significant promise in symptom reduction and misfolding reversal. We explore, through atomistic simulations, potential reaction pathways for the chelation of Cu^2+ from the metal binding site in our representation of a partially misfolded α-synuclein, the protein implicated in PD. Our ab initio simulations use Density Functional Theory (DFT) and nudged elastic band to obtain the minimized energy coordinates of this reaction. Our simulations include ab initio water at the interaction site and in its first solvation shells, while the remainder is fully solvated with orbital-free DFT water representation [1]. Our ongoing studies of viable chelation agents include nicotine, caffeine and other potential reagents, we will review the best case agents in this presentation. [4pt] [1] Hodak M, Lu W, Bernholc J. Hybrid ab initio Kohn-Sham density functional theory/frozen-density orbital-free density functional theory simulation method suitable for biological systems. J. Chem. Phys. 2008 Jan;128(1):014101-9.

Time-dependent Data System (TDDS); an interactive program to assemble, manage, and appraise input data and numerical output of flow/transport simulation models

USGS Publications Warehouse

Regan, R.S.; Schaffranek, R.W.; Baltzer, R.A.

1996-01-01

A system of functional utilities and computer routines, collectively identified as the Time-Dependent Data System CI DDS), has been developed and documented by the U.S. Geological Survey. The TDDS is designed for processing time sequences of discrete, fixed-interval, time-varying geophysical data--in particular, hydrologic data. Such data include various, dependent variables and related parameters typically needed as input for execution of one-, two-, and three-dimensional hydrodynamic/transport and associated water-quality simulation models. Such data can also include time sequences of results generated by numerical simulation models. Specifically, TDDS provides the functional capabilities to process, store, retrieve, and compile data in a Time-Dependent Data Base (TDDB) in response to interactive user commands or pre-programmed directives. Thus, the TDDS, in conjunction with a companion TDDB, provides a ready means for processing, preparation, and assembly of time sequences of data for input to models; collection, categorization, and storage of simulation results from models; and intercomparison of field data and simulation results. The TDDS can be used to edit and verify prototype, time-dependent data to affirm that selected sequences of data are accurate, contiguous, and appropriate for numerical simulation modeling. It can be used to prepare time-varying data in a variety of formats, such as tabular lists, sequential files, arrays, graphical displays, as well as line-printer plots of single or multiparameter data sets. The TDDB is organized and maintained as a direct-access data base by the TDDS, thus providing simple, yet efficient, data management and access. A single, easily used, program interface that provides all access to and from a particular TDDB is available for use directly within models, other user-provided programs, and other data systems. This interface, together with each major functional utility of the TDDS, is described and documented in this report.

Evaluating gyro-viscosity in the Kelvin-Helmholtz instability by kinetic simulations

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

Umeda, Takayuki, E-mail: taka.umeda@nagoya-u.jp; Yamauchi, Natsuki; Wada, Yasutaka

2016-05-15

In the present paper, the finite-Larmor-radius (gyro-viscous) term [K. V. Roberts and J. B. Taylor, Phys. Rev. Lett. 8, 197–198 (1962)] is evaluated by using a full kinetic Vlasov simulation result of the Kelvin-Helmholtz instability (KHI). The velocity field and the pressure tensor are calculated from the high-resolution data of the velocity distribution functions obtained by the Vlasov simulation, which are used to approximate the Finite-Larmor-Radius (FLR) term according to Roberts and Taylor [Phys. Rev. Lett. 8, 197–198 (1962)]. The direct comparison between the pressure tensor and the FLR term shows an agreement. It is also shown that the anisotropicmore » pressure gradient enhanced the linear growth of the KHI when the inner product between the vorticity of the primary velocity shear layer and the magnetic field is negative, which is consistent with the previous FLR-magnetohydrodynamic simulation result. This result suggests that it is not sufficient for reproducing the kinetic simulation result by fluid simulations to include the FLR term (or the pressure tensor) only in the equation of motion for fluid.« less

Using special functions to model the propagation of airborne diseases

NASA Astrophysics Data System (ADS)

Bolaños, Daniela

2014-06-01

Some special functions of the mathematical physics are using to obtain a mathematical model of the propagation of airborne diseases. In particular we study the propagation of tuberculosis in closed rooms and we model the propagation using the error function and the Bessel function. In the model, infected individual emit pathogens to the environment and this infect others individuals who absorb it. The evolution in time of the concentration of pathogens in the environment is computed in terms of error functions. The evolution in time of the number of susceptible individuals is expressed by a differential equation that contains the error function and it is solved numerically for different parametric simulations. The evolution in time of the number of infected individuals is plotted for each numerical simulation. On the other hand, the spatial distribution of the pathogen around the source of infection is represented by the Bessel function K0. The spatial and temporal distribution of the number of infected individuals is computed and plotted for some numerical simulations. All computations were made using software Computer algebra, specifically Maple. It is expected that the analytical results that we obtained allow the design of treatment rooms and ventilation systems that reduce the risk of spread of tuberculosis.

A Laboratory Glass-Cockpit Flight Simulator for Automation and Communications Research

NASA Technical Reports Server (NTRS)

Pisanich, Gregory M.; Heers, Susan T.; Shafto, Michael G. (Technical Monitor)

1995-01-01

A laboratory glass-cockpit flight simulator supporting research on advanced commercial flight deck and Air Traffic Control (ATC) automation and communication interfaces has been developed at the Aviation Operations Branch at the NASA Ames Research Center. This system provides independent and integrated flight and ATC simulator stations, party line voice and datalink communications, along with video and audio monitoring and recording capabilities. Over the last several years, it has been used to support the investigation of flight human factors research issues involving: communication modality; message content and length; graphical versus textual presentation of information, and human accountability for automation. This paper updates the status of this simulator, describing new functionality in the areas of flight management system, EICAS display, and electronic checklist integration. It also provides an overview of several experiments performed using this simulator, including their application areas and results. Finally future enhancements to its ATC (integration of CTAS software) and flight deck (full crew operations) functionality are described.

Functional mapping of reaction norms to multiple environmental signals through nonparametric covariance estimation

PubMed Central

2011-01-01

Background The identification of genes or quantitative trait loci that are expressed in response to different environmental factors such as temperature and light, through functional mapping, critically relies on precise modeling of the covariance structure. Previous work used separable parametric covariance structures, such as a Kronecker product of autoregressive one [AR(1)] matrices, that do not account for interaction effects of different environmental factors. Results We implement a more robust nonparametric covariance estimator to model these interactions within the framework of functional mapping of reaction norms to two signals. Our results from Monte Carlo simulations show that this estimator can be useful in modeling interactions that exist between two environmental signals. The interactions are simulated using nonseparable covariance models with spatio-temporal structural forms that mimic interaction effects. Conclusions The nonparametric covariance estimator has an advantage over separable parametric covariance estimators in the detection of QTL location, thus extending the breadth of use of functional mapping in practical settings. PMID:21269481

Cryogenic terahertz spectrum of (+)-methamphetamine hydrochloride and assignment using solid-state density functional theory.

PubMed

Hakey, Patrick M; Allis, Damian G; Ouellette, Wayne; Korter, Timothy M

2009-04-30

The cryogenic terahertz spectrum of (+)-methamphetamine hydrochloride from 10.0 to 100.0 cm(-1) is presented, as is the complete structural analysis and vibrational assignment of the compound using solid-state density functional theory. This cryogenic investigation reveals multiple spectral features that were not previously reported in room-temperature terahertz studies of the title compound. Modeling of the compound employed eight density functionals utilizing both solid-state and isolated-molecule methods. The results clearly indicate the necessity of solid-state simulations for the accurate assignment of solid-state THz spectra. Assignment of the observed spectral features to specific atomic motions is based on the BP density functional, which provided the best-fit solid-state simulation of the experimental spectrum. The seven experimental spectral features are the result of thirteen infrared-active vibrational modes predicted at a BP/DNP level of theory with more than 90% of the total spectral intensity associated with external crystal vibrations.

Validation of Variations in Mental Workload as a Function of Scenario Difficulty: Traffic Density and Visibility

NASA Technical Reports Server (NTRS)

2003-01-01

Fluctuations in mental workload can be expected as a function of traffic density and visibility. The aim of the current investigation was to establish simulation scenarios that differed in attentional processing requirements. Four scenarios were created and tested representing two levels of traffic density (urban versus freeway) and two levels of visibility (clear versus foggy). An array of mental workload assessment measures were used to exam changes in attentional processing requirements in each scenario. The assessment array consisted of physiological (P300 amplitude and latency) and behavioral (RT and accuracy) indices. Preliminary results indicate that workload differs significantly as a function of traffic density in rural versus freeway scenarios. Workload also differs significantly in rural versus freeway scenarios as a function of visibility as observed by a significant interaction between the two variables of interest. Results are discussed in terms of their application for validating the difficulty level of simulation scenarios as a format for examining mental workload.

Prediction of sound transmission loss through multilayered panels by using Gaussian distribution of directional incident energy

PubMed

Kang; Ih; Kim; Kim

2000-03-01

In this study, a new prediction method is suggested for sound transmission loss (STL) of multilayered panels of infinite extent. Conventional methods such as random or field incidence approach often given significant discrepancies in predicting STL of multilayered panels when compared with the experiments. In this paper, appropriate directional distributions of incident energy to predict the STL of multilayered panels are proposed. In order to find a weighting function to represent the directional distribution of incident energy on the wall in a reverberation chamber, numerical simulations by using a ray-tracing technique are carried out. Simulation results reveal that the directional distribution can be approximately expressed by the Gaussian distribution function in terms of the angle of incidence. The Gaussian function is applied to predict the STL of various multilayered panel configurations as well as single panels. The compared results between the measurement and the prediction show good agreements, which validate the proposed Gaussian function approach.

Functional requirements for design of the Space Ultrareliable Modular Computer (SUMC) system simulator

NASA Technical Reports Server (NTRS)

Curran, R. T.; Hornfeck, W. A.

1972-01-01

The functional requirements for the design of an interpretive simulator for the space ultrareliable modular computer (SUMC) are presented. A review of applicable existing computer simulations is included along with constraints on the SUMC simulator functional design. Input requirements, output requirements, and language requirements for the simulator are discussed in terms of a SUMC configuration which may vary according to the application.

Beware the black box: investigating the sensitivity of FEA simulations to modelling factors in comparative biomechanics.

PubMed

Walmsley, Christopher W; McCurry, Matthew R; Clausen, Phillip D; McHenry, Colin R

2013-01-01

Finite element analysis (FEA) is a computational technique of growing popularity in the field of comparative biomechanics, and is an easily accessible platform for form-function analyses of biological structures. However, its rapid evolution in recent years from a novel approach to common practice demands some scrutiny in regards to the validity of results and the appropriateness of assumptions inherent in setting up simulations. Both validation and sensitivity analyses remain unexplored in many comparative analyses, and assumptions considered to be 'reasonable' are often assumed to have little influence on the results and their interpretation. HERE WE REPORT AN EXTENSIVE SENSITIVITY ANALYSIS WHERE HIGH RESOLUTION FINITE ELEMENT (FE) MODELS OF MANDIBLES FROM SEVEN SPECIES OF CROCODILE WERE ANALYSED UNDER LOADS TYPICAL FOR COMPARATIVE ANALYSIS: biting, shaking, and twisting. Simulations explored the effect on both the absolute response and the interspecies pattern of results to variations in commonly used input parameters. Our sensitivity analysis focuses on assumptions relating to the selection of material properties (heterogeneous or homogeneous), scaling (standardising volume, surface area, or length), tooth position (front, mid, or back tooth engagement), and linear load case (type of loading for each feeding type). Our findings show that in a comparative context, FE models are far less sensitive to the selection of material property values and scaling to either volume or surface area than they are to those assumptions relating to the functional aspects of the simulation, such as tooth position and linear load case. Results show a complex interaction between simulation assumptions, depending on the combination of assumptions and the overall shape of each specimen. Keeping assumptions consistent between models in an analysis does not ensure that results can be generalised beyond the specific set of assumptions used. Logically, different comparative datasets would also be sensitive to identical simulation assumptions; hence, modelling assumptions should undergo rigorous selection. The accuracy of input data is paramount, and simulations should focus on taking biological context into account. Ideally, validation of simulations should be addressed; however, where validation is impossible or unfeasible, sensitivity analyses should be performed to identify which assumptions have the greatest influence upon the results.

Beware the black box: investigating the sensitivity of FEA simulations to modelling factors in comparative biomechanics

PubMed Central

McCurry, Matthew R.; Clausen, Phillip D.; McHenry, Colin R.

2013-01-01

Finite element analysis (FEA) is a computational technique of growing popularity in the field of comparative biomechanics, and is an easily accessible platform for form-function analyses of biological structures. However, its rapid evolution in recent years from a novel approach to common practice demands some scrutiny in regards to the validity of results and the appropriateness of assumptions inherent in setting up simulations. Both validation and sensitivity analyses remain unexplored in many comparative analyses, and assumptions considered to be ‘reasonable’ are often assumed to have little influence on the results and their interpretation. Here we report an extensive sensitivity analysis where high resolution finite element (FE) models of mandibles from seven species of crocodile were analysed under loads typical for comparative analysis: biting, shaking, and twisting. Simulations explored the effect on both the absolute response and the interspecies pattern of results to variations in commonly used input parameters. Our sensitivity analysis focuses on assumptions relating to the selection of material properties (heterogeneous or homogeneous), scaling (standardising volume, surface area, or length), tooth position (front, mid, or back tooth engagement), and linear load case (type of loading for each feeding type). Our findings show that in a comparative context, FE models are far less sensitive to the selection of material property values and scaling to either volume or surface area than they are to those assumptions relating to the functional aspects of the simulation, such as tooth position and linear load case. Results show a complex interaction between simulation assumptions, depending on the combination of assumptions and the overall shape of each specimen. Keeping assumptions consistent between models in an analysis does not ensure that results can be generalised beyond the specific set of assumptions used. Logically, different comparative datasets would also be sensitive to identical simulation assumptions; hence, modelling assumptions should undergo rigorous selection. The accuracy of input data is paramount, and simulations should focus on taking biological context into account. Ideally, validation of simulations should be addressed; however, where validation is impossible or unfeasible, sensitivity analyses should be performed to identify which assumptions have the greatest influence upon the results. PMID:24255817

Validation: Codes to compare simulation data to various observations

NASA Astrophysics Data System (ADS)

Cohn, J. D.

2017-02-01

Validation provides codes to compare several observations to simulated data with stellar mass and star formation rate, simulated data stellar mass function with observed stellar mass function from PRIMUS or SDSS-GALEX in several redshift bins from 0.01-1.0, and simulated data B band luminosity function with observed stellar mass function, and to create plots for various attributes, including stellar mass functions, and stellar mass to halo mass. These codes can model predictions (in some cases alongside observational data) to test other mock catalogs.

Parallel proton fire hose instability in the expanding solar wind: Hybrid simulations

NASA Astrophysics Data System (ADS)

Matteini, Lorenzo; Landi, Simone; Hellinger, Petr; Velli, Marco

2006-10-01

We report a study of the properties of the parallel proton fire hose instability comparing the results obtained by the linear analysis, from one-dimensional (1-D) standard hybrid simulations and 1-D hybrid expanding box simulations. The three different approaches converge toward the same instability threshold condition which is in good agreement with in situ observations, suggesting that such instability is relevant in the solar wind context. We investigate also the effect of the wave-particle interactions on shaping the proton distribution function and on the evolution of the spectrum of the magnetic fluctuations during the expansion. We find that the resonant interaction can provide the proton distribution function to depart from the bi-Maxwellian form.

"First-principles" kinetic Monte Carlo simulations revisited: CO oxidation over RuO2 (110).

PubMed

Hess, Franziska; Farkas, Attila; Seitsonen, Ari P; Over, Herbert

2012-03-15

First principles-based kinetic Monte Carlo (kMC) simulations are performed for the CO oxidation on RuO(2) (110) under steady-state reaction conditions. The simulations include a set of elementary reaction steps with activation energies taken from three different ab initio density functional theory studies. Critical comparison of the simulation results reveals that already small variations in the activation energies lead to distinctly different reaction scenarios on the surface, even to the point where the dominating elementary reaction step is substituted by another one. For a critical assessment of the chosen energy parameters, it is not sufficient to compare kMC simulations only to experimental turnover frequency (TOF) as a function of the reactant feed ratio. More appropriate benchmarks for kMC simulations are the actual distribution of reactants on the catalyst's surface during steady-state reaction, as determined by in situ infrared spectroscopy and in situ scanning tunneling microscopy, and the temperature dependence of TOF in the from of Arrhenius plots. Copyright © 2012 Wiley Periodicals, Inc.

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.

Engineering design of sub-micron topographies for simultaneously adherent and reflective metal-polymer interfaces

NASA Technical Reports Server (NTRS)

Brown, Christopher A.

1993-01-01

The approach of the project is to base the design of multi-function, reflective topographies on the theory that topographically dependent phenomena react with surfaces and interfaces at certain scales. The first phase of the project emphasizes the development of methods for understanding the sizes of topographic features which influence reflectivity. Subsequent phases, if necessary, will address the scales of interaction for adhesion and manufacturing processes. A simulation of the interaction of electromagnetic radiation, or light, with a reflective surface is performed using specialized software. Reflectivity of the surface as a function of scale is evaluated and the results from the simulation are compared with reflectivity measurements made on multi-function, reflective surfaces.

Predicting receptor functionality of signaling lymphocyte activation molecule for measles virus hemagglutinin by docking simulation.

PubMed

Suzuki, Yoshiyuki

2017-05-01

Predicting susceptibility of various species to a virus assists assessment of risk of interspecies transmission. Evaluation of receptor functionality may be useful in screening for susceptibility. In this study, docking simulation was conducted for measles virus hemagglutinin (MV-H) and immunoglobulin-like variable domain of signaling lymphocyte activation molecule (SLAM-V). It was observed that the docking scores for MV-H and SLAM-V correlated with the activity of SLAM as an MV receptor. These results suggest that the receptor functionality may be predicted from the docking scores of virion surface proteins and cellular receptor molecules. © 2017 The Societies and John Wiley & Sons Australia, Ltd.

New Computer Simulations of Macular Neural Functioning

NASA Technical Reports Server (NTRS)

Ross, Muriel D.; Doshay, D.; Linton, S.; Parnas, B.; Montgomery, K.; Chimento, T.

1994-01-01

We use high performance graphics workstations and supercomputers to study the functional significance of the three-dimensional (3-D) organization of gravity sensors. These sensors have a prototypic architecture foreshadowing more complex systems. Scaled-down simulations run on a Silicon Graphics workstation and scaled-up, 3-D versions run on a Cray Y-MP supercomputer. A semi-automated method of reconstruction of neural tissue from serial sections studied in a transmission electron microscope has been developed to eliminate tedious conventional photography. The reconstructions use a mesh as a step in generating a neural surface for visualization. Two meshes are required to model calyx surfaces. The meshes are connected and the resulting prisms represent the cytoplasm and the bounding membranes. A finite volume analysis method is employed to simulate voltage changes along the calyx in response to synapse activation on the calyx or on calyceal processes. The finite volume method insures that charge is conserved at the calyx-process junction. These and other models indicate that efferent processes act as voltage followers, and that the morphology of some afferent processes affects their functioning. In a final application, morphological information is symbolically represented in three dimensions in a computer. The possible functioning of the connectivities is tested using mathematical interpretations of physiological parameters taken from the literature. Symbolic, 3-D simulations are in progress to probe the functional significance of the connectivities. This research is expected to advance computer-based studies of macular functioning and of synaptic plasticity.

Effects of data structure on the estimation of covariance functions to describe genotype by environment interactions in a reaction norm model

PubMed Central

Calus, Mario PL; Bijma, Piter; Veerkamp, Roel F

2004-01-01

Covariance functions have been proposed to predict breeding values and genetic (co)variances as a function of phenotypic within herd-year averages (environmental parameters) to include genotype by environment interaction. The objective of this paper was to investigate the influence of definition of environmental parameters and non-random use of sires on expected breeding values and estimated genetic variances across environments. Breeding values were simulated as a linear function of simulated herd effects. The definition of environmental parameters hardly influenced the results. In situations with random use of sires, estimated genetic correlations between the trait expressed in different environments were 0.93, 0.93 and 0.97 while simulated at 0.89 and estimated genetic variances deviated up to 30% from the simulated values. Non random use of sires, poor genetic connectedness and small herd size had a large impact on the estimated covariance functions, expected breeding values and calculated environmental parameters. Estimated genetic correlations between a trait expressed in different environments were biased upwards and breeding values were more biased when genetic connectedness became poorer and herd composition more diverse. The best possible solution at this stage is to use environmental parameters combining large numbers of animals per herd, while losing some information on genotype by environment interaction in the data. PMID:15339629

Continuum-kinetic approach to sheath simulations

NASA Astrophysics Data System (ADS)

Cagas, Petr; Hakim, Ammar; Srinivasan, Bhuvana

2016-10-01

Simulations of sheaths are performed using a novel continuum-kinetic model with collisions including ionization/recombination. A discontinuous Galerkin method is used to directly solve the Boltzmann-Poisson system to obtain a particle distribution function. Direct discretization of the distribution function has advantages of being noise-free compared to particle-in-cell methods. The distribution function, which is available at each node of the configuration space, can be readily used to calculate the collision integrals in order to get ionization and recombination operators. Analytical models are used to obtain the cross-sections as a function of energy. Results will be presented incorporating surface physics with a classical sheath in Hall thruster-relevant geometry. This work was sponsored by the Air Force Office of Scientific Research under Grant Number FA9550-15-1-0193.

Displacement cascades and defect annealing in tungsten, Part II: Object kinetic Monte Carlo Simulation of Tungsten Cascade Aging

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

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

2015-07-01

The results of object kinetic Monte Carlo (OKMC) simulations of the annealing of primary cascade damage in bulk tungsten using a comprehensive database of cascades obtained from molecular dynamics (Setyawan et al.) are described as a function of primary knock-on atom (PKA) energy at temperatures of 300, 1025 and 2050 K. An increase in SIA clustering coupled with a decrease in vacancy clustering with increasing temperature, in addition to the disparate mobilities of SIAs versus vacancies, causes an interesting effect of temperature on cascade annealing. The annealing efficiency (the ratio of the number of defects after and before annealing) exhibitsmore » an inverse U-shape curve as a function of temperature. The capabilities of the newly developed OKMC code KSOME (kinetic simulations of microstructure evolution) used to carry out these simulations are described.« less

Attractive particle interaction forces and packing density of fine glass powders

PubMed Central

Parteli, Eric J. R.; Schmidt, Jochen; Blümel, Christina; Wirth, Karl-Ernst; Peukert, Wolfgang; Pöschel, Thorsten

2014-01-01

We study the packing of fine glass powders of mean particle diameter in the range (4–52) μm both experimentally and by numerical DEM simulations. We obtain quantitative agreement between the experimental and numerical results, if both types of attractive forces of particle interaction, adhesion and non-bonded van der Waals forces are taken into account. Our results suggest that considering only viscoelastic and adhesive forces in DEM simulations may lead to incorrect numerical predictions of the behavior of fine powders. Based on the results from simulations and experiments, we propose a mathematical expression to estimate the packing fraction of fine polydisperse powders as a function of the average particle size. PMID:25178812

No Escaping the Rat Race: Simulated Night Shift Work Alters the Time-of-Day Variation in BMAL1 Translational Activity in the Prefrontal Cortex.

PubMed

Marti, Andrea R; Patil, Sudarshan; Mrdalj, Jelena; Meerlo, Peter; Skrede, Silje; Pallesen, Ståle; Pedersen, Torhild T; Bramham, Clive R; Grønli, Janne

2017-01-01

Millions of people worldwide work during the night, resulting in disturbed circadian rhythms and sleep loss. This may cause deficits in cognitive functions, impaired alertness and increased risk of errors and accidents. Disturbed circadian rhythmicity resulting from night shift work could impair brain function and cognition through disrupted synthesis of proteins involved in synaptic plasticity and neuronal function. Recently, the circadian transcription factor brain-and-muscle arnt-like protein 1 (BMAL1) has been identified as a promoter of mRNA translation initiation, the most highly regulated step in protein synthesis, through binding to the mRNA "cap". In this study we investigated the effects of simulated shift work on protein synthesis markers. Male rats ( n = 40) were exposed to forced activity, either in their rest phase (simulated night shift work) or in their active phase (simulated day shift work) for 3 days. Following the third work shift, experimental animals and time-matched undisturbed controls were euthanized (rest work at ZT12; active work at ZT0). Tissue lysates from two brain regions (prefrontal cortex, PFC and hippocampus) implicated in cognition and sleep loss, were analyzed with m 7 GTP (cap) pull-down to examine time-of-day variation and effects of simulated shift work on cap-bound protein translation. The results show time-of-day variation of protein synthesis markers in PFC, with increased protein synthesis at ZT12. In the hippocampus there was little difference between ZT0 and ZT12. Active phase work did not induce statistically significant changes in protein synthesis markers at ZT0 compared to time-matched undisturbed controls. Rest work, however, resulted in distinct brain-region specific changes of protein synthesis markers compared to time-matched controls at ZT12. While no changes were observed in the hippocampus, phosphorylation of cap-bound BMAL1 and its regulator S6 kinase beta-1 (S6K1) was significantly reduced in the PFC, together with significant reduction in the synaptic plasticity associated protein activity-regulatedcytoskeleton-associated protein (Arc). Our results indicate considerable time-of-day and brain-region specific variation in cap-dependent translation initiation. We concludethat simulated night shift work in rats disrupts the pathways regulating the circadian component of the translation of mRNA in the PFC, and that this may partly explain impaired waking function during night shift work.

