WorldWideScience

Sample records for simulating temporal dynamics

  1. Temporal languages for simulation and analysis of the dynamics within an organisation.

    NARCIS (Netherlands)

    Jonker, C.M.; Treur, J.; Wijngaards, W.C.A.

    2002-01-01

    In this paper a modelling approach to the dynamics within a multi- agent organisation is presented. A declarative, executable temporal modelling language for organisation dynamics is proposed as a basis for simulation. Moreover, to be able to specify and analyse dynamic properties, another temporal

  2. Discrete simulations of spatio-temporal dynamics of small water bodies under varied stream flow discharges

    Science.gov (United States)

    Daya Sagar, B. S.

    2005-01-01

    Spatio-temporal patterns of small water bodies (SWBs) under the influence of temporally varied stream flow discharge are simulated in discrete space by employing geomorphologically realistic expansion and contraction transformations. Cascades of expansion-contraction are systematically performed by synchronizing them with stream flow discharge simulated via the logistic map. Templates with definite characteristic information are defined from stream flow discharge pattern as the basis to model the spatio-temporal organization of randomly situated surface water bodies of various sizes and shapes. These spatio-temporal patterns under varied parameters (λs) controlling stream flow discharge patterns are characterized by estimating their fractal dimensions. At various λs, nonlinear control parameters, we show the union of boundaries of water bodies that traverse the water body and non-water body spaces as geomorphic attractors. The computed fractal dimensions of these attractors are 1.58, 1.53, 1.78, 1.76, 1.84, and 1.90, respectively, at λs of 1, 2, 3, 3.46, 3.57, and 3.99. These values are in line with general visual observations.

  3. Discrete simulations of spatio-temporal dynamics of small water bodies under varied stream flow discharges

    Directory of Open Access Journals (Sweden)

    B. S. Daya Sagar

    2005-01-01

    Full Text Available Spatio-temporal patterns of small water bodies (SWBs under the influence of temporally varied stream flow discharge are simulated in discrete space by employing geomorphologically realistic expansion and contraction transformations. Cascades of expansion-contraction are systematically performed by synchronizing them with stream flow discharge simulated via the logistic map. Templates with definite characteristic information are defined from stream flow discharge pattern as the basis to model the spatio-temporal organization of randomly situated surface water bodies of various sizes and shapes. These spatio-temporal patterns under varied parameters (λs controlling stream flow discharge patterns are characterized by estimating their fractal dimensions. At various λs, nonlinear control parameters, we show the union of boundaries of water bodies that traverse the water body and non-water body spaces as geomorphic attractors. The computed fractal dimensions of these attractors are 1.58, 1.53, 1.78, 1.76, 1.84, and 1.90, respectively, at λs of 1, 2, 3, 3.46, 3.57, and 3.99. These values are in line with general visual observations.

  4. Temporal dynamics of online petitions.

    Science.gov (United States)

    Böttcher, Lucas; Woolley-Meza, Olivia; Brockmann, Dirk

    2017-01-01

    Online petitions are an important avenue for direct political action, yet the dynamics that determine when a petition will be successful are not well understood. Here we analyze the temporal characteristics of online-petition signing behavior in order to identify systematic differences between popular petitions, which receive a high volume of signatures, and unpopular ones. We find that, in line with other temporal characterizations of human activity, the signing process is typically non-Poissonian and non-homogeneous in time. However, this process exhibits anomalously high memory for human activity, possibly indicating that synchronized external influence or contagion play and important role. More interestingly, we find clear differences in the characteristics of the inter-event time distributions depending on the total number of signatures that petitions receive, independently of the total duration of the petitions. Specifically, popular petitions that attract a large volume of signatures exhibit more variance in the distribution of inter-event times than unpopular petitions with only a few signatures, which could be considered an indication that the former are more bursty. However, petitions with large signature volume are less bursty according to measures that consider the time ordering of inter-event times. Our results, therefore, emphasize the importance of accounting for time ordering to characterize human activity.