A stochastic modeling of isotope exchange reactions in glutamine synthetase

NASA Astrophysics Data System (ADS)

Kazmiruk, N. V.; Boronovskiy, S. E.; Nartsissov, Ya R.

2017-11-01

The model presented in this work allows simulation of isotopic exchange reactions at chemical equilibrium catalyzed by a glutamine synthetase. To simulate the functioning of the enzyme the algorithm based on the stochastic approach was applied. The dependence of exchange rates for 14C and 32P on metabolite concentration was estimated. The simulation results confirmed the hypothesis of the ascertained validity for preferred order random binding mechanism. Corresponding values of K0.5 were also obtained.

B-1 Systems Approach to Training. Simulation Technology Assessment Report (STAR)

DTIC Science & Technology

1975-07-01

Psychology in the Air Force, 1974. Creelman , J.A., Evaluation of Approach Training Procedures, U.S. Naval School of Aviation Med., Proj. No. NM001-109-107...training. 3.2 PHYSICAL VERSUS PSYCHOLOGICAL SIMULATION In the previous section, the term "physical simulation" was used to represent the case where... psychology that there is no "step function" threshold. Rather, detection capability plotted against phys- ical parameter strength results in an ogival

Semi-physical Simulation Platform of a Parafoil Nonlinear Dynamic System

NASA Astrophysics Data System (ADS)

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

2013-11-01

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

Coupling of Charged Particles Via Coulombic Interactions: Numerical Simulations and Resultant Kappa-Like Velocity Space Distribution Functions

NASA Technical Reports Server (NTRS)

Randol, Brent M.; Christian, Eric R.

2016-01-01

A parametric study is performed using the electrostatic simulations of Randol and Christian (2014) in which the number density, n, and initial thermal speed, theta, are varied. The range of parameters covers an extremely broad plasma regime, all the way from the very weak coupling of space plasmas to the very strong coupling of solid plasmas. The first result is that simulations at the same Lambda(sub D), where Lambda(sub D) is the plasma coupling parameter, but at different combinations of n and theta, behave exactly the same. As a function of Lambda(sub D), the form of p(v), the velocity distribution function of v, the magnitude of v, the velocity vector, is studied. For intermediate to high D, heating is observed in p(v) that obeys conservation of energy, and a suprathermal tail is formed, with a spectral index that depends on Lambda(sub D). For strong coupling (Lambda(sub D) much > 1), the form of the tail is v5, consistent with the findings of Randol and Christian (2014). For weak coupling (Lambda(sub D much <1), no acceleration or heating occurs, as there is no free energy. The dependence on N, the number of particles in the simulation, is also explored. There is a subtle dependence in the index of the tail, such that v5 appears to be the N approaches infinity limit.

A task-related and resting state realistic fMRI simulator for fMRI data validation

NASA Astrophysics Data System (ADS)

Hill, Jason E.; Liu, Xiangyu; Nutter, Brian; Mitra, Sunanda

2017-02-01

After more than 25 years of published functional magnetic resonance imaging (fMRI) studies, careful scrutiny reveals that most of the reported results lack fully decisive validation. The complex nature of fMRI data generation and acquisition results in unavoidable uncertainties in the true estimation and interpretation of both task-related activation maps and resting state functional connectivity networks, despite the use of various statistical data analysis methodologies. The goal of developing the proposed STANCE (Spontaneous and Task-related Activation of Neuronally Correlated Events) simulator is to generate realistic task-related and/or resting-state 4D blood oxygenation level dependent (BOLD) signals, given the experimental paradigm and scan protocol, by using digital phantoms of twenty normal brains available from BrainWeb (http://brainweb.bic.mni.mcgill.ca/brainweb/). The proposed simulator will include estimated system and modelled physiological noise as well as motion to serve as a reference to measured brain activities. In its current form, STANCE is a MATLAB toolbox with command line functions serving as an open-source add-on to SPM8 (http://www.fil.ion.ucl.ac.uk/spm/software/spm8/). The STANCE simulator has been designed in a modular framework so that the hemodynamic response (HR) and various noise models can be iteratively improved to include evolving knowledge about such models.

Coupling of charged particles via Coulombic interactions: Numerical simulations and resultant kappa-like velocity space distribution functions

NASA Astrophysics Data System (ADS)

Randol, Brent M.; Christian, Eric R.

2016-03-01

A parametric study is performed using the electrostatic simulations of Randol and Christian in which the number density, n, and initial thermal speed, θ, are varied. The range of parameters covers an extremely broad plasma regime, all the way from the very weak coupling of space plasmas to the very strong coupling of solid plasmas. The first result is that simulations at the same ΓD, where ΓD (∝ n1/3θ-2) is the plasma coupling parameter, but at different combinations of n and θ, behave exactly the same. As a function of ΓD, the form of p(v), the velocity distribution function of v, the magnitude of v, the velocity vector, is studied. For intermediate to high ΓD, heating is observed in p(v) that obeys conservation of energy, and a suprathermal tail is formed, with a spectral index that depends on ΓD. For strong coupling (ΓD≫1), the form of the tail is v-5, consistent with the findings of Randol and Christian). For weak coupling (ΓD≪1), no acceleration or heating occurs, as there is no free energy. The dependence on N, the number of particles in the simulation, is also explored. There is a subtle dependence in the index of the tail, such that v-5 appears to be the N→∞ limit.

Probabilistic biosphere modeling for the long-term safety assessment of geological disposal facilities for radioactive waste using first- and second-order Monte Carlo simulation.

PubMed

Ciecior, Willy; Röhlig, Klaus-Jürgen; Kirchner, Gerald

2018-10-01

In the present paper, deterministic as well as first- and second-order probabilistic biosphere modeling approaches are compared. Furthermore, the sensitivity of the influence of the probability distribution function shape (empirical distribution functions and fitted lognormal probability functions) representing the aleatory uncertainty (also called variability) of a radioecological model parameter as well as the role of interacting parameters are studied. Differences in the shape of the output distributions for the biosphere dose conversion factor from first-order Monte Carlo uncertainty analysis using empirical and fitted lognormal distribution functions for input parameters suggest that a lognormal approximation is possibly not always an adequate representation of the aleatory uncertainty of a radioecological parameter. Concerning the comparison of the impact of aleatory and epistemic parameter uncertainty on the biosphere dose conversion factor, the latter here is described using uncertain moments (mean, variance) while the distribution itself represents the aleatory uncertainty of the parameter. From the results obtained, the solution space of second-order Monte Carlo simulation is much larger than that from first-order Monte Carlo simulation. Therefore, the influence of epistemic uncertainty of a radioecological parameter on the output result is much larger than that one caused by its aleatory uncertainty. Parameter interactions are only of significant influence in the upper percentiles of the distribution of results as well as only in the region of the upper percentiles of the model parameters. Copyright © 2018 Elsevier Ltd. All rights reserved.

Numerical simulation of terahertz transmission of bilayer metallic meshes with different thickness of substrates

NASA Astrophysics Data System (ADS)

Zhang, Gaohui; Zhao, Guozhong; Zhang, Shengbo

2012-12-01

The terahertz transmission characteristics of bilayer metallic meshes are studied based on the finite difference time domain method. The bilayer well-shaped grid, the array of complementary square metallic pill and the cross wire-hole array were investigated. The results show that the bilayer well-shaped grid achieves a high-pass of filter function, while the bilayer array of complementary square metallic pill achieves a low-pass of filter function, the bilayer cross wire-hole array achieves a band-pass of filter function. Between two metallic microstructures, the medium need to be deposited. Obviously, medium thicknesses have an influence on the terahertz transmission characteristics of metallic microstructures. Simulation results show that with increasing the thicknesses of the medium the cut-off frequency of high-pass filter and low-pass filter move to low frequency. But the bilayer cross wire-hole array possesses two transmission peaks which display competition effect.

Computer aided planning of orthopaedic surgeries: the definition of generic planning steps for bone removal procedures.

PubMed

Putzer, David; Moctezuma, Jose Luis; Nogler, Michael

2017-11-01

An increasing number of orthopaedic surgeons are using computer aided planning tools for bone removal applications. The aim of the study was to consolidate a set of generic functions to be used for a 3D computer assisted planning or simulation. A limited subset of 30 surgical procedures was analyzed and verified in 243 surgical procedures of a surgical atlas. Fourteen generic functions to be used in 3D computer assisted planning and simulations were extracted. Our results showed that the average procedure comprises 14 ± 10 (SD) steps with ten different generic planning steps and four generic bone removal steps. In conclusion, the study shows that with a limited number of 14 planning functions it is possible to perform 243 surgical procedures out of Campbell's Operative Orthopedics atlas. The results may be used as a basis for versatile generic intraoperative planning software.

Improving Advanced Inverter Control Convergence in Distribution Power Flow

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

Nagarajan, Adarsh; Palmintier, Bryan; Ding, Fei

Simulation of modern distribution system powerflow increasingly requires capturing the impact of advanced PV inverter voltage regulation on powerflow. With Volt/var control, the inverter adjusts its reactive power flow as a function of the point of common coupling (PCC) voltage. Similarly, Volt/watt control curtails active power production as a function of PCC voltage. However, with larger systems and higher penetrations of PV, this active/reactive power flow itself can cause significant changes to the PCC voltage potentially introducing oscillations that slow the convergence of system simulations. Improper treatment of these advanced inverter functions could potentially lead to incorrect results. This papermore » explores a simple approach to speed such convergence by blending in the previous iteration's reactive power estimate to dampen these oscillations. Results with a single large (5MW) PV system and with multiple 500kW advanced inverters show dramatic improvements using this approach.« less

Dynamic Biological Functioning Important for Simulating and Stabilizing Ocean Biogeochemistry

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

A CONTINUUM HARD-SPHERE MODEL OF PROTEIN ADSORPTION

PubMed Central

Finch, Craig; Clarke, Thomas; Hickman, James J.

2012-01-01

Protein adsorption plays a significant role in biological phenomena such as cell-surface interactions and the coagulation of blood. Two-dimensional random sequential adsorption (RSA) models are widely used to model the adsorption of proteins on solid surfaces. Continuum equations have been developed so that the results of RSA simulations can be used to predict the kinetics of adsorption. Recently, Brownian dynamics simulations have become popular for modeling protein adsorption. In this work a continuum model was developed to allow the results from a Brownian dynamics simulation to be used as the boundary condition in a computational fluid dynamics (CFD) simulation. Brownian dynamics simulations were used to model the diffusive transport of hard-sphere particles in a liquid and the adsorption of the particles onto a solid surface. The configuration of the adsorbed particles was analyzed to quantify the chemical potential near the surface, which was found to be a function of the distance from the surface and the fractional surface coverage. The near-surface chemical potential was used to derive a continuum model of adsorption that incorporates the results from the Brownian dynamics simulations. The equations of the continuum model were discretized and coupled to a CFD simulation of diffusive transport to the surface. The kinetics of adsorption predicted by the continuum model closely matched the results from the Brownian dynamics simulation. This new model allows the results from mesoscale simulations to be incorporated into micro- or macro-scale CFD transport simulations of protein adsorption in practical devices. PMID:23729843

Impact of High-Fidelity Simulation and Pharmacist-Specific Didactic Lectures in Addition to ACLS Provider Certification on Pharmacy Resident ACLS Performance.

PubMed

Bartel, Billie J

2014-08-01

This pilot study explored the use of multidisciplinary high-fidelity simulation and additional pharmacist-focused training methods in training postgraduate year 1 (PGY1) pharmacy residents to provide Advanced Cardiovascular Life Support (ACLS) care. Pharmacy resident confidence and comfort level were assessed after completing these training requirements. The ACLS training requirements for pharmacy residents were revised to include didactic instruction on ACLS pharmacology and rhythm recognition and participation in multidisciplinary high-fidelity simulation ACLS experiences in addition to ACLS provider certification. Surveys were administered to participating residents to assess the impact of this additional education on resident confidence and comfort level in cardiopulmonary arrest situations. The new ACLS didactic and simulation training requirements resulted in increased resident confidence and comfort level in all assessed functions. Residents felt more confident in all areas except providing recommendations for dosing and administration of medications and rhythm recognition after completing the simulation scenarios than with ACLS certification training and the didactic components alone. All residents felt the addition of lectures and simulation experiences better prepared them to function as a pharmacist in the ACLS team. Additional ACLS training requirements for pharmacy residents increased overall awareness of pharmacist roles and responsibilities and greatly improved resident confidence and comfort level in performing most essential pharmacist functions during ACLS situations. © The Author(s) 2013.

Insights into the use of time-lapse GPR data as observations for inverse multiphase flow simulations of DNAPL migration

USGS Publications Warehouse

Johnson, R.H.; Poeter, E.P.

2007-01-01

Perchloroethylene (PCE) saturations determined from GPR surveys were used as observations for inversion of multiphase flow simulations of a PCE injection experiment (Borden 9??m cell), allowing for the estimation of optimal bulk intrinsic permeability values. The resulting fit statistics and analysis of residuals (observed minus simulated PCE saturations) were used to improve the conceptual model. These improvements included adjustment of the elevation of a permeability contrast, use of the van Genuchten versus Brooks-Corey capillary pressure-saturation curve, and a weighting scheme to account for greater measurement error with larger saturation values. A limitation in determining PCE saturations through one-dimensional GPR modeling is non-uniqueness when multiple GPR parameters are unknown (i.e., permittivity, depth, and gain function). Site knowledge, fixing the gain function, and multiphase flow simulations assisted in evaluating non-unique conceptual models of PCE saturation, where depth and layering were reinterpreted to provide alternate conceptual models. Remaining bias in the residuals is attributed to the violation of assumptions in the one-dimensional GPR interpretation (which assumes flat, infinite, horizontal layering) resulting from multidimensional influences that were not included in the conceptual model. While the limitations and errors in using GPR data as observations for inverse multiphase flow simulations are frustrating and difficult to quantify, simulation results indicate that the error and bias in the PCE saturation values are small enough to still provide reasonable optimal permeability values. The effort to improve model fit and reduce residual bias decreases simulation error even for an inversion based on biased observations and provides insight into alternate GPR data interpretations. Thus, this effort is warranted and provides information on bias in the observation data when this bias is otherwise difficult to assess. ?? 2006 Elsevier B.V. All rights reserved.

nth-Nearest-neighbor distribution functions of an interacting fluid from the pair correlation function: a hierarchical approach.

PubMed

Bhattacharjee, Biplab

2003-04-01

The paper presents a general formalism for the nth-nearest-neighbor distribution (NND) of identical interacting particles in a fluid confined in a nu-dimensional space. The nth-NND functions, W(n,r) (for n=1,2,3, em leader) in a fluid are obtained hierarchically in terms of the pair correlation function and W(n-1,r) alone. The radial distribution function (RDF) profiles obtained from the molecular dynamics (MD) simulation of Lennard-Jones (LJ) fluid is used to illustrate the results. It is demonstrated that the collective structural information contained in the maxima and minima of the RDF profiles being resolved in terms of individual NND functions may provide more insights about the microscopic neighborhood structure around a reference particle in a fluid. Representative comparison between the results obtained from the formalism and the MD simulation data shows good agreement. Apart from the quantities such as nth-NND functions and nth-nearest-neighbor distances, the average neighbor population number is defined. These quantities are evaluated for the LJ model system and interesting density dependence of the microscopic neighborhood shell structures are discussed in terms of them. The relevance of the NND functions in various phenomena is also pointed out.

nth-nearest-neighbor distribution functions of an interacting fluid from the pair correlation function: A hierarchical approach

NASA Astrophysics Data System (ADS)

Bhattacharjee, Biplab

2003-04-01

The paper presents a general formalism for the nth-nearest-neighbor distribution (NND) of identical interacting particles in a fluid confined in a ν-dimensional space. The nth-NND functions, W(n,r¯) (for n=1,2,3,…) in a fluid are obtained hierarchically in terms of the pair correlation function and W(n-1,r¯) alone. The radial distribution function (RDF) profiles obtained from the molecular dynamics (MD) simulation of Lennard-Jones (LJ) fluid is used to illustrate the results. It is demonstrated that the collective structural information contained in the maxima and minima of the RDF profiles being resolved in terms of individual NND functions may provide more insights about the microscopic neighborhood structure around a reference particle in a fluid. Representative comparison between the results obtained from the formalism and the MD simulation data shows good agreement. Apart from the quantities such as nth-NND functions and nth-nearest-neighbor distances, the average neighbor population number is defined. These quantities are evaluated for the LJ model system and interesting density dependence of the microscopic neighborhood shell structures are discussed in terms of them. The relevance of the NND functions in various phenomena is also pointed out.

Numerical simulation and analysis of accurate blood oxygenation measurement by using optical resolution photoacoustic microscopy

NASA Astrophysics Data System (ADS)

Yu, Tianhao; Li, Qian; Li, Lin; Zhou, Chuanqing

2016-10-01

Accuracy of photoacoustic signal is the crux on measurement of oxygen saturation in functional photoacoustic imaging, which is influenced by factors such as defocus of laser beam, curve shape of large vessels and nonlinear saturation effect of optical absorption in biological tissues. We apply Monte Carlo model to simulate energy deposition in tissues and obtain photoacoustic signals reaching a simulated focused surface detector to investigate corresponding influence of these factors. We also apply compensation on photoacoustic imaging of in vivo cat cerebral cortex blood vessels, in which signals from different lateral positions of vessels are corrected based on simulation results. And this process on photoacoustic images can improve the smoothness and accuracy of oxygen saturation results.

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

Modeling winter wheat phenological responses to water deficits in the Unified Plant Growth Model (UPGM) component of the spatially distributed Agricultural Ecosystem Services (AgES) model

USDA-ARS?s Scientific Manuscript database

Accurately predicting phenology in crop simulation models is critical for correctly simulating crop production. While extensive work in modeling phenology has focused on the temperature response function (resulting in robust phenology models), limited work on quantifying the phenological responses t...

Comparison of the analytical and simulation results of the equilibrium beam profile

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

Liu, Z. J.; Zhu Shaoping; Cao, L. H.

2007-10-15

The evolution of high current electron beams in dense plasmas has been investigated by using two-dimensional particle-in-cell (PIC) simulations with immobile ions. It is shown that electron beams are split into many filaments at the beginning due to the Weibel instability, and then different filamentation beams attract each other and coalesce. The profile of the filaments can be described by formulas. Hammer et al. [Phys. Fluids 13, 1831 (1970)] developed a self-consistent relativistic electron beam model that allows the propagation of relativistic electron fluxes in excess of the Alfven-Lawson critical-current limit for a fully neutralized beam. The equilibrium solution hasmore » been observed in the simulation results, but the electron distribution function assumed by Hammer et al. is different from the simulation results.« less

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.

A Dynamic Simulation of Musculoskeletal Function in the Mouse Hindlimb During Trotting Locomotion

PubMed Central

Charles, James P.; Cappellari, Ornella; Hutchinson, John R.

2018-01-01

Mice are often used as animal models of various human neuromuscular diseases, and analysis of these models often requires detailed gait analysis. However, little is known of the dynamics of the mouse musculoskeletal system during locomotion. In this study, we used computer optimization procedures to create a simulation of trotting in a mouse, using a previously developed mouse hindlimb musculoskeletal model in conjunction with new experimental data, allowing muscle forces, activation patterns, and levels of mechanical work to be estimated. Analyzing musculotendon unit (MTU) mechanical work throughout the stride allowed a deeper understanding of their respective functions, with the rectus femoris MTU dominating the generation of positive and negative mechanical work during the swing and stance phases. This analysis also tested previous functional inferences of the mouse hindlimb made from anatomical data alone, such as the existence of a proximo-distal gradient of muscle function, thought to reflect adaptations for energy-efficient locomotion. The results do not strongly support the presence of this gradient within the mouse musculoskeletal system, particularly given relatively high negative net work output from the ankle plantarflexor MTUs, although more detailed simulations could test this further. This modeling analysis lays a foundation for future studies of the control of vertebrate movement through the development of neuromechanical simulations. PMID:29868576

A reappraisal of drug release laws using Monte Carlo simulations: the prevalence of the Weibull function.

PubMed

Kosmidis, Kosmas; Argyrakis, Panos; Macheras, Panos

2003-07-01

To verify the Higuchi law and study the drug release from cylindrical and spherical matrices by means of Monte Carlo computer simulation. A one-dimensional matrix, based on the theoretical assumptions of the derivation of the Higuchi law, was simulated and its time evolution was monitored. Cylindrical and spherical three-dimensional lattices were simulated with sites at the boundary of the lattice having been denoted as leak sites. Particles were allowed to move inside it using the random walk model. Excluded volume interactions between the particles was assumed. We have monitored the system time evolution for different lattice sizes and different initial particle concentrations. The Higuchi law was verified using the Monte Carlo technique in a one-dimensional lattice. It was found that Fickian drug release from cylindrical matrices can be approximated nicely with the Weibull function. A simple linear relation between the Weibull function parameters and the specific surface of the system was found. Drug release from a matrix, as a result of a diffusion process assuming excluded volume interactions between the drug molecules, can be described using a Weibull function. This model, although approximate and semiempirical, has the benefit of providing a simple physical connection between the model parameters and the system geometry, which was something missing from other semiempirical models.

First-principles-based kinetic Monte Carlo simulation of nitric oxide decomposition over Pt and Rh surfaces under lean-burn conditions

NASA Astrophysics Data System (ADS)

Mei, Donghai; Ge, Qingfeng; Neurock, Matthew; Kieken, Laurent; Lerou, Jan

First-principles-based kinetic Monte Carlo simulation was used to track the elementary surface transformations involved in the catalytic decomposition of NO over Pt(100) and Rh(100) surfaces under lean-burn operating conditions. Density functional theory (DFT) calculations were carried out to establish the structure and energetics for all reactants, intermediates and products over Pt(100) and Rh(100). Lateral interactions which arise from neighbouring adsorbates were calculated by examining changes in the binding energies as a function of coverage and different coadsorbed configurations. These data were fitted to a bond order conservation (BOC) model which is subsequently used to establish the effects of coverage within the simulation. The intrinsic activation barriers for all the elementary reaction steps in the proposed mechanism of NO reduction over Pt(100) were calculated by using DFT. These values are corrected for coverage effects by using the parametrized BOC model internally within the simulation. This enables a site-explicit kinetic Monte Carlo simulation that can follow the kinetics of NO decomposition over Pt(100) and Rh(100) in the presence of excess oxygen. The simulations are used here to model various experimental protocols including temperature programmed desorption as well as batch catalytic kinetics. The simulation results for the temperature programmed desorption and decomposition of NO over Pt(100) and Rh(100) under vacuum condition were found to be in very good agreement with experimental results. NO decomposition is strongly tied to the temporal number of sites that remain vacant. Experimental results show that Pt is active in the catalytic reaction of NO into N2 and NO2 under lean-burn conditions. The simulated reaction orders for NO and O2 were found to be +0.9 and -0.4 at 723 K, respectively. The simulation also indicates that there is no activity over Rh(100) since the surface becomes poisoned by oxygen.

Geological terrain models

NASA Technical Reports Server (NTRS)

Kaupp, V. H.; Macdonald, H. C.; Waite, W. P.

1981-01-01

The initial phase of a program to determine the best interpretation strategy and sensor configuration for a radar remote sensing system for geologic applications is discussed. In this phase, terrain modeling and radar image simulation were used to perform parametric sensitivity studies. A relatively simple computer-generated terrain model is presented, and the data base, backscatter file, and transfer function for digital image simulation are described. Sets of images are presented that simulate the results obtained with an X-band radar from an altitude of 800 km and at three different terrain-illumination angles. The simulations include power maps, slant-range images, ground-range images, and ground-range images with statistical noise incorporated. It is concluded that digital image simulation and computer modeling provide cost-effective methods for evaluating terrain variations and sensor parameter changes, for predicting results, and for defining optimum sensor parameters.

FLUKA simulation of TEPC response to cosmic radiation.

PubMed

Beck, P; Ferrari, A; Pelliccioni, M; Rollet, S; Villari, R

2005-01-01

The aircrew exposure to cosmic radiation can be assessed by calculation with codes validated by measurements. However, the relationship between doses in the free atmosphere, as calculated by the codes and from results of measurements performed within the aircraft, is still unclear. The response of a tissue-equivalent proportional counter (TEPC) has already been simulated successfully by the Monte Carlo transport code FLUKA. Absorbed dose rate and ambient dose equivalent rate distributions as functions of lineal energy have been simulated for several reference sources and mixed radiation fields. The agreement between simulation and measurements has been well demonstrated. In order to evaluate the influence of aircraft structures on aircrew exposure assessment, the response of TEPC in the free atmosphere and on-board is now simulated. The calculated results are discussed and compared with other calculations and measurements.

Evaluation of the grand-canonical partition function using expanded Wang-Landau simulations. III. Impact of combining rules on mixtures properties

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

Desgranges, Caroline; Delhommelle, Jerome

2014-03-14

Combining rules, such as the Lorentz-Berthelot rules, are routinely used to calculate the thermodynamic properties of mixtures using molecular simulations. Here we extend the expanded Wang-Landau simulation approach to determine the impact of the combining rules on the value of the partition function of binary systems, and, in turn, on the phase coexistence and thermodynamics of these mixtures. We study various types of mixtures, ranging from systems of rare gases to biologically and technologically relevant mixtures, such as water-urea and water-carbon dioxide. Comparing the simulation results to the experimental data on mixtures of rare gases allows us to rank themore » performance of combining rules. We find that the widely used Lorentz-Berthelot rules exhibit the largest deviations from the experimental data, both for the bulk and at coexistence, while the Kong and Waldman-Hagler provide much better alternatives. In particular, in the case of aqueous solutions of urea, we show that the use of the Lorentz-Berthelot rules has a strong impact on the Gibbs free energy of the solute, overshooting the value predicted by the Waldman-Hagler rules by 7%. This result emphasizes the importance of the combining rule for the determination of hydration free energies using molecular simulations.« less

Impact of Missing Data on the Detection of Differential Item Functioning: The Case of Mantel-Haenszel and Logistic Regression Analysis

ERIC Educational Resources Information Center

Robitzsch, Alexander; Rupp, Andre A.

2009-01-01

This article describes the results of a simulation study to investigate the impact of missing data on the detection of differential item functioning (DIF). Specifically, it investigates how four methods for dealing with missing data (listwise deletion, zero imputation, two-way imputation, response function imputation) interact with two methods of…

A Method for Functional Task Alignment Analysis of an Arthrocentesis Simulator.

PubMed

Adams, Reid A; Gilbert, Gregory E; Buckley, Lisa A; Nino Fong, Rodolfo; Fuentealba, I Carmen; Little, Erika L

2018-05-16

During simulation-based education, simulators are subjected to procedures composed of a variety of tasks and processes. Simulators should functionally represent a patient in response to the physical action of these tasks. The aim of this work was to describe a method for determining whether a simulator does or does not have sufficient functional task alignment (FTA) to be used in a simulation. Potential performance checklist items were gathered from published arthrocentesis guidelines and aggregated into a performance checklist using Lawshe's method. An expert panel used this performance checklist and an FTA analysis questionnaire to evaluate a simulator's ability to respond to the physical actions required by the performance checklist. Thirteen items, from a pool of 39, were included on the performance checklist. Experts had mixed reviews of the simulator's FTA and its suitability for use in simulation. Unexpectedly, some positive FTA was found for several tasks where the simulator lacked functionality. By developing a detailed list of specific tasks required to complete a clinical procedure, and surveying experts on the simulator's response to those actions, educators can gain insight into the simulator's clinical accuracy and suitability. Unexpected of positive FTA ratings of function deficits suggest that further revision of the survey method is required.

Comparative study of popular objective functions for damping power system oscillations in multimachine system.

PubMed

Islam, Naz Niamul; Hannan, M A; Shareef, Hussain; Mohamed, Azah; Salam, M A

2014-01-01

Power oscillation damping controller is designed in linearized model with heuristic optimization techniques. Selection of the objective function is very crucial for damping controller design by optimization algorithms. In this research, comparative analysis has been carried out to evaluate the effectiveness of popular objective functions used in power system oscillation damping. Two-stage lead-lag damping controller by means of power system stabilizers is optimized using differential search algorithm for different objective functions. Linearized model simulations are performed to compare the dominant mode's performance and then the nonlinear model is continued to evaluate the damping performance over power system oscillations. All the simulations are conducted in two-area four-machine power system to bring a detailed analysis. Investigated results proved that multiobjective D-shaped function is an effective objective function in terms of moving unstable and lightly damped electromechanical modes into stable region. Thus, D-shape function ultimately improves overall system damping and concurrently enhances power system reliability.

Implementation of an integrated op-amp based chaotic neuron model and observation of its chaotic dynamics

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

Jung, Jinwoo; Lee, Jewon; Song, Hanjung

2011-03-15

This paper presents a fully integrated circuit implementation of an operational amplifier (op-amp) based chaotic neuron model with a bipolar output function, experimental measurements, and analyses of its chaotic behavior. The proposed chaotic neuron model integrated circuit consists of several op-amps, sample and hold circuits, a nonlinear function block for chaotic signal generation, a clock generator, a nonlinear output function, etc. Based on the HSPICE (circuit program) simulation results, approximated empirical equations for analyses were formulated. Then, the chaotic dynamical responses such as bifurcation diagrams, time series, and Lyapunov exponent were calculated using these empirical equations. In addition, we performedmore » simulations about two chaotic neuron systems with four synapses to confirm neural network connections and got normal behavior of the chaotic neuron such as internal state bifurcation diagram according to the synaptic weight variation. The proposed circuit was fabricated using a 0.8-{mu}m single poly complementary metal-oxide semiconductor technology. Measurements of the fabricated single chaotic neuron with {+-}2.5 V power supplies and a 10 kHz sampling clock frequency were carried out and compared with the simulated results.« less

Fluctuations, noise, and numerical methods in gyrokinetic particle-in-cell simulations

NASA Astrophysics Data System (ADS)

Jenkins, Thomas Grant

In this thesis, the role of the "marker weight" (or "particle weight") used in gyrokinetic particle-in-cell (PIC) simulations is explored. Following a review of the foundations and major developments of gyrokinetic theory, key concepts of the Monte Carlo methods which form the basis for PIC simulations are set forth. Consistent with these methods, a Klimontovich representation for the set of simulation markers is developed in the extended phase space {R, v||, v ⊥, W, P} (with the additional coordinates representing weight fields); clear distinctions are consequently established between the marker distribution function and various physical distribution functions (arising from diverse moments of the marker distribution). Equations describing transport in the simulation are shown to be easily derivable using the formalism. The necessity of a two-weight model for nonequilibrium simulations is demonstrated, and a simple method for calculating the second (background-related) weight is presented. Procedures for arbitrary marker loading schemes in gyrokinetic PIC simulations are outlined; various initialization methods for simulations are compared. Possible effects of inadequate velocity-space resolution in gyrokinetic continuum simulations are explored. The "partial-f" simulation method is developed and its limitations indicated. A quasilinear treatment of electrostatic drift waves is shown to correctly predict nonlinear saturation amplitudes, and the relevance of the gyrokinetic fluctuation-dissipation theorem in assessing the effects of discrete-marker-induced statistical noise on the resulting marginally stable states is demonstrated.

Imagining the future: The core episodic simulation network dissociates as a function of timecourse and the amount of simulated information

PubMed Central

Thakral, Preston P.; Benoit, Roland G.; Schacter, Daniel L.

2017-01-01

Neuroimaging data indicate that episodic memory (i.e., remembering specific past experiences) and episodic simulation (i.e., imagining specific future experiences) are associated with enhanced activity in a common set of neural regions, often referred to as the core network. This network comprises the hippocampus, parahippocampal cortex, lateral and medial parietal cortex, lateral temporal cortex, and medial prefrontal cortex. Evidence for a core network has been taken as support for the idea that episodic memory and episodic simulation are supported by common processes. Much remains to be learned about how specific core network regions contribute to specific aspects of episodic simulation. Prior neuroimaging studies of episodic memory indicate that certain regions within the core network are differentially sensitive to the amount of information recollected (e.g., the left lateral parietal cortex). In addition, certain core network regions dissociate as a function of their timecourse of engagement during episodic memory (e.g., transient activity in the posterior hippocampus and sustained activity in the left lateral parietal cortex). In the current study, we assessed whether similar dissociations could be observed during episodic simulation. We found that the left lateral parietal cortex modulates as a function of the amount of simulated details. Of particular interest, while the hippocampus was insensitive to the amount of simulated details, we observed a temporal dissociation within the hippocampus: transient activity occurred in relatively posterior portions of the hippocampus and sustained activity occurred in anterior portions. Because the posterior hippocampal and lateral parietal findings parallel those observed previously during episodic memory, the present results add to the evidence that episodic memory and episodic simulation are supported by common processes. Critically, the present study also provides evidence that regions within the core network support dissociable processes. PMID:28324695

GridPV Toolbox

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

Broderick, Robert; Quiroz, Jimmy; Grijalva, Santiago

2014-07-15

Matlab Toolbox for simulating the impact of solar energy on the distribution grid. The majority of the functions are useful for interfacing OpenDSS and MATLAB, and they are of generic use for commanding OpenDSS from MATLAB and retrieving GridPV Toolbox information from simulations. A set of functions is also included for modeling PV plant output and setting up the PV plant in the OpenDSS simulation. The toolbox contains functions for modeling the OpenDSS distribution feeder on satellite images with GPS coordinates. Finally, example simulations functions are included to show potential uses of the toolbox functions.

Pilot Subjective Assessments During an Investigation of Separation Function Allocation Using a Human-In-The-Loop Simulation

NASA Technical Reports Server (NTRS)

Burke, Kelly A.; Wing, David J.; Lewis, Timothy

2013-01-01

Two human-in-the-loop simulation experiments were conducted to investigate allocation of separation assurance functions between ground and air and between humans and automation. The experiments modeled a mixed-operations concept in which aircraft receiving ground-based separation services shared the airspace with aircraft providing their own separation service (i.e., self-separation). The two experiments, one pilot-focused and the other controller-focused, addressed selected key issues of mixed operations and modeling an emergence of NextGen technologies and procedures. This paper focuses on the results of the subjective assessments of pilots collected during the pilot-focused human-in-the-loop simulation, specifically workload and situation awareness. Generally the results revealed that across all conditions, pilots' perceived workload was low to medium, with the highest reported levels of workload occurring when the pilots experienced a loss of separation during the scenario. Furthermore, the results from the workload data and situation awareness data were complimentary such that when pilots reported lower levels of workload they also experienced higher levels of situation awareness.

Trait-based Modeling Reveals How Plankton Biodiversity-Ecosystem Function (BEF) Relationships Depend on Environmental Variability

NASA Astrophysics Data System (ADS)

Smith, S. L.; Chen, B.; Vallina, S. M.

2017-12-01

Biodiversity-Ecosystem Function (BEF) relationships, which are most commonly quantified in terms of productivity or total biomass yield, are known to depend on the timescale of the experiment or field study, both for terrestrial plants and phytoplankton, which have each been widely studied as model ecosystems. Although many BEF relationships are positive (i.e., increasing biodiversity enhances function), in some cases there is an optimal intermediate diversity level (i.e., a uni-modal relationship), and in other cases productivity decreases with certain measures of biodiversity. These differences in BEF relationships cannot be reconciled merely by differences in the timescale of experiments. We will present results from simulation experiments applying recently developed trait-based models of phytoplankton communities and ecosystems, using the `adaptive dynamics' framework to represent continuous distributions of size and other key functional traits. Controlled simulation experiments were conducted with different levels of phytoplankton size-diversity, which through trait-size correlations implicitly represents functional-diversity. One recent study applied a theoretical box model for idealized simulations at different frequencies of disturbance. This revealed how the shapes of BEF relationships depend systematically on the frequency of disturbance and associated nutrient supply. We will also present more recent results obtained using a trait-based plankton ecosystem model embedded in a three-dimensional ocean model applied to the North Pacific. This reveals essentially the same pattern in a spatially explicit model with more realistic environmental forcing. In the relatively more variable subarctic, productivity tends to increase with the size (and hence functional) diversity of phytoplankton, whereas productivity tends to decrease slightly with increasing size-diversity in the relatively calm subtropics. Continuous trait-based models can capture essential features of BEF relationships, while requiring far fewer calculations compared to typical plankton diversity models that explicitly simulate a great many idealized species.

Linkage mechanisms in the vertebrate skull: Structure and function of three-dimensional, parallel transmission systems.

PubMed

Olsen, Aaron M; Westneat, Mark W

2016-12-01

Many musculoskeletal systems, including the skulls of birds, fishes, and some lizards consist of interconnected chains of mobile skeletal elements, analogous to linkage mechanisms used in engineering. Biomechanical studies have applied linkage models to a diversity of musculoskeletal systems, with previous applications primarily focusing on two-dimensional linkage geometries, bilaterally symmetrical pairs of planar linkages, or single four-bar linkages. Here, we present new, three-dimensional (3D), parallel linkage models of the skulls of birds and fishes and use these models (available as free kinematic simulation software), to investigate structure-function relationships in these systems. This new computational framework provides an accessible and integrated workflow for exploring the evolution of structure and function in complex musculoskeletal systems. Linkage simulations show that kinematic transmission, although a suitable functional metric for linkages with single rotating input and output links, can give misleading results when applied to linkages with substantial translational components or multiple output links. To take into account both linear and rotational displacement we define force mechanical advantage for a linkage (analogous to lever mechanical advantage) and apply this metric to measure transmission efficiency in the bird cranial mechanism. For linkages with multiple, expanding output points we propose a new functional metric, expansion advantage, to measure expansion amplification and apply this metric to the buccal expansion mechanism in fishes. Using the bird cranial linkage model, we quantify the inaccuracies that result from simplifying a 3D geometry into two dimensions. We also show that by combining single-chain linkages into parallel linkages, more links can be simulated while decreasing or maintaining the same number of input parameters. This generalized framework for linkage simulation and analysis can accommodate linkages of differing geometries and configurations, enabling novel interpretations of the mechanics of force transmission across a diversity of vertebrate feeding mechanisms and enhancing our understanding of musculoskeletal function and evolution. J. Morphol. 277:1570-1583, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Update on Controlling Herds of Cooperative Robots

NASA Technical Reports Server (NTRS)

Quadrelli, Marco; Chang, Johnny

2007-01-01

A document presents further information on the subject matter of "Controlling Herds of Cooperative Robots". The document describes the results of the computational simulations of a one-blimp, three-surface-sonde herd in various operational scenarios, including sensitivity studies as a function of distributed communication and processing delays between the sondes and the blimp. From results of the simulations, it is concluded that the methodology is feasible, even if there are significant uncertainties in the dynamical models.

Small Business Innovations

NASA Technical Reports Server (NTRS)

1992-01-01

The purpose of QASE RT is to enable system analysts and software engineers to evaluate performance and reliability implications of design alternatives. The program resulted from two Small Business Innovation Research (SBIR) projects. After receiving a description of the system architecture and workload from the user, QASE RT translates the system description into simulation models and executes them. Simulation provides detailed performance evaluation. The results of the evaluations are service and response times, offered load and device utilizations and functional availability.

Modeling and Simulation of Variable Mass, Flexible Structures

NASA Technical Reports Server (NTRS)

Tobbe, Patrick A.; Matras, Alex L.; Wilson, Heath E.

2009-01-01

The advent of the new Ares I launch vehicle has highlighted the need for advanced dynamic analysis tools for variable mass, flexible structures. This system is composed of interconnected flexible stages or components undergoing rapid mass depletion through the consumption of solid or liquid propellant. In addition to large rigid body configuration changes, the system simultaneously experiences elastic deformations. In most applications, the elastic deformations are compatible with linear strain-displacement relationships and are typically modeled using the assumed modes technique. The deformation of the system is approximated through the linear combination of the products of spatial shape functions and generalized time coordinates. Spatial shape functions are traditionally composed of normal mode shapes of the system or even constraint modes and static deformations derived from finite element models of the system. Equations of motion for systems undergoing coupled large rigid body motion and elastic deformation have previously been derived through a number of techniques [1]. However, in these derivations, the mode shapes or spatial shape functions of the system components were considered constant. But with the Ares I vehicle, the structural characteristics of the system are changing with the mass of the system. Previous approaches to solving this problem involve periodic updates to the spatial shape functions or interpolation between shape functions based on system mass or elapsed mission time. These solutions often introduce misleading or even unstable numerical transients into the system. Plus, interpolation on a shape function is not intuitive. This paper presents an approach in which the shape functions are held constant and operate on the changing mass and stiffness matrices of the vehicle components. Each vehicle stage or component finite element model is broken into dry structure and propellant models. A library of propellant models is used to describe the distribution of mass in the fuel tank or Solid Rocket Booster (SRB) case for various propellant levels. Based on the mass consumed by the liquid engine or SRB, the appropriate propellant model is coupled with the dry structure model for the stage. Then using vehicle configuration data, the integrated vehicle model is assembled and operated on by the constant system shape functions. The system mode shapes and frequencies can then be computed from the resulting generalized mass and stiffness matrices for that mass configuration. The rigid body mass properties of the vehicle are derived from the integrated vehicle model. The coupling terms between the vehicle rigid body motion and elastic deformation are also updated from the constant system shape functions and the integrated vehicle model. This approach was first used to analyze variable mass spinning beams and then prototyped into a generic dynamics simulation engine. The resulting code was tested against Crew Launch Vehicle (CLV-)class problems worked in the TREETOPS simulation package and by Wilson [2]. The Ares I System Integration Laboratory (SIL) is currently being developed at the Marshall Space Flight Center (MSFC) to test vehicle avionics hardware and software in a hardware-in-the-loop (HWIL) environment and certify that the integrated system is prepared for flight. The Ares I SIL utilizes the Ares Real-Time Environment for Modeling, Integration, and Simulation (ARTEMIS) tool to simulate the launch vehicle and stimulate avionics hardware. Due to the presence of vehicle control system filters and the thrust oscillation suppression system, which are tuned to the structural characteristics of the vehicle, ARTEMIS must incorporate accurate structural models of the Ares I launch vehicle. The ARTEMIS core dynamics simulation models the highly coupled nature of the vehicle flexible body dynamics, propellant slosh, and vehicle nozzle inertia effects combined with mass and flexible body properties that vary significant with time during the flight. All forces that act on the vehicle during flight must be simulated, including deflected engine thrust force, spatially distributed aerodynamic forces, gravity, and reaction control jet thrust forces. These forces are used to excite an integrated flexible vehicle, slosh, and nozzle dynamics model for the vehicle stack that simulates large rigid body translations and rotations along with small elastic deformations. Highly effective matrix math operations on a distributed, threaded high-performance simulation node allow ARTEMIS to retain up to 30 modes of flex for real-time simulation. Stage elements that separate from the stack during flight are propagated as independent rigid six degrees of freedom (6DOF) bodies. This paper will present the formulation of the resulting equations of motion, solutions to example problems, and describe the resulting dynamics simulation engine within ARTEMIS.

Improving material removal determinacy based on the compensation of tool influence function

NASA Astrophysics Data System (ADS)

Zhong, Bo; Chen, Xian-hua; Deng, Wen-hui; Zhao, Shi-jie; Zheng, Nan

2018-03-01

In the process of computer-controlled optical surfacing (CCOS), the key of correcting the surface error of optical components is to ensure the consistency between the simulated tool influence function and the actual tool influence function (TIF). The existing removal model usually adopts the fixed-point TIF to remove the material with the planning path and velocity, and it considers that the polishing process is linear and time invariant. However, in the actual polishing process, the TIF is a function related to the feed speed. In this paper, the relationship between the actual TIF and the feed speed (i.e. the compensation relationship between static removal and dynamic removal) is determined by experimental method. Then, the existing removal model is modified based on the compensation relationship, to improve the conformity between simulated and actual processing. Finally, the surface error modification correction test are carried out. The results show that the fitting degree of the simulated surface and the experimental surface is better than 88%, and the surface correction accuracy can be better than 1/10 λ (Λ=632.8nm).

Signals of dynamical and statistical process from IMF-IMF correlation function

NASA Astrophysics Data System (ADS)

Pagano, E. V.; Acosta, L.; Auditore, L.; Baran, V.; Cap, T.; Cardella, G.; Colonna, M.; De Luca, S.; De Filippo, E.; Dell'Aquila, D.; Francalanza, L.; Gnoffo, B.; Lanzalone, G.; Lombardo, I.; Maiolino, C.; Martorana, N. S.; Norella, S.; Pagano, A.; Papa, M.; Piasecki, E.; Pirrone, S.; Politi, G.; Porto, F.; Quattrocchi, L.; Rizzo, F.; Rosato, E.; Russotto, P.; Siwek-Wilczyńska, K.; Trifiro, A.; Trimarchi, M.; Verde, G.; Vigilante, M.; Wilczyńsky, J.

2017-11-01

In this paper we briefly discuss about a novel application of the IMF-IMF correlation function to the physical case of binary massive projectile-like (PLF) splitting for dynamical and statistical breakup/fission in heavy ion collisions at Fermi energy. Theoretical simulations are also shown for comparisons with the data. These preliminary results have been obtained for the reverse kinematics reaction 124Sn + 64Ni at 35 AMeV that was studied using the forward part of CHIMERA detector. In that reaction a strong competition between a dynamical and a statistical components and its evolution with the charge asymmetry of the binary break up was already shown. In this work we show that the IMF-IMF correlation function can be used to pin down the timescale of the fragments production in binary fission-like phenomena. We also made simulations with the CoMDII model in order to compare to the experimental IMF-IMF correlation function. In future we plan to extend these studies to different reaction mechanisms and nuclear systems and to compare with different theoretical transport simulations.

Free energy profiles for two ubiquitous damaging agents: methylation and hydroxylation of guanine in B-DNA.

PubMed

Grüber, R; Aranda, J; Bellili, A; Tuñón, I; Dumont, E

2017-06-07

DNA methylation and hydroxylation are two ubiquitous reactions in DNA damage induction, yet insights are scarce concerning the free energy of activation within B-DNA. We resort to multiscale simulations to investigate the attack of a hydroxyl radical and of the primary diazonium onto a guanine embedded in a solvated dodecamer. Reaction free energy profiles characterize two strongly exergonic processes, yet allow unprecedented quantification of the barrier towards this damage reaction, not higher than 6 kcal mol -1 and sometimes inexistent, and of the exergonicities. In the case of the [G(C8)-OH]˙ intermediate, we challenge the functional dependence of such simulations: recently-proposed functionals, such as M06-2X and LC-BLYP, agree on a ∼4 kcal mol -1 barrier, whereas the hybrid GGA B3LYP functional predicts a barrier-less pathway. In the long term, multiscale approaches can help build up a unified panorama of DNA lesion induction. These results stress the importance of DFT/MM-MD simulations involving new functionals towards the sound modelling of biomolecule damage even in the ground state.

A Digital Sensor Simulator of the Pushbroom Offner Hyperspectral Imaging Spectrometer

PubMed Central

Tao, Dongxing; Jia, Guorui; Yuan, Yan; Zhao, Huijie

2014-01-01

Sensor simulators can be used in forecasting the imaging quality of a new hyperspectral imaging spectrometer, and generating simulated data for the development and validation of the data processing algorithms. This paper presents a novel digital sensor simulator for the pushbroom Offner hyperspectral imaging spectrometer, which is widely used in the hyperspectral remote sensing. Based on the imaging process, the sensor simulator consists of a spatial response module, a spectral response module, and a radiometric response module. In order to enhance the simulation accuracy, spatial interpolation-resampling, which is implemented before the spatial degradation, is developed to compromise the direction error and the extra aliasing effect. Instead of using the spectral response function (SRF), the dispersive imaging characteristics of the Offner convex grating optical system is accurately modeled by its configuration parameters. The non-uniformity characteristics, such as keystone and smile effects, are simulated in the corresponding modules. In this work, the spatial, spectral and radiometric calibration processes are simulated to provide the parameters of modulation transfer function (MTF), SRF and radiometric calibration parameters of the sensor simulator. Some uncertainty factors (the stability, band width of the monochromator for the spectral calibration, and the integrating sphere uncertainty for the radiometric calibration) are considered in the simulation of the calibration process. With the calibration parameters, several experiments were designed to validate the spatial, spectral and radiometric response of the sensor simulator, respectively. The experiment results indicate that the sensor simulator is valid. PMID:25615727

Simulation of Laser Induced Thermal Damage in Nd:YVO4 Crystals

NASA Astrophysics Data System (ADS)

Nagi, Richie

Neodymium-doped yttrium orthovanadate (Nd:YVO4) is a commonly used gain medium in Diode Pumped Solid State (DPSS) lasers, but high heat loading of Nd:YVO4 at high pump powers (≥ 5 W) leads to thermal distortions and crystal fracture, which limits the utility of Nd:YVO 4 for high power applications. In this thesis, a Nd:YVO4 crystal suffered thermal damage during experiments for investigating the optical gain characteristics of the crystal. This thesis examines the thermal damage mechanisms in detail. Principally, laser induced melting, as well as laser induced thermal stress fracture were studied, all in the absence of stimulated emission in the crystal. The optical system for coupling the pump laser light into the crystal was first simulated in Zemax, an optical design software, and the simulations were then compared to the experimental coupling efficiency results, which were found to be in agreement. The simulations for the laser coupling system were then used in conjunction with LASCAD, a finite element analysis software, to obtain the temperatures inside the crystal, as a function of optical power coupled into the crystal. The temperature simulations were then compared to the experimental results, which were in excellent agreement, and the temperature simulations were then generalized to other crystal geometries and Nd doping levels. Zemax and LASCAD were also used to simulate the thermal stress in the crystal as a function of the coupled optical power, and the simulations were compared to experiments, both of which were found to be in agreement. The thermal stress simulations were then generalized to different crystal geometries and Nd doping levels as well.