  5. The temporal dynamics of speeded decision making

    NARCIS (Netherlands)

    Dutilh, G.

    2012-01-01

    This dissertation sheds light on the temporal dynamics of behavior in speeded decision making. Participants on reaction time (RT) tasks learn, get distracted, speed up, slow down, get confused, get bored, and eventually may start guessing. One can safely say that participants' behavior is dynamic.

  6. Temporal fidelity in dynamic social networks

    DEFF Research Database (Denmark)

    Stopczynski, Arkadiusz; Sapiezynski, Piotr; Pentland, Alex ‘Sandy’

    2015-01-01

    of the network dynamics can be used to inform the process of measuring social networks. The details of measurement are of particular importance when considering dynamic processes where minute-to-minute details are important, because collection of physical proximity interactions with high temporal resolution...

  7. Analysing the temporal dynamics of model performance for hydrological models

    NARCIS (Netherlands)

    Reusser, D.E.; Blume, T.; Schaefli, B.; Zehe, E.

    2009-01-01

    The temporal dynamics of hydrological model performance gives insights into errors that cannot be obtained from global performance measures assigning a single number to the fit of a simulated time series to an observed reference series. These errors can include errors in data, model parameters, or

  8. Memory for temporally dynamic scenes.

    Science.gov (United States)

    Ferguson, Ryan; Homa, Donald; Ellis, Derek

    2017-07-01

    Recognition memory was investigated for individual frames extracted from temporally continuous, visually rich film segments of 5-15 min. Participants viewed a short clip from a film in either a coherent or a jumbled order, followed by a recognition test of studied frames. Foils came either from an earlier or a later part of the film (Experiment 1) or from deleted segments selected from random cuts of varying duration (0.5 to 30 s) within the film itself (Experiment 2). When the foils came from an earlier or later part of the film (Experiment 1), recognition was excellent, with the hit rate far exceeding the false-alarm rate (.78 vs. 18). In Experiment 2, recognition was far worse, with the hit rate (.76) exceeding the false-alarm rate only for foils drawn from the longest cuts (15 and 30 s) and matching the false-alarm rate for the 5 s segments. When the foils were drawn from the briefest cuts (0.5 and 1.0 s), the false-alarm rate exceeded the hit rate. Unexpectedly, jumbling had no effect on recognition in either experiment. These results are consistent with the view that memory for complex visually temporal events is excellent, with the integrity unperturbed by disruption of the global structure of the visual stream. Disruption of memory was observed only when foils were drawn from embedded segments of duration less than 5 s, an outcome consistent with the view that memory at these shortest durations are consolidated with expectations drawn from the previous stream.

  9. Dynamic perfusion patterns in temporal lobe epilepsy

    International Nuclear Information System (INIS)

    Dupont, Patrick; Paesschen, Wim van; Zaknun, John J.; Maes, Alex; Tepmongkol, Supatporn; Locharernkul, Chaichon; Vasquez, Silvia; Carpintiero, Silvina; Bal, C.S.; Dondi, Maurizio

    2009-01-01

    To investigate dynamic ictal perfusion changes during temporal lobe epilepsy (TLE). We investigated 37 patients with TLE by ictal and interictal SPECT. All ictal injections were performed within 60 s of seizure onset. Statistical parametric mapping was used to analyse brain perfusion changes and temporal relationships with injection time and seizure duration as covariates. The analysis revealed significant ictal hyperperfusion in the ipsilateral temporal lobe extending to subcortical regions. Hypoperfusion was observed in large extratemporal areas. There were also significant dynamic changes in several extratemporal regions: ipsilateral orbitofrontal and bilateral superior frontal gyri and the contralateral cerebellum and ipsilateral striatum. The study demonstrated early dynamic perfusion changes in extratemporal regions probably involved in both propagation of epileptic activity and initiation of inhibitory mechanisms. (orig.)

  10. Dynamic perfusion patterns in temporal lobe epilepsy

    Energy Technology Data Exchange (ETDEWEB)

    Dupont, Patrick; Paesschen, Wim van [KU Leuven/UZ Gasthuisberg, Nuclear Medicine, Medical Imaging Center and Neurology, Leuven (Belgium); Zaknun, John J. [International Atomic Energy Agency (IAEA), Nuclear Medicine Section, Division of Human Health, Wagramer Strasse 5, PO BOX 200, Vienna (Austria); University Hospital of Innsbruck, Department of Nuclear Medicine, Innsbruck (Austria); Maes, Alex [KU Leuven/UZ Gasthuisberg, Nuclear Medicine, Medical Imaging Center and Neurology, Leuven (Belgium); AZ Groeninge, Nuclear Medicine, Kortrijk (Belgium); Tepmongkol, Supatporn; Locharernkul, Chaichon [Chulalongkorn University, Nuclear Medicine and Neurology, Bangkok (Thailand); Vasquez, Silvia; Carpintiero, Silvina [Fleni Instituto de Investigaciones Neurologicas, Nuclear Medicine, Buenos Aires (Argentina); Bal, C.S. [All India Institute of Medical Sciences, Nuclear Medicine, New Delhi (India); Dondi, Maurizio [International Atomic Energy Agency (IAEA), Nuclear Medicine Section, Division of Human Health, Wagramer Strasse 5, PO BOX 200, Vienna (Austria); Ospedale Maggiore, Nuclear Medicine, Bologna (Italy)

    2009-05-15

    To investigate dynamic ictal perfusion changes during temporal lobe epilepsy (TLE). We investigated 37 patients with TLE by ictal and interictal SPECT. All ictal injections were performed within 60 s of seizure onset. Statistical parametric mapping was used to analyse brain perfusion changes and temporal relationships with injection time and seizure duration as covariates. The analysis revealed significant ictal hyperperfusion in the ipsilateral temporal lobe extending to subcortical regions. Hypoperfusion was observed in large extratemporal areas. There were also significant dynamic changes in several extratemporal regions: ipsilateral orbitofrontal and bilateral superior frontal gyri and the contralateral cerebellum and ipsilateral striatum. The study demonstrated early dynamic perfusion changes in extratemporal regions probably involved in both propagation of epileptic activity and initiation of inhibitory mechanisms. (orig.)

  11. Interactive Dynamic-System Simulation

    CERN Document Server

    Korn, Granino A

    2010-01-01

    Showing you how to use personal computers for modeling and simulation, Interactive Dynamic-System Simulation, Second Edition provides a practical tutorial on interactive dynamic-system modeling and simulation. It discusses how to effectively simulate dynamical systems, such as aerospace vehicles, power plants, chemical processes, control systems, and physiological systems. Written by a pioneer in simulation, the book introduces dynamic-system models and explains how software for solving differential equations works. After demonstrating real simulation programs with simple examples, the author

  12. Concurrency-Induced Transitions in Epidemic Dynamics on Temporal Networks.

    Science.gov (United States)

    Onaga, Tomokatsu; Gleeson, James P; Masuda, Naoki

    2017-09-08

    Social contact networks underlying epidemic processes in humans and animals are highly dynamic. The spreading of infections on such temporal networks can differ dramatically from spreading on static networks. We theoretically investigate the effects of concurrency, the number of neighbors that a node has at a given time point, on the epidemic threshold in the stochastic susceptible-infected-susceptible dynamics on temporal network models. We show that network dynamics can suppress epidemics (i.e., yield a higher epidemic threshold) when the node's concurrency is low, but can also enhance epidemics when the concurrency is high. We analytically determine different phases of this concurrency-induced transition, and confirm our results with numerical simulations.