A method to assess the situation of air combat based on the missile attack zone

NASA Astrophysics Data System (ADS)

Shi, Zhenqing; Liang, Xiao Long; Zhang, Jiaqiang; Liu, Liu

2018-04-01

Aiming at the question that we rarely consider the impact of target's attack zone in traditional situation assessment so that the assessment result is not comprehensive enough, a method that takes target's attack zone into account is presented. This paper has obtained the attack zone and the non-escape zone as the basis for quantitative analysis using the rapid simulation method and the air-to-air missile mathematical model. The situation of air combat is assessed by the ratio of the advantage function values of both sides, and the advantage function is constructed based on some influential factors such as height, speed, distance and angle. The simulation results have shown the effectiveness of this method.

Interacting steps with finite-range interactions: Analytical approximation and numerical results

NASA Astrophysics Data System (ADS)

Jaramillo, Diego Felipe; Téllez, Gabriel; González, Diego Luis; Einstein, T. L.

2013-05-01

We calculate an analytical expression for the terrace-width distribution P(s) for an interacting step system with nearest- and next-nearest-neighbor interactions. Our model is derived by mapping the step system onto a statistically equivalent one-dimensional system of classical particles. The validity of the model is tested with several numerical simulations and experimental results. We explore the effect of the range of interactions q on the functional form of the terrace-width distribution and pair correlation functions. For physically plausible interactions, we find modest changes when next-nearest neighbor interactions are included and generally negligible changes when more distant interactions are allowed. We discuss methods for extracting from simulated experimental data the characteristic scale-setting terms in assumed potential forms.

Improving Project Management with Simulation and Completion Distribution Functions

NASA Technical Reports Server (NTRS)

Cates, Grant R.

2004-01-01

Despite the critical importance of project completion timeliness, management practices in place today remain inadequate for addressing the persistent problem of project completion tardiness. A major culprit in late projects is uncertainty, which most, if not all, projects are inherently subject to. This uncertainty resides in the estimates for activity durations, the occurrence of unplanned and unforeseen events, and the availability of critical resources. In response to this problem, this research developed a comprehensive simulation based methodology for conducting quantitative project completion time risk analysis. It is called the Project Assessment by Simulation Technique (PAST). This new tool enables project stakeholders to visualize uncertainty or risk, i.e. the likelihood of their project completing late and the magnitude of the lateness, by providing them with a completion time distribution function of their projects. Discrete event simulation is used within PAST to determine the completion distribution function for the project of interest. The simulation is populated with both deterministic and stochastic elements. The deterministic inputs include planned project activities, precedence requirements, and resource requirements. The stochastic inputs include activity duration growth distributions, probabilities for events that can impact the project, and other dynamic constraints that may be placed upon project activities and milestones. These stochastic inputs are based upon past data from similar projects. The time for an entity to complete the simulation network, subject to both the deterministic and stochastic factors, represents the time to complete the project. Repeating the simulation hundreds or thousands of times allows one to create the project completion distribution function. The Project Assessment by Simulation Technique was demonstrated to be effective for the on-going NASA project to assemble the International Space Station. Approximately $500 million per month is being spent on this project, which is scheduled to complete by 2010. NASA project stakeholders participated in determining and managing completion distribution functions produced from PAST. The first result was that project stakeholders improved project completion risk awareness. Secondly, using PAST, mitigation options were analyzed to improve project completion performance and reduce total project cost.

Influence of speckle image reconstruction on photometric precision for large solar telescopes

NASA Astrophysics Data System (ADS)

Peck, C. L.; Wöger, F.; Marino, J.

2017-11-01

Context. High-resolution observations from large solar telescopes require adaptive optics (AO) systems to overcome image degradation caused by Earth's turbulent atmosphere. AO corrections are, however, only partial. Achieving near-diffraction limited resolution over a large field of view typically requires post-facto image reconstruction techniques to reconstruct the source image. Aims: This study aims to examine the expected photometric precision of amplitude reconstructed solar images calibrated using models for the on-axis speckle transfer functions and input parameters derived from AO control data. We perform a sensitivity analysis of the photometric precision under variations in the model input parameters for high-resolution solar images consistent with four-meter class solar telescopes. Methods: Using simulations of both atmospheric turbulence and partial compensation by an AO system, we computed the speckle transfer function under variations in the input parameters. We then convolved high-resolution numerical simulations of the solar photosphere with the simulated atmospheric transfer function, and subsequently deconvolved them with the model speckle transfer function to obtain a reconstructed image. To compute the resulting photometric precision, we compared the intensity of the original image with the reconstructed image. Results: The analysis demonstrates that high photometric precision can be obtained for speckle amplitude reconstruction using speckle transfer function models combined with AO-derived input parameters. Additionally, it shows that the reconstruction is most sensitive to the input parameter that characterizes the atmospheric distortion, and sub-2% photometric precision is readily obtained when it is well estimated.

Investigation of Transport Parameters of Graphene-Based Nanostructures

NASA Astrophysics Data System (ADS)

Sergeyev, D. M.; Shunkeyev, K. Sh.

2018-03-01

The paper presents results of computer simulation of the main transport parameters of nanostructures obtained through the row-by-row removal of carbon atoms from graphene ribbon. Research into the electrical parameters is carried out within the density functional theory using the non-equilibrium Green functions in the local-density approximation. Virtual NanoLab based on Atomistix ToolKit is used to construct structures and analyze simulation results. Current-voltage characteristics, differential conductivity and transmittance spectra of nanostructures are calculated at different values of bias voltage. It is found that there is a large region of negative differential resistance in current-voltage characteristics of nanostructures caused by resonant tunneling of quasi-particles. Differential (dI/dV) characteristic also has similar changes. The obtained results can be useful for building novel electronic devices in the field of nanoelectronics.

Effect of simulated sampling disturbance on creep behaviour of rock salt

NASA Astrophysics Data System (ADS)

Guessous, Z.; Gill, D. E.; Ladanyi, B.

1987-10-01

This article presents the results of an experimental study of creep behaviour of a rock salt under uniaxial compression as a function of prestrain, simulating sampling disturbance. The prestrain was produced by radial compressive loading of the specimens prior to creep testing. The tests were conducted on an artifical salt to avoid excessive scattering of the results. The results obtained from several series of single-stage creep tests show that, at short-term, the creep response of salt is strongly affected by the preloading history of samples. The nature of this effect depends upon the intensity of radial compressive preloading, and its magnitude is a function of the creep stress level. The effect, however, decreases with increasing plastic deformation, indicating that large creep strains may eventually lead to a complete loss of preloading memory.

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.

Dynamical properties of magnetized two-dimensional one-component plasma

NASA Astrophysics Data System (ADS)

Dubey, Girija S.; Gumbs, Godfrey; Fessatidis, Vassilios

2018-05-01

Molecular dynamics simulation are used to examine the effect of a uniform perpendicular magnetic field on a two-dimensional interacting electron system. In this simulation we include the effect of the magnetic field classically through the Lorentz force. Both the Coulomb and the magnetic forces are included directly in the electron dynamics to study their combined effect on the dynamical properties of the 2D system. Results are presented for the velocity autocorrelation function and the diffusion constants in the presence and absence of an external magnetic field. Our simulation results clearly show that the external magnetic field has an effect on the dynamical properties of the system.

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.

Experimental verification and simulation of negative index of refraction using Snell's law.

PubMed

Parazzoli, C G; Greegor, R B; Li, K; Koltenbah, B E C; Tanielian, M

2003-03-14

We report the results of a Snell's law experiment on a negative index of refraction material in free space from 12.6 to 13.2 GHz. Numerical simulations using Maxwell's equations solvers show good agreement with the experimental results, confirming the existence of negative index of refraction materials. The index of refraction is a function of frequency. At 12.6 GHz we measure and compute the real part of the index of refraction to be -1.05. The measurements and simulations of the electromagnetic field profiles were performed at distances of 14lambda and 28lambda from the sample; the fields were also computed at 100lambda.

Image reconstruction through thin scattering media by simulated annealing algorithm

NASA Astrophysics Data System (ADS)

Fang, Longjie; Zuo, Haoyi; Pang, Lin; Yang, Zuogang; Zhang, Xicheng; Zhu, Jianhua

2018-07-01

An idea for reconstructing the image of an object behind thin scattering media is proposed by phase modulation. The optimized phase mask is achieved by modulating the scattered light using simulated annealing algorithm. The correlation coefficient is exploited as a fitness function to evaluate the quality of reconstructed image. The reconstructed images optimized from simulated annealing algorithm and genetic algorithm are compared in detail. The experimental results show that our proposed method has better definition and higher speed than genetic algorithm.

Low energy electron transport in furfural

NASA Astrophysics Data System (ADS)

Lozano, Ana I.; Krupa, Kateryna; Ferreira da Silva, Filipe; Limão-Vieira, Paulo; Blanco, Francisco; Muñoz, Antonio; Jones, Darryl B.; Brunger, Michael J.; García, Gustavo

2017-09-01

We report on an initial investigation into the transport of electrons through a gas cell containing 1 mTorr of gaseous furfural. Results from our Monte Carlo simulation are implicitly checked against those from a corresponding electron transmission measurement. To enable this simulation a self-consistent cross section data base was constructed. This data base is benchmarked through new total cross section measurements which are also described here. In addition, again to facilitate the simulation, our preferred energy loss distribution function is presented and discussed.

Prior-knowledge-based feedforward network simulation of true boiling point curve of crude oil.

PubMed

Chen, C W; Chen, D Z

2001-11-01

Theoretical results and practical experience indicate that feedforward networks can approximate a wide class of functional relationships very well. This property is exploited in modeling chemical processes. Given finite and noisy training data, it is important to encode the prior knowledge in neural networks to improve the fit precision and the prediction ability of the model. In this paper, as to the three-layer feedforward networks and the monotonic constraint, the unconstrained method, Joerding's penalty function method, the interpolation method, and the constrained optimization method are analyzed first. Then two novel methods, the exponential weight method and the adaptive method, are proposed. These methods are applied in simulating the true boiling point curve of a crude oil with the condition of increasing monotonicity. The simulation experimental results show that the network models trained by the novel methods are good at approximating the actual process. Finally, all these methods are discussed and compared with each other.

Local Elastic Constants for Epoxy-Nanotube Composites from Molecular Dynamics Simulation

NASA Technical Reports Server (NTRS)

Frankland, S. J. V.; Gates, T. S.

2007-01-01

A method from molecular dynamics simulation is developed for determining local elastic constants of an epoxy/nanotube composite. The local values of C11, C33, K12, and K13 elastic constants are calculated for an epoxy/nanotube composite as a function of radial distance from the nanotube. While the results possess a significant amount of statistical uncertainty resulting from both the numerical analysis and the molecular fluctuations during the simulation, the following observations can be made. If the size of the region around the nanotube is increased from shells of 1 to 6 in thickness, then the scatter in the data reduces enough to observe trends. All the elastic constants determined are at a minimum 20 from the center of the nanotube. The C11, C33, and K12 follow similar trends as a function of radial distance from the nanotube. The K13 decreases greater distances from the nanotube and becomes negative which may be a symptom of the statistical averaging.

Evaluation of protective shielding thickness for diagnostic radiology rooms: theory and computer simulation.

PubMed

Costa, Paulo R; Caldas, Linda V E

2002-01-01

This work presents the development and evaluation using modern techniques to calculate radiation protection barriers in clinical radiographic facilities. Our methodology uses realistic primary and scattered spectra. The primary spectra were computer simulated using a waveform generalization and a semiempirical model (the Tucker-Barnes-Chakraborty model). The scattered spectra were obtained from published data. An analytical function was used to produce attenuation curves from polychromatic radiation for specified kVp, waveform, and filtration. The results of this analytical function are given in ambient dose equivalent units. The attenuation curves were obtained by application of Archer's model to computer simulation data. The parameters for the best fit to the model using primary and secondary radiation data from different radiographic procedures were determined. They resulted in an optimized model for shielding calculation for any radiographic room. The shielding costs were about 50% lower than those calculated using the traditional method based on Report No. 49 of the National Council on Radiation Protection and Measurements.

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.

Digital simulation of two-dimensional random fields with arbitrary power spectra and non-Gaussian probability distribution functions.

PubMed

Yura, Harold T; Hanson, Steen G

2012-04-01

Methods for simulation of two-dimensional signals with arbitrary power spectral densities and signal amplitude probability density functions are disclosed. The method relies on initially transforming a white noise sample set of random Gaussian distributed numbers into a corresponding set with the desired spectral distribution, after which this colored Gaussian probability distribution is transformed via an inverse transform into the desired probability distribution. In most cases the method provides satisfactory results and can thus be considered an engineering approach. Several illustrative examples with relevance for optics are given.

Statistics of velocity gradients in two-dimensional Navier-Stokes and ocean turbulence.

PubMed

Schorghofer, Norbert; Gille, Sarah T

2002-02-01

Probability density functions and conditional averages of velocity gradients derived from upper ocean observations are compared with results from forced simulations of the two-dimensional Navier-Stokes equations. Ocean data are derived from TOPEX satellite altimeter measurements. The simulations use rapid forcing on large scales, characteristic of surface winds. The probability distributions of transverse velocity derivatives from the ocean observations agree with the forced simulations, although they differ from unforced simulations reported elsewhere. The distribution and cross correlation of velocity derivatives provide clear evidence that large coherent eddies play only a minor role in generating the observed statistics.

Design analysis and computer-aided performance evaluation of shuttle orbiter electrical power system. Volume 1: Summary

NASA Technical Reports Server (NTRS)

1974-01-01

Studies were conducted to develop appropriate space shuttle electrical power distribution and control (EPDC) subsystem simulation models and to apply the computer simulations to systems analysis of the EPDC. A previously developed software program (SYSTID) was adapted for this purpose. The following objectives were attained: (1) significant enhancement of the SYSTID time domain simulation software, (2) generation of functionally useful shuttle EPDC element models, and (3) illustrative simulation results in the analysis of EPDC performance, under the conditions of fault, current pulse injection due to lightning, and circuit protection sizing and reaction times.

Instrumental resolution of the chopper spectrometer 4SEASONS evaluated by Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Kajimoto, Ryoichi; Sato, Kentaro; Inamura, Yasuhiro; Fujita, Masaki

2018-05-01

We performed simulations of the resolution function of the 4SEASONS spectrometer at J-PARC by using the Monte Carlo simulation package McStas. The simulations showed reasonably good agreement with analytical calculations of energy and momentum resolutions by using a simplified description. We implemented new functionalities in Utsusemi, the standard data analysis tool used in 4SEASONS, to enable visualization of the simulated resolution function and predict its shape for specific experimental configurations.

Stochastic simulation of biological reactions, and its applications for studying actin polymerization.

PubMed

Ichikawa, Kazuhisa; Suzuki, Takashi; Murata, Noboru

2010-11-30

Molecular events in biological cells occur in local subregions, where the molecules tend to be small in number. The cytoskeleton, which is important for both the structural changes of cells and their functions, is also a countable entity because of its long fibrous shape. To simulate the local environment using a computer, stochastic simulations should be run. We herein report a new method of stochastic simulation based on random walk and reaction by the collision of all molecules. The microscopic reaction rate P(r) is calculated from the macroscopic rate constant k. The formula involves only local parameters embedded for each molecule. The results of the stochastic simulations of simple second-order, polymerization, Michaelis-Menten-type and other reactions agreed quite well with those of deterministic simulations when the number of molecules was sufficiently large. An analysis of the theory indicated a relationship between variance and the number of molecules in the system, and results of multiple stochastic simulation runs confirmed this relationship. We simulated Ca²(+) dynamics in a cell by inward flow from a point on the cell surface and the polymerization of G-actin forming F-actin. Our results showed that this theory and method can be used to simulate spatially inhomogeneous events.

Using block pulse functions for seismic vibration semi-active control of structures with MR dampers

NASA Astrophysics Data System (ADS)

Rahimi Gendeshmin, Saeed; Davarnia, Daniel

2018-03-01

This article applied the idea of block pulse functions in the semi-active control of structures. The BP functions give effective tools to approximate complex problems. The applied control algorithm has a major effect on the performance of the controlled system and the requirements of the control devices. In control problems, it is important to devise an accurate analytical technique with less computational cost. It is proved that the BP functions are fundamental tools in approximation problems which have been applied in disparate areas in last decades. This study focuses on the employment of BP functions in control algorithm concerning reduction the computational cost. Magneto-rheological (MR) dampers are one of the well-known semi-active tools that can be used to control the response of civil Structures during earthquake. For validation purposes, numerical simulations of a 5-story shear building frame with MR dampers are presented. The results of suggested method were compared with results obtained by controlling the frame by the optimal control method based on linear quadratic regulator theory. It can be seen from simulation results that the suggested method can be helpful in reducing seismic structural responses. Besides, this method has acceptable accuracy and is in agreement with optimal control method with less computational costs.

Properties of a planar electric double layer under extreme conditions investigated by classical density functional theory and Monte Carlo simulations.

PubMed

Zhou, Shiqi; Lamperski, Stanisław; Zydorczak, Maria

2014-08-14

Monte Carlo (MC) simulation and classical density functional theory (DFT) results are reported for the structural and electrostatic properties of a planar electric double layer containing ions having highly asymmetric diameters or valencies under extreme concentration condition. In the applied DFT, for the excess free energy contribution due to the hard sphere repulsion, a recently elaborated extended form of the fundamental measure functional is used, and coupling of Coulombic and short range hard-sphere repulsion is described by a traditional second-order functional perturbation expansion approximation. Comparison between the MC and DFT results indicates that validity interval of the traditional DFT approximation expands to high ion valences running up to 3 and size asymmetry high up to diameter ratio of 4 whether the high valence ions or the large size ion are co- or counter-ions; and to a high bulk electrolyte concentration being close to the upper limit of the electrolyte mole concentration the MC simulation can deal with well. The DFT accuracy dependence on the ion parameters can be self-consistently explained using arguments of liquid state theory, and new EDL phenomena such as overscreening effect due to monovalent counter-ions, extreme layering effect of counter-ions, and appearance of a depletion layer with almost no counter- and co-ions are observed.

Translational simulation: not 'where?' but 'why?' A functional view of in situ simulation.

PubMed

Brazil, Victoria

2017-01-01

Healthcare simulation has been widely adopted for health professional education at all stages of training and practice and across cognitive, procedural, communication and teamwork domains. Recent enthusiasm for in situ simulation-delivered in the real clinical environment-cites improved transfer of knowledge and skills into real-world practice, as well as opportunities to identify latent safety threats and other workplace-specific issues. However, describing simulation type according to place may not be helpful. Instead, I propose the term translational simulation as a functional term for how simulation may be connected directly with health service priorities and patient outcomes, through interventional and diagnostic functions, independent of the location of the simulation activity.

AB INITIO Molecular Dynamics Simulations on Local Structure and Electronic Properties in Liquid MgxBi1-x Alloys

NASA Astrophysics Data System (ADS)

Hao, Qing-Hai; You, Yu-Wei; Kong, Xiang-Shan; Liu, C. S.

2013-03-01

The microscopic structure and dynamics of liquid MgxBi1-x(x = 0.5, 0.6, 0.7) alloys together with pure liquid Mg and Bi metals were investigated by means of ab initio molecular dynamics simulations. We present results of structure properties including pair correlation function, structural factor, bond-angle distribution function and bond order parameter, and their composition dependence. The dynamical and electronic properties have also been studied. The structure factor and pair correlation function are in agreement with the available experimental data. The calculated bond-angle distribution function and bond order parameter suggest that the stoichiometric composition Mg3Bi2 exhibits a different local structure order compared with other concentrations, which help us understand the appearance of the minimum electronic conductivity at this composition observed in previous experiments.

Solvation and Ion Pair Association in Aqueous Metal Sulfates: Interpretation of NDIS raw data by isobaric-isothermal molecular dynamics simulation.

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

Chialvo, Ariel A; Simonson, J Michael

2010-01-01

We analyzed the solvation behavior of aqueous lithium, nickel, and ytterbium sulfates at ambient conditions in terms of the relevant radial distributions functions and the corresponding first-order difference of the sulfur-site neutronweighted distribution functions generated by isothermal-isobaric molecular dynamics simulation. We determined of the partial contributions to the neutronweighted distribution functions, to identify the main peaks, and the effect of the contact ion-pair configuration on the resulting H ! S coordination number. Finally, we assessed the extent of the ion-pair formation according to Poirier- DeLap formalism and highlighted the significant increase of the ion-pair association exhibited by these salts withmore » cation charge.« less

Simulation Of Wave Function And Probability Density Of Modified Poschl Teller Potential Derived Using Supersymmetric Quantum Mechanics

NASA Astrophysics Data System (ADS)

Angraini, Lily Maysari; Suparmi, Variani, Viska Inda

2010-12-01

SUSY quantum mechanics can be applied to solve Schrodinger equation for high dimensional system that can be reduced into one dimensional system and represented in lowering and raising operators. Lowering and raising operators can be obtained using relationship between original Hamiltonian equation and the (super) potential equation. In this paper SUSY quantum mechanics is used as a method to obtain the wave function and the energy level of the Modified Poschl Teller potential. The graph of wave function equation and probability density is simulated by using Delphi 7.0 programming language. Finally, the expectation value of quantum mechanics operator could be calculated analytically using integral form or probability density graph resulted by the programming.

Assessment of the adsorption mechanism of Flutamide anticancer drug on the functionalized single-walled carbon nanotube surface as a drug delivery vehicle: An alternative theoretical approach based on DFT and MD

NASA Astrophysics Data System (ADS)

Kamel, Maedeh; Raissi, Heidar; Morsali, Ali; Shahabi, Mahnaz

2018-03-01

In the present work, we have studied the drug delivery performance of the functionalized (5, 5) single-walled carbon nanotube with a carboxylic acid group for Flutamide anticancer drug in the gas phase as well as water solution by means of density functional theory calculations. The obtained results confirmed the energetic stability of the optimized geometries and revealed that the nature of drug adsorption on the functionalized carbon nanotube is physical. Our computations showed that the hydrogen bonding between active sites of Flutamide molecule and the carboxyl functional group of the nanotube plays a vital role in the stabilization of the considered configurations. The natural bond orbital analysis suggested that the functionalized nanotube plays the role of an electron donor and Flutamide molecule acts as an electron acceptor at the investigated complexes. In addition, molecular dynamics simulation is also utilized to investigate the effect of functionalized carbon nanotube chirality on the dynamic process of drug molecule adsorption on the nanotube surface. Simulation results demonstrated that drug molecules are strongly adsorbed on the functionalized nanotube surface with (10,5) chirality, as reflected by the most negative van der Waals interaction energy and a high number of hydrogen bonds between the functionalized nanotube and drug molecules.

Computer simulations of equilibrium magnetization and microstructure in magnetic fluids

NASA Astrophysics Data System (ADS)

Rosa, A. P.; Abade, G. C.; Cunha, F. R.

2017-09-01

In this work, Monte Carlo and Brownian Dynamics simulations are developed to compute the equilibrium magnetization of a magnetic fluid under action of a homogeneous applied magnetic field. The particles are free of inertia and modeled as hard spheres with the same diameters. Two different periodic boundary conditions are implemented: the minimum image method and Ewald summation technique by replicating a finite number of particles throughout the suspension volume. A comparison of the equilibrium magnetization resulting from the minimum image approach and Ewald sums is performed by using Monte Carlo simulations. The Monte Carlo simulations with minimum image and lattice sums are used to investigate suspension microstructure by computing the important radial pair-distribution function go(r), which measures the probability density of finding a second particle at a distance r from a reference particle. This function provides relevant information on structure formation and its anisotropy through the suspension. The numerical results of go(r) are compared with theoretical predictions based on quite a different approach in the absence of the field and dipole-dipole interactions. A very good quantitative agreement is found for a particle volume fraction of 0.15, providing a validation of the present simulations. In general, the investigated suspensions are dominated by structures like dimmer and trimmer chains with trimmers having probability to form an order of magnitude lower than dimmers. Using Monte Carlo with lattice sums, the density distribution function g2(r) is also examined. Whenever this function is different from zero, it indicates structure-anisotropy in the suspension. The dependence of the equilibrium magnetization on the applied field, the magnetic particle volume fraction, and the magnitude of the dipole-dipole magnetic interactions for both boundary conditions are explored in this work. Results show that at dilute regimes and with moderate dipole-dipole interactions, the standard method of minimum image is both accurate and computationally efficient. Otherwise, lattice sums of magnetic particle interactions are required to accelerate convergence of the equilibrium magnetization. The accuracy of the numerical code is also quantitatively verified by comparing the magnetization obtained from numerical results with asymptotic predictions of high order in the particle volume fraction, in the presence of dipole-dipole interactions. In addition, Brownian Dynamics simulations are used in order to examine magnetization relaxation of a ferrofluid and to calculate the magnetic relaxation time as a function of the magnetic particle interaction strength for a given particle volume fraction and a non-dimensional applied field. The simulations of magnetization relaxation have shown the existence of a critical value of the dipole-dipole interaction parameter. For strength of the interactions below the critical value at a given particle volume fraction, the magnetic relaxation time is close to the Brownian relaxation time and the suspension has no appreciable memory. On the other hand, for strength of dipole interactions beyond its critical value, the relaxation time increases exponentially with the strength of dipole-dipole interaction. Although we have considered equilibrium conditions, the obtained results have far-reaching implications for the analysis of magnetic suspensions under external flow.