  13. Concurrency-Induced Transitions in Epidemic Dynamics on Temporal Networks

    Science.gov (United States)

    Onaga, Tomokatsu; Gleeson, James P.; Masuda, Naoki

    2017-09-01

    Social contact networks underlying epidemic processes in humans and animals are highly dynamic. The spreading of infections on such temporal networks can differ dramatically from spreading on static networks. We theoretically investigate the effects of concurrency, the number of neighbors that a node has at a given time point, on the epidemic threshold in the stochastic susceptible-infected-susceptible dynamics on temporal network models. We show that network dynamics can suppress epidemics (i.e., yield a higher epidemic threshold) when the node's concurrency is low, but can also enhance epidemics when the concurrency is high. We analytically determine different phases of this concurrency-induced transition, and confirm our results with numerical simulations.

  14. A temporal interpolation approach for dynamic reconstruction in perfusion CT

    International Nuclear Information System (INIS)

    Montes, Pau; Lauritsch, Guenter

    2007-01-01

    This article presents a dynamic CT reconstruction algorithm for objects with time dependent attenuation coefficient. Projection data acquired over several rotations are interpreted as samples of a continuous signal. Based on this idea, a temporal interpolation approach is proposed which provides the maximum temporal resolution for a given rotational speed of the CT scanner. Interpolation is performed using polynomial splines. The algorithm can be adapted to slow signals, reducing the amount of data acquired and the computational cost. A theoretical analysis of the approximations made by the algorithm is provided. In simulation studies, the temporal interpolation approach is compared with three other dynamic reconstruction algorithms based on linear regression, linear interpolation, and generalized Parker weighting. The presented algorithm exhibits the highest temporal resolution for a given sampling interval. Hence, our approach needs less input data to achieve a certain quality in the reconstruction than the other algorithms discussed or, equivalently, less x-ray exposure and computational complexity. The proposed algorithm additionally allows the possibility of using slow rotating scanners for perfusion imaging purposes

  15. Molecular dynamics simulations

    International Nuclear Information System (INIS)

    Alder, B.J.

    1985-07-01

    The molecular dynamics computer simulation discovery of the slow decay of the velocity autocorrelation function in fluids is briefly reviewed in order to contrast that long time tail with those observed for the stress autocorrelation function in fluids and the velocity autocorrelation function in the Lorentz gas. For a non-localized particle in the Lorentz gas it is made plausible that even if it behaved quantum mechanically its long time tail would be the same as the classical one. The generalization of Fick's law for diffusion for the Lorentz gas, necessary to avoid divergences due to the slow decay of correlations, is presented. For fluids, that generalization has not yet been established, but the region of validity of generalized hydrodynamics is discussed. 20 refs., 5 figs

  16. Spatio-temporal diffusion of dynamic PET images

    International Nuclear Information System (INIS)

    Tauber, C; Chalon, S; Guilloteau, D; Stute, S; Buvat, I; Chau, M; Spiteri, P

    2011-01-01

    Positron emission tomography (PET) images are corrupted by noise. This is especially true in dynamic PET imaging where short frames are required to capture the peak of activity concentration after the radiotracer injection. High noise results in a possible bias in quantification, as the compartmental models used to estimate the kinetic parameters are sensitive to noise. This paper describes a new post-reconstruction filter to increase the signal-to-noise ratio in dynamic PET imaging. It consists in a spatio-temporal robust diffusion of the 4D image based on the time activity curve (TAC) in each voxel. It reduces the noise in homogeneous areas while preserving the distinct kinetics in regions of interest corresponding to different underlying physiological processes. Neither anatomical priors nor the kinetic model are required. We propose an automatic selection of the scale parameter involved in the diffusion process based on a robust statistical analysis of the distances between TACs. The method is evaluated using Monte Carlo simulations of brain activity distributions. We demonstrate the usefulness of the method and its superior performance over two other post-reconstruction spatial and temporal filters. Our simulations suggest that the proposed method can be used to significantly increase the signal-to-noise ratio in dynamic PET imaging.

  17. Temporal dynamics of divided spatial attention.

    Science.gov (United States)

    Itthipuripat, Sirawaj; Garcia, Javier O; Serences, John T

    2013-05-01

    In naturalistic settings, observers often have to monitor multiple objects dispersed throughout the visual scene. However, the degree to which spatial attention can be divided across spatially noncontiguous objects has long been debated, particularly when those objects are in close proximity. Moreover, the temporal dynamics of divided attention are unclear: is the process of dividing spatial attention gradual and continuous, or does it onset in a discrete manner? To address these issues, we recorded steady-state visual evoked potentials (SSVEPs) as subjects covertly monitored two flickering targets while ignoring an intervening distractor that flickered at a different frequency. All three stimuli were clustered within either the lower left or the lower right quadrant, and our dependent measure was SSVEP power at the target and distractor frequencies measured over time. In two experiments, we observed a temporally discrete increase in power for target- vs. distractor-evoked SSVEPs extending from ∼350 to 150 ms prior to correct (but not incorrect) responses. The divergence in SSVEP power immediately prior to a correct response suggests that spatial attention can be divided across noncontiguous locations, even when the targets are closely spaced within a single quadrant. In addition, the division of spatial attention appears to be relatively discrete, as opposed to slow and continuous. Finally, the predictive relationship between SSVEP power and behavior demonstrates that these neurophysiological measures of divided attention are meaningfully related to cognitive function.

  18. Temporal information encoding in dynamic memristive devices

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Wen; Chen, Lin; Du, Chao; Lu, Wei D., E-mail: wluee@eecs.umich.edu [Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan 48109 (United States)

    2015-11-09

    We show temporal and frequency information can be effectively encoded in memristive devices with inherent short-term dynamics. Ag/Ag{sub 2}S/Pd based memristive devices with low programming voltage (∼100 mV) were fabricated and tested. At weak programming conditions, the devices exhibit inherent decay due to spontaneous diffusion of the Ag atoms. When the devices were subjected to pulse train inputs emulating different spiking patterns, the switching probability distribution function diverges from the standard Poisson distribution and evolves according to the input pattern. The experimentally observed switching probability distributions and the associated cumulative probability functions can be well-explained using a model accounting for the short-term decay effects. Such devices offer an intriguing opportunity to directly encode neural signals for neural information storage and analysis.

  19. Spatio-Temporal Process Simulation of Dam-Break Flood Based on SPH

    Science.gov (United States)

    Wang, H.; Ye, F.; Ouyang, S.; Li, Z.

    2018-04-01

    On the basis of introducing the SPH (Smooth Particle Hydrodynamics) simulation method, the key research problems were given solutions in this paper, which ere the spatial scale and temporal scale adapting to the GIS(Geographical Information System) application, the boundary condition equations combined with the underlying surface, and the kernel function and parameters applicable to dam-break flood simulation. In this regards, a calculation method of spatio-temporal process emulation with elaborate particles for dam-break flood was proposed. Moreover the spatio-temporal process was dynamic simulated by using GIS modelling and visualization. The results show that the method gets more information, objectiveness and real situations.

  20. Ananke: temporal clustering reveals ecological dynamics of microbial communities

    Directory of Open Access Journals (Sweden)