A computer simulation of an adaptive noise canceler with a single input

NASA Astrophysics Data System (ADS)

Albert, Stuart D.

1991-06-01

A description of an adaptive noise canceler using Widrows' LMS algorithm is presented. A computer simulation of canceler performance (adaptive convergence time and frequency transfer function) was written for use as a design tool. The simulations, assumptions, and input parameters are described in detail. The simulation is used in a design example to predict the performance of an adaptive noise canceler in the simultaneous presence of both strong and weak narrow-band signals (a cosited frequency hopping radio scenario). On the basis of the simulation results, it is concluded that the simulation is suitable for use as an adaptive noise canceler design tool; i.e., it can be used to evaluate the effect of design parameter changes on canceler performance.

Structure refinement of membrane proteins via molecular dynamics simulations.

PubMed

Dutagaci, Bercem; Heo, Lim; Feig, Michael

2018-07-01

A refinement protocol based on physics-based techniques established for water soluble proteins is tested for membrane protein structures. Initial structures were generated by homology modeling and sampled via molecular dynamics simulations in explicit lipid bilayer and aqueous solvent systems. Snapshots from the simulations were selected based on scoring with either knowledge-based or implicit membrane-based scoring functions and averaged to obtain refined models. The protocol resulted in consistent and significant refinement of the membrane protein structures similar to the performance of refinement methods for soluble proteins. Refinement success was similar between sampling in the presence of lipid bilayers and aqueous solvent but the presence of lipid bilayers may benefit the improvement of lipid-facing residues. Scoring with knowledge-based functions (DFIRE and RWplus) was found to be as good as scoring using implicit membrane-based scoring functions suggesting that differences in internal packing is more important than orientations relative to the membrane during the refinement of membrane protein homology models. © 2018 Wiley Periodicals, Inc.

Simulation-Based Validation of the p53 Transcriptional Activity with Hybrid Functional Petri Net.

PubMed

Doi, Atsushi; Nagasaki, Masao; Matsuno, Hiroshi; Miyano, Satoru

2011-01-01

MDM2 and p19ARF are essential proteins in cancer pathways forming a complex with protein p53 to control the transcriptional activity of protein p53. It is confirmed that protein p53 loses its transcriptional activity by forming the functional dimer with protein MDM2. However, it is still unclear that protein p53 keeps its transcriptional activity when it forms the trimer with proteins MDM2 and p19ARF. We have observed mutual behaviors among genes p53, MDM2, p19ARF and their products on a computational model with hybrid functional Petri net (HFPN) which is constructed based on information described in the literature. The simulation results suggested that protein p53 should have the transcriptional activity in the forms of the trimer of proteins p53, MDM2, and p19ARF. This paper also discusses the advantages of HFPN based modeling method in terms of pathway description for simulations.

The Researches on Damage Detection Method for Truss Structures

NASA Astrophysics Data System (ADS)

Wang, Meng Hong; Cao, Xiao Nan

2018-06-01

This paper presents an effective method to detect damage in truss structures. Numerical simulation and experimental analysis were carried out on a damaged truss structure under instantaneous excitation. The ideal excitation point and appropriate hammering method were determined to extract time domain signals under two working conditions. The frequency response function and principal component analysis were used for data processing, and the angle between the frequency response function vectors was selected as a damage index to ascertain the location of a damaged bar in the truss structure. In the numerical simulation, the time domain signal of all nodes was extracted to determine the location of the damaged bar. In the experimental analysis, the time domain signal of a portion of the nodes was extracted on the basis of an optimal sensor placement method based on the node strain energy coefficient. The results of the numerical simulation and experimental analysis showed that the damage detection method based on the frequency response function and principal component analysis could locate the damaged bar accurately.

Microsecond Simulations of DNA and Ion Transport in Nanopores with Novel Ion-Ion and Ion-Nucleotides Effective Potentials

PubMed Central

De Biase, Pablo M.; Markosyan, Suren; Noskov, Sergei

2014-01-01

We developed a novel scheme based on the Grand-Canonical Monte-Carlo/Brownian Dynamics (GCMC/BD) simulations and have extended it to studies of ion currents across three nanopores with the potential for ssDNA sequencing: solid-state nanopore Si3N4, α-hemolysin, and E111N/M113Y/K147N mutant. To describe nucleotide-specific ion dynamics compatible with ssDNA coarse-grained model, we used the Inverse Monte-Carlo protocol, which maps the relevant ion-nucleotide distribution functions from an all-atom MD simulations. Combined with the previously developed simulation platform for Brownian Dynamic (BD) simulations of ion transport, it allows for microsecond- and millisecond-long simulations of ssDNA dynamics in nanopore with a conductance computation accuracy that equals or exceeds that of all-atom MD simulations. In spite of the simplifications, the protocol produces results that agree with the results of previous studies on ion conductance across open channels and provide direct correlations with experimentally measured blockade currents and ion conductances that have been estimated from all-atom MD simulations. PMID:24738152

LiquidLib: A comprehensive toolbox for analyzing classical and ab initio molecular dynamics simulations of liquids and liquid-like matter with applications to neutron scattering experiments

NASA Astrophysics Data System (ADS)

Walter, Nathan P.; Jaiswal, Abhishek; Cai, Zhikun; Zhang, Yang

2018-07-01

Neutron scattering is a powerful experimental technique for characterizing the structure and dynamics of materials on the atomic or molecular scale. However, the interpretation of experimental data from neutron scattering is oftentimes not trivial, partly because scattering methods probe ensemble-averaged information in the reciprocal space. Therefore, computer simulations, such as classical and ab initio molecular dynamics, are frequently used to unravel the time-dependent atomistic configurations that can reproduce the scattering patterns and thus assist in the understanding of the microscopic origin of certain properties of materials. LiquidLib is a post-processing package for analyzing the trajectory of atomistic simulations of liquids and liquid-like matter with application to neutron scattering experiments. From an atomistic simulation, LiquidLib provides the computation of various statistical quantities including the pair distribution function, the weighted and unweighted structure factors, the mean squared displacement, the non-Gaussian parameter, the four-point correlation function, the velocity auto correlation function, the self and collective van Hove correlation functions, the self and collective intermediate scattering functions, and the bond orientational order parameter. LiquidLib analyzes atomistic trajectories generated from packages such as LAMMPS, GROMACS, and VASP. It also offers an extendable platform to conveniently integrate new quantities into the library and integrate simulation trajectories of other file formats for analysis. Weighting the quantities by element-specific neutron-scattering lengths provides results directly comparable to neutron scattering measurements. Lastly, LiquidLib is independent of dimensionality, which allows analysis of trajectories in two, three, and higher dimensions. The code is beginning to find worldwide use.

First results from the IllustrisTNG simulations: matter and galaxy clustering

NASA Astrophysics Data System (ADS)

Springel, Volker; Pakmor, Rüdiger; Pillepich, Annalisa; Weinberger, Rainer; Nelson, Dylan; Hernquist, Lars; Vogelsberger, Mark; Genel, Shy; Torrey, Paul; Marinacci, Federico; Naiman, Jill

2018-03-01

Hydrodynamical simulations of galaxy formation have now reached sufficient volume to make precision predictions for clustering on cosmologically relevant scales. Here, we use our new IllustrisTNG simulations to study the non-linear correlation functions and power spectra of baryons, dark matter, galaxies, and haloes over an exceptionally large range of scales. We find that baryonic effects increase the clustering of dark matter on small scales and damp the total matter power spectrum on scales up to k ˜ 10 h Mpc-1 by 20 per cent. The non-linear two-point correlation function of the stellar mass is close to a power-law over a wide range of scales and approximately invariant in time from very high redshift to the present. The two-point correlation function of the simulated galaxies agrees well with Sloan Digital Sky Survey at its mean redshift z ≃ 0.1, both as a function of stellar mass and when split according to galaxy colour, apart from a mild excess in the clustering of red galaxies in the stellar mass range of109-1010 h-2 M⊙. Given this agreement, the TNG simulations can make valuable theoretical predictions for the clustering bias of different galaxy samples. We find that the clustering length of the galaxy autocorrelation function depends strongly on stellar mass and redshift. Its power-law slope γ is nearly invariant with stellar mass, but declines from γ ˜ 1.8 at redshift z = 0 to γ ˜ 1.6 at redshift z ˜ 1, beyond which the slope steepens again. We detect significant scale dependences in the bias of different observational tracers of large-scale structure, extending well into the range of the baryonic acoustic oscillations and causing nominal (yet fortunately correctable) shifts of the acoustic peaks of around ˜ 5 per cent.

Computer Simulation of Global Profiles of Carbon Dioxide Using a Pulsed, 2-Micron, Coherent-Detection, Column-Content DIAL System

NASA Technical Reports Server (NTRS)

Kavaya, Michael J.; Singh, Upendra N.; Koch, Grady J.; Yu, Jirong; Frehlich, Rod G.

2009-01-01

We present preliminary results of computer simulations of the error in measuring carbon dioxide mixing ratio profiles from earth orbit. The simulated sensor is a pulsed, 2-micron, coherent-detection lidar alternately operating on at least two wavelengths. The simulated geometry is a nadir viewing lidar measuring the column content signal. Atmospheric absorption is modeled using FASCODE3P software with the HITRAN 2004 absorption line data base. Lidar shot accumulation is employed up to the horizontal resolution limit. Horizontal resolutions of 50, 100, and 200 km are shown. Assuming a 400 km spacecraft orbit, the horizontal resolutions correspond to measurement times of about 7, 14, and 28 s. We simulate laser pulse-pair repetition frequencies from 1 Hz to 100 kHz. The range of shot accumulation is 7 to 2.8 million pulse-pairs. The resultant error is shown as a function of horizontal resolution, laser pulse-pair repetition frequency, and laser pulse energy. The effect of different on and off pulse energies is explored. The results are compared to simulation results of others and to demonstrated 2-micron operating points at NASA Langley.

Implementation and simulations of the sphere solution in FAST

NASA Astrophysics Data System (ADS)

Murgolo, F. P.; Schirone, M. G.; Lattanzi, M.; Bernacca, P. L.

1989-06-01

The details of the implementation of the sphere solution software in the Fundamental Astronomy by Space Techniques (FAST) consortium, are described. The simulation results for realistic data sets, both with and without grid-step errors are given. Expected errors on the astrometric parameters of the primary stars and the precision of the reference great circle zero points, are provided as a function of mission duration. The design matrix, the diagrams of the context processor and the processors experimental results are given.

Integration of OpenMC methods into MAMMOTH and Serpent

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

Kerby, Leslie; DeHart, Mark; Tumulak, Aaron

OpenMC, a Monte Carlo particle transport simulation code focused on neutron criticality calculations, contains several methods we wish to emulate in MAMMOTH and Serpent. First, research coupling OpenMC and the Multiphysics Object-Oriented Simulation Environment (MOOSE) has shown promising results. Second, the utilization of Functional Expansion Tallies (FETs) allows for a more efficient passing of multiphysics data between OpenMC and MOOSE. Both of these capabilities have been preliminarily implemented into Serpent. Results are discussed and future work recommended.

Protein's electronic polarization contributes significantly to its catalytic function

NASA Astrophysics Data System (ADS)

Xiang, Yun; Duan, Lili; Zhang, John Z. H.

2011-05-01

Ab initio quantum mechanical/molecular mechanical method is combined with the polarized protein-specific charge to study the chemical reactions catalyzed by protein enzymes. Significant improvement in the accuracy and efficiency of free-energy simulation is demonstrated by calculating the free-energy profile of the primary proton transfer reaction in triosephosphate isomerase. Quantitative agreement with experimental results is achieved. Our simulation results indicate that electronic polarization makes important contribution to enzyme catalysis by lowering the energy barrier by as much as 3 kcal/mol.

Simulation of electric double-layer capacitors: evaluation of constant potential method

NASA Astrophysics Data System (ADS)

Wang, Zhenxing; Laird, Brian; Yang, Yang; Olmsted, David; Asta, Mark

2014-03-01

Atomistic simulations can play an important role in understanding electric double-layer capacitors (EDLCs) at a molecular level. In such simulations, typically the electrode surface is modeled using fixed surface charges, which ignores the charge fluctuation induced by local fluctuations in the electrolyte solution. In this work we evaluate an explicit treatment of charges, namely constant potential method (CPM)[1], in which the electrode charges are dynamically updated to maintain constant electrode potential. We employ a model system with a graphite electrode and a LiClO4/acetonitrile electrolyte, examined as a function of electrode potential differences. Using various molecular and macroscopic properties as metrics, we compare CPM simulations on this system to results using fixed surface charges. Specifically, results for predicted capacity, electric potential gradient and solvent density profile are identical between the two methods; However, ion density profiles and solvation structure yield significantly different results.

Intercepting real and simulated falling objects: what is the difference?

PubMed

Baurès, Robin; Benguigui, Nicolas; Amorim, Michel-Ange; Hecht, Heiko

2009-10-30

The use of virtual reality is nowadays common in many studies in the field of human perception and movement control, particularly in interceptive actions. However, the ecological validity of the simulation is often taken for granted without having been formally established. If participants were to perceive the real situation and its virtual equivalent in a different fashion, the generalization of the results obtained in virtual reality to real life would be highly questionable. We tested the ecological validity of virtual reality in this context by comparing the timing of interceptive actions based upon actually falling objects and their simulated counterparts. The results show very limited differences as a function of whether participants were confronted with a real ball or a simulation thereof. And when present, such differences were limited to the first trial only. This result validates the use of virtual reality when studying interceptive actions of accelerated stimuli.

Photomechanical Deformation of Azobenzene-Functionalized Polyimides Synthesized with Bulky Substituents (Postprint)

DTIC Science & Technology

2017-12-06

mechanical response of the azobenzene- functionalized polyimide is correlated to the rotational freedom of the polyimide chains (resulting in extensive... correlated to the rotational freedom of the polyimide chains (resulting in extensive segmental mobility) and fractional free volume (FFV > 0.1...response has been described,34 and a recent simulation study on the stress relaxation dynamics of azo-polyimides has provided insights into the correlation

Unsteady Aerodynamic Modeling of A Maneuvering Aircraft Using Indicial Functions

DTIC Science & Technology

2016-03-30

indicial functions are directly calculated using the results of unsteady Reynolds-averaged Navier - Stokes simulation and a grid-movement tool. Results are...but meanwhile, the full-order model based on Unsteady Reynolds-averaged Navier - Stokes (URANS) equation is too computationally expensive to be used...The flow solver used in this study solves the unsteady, three-dimensional and compressible Navier - Stokes equations. The equations in terms of

Evaluation of hazard and integrity monitor functions for integrated alerting and notification using a sensor simulation framework

NASA Astrophysics Data System (ADS)

Bezawada, Rajesh; Uijt de Haag, Maarten

2010-04-01

This paper discusses the results of an initial evaluation study of hazard and integrity monitor functions for use with integrated alerting and notification. The Hazard and Integrity Monitor (HIM) (i) allocates information sources within the Integrated Intelligent Flight Deck (IIFD) to required functionality (like conflict detection and avoidance) and determines required performance of these information sources as part of that function; (ii) monitors or evaluates the required performance of the individual information sources and performs consistency checks among various information sources; (iii) integrates the information to establish tracks of potential hazards that can be used for the conflict probes or conflict prediction for various time horizons including the 10, 5, 3, and <3 minutes used in our scenario; (iv) detects and assesses the class of the hazard and provide possible resolutions. The HIM monitors the operation-dependent performance parameters related to the potential hazards in a manner similar to the Required Navigation Performance (RNP). Various HIM concepts have been implemented and evaluated using a previously developed sensor simulator/synthesizer. Within the simulation framework, various inputs to the IIFD and its subsystems are simulated, synthesized from actual collected data, or played back from actual flight test sensor data. The framework and HIM functions are implemented in SimulinkR, a modeling language developed by The MathworksTM. This modeling language allows for test and evaluation of various sensor and communication link configurations as well as the inclusion of feedback from the pilot on the performance of the aircraft.

A Genetic Algorithm for the Generation of Packetization Masks for Robust Image Communication

PubMed Central

Zapata-Quiñones, Katherine; Duran-Faundez, Cristian; Gutiérrez, Gilberto; Lecuire, Vincent; Arredondo-Flores, Christopher; Jara-Lipán, Hugo

2017-01-01

Image interleaving has proven to be an effective solution to provide the robustness of image communication systems when resource limitations make reliable protocols unsuitable (e.g., in wireless camera sensor networks); however, the search for optimal interleaving patterns is scarcely tackled in the literature. In 2008, Rombaut et al. presented an interesting approach introducing a packetization mask generator based in Simulated Annealing (SA), including a cost function, which allows assessing the suitability of a packetization pattern, avoiding extensive simulations. In this work, we present a complementary study about the non-trivial problem of generating optimal packetization patterns. We propose a genetic algorithm, as an alternative to the cited work, adopting the mentioned cost function, then comparing it to the SA approach and a torus automorphism interleaver. In addition, we engage the validation of the cost function and provide results attempting to conclude about its implication in the quality of reconstructed images. Several scenarios based on visual sensor networks applications were tested in a computer application. Results in terms of the selected cost function and image quality metric PSNR show that our algorithm presents similar results to the other approaches. Finally, we discuss the obtained results and comment about open research challenges. PMID:28452934

Estimation and Simulation of Slow Crack Growth Parameters from Constant Stress Rate Data

NASA Technical Reports Server (NTRS)

Salem, Jonathan A.; Weaver, Aaron S.

2003-01-01

Closed form, approximate functions for estimating the variances and degrees-of-freedom associated with the slow crack growth parameters n, D, B, and A(sup *) as measured using constant stress rate ('dynamic fatigue') testing were derived by using propagation of errors. Estimates made with the resulting functions and slow crack growth data for a sapphire window were compared to the results of Monte Carlo simulations. The functions for estimation of the variances of the parameters were derived both with and without logarithmic transformation of the initial slow crack growth equations. The transformation was performed to make the functions both more linear and more normal. Comparison of the Monte Carlo results and the closed form expressions derived with propagation of errors indicated that linearization is not required for good estimates of the variances of parameters n and D by the propagation of errors method. However, good estimates variances of the parameters B and A(sup *) could only be made when the starting slow crack growth equation was transformed and the coefficients of variation of the input parameters were not too large. This was partially a result of the skewered distributions of B and A(sup *). Parametric variation of the input parameters was used to determine an acceptable range for using closed form approximate equations derived from propagation of errors.

Evaluation of various energy windows at different radionuclides for scatter and attenuation correction in nuclear medicine.

PubMed

Asgari, Afrouz; Ashoor, Mansour; Sohrabpour, Mostafa; Shokrani, Parvaneh; Rezaei, Ali

2015-05-01

Improving signal to noise ratio (SNR) and qualified images by the various methods is very important for detecting the abnormalities at the body organs. Scatter and attenuation of photons by the organs lead to errors in radiopharmaceutical estimation as well as degradation of images. The choice of suitable energy window and the radionuclide have a key role in nuclear medicine which appearing the lowest scatter fraction as well as having a nearly constant linear attenuation coefficient as a function of phantom thickness. The energy windows of symmetrical window (SW), asymmetric window (ASW), high window (WH) and low window (WL) using Tc-99m and Sm-153 radionuclide with solid water slab phantom (RW3) and Teflon bone phantoms have been compared, and Matlab software and Monte Carlo N-Particle (MCNP4C) code were modified to simulate these methods and obtaining the amounts of FWHM and full width at tenth maximum (FWTM) using line spread functions (LSFs). The experimental data were obtained from the Orbiter Scintron gamma camera. Based on the results of the simulation as well as experimental work, the performance of WH and ASW display of the results, lowest scatter fraction as well as constant linear attenuation coefficient as a function of phantom thickness. WH and ASW were optimal windows in nuclear medicine imaging for Tc-99m in RW3 phantom and Sm-153 in Teflon bone phantom. Attenuation correction was done for WH and ASW optimal windows and for these radionuclides using filtered back projection algorithm. Results of simulation and experimental show that very good agreement between the set of experimental with simulation as well as theoretical values with simulation data were obtained which was nominally less than 7.07 % for Tc-99m and less than 8.00 % for Sm-153. Corrected counts were not affected by the thickness of scattering material. The Simulated results of Line Spread Function (LSF) for Sm-153 and Tc-99m in phantom based on four windows and TEW method were indicated that the FWHM and FWTM values were approximately the same in TEW method and WH and ASW, but the sensitivity at the optimal window was more than that of the other one. The suitable determination of energy window width on the energy spectra can be useful in optimal design to improve efficiency and contrast. It is found that the WH is preferred to the ASW and the ASW is preferred to the SW.

Grid Integrated Distributed PV (GridPV) Version 2.

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

Reno, Matthew J.; Coogan, Kyle

2014-12-01

This manual provides the documentation of the MATLAB toolbox of functions for using OpenDSS to simulate the impact of solar energy on the distribution system. The majority of the functio ns are useful for interfacing OpenDSS and MATLAB, and they are of generic use for commanding OpenDSS from MATLAB and retrieving information from simulations. A set of functions is also included for modeling PV plant output and setting up the PV plant in th e OpenDSS simulation. The toolbox contains functions for modeling the OpenDSS distribution feeder on satellite images with GPS coordinates. Finally, example simulations functions are included tomore » show potential uses of the toolbox functions. Each function i n the toolbox is documented with the function use syntax, full description, function input list, function output list, example use, and example output.« less

Segregation formation, thermal and electronic properties of ternary cubic CdZnTe clusters: MD simulations and DFT calculations

NASA Astrophysics Data System (ADS)

Kurban, Mustafa; Erkoç, Şakir

2017-04-01

Surface and core formation, thermal and electronic properties of ternary cubic CdZnTe clusters are investigated by using classical molecular dynamics (MD) simulations and density functional theory (DFT) calculations. In this work, MD simulations of the CdZnTe clusters are performed by means of LAMMPS by using bond order potential (BOP). MD simulations are carried out at different temperatures to study the segregation phenomena of Cd, Zn and Te atoms, and deviation of clusters and heat capacity. After that, using optimized geometries obtained, excess charge on atoms, dipole moments, highest occupied molecular orbitals, lowest unoccupied molecular orbitals, HOMO-LUMO gaps (Eg) , total energies, spin density and the density of states (DOS) have been calculated with DFT. Simulation results such as heat capacity and segregation formation are compared with experimental bulk and theoretical results.

Dynamic Average-Value Modeling of Doubly-Fed Induction Generator Wind Energy Conversion Systems

NASA Astrophysics Data System (ADS)

Shahab, Azin

In a Doubly-fed Induction Generator (DFIG) wind energy conversion system, the rotor of a wound rotor induction generator is connected to the grid via a partial scale ac/ac power electronic converter which controls the rotor frequency and speed. In this research, detailed models of the DFIG wind energy conversion system with Sinusoidal Pulse-Width Modulation (SPWM) scheme and Optimal Pulse-Width Modulation (OPWM) scheme for the power electronic converter are developed in detail in PSCAD/EMTDC. As the computer simulation using the detailed models tends to be computationally extensive, time consuming and even sometimes not practical in terms of speed, two modified approaches (switching-function modeling and average-value modeling) are proposed to reduce the simulation execution time. The results demonstrate that the two proposed approaches reduce the simulation execution time while the simulation results remain close to those obtained using the detailed model simulation.

Kinematics of Globular Cluster: new Perspectives of Energy Equipartition from N-body Simulations

NASA Astrophysics Data System (ADS)

Kim, Hyunwoo; Pasquato, Mario; Yoon, Suk-jin

2018-01-01

Globular clusters (GCs) evolve dynamically through gravitational two-body interactions between stars. We investigated the evolution towards energy equipartition in GCs using direct n-body simulations in NBODY6. If a GC reaches full energy equipartition, the velocity dispersion as a function of stars’ mass becomes a power law with exponent -1/2. However, our n-body simulations never reach full equipartition, which is similar to Trenti & van de Marel (2013) results. Instead we found that in simulations with a shallow mass spectrum the best fit exponent becomes positive slightly before core collapse time. This inversion is a new result, which can be used as a kinematic predictor of core collapse. We are currently exploring applications of this inversion indicator to the detection of intermediate mass black holes.

Initial Data Analysis Results for ATD-2 ISAS HITL Simulation

NASA Technical Reports Server (NTRS)

Lee, Hanbong

2017-01-01

To evaluate the operational procedures and information requirements for the core functional capabilities of the ATD-2 project, such as tactical surface metering tool, APREQ-CFR procedure, and data element exchanges between ramp and tower, human-in-the-loop (HITL) simulations were performed in March, 2017. This presentation shows the initial data analysis results from the HITL simulations. With respect to the different runway configurations and metering values in tactical surface scheduler, various airport performance metrics were analyzed and compared. These metrics include gate holding time, taxi-out in time, runway throughput, queue size and wait time in queue, and TMI flight compliance. In addition to the metering value, other factors affecting the airport performance in the HITL simulation, including run duration, runway changes, and TMI constraints, are also discussed.