    Michael W. Hall

    2017-09-01

    Full Text Available Taxonomic markers such as the 16S ribosomal RNA gene are widely used in microbial community analysis. A common first step in marker-gene analysis is grouping genes into clusters to reduce data sets to a more manageable size and potentially mitigate the effects of sequencing error. Instead of clustering based on sequence identity, marker-gene data sets collected over time can be clustered based on temporal correlation to reveal ecologically meaningful associations. We present Ananke, a free and open-source algorithm and software package that complements existing sequence-identity-based clustering approaches by clustering marker-gene data based on time-series profiles and provides interactive visualization of clusters, including highlighting of internal OTU inconsistencies. Ananke is able to cluster distinct temporal patterns from simulations of multiple ecological patterns, such as periodic seasonal dynamics and organism appearances/disappearances. We apply our algorithm to two longitudinal marker gene data sets: faecal communities from the human gut of an individual sampled over one year, and communities from a freshwater lake sampled over eleven years. Within the gut, the segregation of the bacterial community around a food-poisoning event was immediately clear. In the freshwater lake, we found that high sequence identity between marker genes does not guarantee similar temporal dynamics, and Ananke time-series clusters revealed patterns obscured by clustering based on sequence identity or taxonomy. Ananke is free and open-source software available at https://github.com/beiko-lab/ananke.

  1. Noise-induced temporal dynamics in Turing systems

    KAUST Repository

    Schumacher, Linus J.

    2013-04-25

    We examine the ability of intrinsic noise to produce complex temporal dynamics in Turing pattern formation systems, with particular emphasis on the Schnakenberg kinetics. Using power spectral methods, we characterize the behavior of the system using stochastic simulations at a wide range of points in parameter space and compare with analytical approximations. Specifically, we investigate whether polarity switching of stochastic patterns occurs at a defined frequency. We find that it can do so in individual realizations of a stochastic simulation, but that the frequency is not defined consistently across realizations in our samples of parameter space. Further, we examine the effect of noise on deterministically predicted traveling waves and find them increased in amplitude and decreased in speed. © 2013 American Physical Society.

  2. An investigation of temporal regularization techniques for dynamic PET reconstructions using temporal splines

    International Nuclear Information System (INIS)

    Verhaeghe, Jeroen; D'Asseler, Yves; Vandenberghe, Stefaan; Staelens, Steven; Lemahieu, Ignace

    2007-01-01

    The use of a temporal B-spline basis for the reconstruction of dynamic positron emission tomography data was investigated. Maximum likelihood (ML) reconstructions using an expectation maximization framework and maximum A-posteriori (MAP) reconstructions using the generalized expectation maximization framework were evaluated. Different parameters of the B-spline basis of such as order, number of basis functions and knot placing were investigated in a reconstruction task using simulated dynamic list-mode data. We found that a higher order basis reduced both the bias and variance. Using a higher number of basis functions in the modeling of the time activity curves (TACs) allowed the algorithm to model faster changes of the TACs, however, the TACs became noisier. We have compared ML, Gaussian postsmoothed ML and MAP reconstructions. The noise level in the ML reconstructions was controlled by varying the number of basis functions. The MAP algorithm penalized the integrated squared curvature of the reconstructed TAC. The postsmoothed ML was always outperformed in terms of bias and variance properties by the MAP and ML reconstructions. A simple adaptive knot placing strategy was also developed and evaluated. It is based on an arc length redistribution scheme during the reconstruction. The free knot reconstruction allowed a more accurate reconstruction while reducing the noise level especially for fast changing TACs such as blood input functions. Limiting the number of temporal basis functions combined with the adaptive knot placing strategy is in this case advantageous for regularization purposes when compared to the other regularization techniques

  3. Dynamic simulation of a reboiler

    International Nuclear Information System (INIS)

    Moeck, E.O.; McMorran, P.D.

    1977-07-01

    A hybrid-computer simulation of reboiler dynamics was prepared, comprising models of steam condensation in tubes, heat conduction, steam generation, a surge tank, steam transmission line and flow-control valve. Time and frequency responses were obtained to illustrate the dynamics of this multivariable process. (author)

  4. Simulating temporal variations of nitrogen losses in river networks with a dynamic transport model unravels the coupled effects of hydrological and biogeochemical processes

    Energy Technology Data Exchange (ETDEWEB)