Improving 1D Stellar Models with 3D Atmospheres

NASA Astrophysics Data System (ADS)

Mosumgaard, Jakob Rørsted; Silva Aguirre, Víctor; Weiss, Achim; Christensen-Dalsgaard, Jørgen; Trampedach, Regner

2017-10-01

Stellar evolution codes play a major role in present-day astrophysics, yet they share common issues. In this work we seek to remedy some of those by the use of results from realistic and highly detailed 3D hydrodynamical simulations of stellar atmospheres. We have implemented a new temperature stratification extracted directly from the 3D simulations into the Garching Stellar Evolution Code to replace the simplified atmosphere normally used. Secondly, we have implemented the use of a variable mixing-length parameter, which changes as a function of the stellar surface gravity and temperature - also derived from the 3D simulations. Furthermore, to make our models consistent, we have calculated new opacity tables to match the atmospheric simulations. Here, we present the modified code and initial results on stellar evolution using it.

Unscrambling micro-solvation of -COOH and -NH groups in neat dimethyl sulfoxide: insights from 1H-NMR spectroscopy and computational studies.

PubMed

Takis, Panteleimon G; Papavasileiou, Konstantinos D; Peristeras, Loukas D; Boulougouris, Georgios C; Melissas, Vasilios S; Troganis, Anastassios N

2017-05-31

Dimethyl sulfoxide (DMSO) has a significant, multi-faceted role in medicine, pharmacy, and biology as well as in biophysical chemistry and catalysis. Its physical properties and impact on biomolecular structures still attract major scientific interest, especially the interactions of DMSO with biomolecular functional groups. In the present study, we shed light on the "isolated" carboxylic (-COOH) and amide (-NH) interactions in neat DMSO via 1 H NMR studies along with extensive theoretical approaches, i.e. molecular dynamics (MD) simulations, density functional theory (DFT), and ab initio calculations, applied on model compounds (i.e. acetic and benzoic acid, ethyl acetamidocyanoacetate). Both experimental and theoretical results show excellent agreement, thereby permitting the calculation of the association constants between the studied compounds and DMSO molecules. Our coupled MD simulations, DFT and ab initio calculations, and NMR spectroscopy results indicated that complex formation is entropically driven and DMSO molecules undergo multiple strong interactions with the studied molecules, particularly with the -COOH groups. The combined experimental and theoretical techniques unraveled the interactions of DMSO with the most abundant functional groups of peptides (i.e. peptide bonds, side chain and terminal carboxyl groups) in high detail, providing significant insights on the underlying thermodynamics driving these interactions. Moreover, the developed methodology for the analysis of the simulation results could serve as a template for future thermodynamic and kinetic studies of similar systems.

Renal function alterations during skeletal muscle disuse in simulated microgravity

NASA Technical Reports Server (NTRS)

Tucker, Bryan J.

1992-01-01

This project was to examine the alterations in renal functions during skeletal muscle disuse in simulated microgravity. Although this area could cover a wide range of investigative efforts, the limited funding resulted in the selection of two projects. These projects would result in data contributing to an area of research deemed high priority by NASA and would address issues of the alterations in renal response to vasoactive stimuli during conditions of skeletal muscle disuse as well as investigate the contribution of skeletal muscle disuse, conditions normally found in long term human exposure to microgravity, to the balance of fluid and macromolecules within the vasculature versus the interstitium. These two projects selected are as follows: investigate the role of angiotensin 2 on renal function during periods of simulated microgravity and skeletal muscle disuse to determine if the renal response is altered to changes in circulating concentrations of angiotensin 2 compared to appropriate controls; and determine if the shift of fluid balance from vasculature to the interstitium, the two components of extracellular fluid volume, that occur during prolonged exposure to microgravity and skeletal muscle disuse is a result, in part, to alterations in the fluid and macromolecular balance in the peripheral capillary beds, of which the skeletal muscle contains the majority of recruitment capillaries. A recruitment capillary bed would be most sensitive to alterations in Starling forces and fluid and macromolecular permeability.

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

PubMed

Richings, Gareth W; Habershon, Scott

2017-09-12

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

Two-dimensional quasistatic stationary short range surface plasmons in flat nanoprisms.

PubMed

Nelayah, J; Kociak, M; Stéphan, O; Geuquet, N; Henrard, L; García de Abajo, F J; Pastoriza-Santos, I; Liz-Marzán, L M; Colliex, C

2010-03-10

We report on the nanometer scale spectral imaging of surface plasmons within individual silver triangular nanoprisms by electron energy loss spectroscopy and on related discrete dipole approximation simulations. A dependence of the energy and intensity of the three detected modes as function of the edge length is clearly identified both experimentally and with simulations. We show that for experimentally available prisms (edge lengths ca. 70 to 300 nm) the energies and intensities of the different modes show a monotonic dependence as function of the aspect ratio of the prisms. For shorter or longer prisms, deviations to this behavior are identified thanks to simulations. These modes have symmetric charge distribution and result from the strong coupling of the upper and lower triangular surfaces. They also form a standing wave in the in-plane direction and are identified as quasistatic short range surface plasmons of different orders as emphasized within a continuum dielectric model. This model explains in simple terms the measured and simulated energy and intensity changes as function of geometric parameters. By providing a unified vision of surface plasmons in platelets, such a model should be useful for engineering of the optical properties of metallic nanoplatelets.

Concurrent atomistic and continuum simulation of bi-crystal strontium titanate with tilt grain boundary

PubMed Central

Yang, Shengfeng; Chen, Youping

2015-01-01

In this paper, we present the development of a concurrent atomistic–continuum (CAC) methodology for simulation of the grain boundary (GB) structures and their interaction with other defects in ionic materials. Simulation results show that the CAC simulation allows a smooth passage of cracks through the atomistic–continuum interface without the need for additional constitutive rules or special numerical treatment; both the atomic-scale structures and the energies of the four different [001] tilt GBs in bi-crystal strontium titanate obtained by CAC compare well with those obtained by existing experiments and density function theory calculations. Although 98.4% of the degrees of freedom of the simulated atomistic system have been eliminated in a coarsely meshed finite-element region, the CAC results, including the stress–strain responses, the GB–crack interaction mechanisms and the effect of the interaction on the fracture strength, are comparable with that of all-atom molecular dynamics simulation results. In addition, CAC simulation results show that the GB–crack interaction has a significant effect on the fracture behaviour of bi-crystal strontium titanate; not only the misorientation angle but also the atomic-level details of the GB structure influence the effect of the GB on impeding crack propagation. PMID:25792957

Shock compression of strongly correlated oxides: A liquid-regime equation of state for cerium(IV) oxide

NASA Astrophysics Data System (ADS)

Weck, Philippe F.; Cochrane, Kyle R.; Root, Seth; Lane, J. Matthew D.; Shulenburger, Luke; Carpenter, John H.; Sjostrom, Travis; Mattsson, Thomas R.; Vogler, Tracy J.

2018-03-01

The shock Hugoniot for full-density and porous CeO2 was investigated in the liquid regime using ab initio molecular dynamics (AIMD) simulations with Erpenbeck's approach based on the Rankine-Hugoniot jump conditions. The phase space was sampled by carrying out NVT simulations for isotherms between 6000 and 100 000 K and densities ranging from ρ =2.5 to 20 g /cm3 . The impact of on-site Coulomb interaction corrections +U on the equation of state (EOS) obtained from AIMD simulations was assessed by direct comparison with results from standard density functional theory simulations. Classical molecular dynamics (CMD) simulations were also performed to model atomic-scale shock compression of larger porous CeO2 models. Results from AIMD and CMD compression simulations compare favorably with Z-machine shock data to 525 GPa and gas-gun data to 109 GPa for porous CeO2 samples. Using results from AIMD simulations, an accurate liquid-regime Mie-Grüneisen EOS was built for CeO2. In addition, a revised multiphase SESAME-type EOS was constrained using AIMD results and experimental data generated in this work. This study demonstrates the necessity of acquiring data in the porous regime to increase the reliability of existing analytical EOS models.

Concurrent atomistic and continuum simulation of bi-crystal strontium titanate with tilt grain boundary.

PubMed

Yang, Shengfeng; Chen, Youping

2015-03-08

In this paper, we present the development of a concurrent atomistic-continuum (CAC) methodology for simulation of the grain boundary (GB) structures and their interaction with other defects in ionic materials. Simulation results show that the CAC simulation allows a smooth passage of cracks through the atomistic-continuum interface without the need for additional constitutive rules or special numerical treatment; both the atomic-scale structures and the energies of the four different [001] tilt GBs in bi-crystal strontium titanate obtained by CAC compare well with those obtained by existing experiments and density function theory calculations. Although 98.4% of the degrees of freedom of the simulated atomistic system have been eliminated in a coarsely meshed finite-element region, the CAC results, including the stress-strain responses, the GB-crack interaction mechanisms and the effect of the interaction on the fracture strength, are comparable with that of all-atom molecular dynamics simulation results. In addition, CAC simulation results show that the GB-crack interaction has a significant effect on the fracture behaviour of bi-crystal strontium titanate; not only the misorientation angle but also the atomic-level details of the GB structure influence the effect of the GB on impeding crack propagation.

Thermal Analysis System

NASA Technical Reports Server (NTRS)

DiStefano, III, Frank James (Inventor); Wobick, Craig A. (Inventor); Chapman, Kirt Auldwin (Inventor); McCloud, Peter L. (Inventor)

2014-01-01

A thermal fluid system modeler including a plurality of individual components. A solution vector is configured and ordered as a function of one or more inlet dependencies of the plurality of individual components. A fluid flow simulator simulates thermal energy being communicated with the flowing fluid and between first and second components of the plurality of individual components. The simulation extends from an initial time to a later time step and bounds heat transfer to be substantially between the flowing fluid, walls of tubes formed in each of the individual components of the plurality, and between adjacent tubes. Component parameters of the solution vector are updated with simulation results for each of the plurality of individual components of the simulation.

Genomic data assimilation for estimating hybrid functional Petri net from time-course gene expression data.

PubMed

Nagasaki, Masao; Yamaguchi, Rui; Yoshida, Ryo; Imoto, Seiya; Doi, Atsushi; Tamada, Yoshinori; Matsuno, Hiroshi; Miyano, Satoru; Higuchi, Tomoyuki

2006-01-01

We propose an automatic construction method of the hybrid functional Petri net as a simulation model of biological pathways. The problems we consider are how we choose the values of parameters and how we set the network structure. Usually, we tune these unknown factors empirically so that the simulation results are consistent with biological knowledge. Obviously, this approach has the limitation in the size of network of interest. To extend the capability of the simulation model, we propose the use of data assimilation approach that was originally established in the field of geophysical simulation science. We provide genomic data assimilation framework that establishes a link between our simulation model and observed data like microarray gene expression data by using a nonlinear state space model. A key idea of our genomic data assimilation is that the unknown parameters in simulation model are converted as the parameter of the state space model and the estimates are obtained as the maximum a posteriori estimators. In the parameter estimation process, the simulation model is used to generate the system model in the state space model. Such a formulation enables us to handle both the model construction and the parameter tuning within a framework of the Bayesian statistical inferences. In particular, the Bayesian approach provides us a way of controlling overfitting during the parameter estimations that is essential for constructing a reliable biological pathway. We demonstrate the effectiveness of our approach using synthetic data. As a result, parameter estimation using genomic data assimilation works very well and the network structure is suitably selected.

Deterministic modelling and stochastic simulation of biochemical pathways using MATLAB.

PubMed

Ullah, M; Schmidt, H; Cho, K H; Wolkenhauer, O

2006-03-01

The analysis of complex biochemical networks is conducted in two popular conceptual frameworks for modelling. The deterministic approach requires the solution of ordinary differential equations (ODEs, reaction rate equations) with concentrations as continuous state variables. The stochastic approach involves the simulation of differential-difference equations (chemical master equations, CMEs) with probabilities as variables. This is to generate counts of molecules for chemical species as realisations of random variables drawn from the probability distribution described by the CMEs. Although there are numerous tools available, many of them free, the modelling and simulation environment MATLAB is widely used in the physical and engineering sciences. We describe a collection of MATLAB functions to construct and solve ODEs for deterministic simulation and to implement realisations of CMEs for stochastic simulation using advanced MATLAB coding (Release 14). The program was successfully applied to pathway models from the literature for both cases. The results were compared to implementations using alternative tools for dynamic modelling and simulation of biochemical networks. The aim is to provide a concise set of MATLAB functions that encourage the experimentation with systems biology models. All the script files are available from www.sbi.uni-rostock.de/ publications_matlab-paper.html.

On the Green's function of the partially diffusion-controlled reversible ABCD reaction for radiation chemistry codes

NASA Astrophysics Data System (ADS)

Plante, Ianik; Devroye, Luc

2015-09-01

Several computer codes simulating chemical reactions in particles systems are based on the Green's functions of the diffusion equation (GFDE). Indeed, many types of chemical systems have been simulated using the exact GFDE, which has also become the gold standard for validating other theoretical models. In this work, a simulation algorithm is presented to sample the interparticle distance for partially diffusion-controlled reversible ABCD reaction. This algorithm is considered exact for 2-particles systems, is faster than conventional look-up tables and uses only a few kilobytes of memory. The simulation results obtained with this method are compared with those obtained with the independent reaction times (IRT) method. This work is part of our effort in developing models to understand the role of chemical reactions in the radiation effects on cells and tissues and may eventually be included in event-based models of space radiation risks. However, as many reactions are of this type in biological systems, this algorithm might play a pivotal role in future simulation programs not only in radiation chemistry, but also in the simulation of biochemical networks in time and space as well.

Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments

PubMed Central

Patmanidis, Ilias

2018-01-01

In bionanotechnology, the field of creating functional materials consisting of bio-inspired molecules, the function and shape of a nanostructure only appear through the assembly of many small molecules together. The large number of building blocks required to define a nanostructure combined with the many degrees of freedom in packing small molecules has long precluded molecular simulations, but recent advances in computational hardware as well as software have made classical simulations available to this strongly expanding field. Here, we review the state of the art in simulations of self-assembling bio-inspired supramolecular systems. We will first discuss progress in force fields, simulation protocols and enhanced sampling techniques using recent examples. Secondly, we will focus on efforts to enable the comparison of experimentally accessible observables and computational results. Experimental quantities that can be measured by microscopy, spectroscopy and scattering can be linked to simulation output either directly or indirectly, via quantum mechanical or semi-empirical techniques. Overall, we aim to provide an overview of the various computational approaches to understand not only the molecular architecture of nanostructures, but also the mechanism of their formation. PMID:29688238

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

Popovich, P.; Carter, T. A.; Friedman, B.

Numerical simulation of plasma turbulence in the Large Plasma Device (LAPD) [W. Gekelman, H. Pfister, Z. Lucky et al., Rev. Sci. Instrum. 62, 2875 (1991)] is presented. The model, implemented in the BOUndary Turbulence code [M. Umansky, X. Xu, B. Dudson et al., Contrib. Plasma Phys. 180, 887 (2009)], includes three-dimensional (3D) collisional fluid equations for plasma density, electron parallel momentum, and current continuity, and also includes the effects of ion-neutral collisions. In nonlinear simulations using measured LAPD density profiles but assuming constant temperature profile for simplicity, self-consistent evolution of instabilities and nonlinearly generated zonal flows results in a saturatedmore » turbulent state. Comparisons of these simulations with measurements in LAPD plasmas reveal good qualitative and reasonable quantitative agreement, in particular in frequency spectrum, spatial correlation, and amplitude probability distribution function of density fluctuations. For comparison with LAPD measurements, the plasma density profile in simulations is maintained either by direct azimuthal averaging on each time step, or by adding particle source/sink function. The inferred source/sink values are consistent with the estimated ionization source and parallel losses in LAPD. These simulations lay the groundwork for more a comprehensive effort to test fluid turbulence simulation against LAPD data.« less

Simulation of wheat growth and development based on organ-level photosynthesis and assimilate allocation.

PubMed

Evers, J B; Vos, J; Yin, X; Romero, P; van der Putten, P E L; Struik, P C

2010-05-01

Intimate relationships exist between form and function of plants, determining many processes governing their growth and development. However, in most crop simulation models that have been created to simulate plant growth and, for example, predict biomass production, plant structure has been neglected. In this study, a detailed simulation model of growth and development of spring wheat (Triticum aestivum) is presented, which integrates degree of tillering and canopy architecture with organ-level light interception, photosynthesis, and dry-matter partitioning. An existing spatially explicit 3D architectural model of wheat development was extended with routines for organ-level microclimate, photosynthesis, assimilate distribution within the plant structure according to organ demands, and organ growth and development. Outgrowth of tiller buds was made dependent on the ratio between assimilate supply and demand of the plants. Organ-level photosynthesis, biomass production, and bud outgrowth were simulated satisfactorily. However, to improve crop simulation results more efforts are needed mechanistically to model other major plant physiological processes such as nitrogen uptake and distribution, tiller death, and leaf senescence. Nevertheless, the work presented here is a significant step forwards towards a mechanistic functional-structural plant model, which integrates plant architecture with key plant processes.

Challenges and solutions for realistic room simulation

NASA Astrophysics Data System (ADS)

Begault, Durand R.

2002-05-01

Virtual room acoustic simulation (auralization) techniques have traditionally focused on answering questions related to speech intelligibility or musical quality, typically in large volumetric spaces. More recently, auralization techniques have been found to be important for the externalization of headphone-reproduced virtual acoustic images. Although externalization can be accomplished using a minimal simulation, data indicate that realistic auralizations need to be responsive to head motion cues for accurate localization. Computational demands increase when providing for the simulation of coupled spaces, small rooms lacking meaningful reverberant decays, or reflective surfaces in outdoor environments. Auditory threshold data for both early reflections and late reverberant energy levels indicate that much of the information captured in acoustical measurements is inaudible, minimizing the intensive computational requirements of real-time auralization systems. Results are presented for early reflection thresholds as a function of azimuth angle, arrival time, and sound-source type, and reverberation thresholds as a function of reverberation time and level within 250-Hz-2-kHz octave bands. Good agreement is found between data obtained in virtual room simulations and those obtained in real rooms, allowing a strategy for minimizing computational requirements of real-time auralization systems.

Distributed Observer Network

NASA Technical Reports Server (NTRS)

Conroy, Michael; Mazzone, Rebecca; Little, William; Elfrey, Priscilla; Mann, David; Mabie, Kevin; Cuddy, Thomas; Loundermon, Mario; Spiker, Stephen; McArthur, Frank;

A Machine Learning Method for the Prediction of Receptor Activation in the Simulation of Synapses

PubMed Central

Montes, Jesus; Gomez, Elena; Merchán-Pérez, Angel; DeFelipe, Javier; Peña, Jose-Maria

2013-01-01

Chemical synaptic transmission involves the release of a neurotransmitter that diffuses in the extracellular space and interacts with specific receptors located on the postsynaptic membrane. Computer simulation approaches provide fundamental tools for exploring various aspects of the synaptic transmission under different conditions. In particular, Monte Carlo methods can track the stochastic movements of neurotransmitter molecules and their interactions with other discrete molecules, the receptors. However, these methods are computationally expensive, even when used with simplified models, preventing their use in large-scale and multi-scale simulations of complex neuronal systems that may involve large numbers of synaptic connections. We have developed a machine-learning based method that can accurately predict relevant aspects of the behavior of synapses, such as the percentage of open synaptic receptors as a function of time since the release of the neurotransmitter, with considerably lower computational cost compared with the conventional Monte Carlo alternative. The method is designed to learn patterns and general principles from a corpus of previously generated Monte Carlo simulations of synapses covering a wide range of structural and functional characteristics. These patterns are later used as a predictive model of the behavior of synapses under different conditions without the need for additional computationally expensive Monte Carlo simulations. This is performed in five stages: data sampling, fold creation, machine learning, validation and curve fitting. The resulting procedure is accurate, automatic, and it is general enough to predict synapse behavior under experimental conditions that are different to the ones it has been trained on. Since our method efficiently reproduces the results that can be obtained with Monte Carlo simulations at a considerably lower computational cost, it is suitable for the simulation of high numbers of synapses and it is therefore an excellent tool for multi-scale simulations. PMID:23894367

Neurite, a Finite Difference Large Scale Parallel Program for the Simulation of Electrical Signal Propagation in Neurites under Mechanical Loading

PubMed Central

García-Grajales, Julián A.; Rucabado, Gabriel; García-Dopico, Antonio; Peña, José-María; Jérusalem, Antoine

2015-01-01

With the growing body of research on traumatic brain injury and spinal cord injury, computational neuroscience has recently focused its modeling efforts on neuronal functional deficits following mechanical loading. However, in most of these efforts, cell damage is generally only characterized by purely mechanistic criteria, functions of quantities such as stress, strain or their corresponding rates. The modeling of functional deficits in neurites as a consequence of macroscopic mechanical insults has been rarely explored. In particular, a quantitative mechanically based model of electrophysiological impairment in neuronal cells, Neurite, has only very recently been proposed. In this paper, we present the implementation details of this model: a finite difference parallel program for simulating electrical signal propagation along neurites under mechanical loading. Following the application of a macroscopic strain at a given strain rate produced by a mechanical insult, Neurite is able to simulate the resulting neuronal electrical signal propagation, and thus the corresponding functional deficits. The simulation of the coupled mechanical and electrophysiological behaviors requires computational expensive calculations that increase in complexity as the network of the simulated cells grows. The solvers implemented in Neurite—explicit and implicit—were therefore parallelized using graphics processing units in order to reduce the burden of the simulation costs of large scale scenarios. Cable Theory and Hodgkin-Huxley models were implemented to account for the electrophysiological passive and active regions of a neurite, respectively, whereas a coupled mechanical model accounting for the neurite mechanical behavior within its surrounding medium was adopted as a link between electrophysiology and mechanics. This paper provides the details of the parallel implementation of Neurite, along with three different application examples: a long myelinated axon, a segmented dendritic tree, and a damaged axon. The capabilities of the program to deal with large scale scenarios, segmented neuronal structures, and functional deficits under mechanical loading are specifically highlighted. PMID:25680098

Full equations utilities (FEQUTL) model for the approximation of hydraulic characteristics of open channels and control structures during unsteady flow

USGS Publications Warehouse

Franz, Delbert D.; Melching, Charles S.

1997-01-01

The Full EQuations UTiLities (FEQUTL) model is a computer program for computation of tables that list the hydraulic characteristics of open channels and control structures as a function of upstream and downstream depths; these tables facilitate the simulation of unsteady flow in a stream system with the Full Equations (FEQ) model. Simulation of unsteady flow requires many iterations for each time period computed. Thus, computation of hydraulic characteristics during the simulations is impractical, and preparation of function tables and application of table look-up procedures facilitates simulation of unsteady flow. Three general types of function tables are computed: one-dimensional tables that relate hydraulic characteristics to upstream flow depth, two-dimensional tables that relate flow through control structures to upstream and downstream flow depth, and three-dimensional tables that relate flow through gated structures to upstream and downstream flow depth and gate setting. For open-channel reaches, six types of one-dimensional function tables contain different combinations of the top width of flow, area, first moment of area with respect to the water surface, conveyance, flux coefficients, and correction coefficients for channel curvilinearity. For hydraulic control structures, one type of one-dimensional function table contains relations between flow and upstream depth, and two types of two-dimensional function tables contain relations among flow and upstream and downstream flow depths. For hydraulic control structures with gates, a three-dimensional function table lists the system of two-dimensional tables that contain the relations among flow and upstream and downstream flow depths that correspond to different gate openings. Hydraulic control structures for which function tables containing flow relations are prepared in FEQUTL include expansions, contractions, bridges, culverts, embankments, weirs, closed conduits (circular, rectangular, and pipe-arch shapes), dam failures, floodways, and underflow gates (sluice and tainter gates). The theory for computation of the hydraulic characteristics is presented for open channels and for each hydraulic control structure. For the hydraulic control structures, the theory is developed from the results of experimental tests of flow through the structure for different upstream and downstream flow depths. These tests were done to describe flow hydraulics for a single, steady-flow design condition and, thus, do not provide complete information on flow transitions (for example, between free- and submerged-weir flow) that may result in simulation of unsteady flow. Therefore, new procedures are developed to approximate the hydraulics of flow transitions for culverts, embankments, weirs, and underflow gates.

Simulation approach for the evaluation of tracking accuracy in radiotherapy: a preliminary study.

PubMed

Tanaka, Rie; Ichikawa, Katsuhiro; Mori, Shinichiro; Sanada, Sigeru

2013-01-01

Real-time tumor tracking in external radiotherapy can be achieved by diagnostic (kV) X-ray imaging with a dynamic flat-panel detector (FPD). It is important to keep the patient dose as low as possible while maintaining tracking accuracy. A simulation approach would be helpful to optimize the imaging conditions. This study was performed to develop a computer simulation platform based on a noise property of the imaging system for the evaluation of tracking accuracy at any noise level. Flat-field images were obtained using a direct-type dynamic FPD, and noise power spectrum (NPS) analysis was performed. The relationship between incident quantum number and pixel value was addressed, and a conversion function was created. The pixel values were converted into a map of quantum number using the conversion function, and the map was then input into the random number generator to simulate image noise. Simulation images were provided at different noise levels by changing the incident quantum numbers. Subsequently, an implanted marker was tracked automatically and the maximum tracking errors were calculated at different noise levels. The results indicated that the maximum tracking error increased with decreasing incident quantum number in flat-field images with an implanted marker. In addition, the range of errors increased with decreasing incident quantum number. The present method could be used to determine the relationship between image noise and tracking accuracy. The results indicated that the simulation approach would aid in determining exposure dose conditions according to the necessary tracking accuracy.

A generic model of real-world non-ideal behaviour of FES-induced muscle contractions: simulation tool

NASA Astrophysics Data System (ADS)

Lynch, Cheryl L.; Graham, Geoff M.; Popovic, Milos R.

2011-08-01

Functional electrical stimulation (FES) applications are frequently evaluated in simulation prior to testing in human subjects. Such simulations are usually based on the typical muscle responses to electrical stimulation, which may result in an overly optimistic assessment of likely real-world performance. We propose a novel method for simulating FES applications that includes non-ideal muscle behaviour during electrical stimulation resulting from muscle fatigue, spasms and tremors. A 'non-idealities' block that can be incorporated into existing FES simulations and provides a realistic estimate of real-world performance is described. An implementation example is included, showing how the non-idealities block can be incorporated into a simulation of electrically stimulated knee extension against gravity for both a proportional-integral-derivative controller and a sliding mode controller. The results presented in this paper illustrate that the real-world performance of a FES system may be vastly different from the performance obtained in simulation using nominal muscle models. We believe that our non-idealities block should be included in future simulations that involve muscle response to FES, as this tool will provide neural engineers with a realistic simulation of the real-world performance of FES systems. This simulation strategy will help engineers and organizations save time and money by preventing premature human testing. The non-idealities block will become available free of charge at www.toronto-fes.ca in late 2011.

A theoretical analysis of anatomical and functional intestinal slow wave re-entry.

PubMed

Du, Peng; O'Grady, Gregory; Cheng, Leo K

2017-07-21

Intestinal bioelectrical slow waves are a key regulator of intestinal motility. Peripheral pacemakers, ectopic initiations and sustained periods of re-entrant activities have all been experimentally observed to be important factors in setting the frequency of intestinal slow waves, but the tissue-level mechanisms underpinning these activities are unclear. This theoretical analysis aimed to define the initiation, maintenance, and termination criteria of two classes of intestinal re-entrant activities: anatomical re-entry and functional re-entry. Anatomical re-entry was modeled in a three-dimensional (3D) cylindrical model, and functional rotor was modeled in a 2D rectangle model. A single-pulse stimulus was used to invoke an anatomical re-entry and a prolonged refractory block was used to invoke the rotor. In both cases, the simulated re-entrant activities operated at frequencies above the baseline entrainment frequency. The anatomical re-entry simulation results demonstrated that a temporary functional refractory block would be required to initiate the re-entrant activity in a single direction around the cylindrical model. The rotor could be terminated by a single-pulse stimulus delivered around the core of the rotor. In conclusion, the simulation results provide the following new insights into the mechanisms of intestinal re-entry: (i) anatomical re-entry is only maintained within a specific range of velocities, outside of which the re-entrant activities become either an ectopic activity or simultaneous activations of the intestinal wall; (ii) a maintained rotor entrained slow waves faster in the antegrade direction than in the retrograde direction. Simulations are shown to be a valuable tool for achieving novel insights into the mechanisms of intestinal slow wave dysrhythmia. Copyright © 2017 Elsevier Ltd. All rights reserved.

Structural and magnetic properties of turmeric functionalized CoFe2O4 nanocomposite powder

NASA Astrophysics Data System (ADS)

Mehran, E.; Farjami Shayesteh, S.; Sheykhan, M.

2016-10-01

The structural and magnetic properties of the synthesized pure and functionalized CoFe2O4 magnetic nanoparticles (NPs) are studied by analyzing the results from the x-ray diffraction (XRD), transmission electron microscopy (TEM), FT-IR spectroscopy, thermogravimetry (TG), and vibrating sample magnetometer (VSM). To extract the structure and lattice parameters from the XRD analysis results, we first apply the pseudo-Voigt model function to the experimental data obtained from XRD analysis and then the Rietveld algorithm is used in order to optimize the model function to estimate the true intensity values. Our simulated intensities are in good agreement with the experimental peaks, therefore, all structural parameters such as crystallite size and lattice constant are achieved through this simulation. Magnetic analysis reveals that the synthesized functionalized NPs have a saturation magnetization almost equal to that of pure nanoparticles (PNPs). It is also found that the presence of the turmeric causes a small reduction in coercivity of the functionalized NPs in comparison with PNP. Our TGA and FTIR results show that the turmeric is bonded very well to the surface of the NPs. So it can be inferred that a nancomposite (NC) powder of turmeric and nanoparticles is produced. As an application, the anti-arsenic characteristic of turmeric makes the synthesized functionalized NPs or NC powder a good candidate for arsenic removal from polluted industrial waste water. Project supported by the University of Guilan and the Iran Nanotechnology Initiative Council.

Functional domain motions in proteins on the ~1-100 ns timescale: comparison of neutron spin-echo spectroscopy of phosphoglycerate kinase with molecular-dynamics simulation.

PubMed

Smolin, N; Biehl, R; Kneller, G R; Richter, D; Smith, J C

2012-03-07

Protein function often requires large-scale domain motion. An exciting new development in the experimental characterization of domain motions in proteins is the application of neutron spin-echo spectroscopy (NSE). NSE directly probes coherent (i.e., pair correlated) scattering on the ~1-100 ns timescale. Here, we report on all-atom molecular-dynamics (MD) simulation of a protein, phosphoglycerate kinase, from which we calculate small-angle neutron scattering (SANS) and NSE scattering properties. The simulation-derived and experimental-solution SANS results are in excellent agreement. The contributions of translational and rotational whole-molecule diffusion to the simulation-derived NSE and potential problems in their estimation are examined. Principal component analysis identifies types of domain motion that dominate the internal motion's contribution to the NSE signal, with the largest being classic hinge bending. The associated free-energy profiles are quasiharmonic and the frictional properties correspond to highly overdamped motion. The amplitudes of the motions derived by MD are smaller than those derived from the experimental analysis, and possible reasons for this difference are discussed. The MD results confirm that a significant component of the NSE arises from internal dynamics. They also demonstrate that the combination of NSE with MD is potentially useful for determining the forms, potentials of mean force, and time dependence of functional domain motions in proteins. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Functional Domain Motions in Proteins on the ∼1–100 ns Timescale: Comparison of Neutron Spin-Echo Spectroscopy of Phosphoglycerate Kinase with Molecular-Dynamics Simulation

PubMed Central

Smolin, N.; Biehl, R.; Kneller, G.R.; Richter, D.; Smith, J.C.

2012-01-01

Protein function often requires large-scale domain motion. An exciting new development in the experimental characterization of domain motions in proteins is the application of neutron spin-echo spectroscopy (NSE). NSE directly probes coherent (i.e., pair correlated) scattering on the ∼1–100 ns timescale. Here, we report on all-atom molecular-dynamics (MD) simulation of a protein, phosphoglycerate kinase, from which we calculate small-angle neutron scattering (SANS) and NSE scattering properties. The simulation-derived and experimental-solution SANS results are in excellent agreement. The contributions of translational and rotational whole-molecule diffusion to the simulation-derived NSE and potential problems in their estimation are examined. Principal component analysis identifies types of domain motion that dominate the internal motion's contribution to the NSE signal, with the largest being classic hinge bending. The associated free-energy profiles are quasiharmonic and the frictional properties correspond to highly overdamped motion. The amplitudes of the motions derived by MD are smaller than those derived from the experimental analysis, and possible reasons for this difference are discussed. The MD results confirm that a significant component of the NSE arises from internal dynamics. They also demonstrate that the combination of NSE with MD is potentially useful for determining the forms, potentials of mean force, and time dependence of functional domain motions in proteins. PMID:22404933

The Role of Parametric Assumptions in Adaptive Bayesian Estimation

ERIC Educational Resources Information Center

Alcala-Quintana, Rocio; Garcia-Perez, Miguel A.

2004-01-01

Variants of adaptive Bayesian procedures for estimating the 5% point on a psychometric function were studied by simulation. Bias and standard error were the criteria to evaluate performance. The results indicated a superiority of (a) uniform priors, (b) model likelihood functions that are odd symmetric about threshold and that have parameter…

Virtual reality simulation training of mastoidectomy - studies on novice performance.

PubMed

Andersen, Steven Arild Wuyts

2016-08-01

Virtual reality (VR) simulation-based training is increasingly used in surgical technical skills training including in temporal bone surgery. The potential of VR simulation in enabling high-quality surgical training is great and VR simulation allows high-stakes and complex procedures such as mastoidectomy to be trained repeatedly, independent of patients and surgical tutors, outside traditional learning environments such as the OR or the temporal bone lab, and with fewer of the constraints of traditional training. This thesis aims to increase the evidence-base of VR simulation training of mastoidectomy and, by studying the final-product performances of novices, investigates the transfer of skills to the current gold-standard training modality of cadaveric dissection, the effect of different practice conditions and simulator-integrated tutoring on performance and retention of skills, and the role of directed, self-regulated learning. Technical skills in mastoidectomy were transferable from the VR simulation environment to cadaveric dissection with significant improvement in performance after directed, self-regulated training in the VR temporal bone simulator. Distributed practice led to a better learning outcome and more consolidated skills than massed practice and also resulted in a more consistent performance after three months of non-practice. Simulator-integrated tutoring accelerated the initial learning curve but also caused over-reliance on tutoring, which resulted in a drop in performance when the simulator-integrated tutor-function was discontinued. The learning curves were highly individual but often plateaued early and at an inadequate level, which related to issues concerning both the procedure and the VR simulator, over-reliance on the tutor function and poor self-assessment skills. Future simulator-integrated automated assessment could potentially resolve some of these issues and provide trainees with both feedback during the procedure and immediate assessment following each procedure. Standard setting by establishing a proficiency level that can be used for mastery learning with deliberate practice could also further sophisticate directed, self-regulated learning in VR simulation-based training. VR simulation-based training should be embedded in a systematic and competency-based training curriculum for high-quality surgical skills training, ultimately leading to improved safety and patient care.

Force-field functor theory: classical force-fields which reproduce equilibrium quantum distributions

PubMed Central

Babbush, Ryan; Parkhill, John; Aspuru-Guzik, Alán

2013-01-01

Feynman and Hibbs were the first to variationally determine an effective potential whose associated classical canonical ensemble approximates the exact quantum partition function. We examine the existence of a map between the local potential and an effective classical potential which matches the exact quantum equilibrium density and partition function. The usefulness of such a mapping rests in its ability to readily improve Born-Oppenheimer potentials for use with classical sampling. We show that such a map is unique and must exist. To explore the feasibility of using this result to improve classical molecular mechanics, we numerically produce a map from a library of randomly generated one-dimensional potential/effective potential pairs then evaluate its performance on independent test problems. We also apply the map to simulate liquid para-hydrogen, finding that the resulting radial pair distribution functions agree well with path integral Monte Carlo simulations. The surprising accessibility and transferability of the technique suggest a quantitative route to adapting Born-Oppenheimer potentials, with a motivation similar in spirit to the powerful ideas and approximations of density functional theory. PMID:24790954

Summary of Research Adaptions of Visceral and Cerebral Resistance Arteries to Simulated Microgravity

NASA Technical Reports Server (NTRS)

Delp, Michael

2003-01-01

The proposed studies were designed address the effects of simulated microgravity on vascular smooth muscle and endothelial cell function in resistance arteries isolated from visceral tissues (spleen, mesentery and kidneys) and cerebrum. Alterations in vascular function induced by microgravity are particularly relevant to the problems of orthostatic intolerance and reduced exercise capacity experienced by astronauts upon re-entry into the earth's gravitational field. Decrements in contractile function or enhanced vasodilatory responsiveness of peripheral resistance arteries could lead to decreased peripheral resistance and orthostatic hypotension. Alternatively, augmentation of contractile function in cerebral resistance arteries could lead to increased cerebral vascular resistance and diminished perfusion of the brain. The Specific Aims and hypotheses were proposed in this grant. Following each of the Specific Aims, progress toward addressing that specific aim is presented. With the exception of Specific Aim VI (see aim for details), all aims have been experimentally addressed as proposed. The final six months of the granting period will be used for manuscript preparation; manuscripts in preparation will contain results from Specific Aims I-IV. Results from Specific Aims V and VI have been published.

Global Simulation of Aviation Operations

NASA Technical Reports Server (NTRS)

Sridhar, Banavar; Sheth, Kapil; Ng, Hok Kwan; Morando, Alex; Li, Jinhua

2016-01-01

The simulation and analysis of global air traffic is limited due to a lack of simulation tools and the difficulty in accessing data sources. This paper provides a global simulation of aviation operations combining flight plans and real air traffic data with historical commercial city-pair aircraft type and schedule data and global atmospheric data. The resulting capability extends the simulation and optimization functions of NASA's Future Air Traffic Management Concept Evaluation Tool (FACET) to global scale. This new capability is used to present results on the evolution of global air traffic patterns from a concentration of traffic inside US, Europe and across the Atlantic Ocean to a more diverse traffic pattern across the globe with accelerated growth in Asia, Australia, Africa and South America. The simulation analyzes seasonal variation in the long-haul wind-optimal traffic patterns in six major regions of the world and provides potential time-savings of wind-optimal routes compared with either great circle routes or current flight-plans if available.

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.

Communication: An exact bound on the bridge function in integral equation theories.

PubMed

Kast, Stefan M; Tomazic, Daniel

2012-11-07

We show that the formal solution of the general closure relation occurring in Ornstein-Zernike-type integral equation theories in terms of the Lambert W function leads to an exact relation between the bridge function and correlation functions, most notably to an inequality that bounds possible bridge values. The analytical results are illustrated on the example of the Lennard-Jones fluid for which the exact bridge function is known from computer simulations under various conditions. The inequality has consequences for the development of bridge function models and rationalizes numerical convergence issues.

Robustness and Uncertainty: Applications for Policy in Climate and Hydrological Modeling

NASA Astrophysics Data System (ADS)

Fields, A. L., III

2015-12-01

Policymakers must often decide how to proceed when presented with conflicting simulation data from hydrological, climatological, and geological models. While laboratory sciences often appeal to the reproducibility of results to argue for the validity of their conclusions, simulations cannot use this strategy for a number of pragmatic and methodological reasons. However, robustness of predictions and causal structures can serve the same function for simulations as reproducibility does for laboratory experiments and field observations in either adjudicating between conflicting results or showing that there is insufficient justification to externally validate the results. Additionally, an interpretation of the argument from robustness is presented that involves appealing to the convergence of many well-built and diverse models rather than the more common version which involves appealing to the probability that one of a set of models is likely to be true. This interpretation strengthens the case for taking robustness as an additional requirement for the validation of simulation results and ultimately supports the idea that computer simulations can provide information about the world that is just as trustworthy as data from more traditional laboratory studies and field observations. Understanding the importance of robust results for the validation of simulation data is especially important for policymakers making decisions on the basis of potentially conflicting models. Applications will span climate, hydrological, and hydroclimatological models.

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

Motevaselian, M. H.; Mashayak, S. Y.; Aluru, N. R., E-mail: aluru@illinois.edu

Empirical potential-based quasi-continuum theory (EQT) provides a route to incorporate atomistic detail into continuum framework such as the Nernst-Planck equation. EQT can also be used to construct a grand potential functional for classical density functional theory (cDFT). The combination of EQT and cDFT provides a simple and fast approach to predict the inhomogeneous density, potential profiles, and thermodynamic properties of confined fluids. We extend the EQT-cDFT approach to confined fluid mixtures and demonstrate it by simulating a mixture of methane and hydrogen inside slit-like channels of graphene. We show that the EQT-cDFT predictions for the structure of the confined fluidmore » mixture compare well with the molecular dynamics simulation results. In addition, our results show that graphene slit nanopores exhibit a selective adsorption of methane over hydrogen.« less

An algorithm for solving the system-level problem in multilevel optimization

NASA Technical Reports Server (NTRS)

Balling, R. J.; Sobieszczanski-Sobieski, J.

1994-01-01

A multilevel optimization approach which is applicable to nonhierarchic coupled systems is presented. The approach includes a general treatment of design (or behavior) constraints and coupling constraints at the discipline level through the use of norms. Three different types of norms are examined: the max norm, the Kreisselmeier-Steinhauser (KS) norm, and the 1(sub p) norm. The max norm is recommended. The approach is demonstrated on a class of hub frame structures which simulate multidisciplinary systems. The max norm is shown to produce system-level constraint functions which are non-smooth. A cutting-plane algorithm is presented which adequately deals with the resulting corners in the constraint functions. The algorithm is tested on hub frames with increasing number of members (which simulate disciplines), and the results are summarized.

The precision segmented reflectors: Moderate mission figure control subsystem

NASA Technical Reports Server (NTRS)

Sevaston, G.; Redding, D.; Lau, K.; Breckenridge, W.; Levine, B.; Nerheim, N.; Sirlin, S.; Kadogawa, H.

1991-01-01

A system concept for a space based segmented reflector telescope figure control subsystem is described. The concept employs a two phase architecture in which figure initialization and figure maintenance are independent functions. Figure initialization is accomplished by image sharpening using natural reference targets. Figure maintenance is performed by monitoring the relative positions and alignments of the telescope components using an optical truss. Actuation is achieved using precision positioners. Computer simulation results of figure initialization by pairwise segment coalignment/cophasing and simulated annealing are presented along with figure maintenance results using a wavefront error regulation algorithm. Both functions are shown to perform at acceptable levels for the class of submillimeter telescopes that are serving as the focus of this technology development effort. Component breadboard work as well as plans for a system testbed are discussed.

AVCS Simulator Test Plan and Design Guide

NASA Technical Reports Server (NTRS)

Shelden, Stephen

2001-01-01

Internal document for communication of AVCS direction and documentation of simulator functionality. Discusses methods for AVCS simulation evaluation of pilot functions, implementation strategy of varying functional representation of pilot tasks (by instantiations of a base AVCS to reasonably approximate the interface of various vehicles -- e.g. Altair, GlobalHawk, etc.).

Comparison of cyclic correlation algorithm implemented in matlab and python

NASA Astrophysics Data System (ADS)

Carr, Richard; Whitney, James

Simulation is a necessary step for all engineering projects. Simulation gives the engineers an approximation of how their devices will perform under different circumstances, without hav-ing to build, or before building a physical prototype. This is especially true for space bound devices, i.e., space communication systems, where the impact of system malfunction or failure is several orders of magnitude over that of terrestrial applications. Therefore having a reliable simulation tool is key in developing these devices and systems. Math Works Matrix Laboratory (MATLAB) is a matrix based software used by scientists and engineers to solve problems and perform complex simulations. MATLAB has a number of applications in a wide variety of fields which include communications, signal processing, image processing, mathematics, eco-nomics and physics. Because of its many uses MATLAB has become the preferred software for many engineers; it is also very expensive, especially for students and startups. One alternative to MATLAB is Python. The Python is a powerful, easy to use, open source programming environment that can be used to perform many of the same functions as MATLAB. Python programming environment has been steadily gaining popularity in niche programming circles. While there are not as many function included in the software as MATLAB, there are many open source functions that have been developed that are available to be downloaded for free. This paper illustrates how Python can implement the cyclic correlation algorithm and com-pares the results to the cyclic correlation algorithm implemented in the MATLAB environment. Some of the characteristics to be compared are the accuracy and precision of the results, and the length of the programs. The paper will demonstrate that Python is capable of performing simulations of complex algorithms such cyclic correlation.

Influence of foam on the stability characteristics of immiscible flow in porous media

NASA Astrophysics Data System (ADS)

van der Meer, J. M.; Farajzadeh, R.; Rossen, W. R.; Jansen, J. D.

2018-01-01

Accurate field-scale simulations of foam enhanced oil recovery are challenging, due to the sharp transition between gas and foam. Hence, unpredictable numerical and physical behavior is often observed, casting doubt on the validity of the simulation results. In this paper, a thorough stability analysis of the foam model is presented to validate the simulation results. We study the effect of a strongly non-monotonous total mobility function arising from foam models on the stability characteristics of the flow. To this end, we apply the linear stability analysis to nearly discontinuous relative permeability functions and compare the results with those of highly accurate numerical simulations. In addition, we present a qualitative analysis of the effect of different reservoir and fluid properties on the foam fingering behavior. In particular, we consider the effect of heterogeneity of the reservoir, injection rates, and foam quality. Relative permeability functions play an important role in the onset of fingering behavior of the injected fluid. Hence, we can deduce that stability properties are highly dependent on the non-linearity of the foam transition. The foam-water interface is governed by a very small total mobility ratio, implying a stable front. The transition between gas and foam, however, exhibits a huge total mobility ratio, leading to instabilities in the form of viscous fingering. This implies that there is an unstable pattern behind the front. We deduce that instabilities are able to grow behind the front but are later absorbed by the expanding wave. Moreover, the stability analysis, validated by numerical simulations, provides valuable insights about the important scales and wavelengths of the foam model. In this way, we remove the ambiguity regarding the effect of grid resolution on the convergence of the solutions. This insight forms an essential step toward the design of a suitable computational solver that captures all the appropriate scales, while retaining computational efficiency.

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

Megala, M.; Rajkumar, Beulah J. M., E-mail: beulah-rajkumar@yahoo.co.in

The electronic and optical transfer properties of Benzene, Benzoic Acid (BA), Nitrobenzene (NB) and Para Nitro Benzoic Acid (PNBA) at ground and first excited state has been investigated by the Density functional theory (DFT)and Time Dependent Density Functional Theory (TDDFT) using SVWN functional/3-21G basis set respectively. Possible intra-molecular charge transfer and n to π* transitions in the ground and the first excitation states have been predicted by the molecular orbitals and the Natural Bond Orbital (NBO) analysis. The simulated absorption spectra have been generated and the result compared with existing experimental results.

Simulations of material mixing in laser-driven reshock experiments

NASA Astrophysics Data System (ADS)

Haines, Brian M.; Grinstein, Fernando F.; Welser-Sherrill, Leslie; Fincke, James R.

2013-02-01

We perform simulations of a laser-driven reshock experiment [Welser-Sherrill et al., High Energy Density Phys. (unpublished)] in the strong-shock high energy-density regime to better understand material mixing driven by the Richtmyer-Meshkov instability. Validation of the simulations is based on direct comparison of simulation and radiographic data. Simulations are also compared with published direct numerical simulation and the theory of homogeneous isotropic turbulence. Despite the fact that the flow is neither homogeneous, isotropic nor fully turbulent, there are local regions in which the flow demonstrates characteristics of homogeneous isotropic turbulence. We identify and isolate these regions by the presence of high levels of turbulent kinetic energy (TKE) and vorticity. After reshock, our analysis shows characteristics consistent with those of incompressible isotropic turbulence. Self-similarity and effective Reynolds number assessments suggest that the results are reasonably converged at the finest resolution. Our results show that in shock-driven transitional flows, turbulent features such as self-similarity and isotropy only fully develop once de-correlation, characteristic vorticity distributions, and integrated TKE, have decayed significantly. Finally, we use three-dimensional simulation results to test the performance of two-dimensional Reynolds-averaged Navier-Stokes simulations. In this context, we also test a presumed probability density function turbulent mixing model extensively used in combustion applications.

A continuous optimization approach for inferring parameters in mathematical models of regulatory networks.

PubMed

Deng, Zhimin; Tian, Tianhai

2014-07-29

The advances of systems biology have raised a large number of sophisticated mathematical models for describing the dynamic property of complex biological systems. One of the major steps in developing mathematical models is to estimate unknown parameters of the model based on experimentally measured quantities. However, experimental conditions limit the amount of data that is available for mathematical modelling. The number of unknown parameters in mathematical models may be larger than the number of observation data. The imbalance between the number of experimental data and number of unknown parameters makes reverse-engineering problems particularly challenging. To address the issue of inadequate experimental data, we propose a continuous optimization approach for making reliable inference of model parameters. This approach first uses a spline interpolation to generate continuous functions of system dynamics as well as the first and second order derivatives of continuous functions. The expanded dataset is the basis to infer unknown model parameters using various continuous optimization criteria, including the error of simulation only, error of both simulation and the first derivative, or error of simulation as well as the first and second derivatives. We use three case studies to demonstrate the accuracy and reliability of the proposed new approach. Compared with the corresponding discrete criteria using experimental data at the measurement time points only, numerical results of the ERK kinase activation module show that the continuous absolute-error criteria using both function and high order derivatives generate estimates with better accuracy. This result is also supported by the second and third case studies for the G1/S transition network and the MAP kinase pathway, respectively. This suggests that the continuous absolute-error criteria lead to more accurate estimates than the corresponding discrete criteria. We also study the robustness property of these three models to examine the reliability of estimates. Simulation results show that the models with estimated parameters using continuous fitness functions have better robustness properties than those using the corresponding discrete fitness functions. The inference studies and robustness analysis suggest that the proposed continuous optimization criteria are effective and robust for estimating unknown parameters in mathematical models.