    Mulholland, Patrick J [ORNL; Alexander, Richard [U.S. Geological Survey; Bohlke, John [U.S. Geological Survey; Boyer, Elizabeth [Pennsylvania State University; Harvey, Judson [U.S. Geological Survey; Seitzinger, Sybil [Rutgers University; Tobias, Craig [University of North Carolina, Wilmington; Tonitto, Christina [Cornell University; Wollheim, Wilfred [University of New Hampshire

    2009-01-01

    The importance of lotic systems as sinks for nitrogen inputs is well recognized. A fraction of nitrogen in streamflow is removed to the atmosphere via denitrification with the remainder exported in streamflow as nitrogen loads. At the watershed scale, there is a keen interest in understanding the factors that control the fate of nitrogen throughout the stream channel network, with particular attention to the processes that deliver large nitrogen loads to sensitive coastal ecosystems. We use a dynamic stream transport model to assess biogeochemical (nitrate loadings, concentration, temperature) and hydrological (discharge, depth, velocity) effects on reach-scale denitrification and nitrate removal in the river networks of two watersheds having widely differing levels of nitrate enrichment but nearly identical discharges. Stream denitrification is estimated by regression as a nonlinear function of nitrate concentration, streamflow, and temperature, using more than 300 published measurements from a variety of US streams. These relations are used in the stream transport model to characterize nitrate dynamics related to denitrification at a monthly time scale in the stream reaches of the two watersheds. Results indicate that the nitrate removal efficiency of streams, as measured by the percentage of the stream nitrate flux removed via denitrification per unit length of channel, is appreciably reduced during months with high discharge and nitrate flux and increases during months of low-discharge and flux. Biogeochemical factors, including land use, nitrate inputs, and stream concentrations, are a major control on reach-scale denitrification, evidenced by the disproportionately lower nitrate removal efficiency in streams of the highly nitrate-enriched watershed as compared with that in similarly sized streams in the less nitrate-enriched watershed. Sensitivity analyses reveal that these important biogeochemical factors and physical hydrological factors contribute nearly

  5. Temporal Gillespie Algorithm: Fast Simulation of Contagion Processes on Time-Varying Networks.

    Science.gov (United States)

    Vestergaard, Christian L; Génois, Mathieu

    2015-10-01

    Stochastic simulations are one of the cornerstones of the analysis of dynamical processes on complex networks, and are often the only accessible way to explore their behavior. The development of fast algorithms is paramount to allow large-scale simulations. The Gillespie algorithm can be used for fast simulation of stochastic processes, and variants of it have been applied to simulate dynamical processes on static networks. However, its adaptation to temporal networks remains non-trivial. We here present a temporal Gillespie algorithm that solves this problem. Our method is applicable to general Poisson (constant-rate) processes on temporal networks, stochastically exact, and up to multiple orders of magnitude faster than traditional simulation schemes based on rejection sampling. We also show how it can be extended to simulate non-Markovian processes. The algorithm is easily applicable in practice, and as an illustration we detail how to simulate both Poissonian and non-Markovian models of epidemic spreading. Namely, we provide pseudocode and its implementation in C++ for simulating the paradigmatic Susceptible-Infected-Susceptible and Susceptible-Infected-Recovered models and a Susceptible-Infected-Recovered model with non-constant recovery rates. For empirical networks, the temporal Gillespie algorithm is here typically from 10 to 100 times faster than rejection sampling.

  6. Noise-induced temporal dynamics in Turing systems

    KAUST Repository

    Schumacher, Linus J.; Woolley, Thomas E.; Baker, Ruth E.

    2013-01-01

    We examine the ability of intrinsic noise to produce complex temporal dynamics in Turing pattern formation systems, with particular emphasis on the Schnakenberg kinetics. Using power spectral methods, we characterize the behavior of the system using

  7. Hat cycle dynamic simulation

    International Nuclear Information System (INIS)

    Trucco, A.; Corallo, C.; Pini Prato, A.; Porro, S.