Propositions for the Analysis of Commutation Phenomena and Modeling of Universal Motors Using the State Function Method

NASA Astrophysics Data System (ADS)

Niwa, Yuta; Akiyama, Yuji; Naruta, Tomokazu

We carried out FEM simulations for modeling ultra-high-speed universal motors by using the state function method and analyzed the phenomenon of commutator sparking, the characteristics of the air gap surface, and the contact condition or contact resistance of the brushes and commutator bars. Thus, we could quantitatively analyze commutator sparking and investigate the configuration of the iron core. The results of FEM analysis were used to develop a model for predicting the configuration of the iron core and for estimating the electromotive force generated by the transformer, armature reaction field, spark voltage, contact resistance between the rotating brushes, and changes in the gap permeance. The results of our simulation were experimental results. This confirmed the validity of our analysis method. Thus, an ultra-high-speed, high-capacity of 1.5kw motor rotating at 30,000rpm can be designed for use in vacuum cleaners.

Dielectric and thermal effects on the optical properties of natural dyes: a case study on solvated cyanin.

PubMed

Malcıoğlu, Osman Bariş; Calzolari, Arrigo; Gebauer, Ralph; Varsano, Daniele; Baroni, Stefano

2011-10-05

The optical properties of the flavylium state of the cyanin dye are simulated numerically by combining Car-Parrinello molecular dynamics and linear-response time-dependent density functional theory calculations. The spectrum of the dye calculated in the gas phase is characterized by two peaks in the yellow and in the blue (green and violet), using a GGA-PBE (hybrid-B3LYP) DFT functional, which would bring about a greenish (bright orange) color incompatible with the dark purple hue observed in nature. Describing the effect of the water solvent through a polarizable continuum model does not modify qualitatively the resulting picture. An explicit simulation of both solvent and thermal effects using ab initio molecular dynamics results instead in a spectrum that is compatible with the observed coloration. This result is analyzed in terms of the spectroscopic effects of the molecular distortions induced by thermal fluctuations.

Neural system modeling and simulation using Hybrid Functional Petri Net.

PubMed

Tang, Yin; Wang, Fei

2012-02-01

The Petri net formalism has been proved to be powerful in biological modeling. It not only boasts of a most intuitive graphical presentation but also combines the methods of classical systems biology with the discrete modeling technique. Hybrid Functional Petri Net (HFPN) was proposed specially for biological system modeling. An array of well-constructed biological models using HFPN yielded very interesting results. In this paper, we propose a method to represent neural system behavior, where biochemistry and electrical chemistry are both included using the Petri net formalism. We built a model for the adrenergic system using HFPN and employed quantitative analysis. Our simulation results match the biological data well, showing that the model is very effective. Predictions made on our model further manifest the modeling power of HFPN and improve the understanding of the adrenergic system. The file of our model and more results with their analysis are available in our supplementary material.

Cross-correlation between EMG and center of gravity during quiet stance: theory and simulations.

PubMed

Kohn, André Fabio

2005-11-01

Several signal processing tools have been employed in the experimental study of the postural control system in humans. Among them, the cross-correlation function has been used to analyze the time relationship between signals such as the electromyogram and the horizontal projection of the center of gravity. The common finding is that the electromyogram precedes the biomechanical signal, a result that has been interpreted in different ways, for example, the existence of feedforward control or the preponderance of a velocity feedback. It is shown here, analytically and by simulation, that the cross-correlation function is dependent in a complicated way on system parameters and on noise spectra. Results similar to those found experimentally, e.g., electromyogram preceding the biomechanical signal may be obtained in a postural control model without any feedforward control and without any velocity feedback. Therefore, correct interpretations of experimentally obtained cross-correlation functions may require additional information about the system. The results extend to other biomedical applications where two signals from a closed loop system are cross-correlated.

Computer simulation of surface and film processes

NASA Technical Reports Server (NTRS)

Tiller, W. A.; Halicioglu, M. T.

1984-01-01

All the investigations which were performed employed in one way or another a computer simulation technique based on atomistic level considerations. In general, three types of simulation methods were used for modeling systems with discrete particles that interact via well defined potential functions: molecular dynamics (a general method for solving the classical equations of motion of a model system); Monte Carlo (the use of Markov chain ensemble averaging technique to model equilibrium properties of a system); and molecular statics (provides properties of a system at T = 0 K). The effects of three-body forces on the vibrational frequencies of triatomic cluster were investigated. The multilayer relaxation phenomena for low index planes of an fcc crystal was analyzed also as a function of the three-body interactions. Various surface properties for Si and SiC system were calculated. Results obtained from static simulation calculations for slip formation were presented. The more elaborate molecular dynamics calculations on the propagation of cracks in two-dimensional systems were outlined.

A Radiation Chemistry Code Based on the Green's Function of the Diffusion Equation

NASA Technical Reports Server (NTRS)

Plante, Ianik; Wu, Honglu

2014-01-01

Stochastic radiation track structure codes are of great interest for space radiation studies and hadron therapy in medicine. These codes are used for a many purposes, notably for microdosimetry and DNA damage studies. In the last two decades, they were also used with the Independent Reaction Times (IRT) method in the simulation of chemical reactions, to calculate the yield of various radiolytic species produced during the radiolysis of water and in chemical dosimeters. Recently, we have developed a Green's function based code to simulate reversible chemical reactions with an intermediate state, which yielded results in excellent agreement with those obtained by using the IRT method. This code was also used to simulate and the interaction of particles with membrane receptors. We are in the process of including this program for use with the Monte-Carlo track structure code Relativistic Ion Tracks (RITRACKS). This recent addition should greatly expand the capabilities of RITRACKS, notably to simulate DNA damage by both the direct and indirect effect.

Computer modelling of the surface tension of the gas-liquid and liquid-liquid interface.

PubMed

Ghoufi, Aziz; Malfreyt, Patrice; Tildesley, Dominic J

2016-03-07

This review presents the state of the art in molecular simulations of interfacial systems and of the calculation of the surface tension from the underlying intermolecular potential. We provide a short account of different methodological factors (size-effects, truncation procedures, long-range corrections and potential models) that can affect the results of the simulations. Accurate calculations are presented for the calculation of the surface tension as a function of the temperature, pressure and composition by considering the planar gas-liquid interface of a range of molecular fluids. In particular, we consider the challenging problems of reproducing the interfacial tension of salt solutions as a function of the salt molality; the simulations of spherical interfaces including the calculation of the sign and size of the Tolman length for a spherical droplet; the use of coarse-grained models in the calculation of the interfacial tension of liquid-liquid surfaces and the mesoscopic simulations of oil-water-surfactant interfacial systems.

Nuclear quantum effects of light and heavy water studied by all-electron first principles path integral simulations

NASA Astrophysics Data System (ADS)

Machida, Masahiko; Kato, Koichiro; Shiga, Motoyuki

2018-03-01

The isotopologs of liquid water, H2O, D2O, and T2O, are studied systematically by first principles PIMD simulations, in which the whole entity of the electrons and nuclei are treated quantum mechanically. The simulation results are in reasonable agreement with available experimental data on isotope effects, in particular, on the peak shift in the radial distributions of H2O and D2O and the shift in the evaporation energies. It is found that, due to differences in nuclear quantum effects, the H atoms in the OH bonds more easily access the dissociative region up to the hydrogen bond center than the D (T) atoms in the OD (OT) bonds. The accuracy and limitation in the use of the current density-functional-theory-based first principles PIMD simulations are also discussed. It is argued that the inclusion of the dispersion correction or relevant improvements in the density functionals are required for the quantitative estimation of isotope effects.

Equation of state of mixtures: density functional theory (DFT) simulations and experiments on Sandia's Z machine

NASA Astrophysics Data System (ADS)

Magyar, R. J.; Root, S.; Haill, T. A.; Schroen, D. G.; Mattsson, T. R.; Flicker, D. G.; Sandia National Laboratories Collaboration

2011-06-01

Mixtures of materials are expected to behave quite differently from their isolated constituents, particularly when the constituents atomic numbers differ significantly. To investigate the mixture behavior, we performed density functional theory (DFT) calculations on xenon/hydrogen, xenon/ethane, and platinum/hydrocarbon mixtures. In addition, we performed shock compression experiments on platinum-doped hydrocarbon foams up to 480 GPa using the Sandia Z-accelerator. Since the DFT simulations treat electrons and nuclei generically, simulations of pure and mix systems are expected to be of comparable accuracy. The DFT and experimental results are compared to hydrodynamic simulations using different mixing models in the equation of state. The role of de-mixing and the relative contributions of the enthalpy of mixing are explored. Sandia National Laboratories is a multi-program laboratory operated by Sandia Corporation, a wholly owned subsidiary of the Lockheed Martin company, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Hybrid General Pattern Search and Simulated Annealing for Industrail Production Planning Problems

NASA Astrophysics Data System (ADS)

Vasant, P.; Barsoum, N.

2010-06-01

In this paper, the hybridization of GPS (General Pattern Search) method and SA (Simulated Annealing) incorporated in the optimization process in order to look for the global optimal solution for the fitness function and decision variables as well as minimum computational CPU time. The real strength of SA approach been tested in this case study problem of industrial production planning. This is due to the great advantage of SA for being easily escaping from trapped in local minima by accepting up-hill move through a probabilistic procedure in the final stages of optimization process. Vasant [1] in his Ph. D thesis has provided 16 different techniques of heuristic and meta-heuristic in solving industrial production problems with non-linear cubic objective functions, eight decision variables and 29 constraints. In this paper, fuzzy technological problems have been solved using hybrid techniques of general pattern search and simulated annealing. The simulated and computational results are compared to other various evolutionary techniques.

Kidney-inspired algorithm for optimization problems

NASA Astrophysics Data System (ADS)

Jaddi, Najmeh Sadat; Alvankarian, Jafar; Abdullah, Salwani

2017-01-01

In this paper, a population-based algorithm inspired by the kidney process in the human body is proposed. In this algorithm the solutions are filtered in a rate that is calculated based on the mean of objective functions of all solutions in the current population of each iteration. The filtered solutions as the better solutions are moved to filtered blood and the rest are transferred to waste representing the worse solutions. This is a simulation of the glomerular filtration process in the kidney. The waste solutions are reconsidered in the iterations if after applying a defined movement operator they satisfy the filtration rate, otherwise it is expelled from the waste solutions, simulating the reabsorption and excretion functions of the kidney. In addition, a solution assigned as better solution is secreted if it is not better than the worst solutions simulating the secreting process of blood in the kidney. After placement of all the solutions in the population, the best of them is ranked, the waste and filtered blood are merged to become a new population and the filtration rate is updated. Filtration provides the required exploitation while generating a new solution and reabsorption gives the necessary exploration for the algorithm. The algorithm is assessed by applying it on eight well-known benchmark test functions and compares the results with other algorithms in the literature. The performance of the proposed algorithm is better on seven out of eight test functions when it is compared with the most recent researches in literature. The proposed kidney-inspired algorithm is able to find the global optimum with less function evaluations on six out of eight test functions. A statistical analysis further confirms the ability of this algorithm to produce good-quality results.

Exploring connectivity with large-scale Granger causality on resting-state functional MRI.

PubMed

DSouza, Adora M; Abidin, Anas Z; Leistritz, Lutz; Wismüller, Axel

2017-08-01

Large-scale Granger causality (lsGC) is a recently developed, resting-state functional MRI (fMRI) connectivity analysis approach that estimates multivariate voxel-resolution connectivity. Unlike most commonly used multivariate approaches, which establish coarse-resolution connectivity by aggregating voxel time-series avoiding an underdetermined problem, lsGC estimates voxel-resolution, fine-grained connectivity by incorporating an embedded dimension reduction. We investigate application of lsGC on realistic fMRI simulations, modeling smoothing of neuronal activity by the hemodynamic response function and repetition time (TR), and empirical resting-state fMRI data. Subsequently, functional subnetworks are extracted from lsGC connectivity measures for both datasets and validated quantitatively. We also provide guidelines to select lsGC free parameters. Results indicate that lsGC reliably recovers underlying network structure with area under receiver operator characteristic curve (AUC) of 0.93 at TR=1.5s for a 10-min session of fMRI simulations. Furthermore, subnetworks of closely interacting modules are recovered from the aforementioned lsGC networks. Results on empirical resting-state fMRI data demonstrate recovery of visual and motor cortex in close agreement with spatial maps obtained from (i) visuo-motor fMRI stimulation task-sequence (Accuracy=0.76) and (ii) independent component analysis (ICA) of resting-state fMRI (Accuracy=0.86). Compared with conventional Granger causality approach (AUC=0.75), lsGC produces better network recovery on fMRI simulations. Furthermore, it cannot recover functional subnetworks from empirical fMRI data, since quantifying voxel-resolution connectivity is not possible as consequence of encountering an underdetermined problem. Functional network recovery from fMRI data suggests that lsGC gives useful insight into connectivity patterns from resting-state fMRI at a multivariate voxel-resolution. Copyright © 2017 Elsevier B.V. All rights reserved.

Alcohol Dose Effects on Brain Circuits During Simulated Driving: An fMRI Study

PubMed Central

Meda, Shashwath A.; Calhoun, Vince D.; Astur, Robert S.; Turner, Beth M.; Ruopp, Kathryn; Pearlson, Godfrey D.

2009-01-01

Driving while intoxicated remains a major public health hazard. Driving is a complex task involving simultaneous recruitment of multiple cognitive functions. The investigators studied the neural substrates of driving and their response to different blood alcohol concentrations (BACs), using functional magnetic resonance imaging (fMRI) and a virtual reality driving simulator. We used independent component analysis (ICA) to isolate spatially independent and temporally correlated driving-related brain circuits in 40 healthy, adult moderate social drinkers. Each subject received three individualized, separate single-blind doses of beverage alcohol to produce BACs of 0.05% (moderate), 0.10% (high), or 0% (placebo). 3 T fMRI scanning and continuous behavioral measurement occurred during simulated driving. Brain function was assessed and compared using both ICA and a conventional general linear model (GLM) analysis. ICA results replicated and significantly extended our previous 1.5T study (Calhoun et al. [2004a]: Neuropsychopharmacology 29:2097–2017). GLM analysis revealed significant dose-related functional differences, complementing ICA data. Driving behaviors including opposite white line crossings and mean speed independently demonstrated significant dose-dependent changes. Behavior-based factors also predicted a frontal-basal-temporal circuit to be functionally impaired with alcohol dosage across baseline scaled, good versus poorly performing drivers. We report neural correlates of driving behavior and found dose-related spatio-temporal disruptions in critical driving-associated regions including the superior, middle and orbito frontal gyri, anterior cingulate, primary/supplementary motor areas, basal ganglia, and cerebellum. Overall, results suggest that alcohol (especially at high doses) causes significant impairment of both driving behavior and brain functionality related to motor planning and control, goal directedness, error monitoring, and memory. PMID:18571794

3D geometric modeling and simulation of laser propagation through turbulence with plenoptic functions

NASA Astrophysics Data System (ADS)

Wu, Chensheng; Nelson, William; Davis, Christopher C.

2014-10-01

Plenoptic functions are functions that preserve all the necessary light field information of optical events. Theoretical work has demonstrated that geometric based plenoptic functions can serve equally well in the traditional wave propagation equation known as the "scalar stochastic Helmholtz equation". However, in addressing problems of 3D turbulence simulation, the dominant methods using phase screen models have limitations both in explaining the choice of parameters (on the transverse plane) in real-world measurements, and finding proper correlations between neighboring phase screens (the Markov assumption breaks down). Though possible corrections to phase screen models are still promising, the equivalent geometric approach based on plenoptic functions begins to show some advantages. In fact, in these geometric approaches, a continuous wave problem is reduced to discrete trajectories of rays. This allows for convenience in parallel computing and guarantees conservation of energy. Besides the pairwise independence of simulated rays, the assigned refractive index grids can be directly tested by temperature measurements with tiny thermoprobes combined with other parameters such as humidity level and wind speed. Furthermore, without loss of generality one can break the causal chain in phase screen models by defining regional refractive centers to allow rays that are less affected to propagate through directly. As a result, our work shows that the 3D geometric approach serves as an efficient and accurate method in assessing relevant turbulence problems with inputs of several environmental measurements and reasonable guesses (such as Cn 2 levels). This approach will facilitate analysis and possible corrections in lateral wave propagation problems, such as image de-blurring, prediction of laser propagation over long ranges, and improvement of free space optic communication systems. In this paper, the plenoptic function model and relevant parallel algorithm computing will be presented, and its primary results and applications are demonstrated.

SPOKES: An end-to-end simulation facility for spectroscopic cosmological surveys

DOE PAGES

Nord, B.; Amara, A.; Refregier, A.; ...

2016-03-03

The nature of dark matter, dark energy and large-scale gravity pose some of the most pressing questions in cosmology today. These fundamental questions require highly precise measurements, and a number of wide-field spectroscopic survey instruments are being designed to meet this requirement. A key component in these experiments is the development of a simulation tool to forecast science performance, define requirement flow-downs, optimize implementation, demonstrate feasibility, and prepare for exploitation. We present SPOKES (SPectrOscopic KEn Simulation), an end-to-end simulation facility for spectroscopic cosmological surveys designed to address this challenge. SPOKES is based on an integrated infrastructure, modular function organization, coherentmore » data handling and fast data access. These key features allow reproducibility of pipeline runs, enable ease of use and provide flexibility to update functions within the pipeline. The cyclic nature of the pipeline offers the possibility to make the science output an efficient measure for design optimization and feasibility testing. We present the architecture, first science, and computational performance results of the simulation pipeline. The framework is general, but for the benchmark tests, we use the Dark Energy Spectrometer (DESpec), one of the early concepts for the upcoming project, the Dark Energy Spectroscopic Instrument (DESI). As a result, we discuss how the SPOKES framework enables a rigorous process to optimize and exploit spectroscopic survey experiments in order to derive high-precision cosmological measurements optimally.« less

Molecular Dynamics Simulations of Intrinsically Disordered Proteins: Force Field Evaluation and Comparison with Experiment.

PubMed

Henriques, João; Cragnell, Carolina; Skepö, Marie

2015-07-14

An increasing number of studies using molecular dynamics (MD) simulations of unfolded and intrinsically disordered proteins (IDPs) suggest that current force fields sample conformations that are overly collapsed. Here, we study the applicability of several state-of-the-art MD force fields, of the AMBER and GROMOS variety, for the simulation of Histatin 5, a short (24 residues) cationic salivary IDP with antimicrobial and antifungal properties. The quality of the simulations is assessed in three complementary analyses: (i) protein shape and size comparison with recent experimental small-angle X-ray scattering data; (ii) secondary structure prediction; (iii) energy landscape exploration and conformational class analysis. Our results show that, indeed, standard force fields sample conformations that are too compact, being systematically unable to reproduce experimental evidence such as the scattering function, the shape of the protein as compared with the Kratky plot, and intrapeptide distances obtained through the pair distance distribution function, p(r). The consistency of this deviation suggests that the problem is not mainly due to protein-protein or water-water interactions, whose parametrization varies the most between force fields and water models. In fact, as originally proposed in [ Best et al. J. Chem. Theory Comput. 2014, 10, 5113 - 5124.], balanced protein-water interactions may be the key to solving this problem. Our simulations using this approach produce results in very good agreement with experiment.

nMoldyn: a program package for a neutron scattering oriented analysis of molecular dynamics simulations.

PubMed

Róg, T; Murzyn, K; Hinsen, K; Kneller, G R

2003-04-15

We present a new implementation of the program nMoldyn, which has been developed for the computation and decomposition of neutron scattering intensities from Molecular Dynamics trajectories (Comp. Phys. Commun 1995, 91, 191-214). The new implementation extends the functionality of the original version, provides a much more convenient user interface (both graphical/interactive and batch), and can be used as a tool set for implementing new analysis modules. This was made possible by the use of a high-level language, Python, and of modern object-oriented programming techniques. The quantities that can be calculated by nMoldyn are the mean-square displacement, the velocity autocorrelation function as well as its Fourier transform (the density of states) and its memory function, the angular velocity autocorrelation function and its Fourier transform, the reorientational correlation function, and several functions specific to neutron scattering: the coherent and incoherent intermediate scattering functions with their Fourier transforms, the memory function of the coherent scattering function, and the elastic incoherent structure factor. The possibility to compute memory function is a new and powerful feature that allows to relate simulation results to theoretical studies. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 657-667, 2003

The application of integral performance criteria to the analysis of discrete maneuvers in a driving simulator

NASA Technical Reports Server (NTRS)

Repa, B. S.; Zucker, R. S.; Wierwille, W. W.

1977-01-01

The influence of vehicle transient response characteristics on driver-vehicle performance in discrete maneuvers as measured by integral performance criteria was investigated. A group of eight ordinary drivers was presented with a series of eight vehicle transfer function configurations in a driving simulator. Performance in two discrete maneuvers was analyzed by means of integral performance criteria. Results are presented.

Population pharmacokinetic–pharmacodynamic analysis for sugammadex-mediated reversal of rocuronium-induced neuromuscular blockade

PubMed Central

Kleijn, Huub J; Zollinger, Daniel P; van den Heuvel, Michiel W; Kerbusch, Thomas

2011-01-01

AIMS An integrated population pharmacokinetic–pharmacodynamic model was developed with the following aims: to simultaneously describe pharmacokinetic behaviour of sugammadex and rocuronium; to establish the pharmacokinetic–pharmacodynamic model for rocuronium-induced neuromuscular blockade and reversal by sugammadex; to evaluate covariate effects; and to explore, by simulation, typical covariate effects on reversal time. METHODS Data (n = 446) from eight sugammadex clinical studies covering men, women, non-Asians, Asians, paediatrics, adults and the elderly, with various degrees of renal impairment, were used. Modelling and simulation techniques based on physiological principles were applied to capture rocuronium and sugammadex pharmacokinetics and pharmacodynamics and to identify and quantify covariate effects. RESULTS Sugammadex pharmacokinetics were affected by renal function, bodyweight and race, and rocuronium pharmacokinetics were affected by age, renal function and race. Sevoflurane potentiated rocuronium-induced neuromuscular blockade. Posterior predictive checks and bootstrapping illustrated the accuracy and robustness of the model. External validation showed concordance between observed and predicted reversal times, but interindividual variability in reversal time was pronounced. Simulated reversal times in typical adults were 0.8, 1.5 and 1.4 min upon reversal with sugammadex 16 mg kg−1 3 min after rocuronium, sugammadex 4 mg kg−1 during deep neuromuscular blockade and sugammadex 2 mg kg−1 during moderate blockade, respectively. Simulations indicated that reversal times were faster in paediatric patients and slightly slower in elderly patients compared with adults. Renal function did not affect reversal time. CONCLUSIONS Simulations of the therapeutic dosing regimens demonstrated limited impact of age, renal function and sevoflurane use, as predicted reversal time in typical subjects was always <2 min. PMID:21535448

An empirical model of H2O, CO2 and CO coma distributions and production rates for comet 67P/Churyumov-Gerasimenko based on ROSINA/DFMS measurements and AMPS-DSMC simulations

NASA Astrophysics Data System (ADS)

Hansen, Kenneth C.; Altwegg, Kathrin; Bieler, Andre; Berthelier, Jean-Jacques; Calmonte, Ursina; Combi, Michael R.; De Keyser, Johan; Fiethe, Björn; Fougere, Nicolas; Fuselier, Stephen; Gombosi, T. I.; Hässig, Myrtha; Huang, Zhenguang; Le Roy, Léna; Rubin, Martin; Tenishev, Valeriy; Toth, Gabor; Tzou, Chia-Yu; ROSINA Team

2016-10-01

We have previously used results from the AMPS DSMC (Adaptive Mesh Particle Simulator Direct Simulation Monte Carlo) model to create an empirical model of the near comet water (H2O) coma of comet 67P/Churyumov-Gerasimenko. In this work we create additional empirical models for the coma distributions of CO2 and CO. The AMPS simulations are based on ROSINA DFMS (Rosetta Orbiter Spectrometer for Ion and Neutral Analysis, Double Focusing Mass Spectrometer) data taken over the entire timespan of the Rosetta mission. The empirical model is created using AMPS DSMC results which are extracted from simulations at a range of radial distances, rotation phases and heliocentric distances. The simulation results are then averaged over a comet rotation and fitted to an empirical model distribution. Model coefficients are then fitted to piecewise-linear functions of heliocentric distance. The final product is an empirical model of the coma distribution which is a function of heliocentric distance, radial distance, and sun-fixed longitude and latitude angles. The model clearly mimics the behavior of water shifting production from North to South across the inbound equinox while the CO2 production is always in the South.The empirical model can be used to de-trend the spacecraft motion from the ROSINA COPS and DFMS data. The ROSINA instrument measures the neutral coma density at a single point and the measured value is influenced by the location of the spacecraft relative to the comet and the comet-sun line. Using the empirical coma model we can correct for the position of the spacecraft and compute a total production rate based on single point measurements. In this presentation we will present the coma production rates as a function of heliocentric distance for the entire Rosetta mission.This work was supported by contracts JPL#1266313 and JPL#1266314 from the US Rosetta Project and NASA grant NNX14AG84G from the Planetary Atmospheres Program.