    1999-01-01

    Among the innovative cycle recently proposed in literature, the Humid Air Turbine Cycle - Hat better seems to fulfil the main energy market requirements of today: High efficiency in a large power ranger, low pollution, low specific capital cost. The previous results of an analysis at partial load and transient conditions are here presented, where the Hat plant has been simulated using the original model implemented in LEGO environment [it

  8. STSE: Spatio-Temporal Simulation Environment Dedicated to Biology

    Directory of Open Access Journals (Sweden)

    Gerber Susanne

    2011-04-01

    Full Text Available Abstract Background Recently, the availability of high-resolution microscopy together with the advancements in the development of biomarkers as reporters of biomolecular interactions increased the importance of imaging methods in molecular cell biology. These techniques enable the investigation of cellular characteristics like volume, size and geometry as well as volume and geometry of intracellular compartments, and the amount of existing proteins in a spatially resolved manner. Such detailed investigations opened up many new areas of research in the study of spatial, complex and dynamic cellular systems. One of the crucial challenges for the study of such systems is the design of a well stuctured and optimized workflow to provide a systematic and efficient hypothesis verification. Computer Science can efficiently address this task by providing software that facilitates handling, analysis, and evaluation of biological data to the benefit of experimenters and modelers. Results The Spatio-Temporal Simulation Environment (STSE is a set of open-source tools provided to conduct spatio-temporal simulations in discrete structures based on microscopy images. The framework contains modules to digitize, represent, analyze, and mathematically model spatial distributions of biochemical species. Graphical user interface (GUI tools provided with the software enable meshing of the simulation space based on the Voronoi concept. In addition, it supports to automatically acquire spatial information to the mesh from the images based on pixel luminosity (e.g. corresponding to molecular levels from microscopy images. STSE is freely available either as a stand-alone version or included in the linux live distribution Systems Biology Operational Software (SB.OS and can be downloaded from http://www.stse-software.org/. The Python source code as well as a comprehensive user manual and video tutorials are also offered to the research community. We discuss main concepts

  9. STSE: Spatio-Temporal Simulation Environment Dedicated to Biology.

    Science.gov (United States)

    Stoma, Szymon; Fröhlich, Martina; Gerber, Susanne; Klipp, Edda

    2011-04-28

    Recently, the availability of high-resolution microscopy together with the advancements in the development of biomarkers as reporters of biomolecular interactions increased the importance of imaging methods in molecular cell biology. These techniques enable the investigation of cellular characteristics like volume, size and geometry as well as volume and geometry of intracellular compartments, and the amount of existing proteins in a spatially resolved manner. Such detailed investigations opened up many new areas of research in the study of spatial, complex and dynamic cellular systems. One of the crucial challenges for the study of such systems is the design of a well stuctured and optimized workflow to provide a systematic and efficient hypothesis verification. Computer Science can efficiently address this task by providing software that facilitates handling, analysis, and evaluation of biological data to the benefit of experimenters and modelers. The Spatio-Temporal Simulation Environment (STSE) is a set of open-source tools provided to conduct spatio-temporal simulations in discrete structures based on microscopy images. The framework contains modules to digitize, represent, analyze, and mathematically model spatial distributions of biochemical species. Graphical user interface (GUI) tools provided with the software enable meshing of the simulation space based on the Voronoi concept. In addition, it supports to automatically acquire spatial information to the mesh from the images based on pixel luminosity (e.g. corresponding to molecular levels from microscopy images). STSE is freely available either as a stand-alone version or included in the linux live distribution Systems Biology Operational Software (SB.OS) and can be downloaded from http://www.stse-software.org/. The Python source code as well as a comprehensive user manual and video tutorials are also offered to the research community. We discuss main concepts of the STSE design and workflow. We

  10. Simulating spatial and temporally related fire weather

    Science.gov (United States)

    Isaac C. Grenfell; Mark Finney; Matt Jolly

    2010-01-01

    Use of fire behavior models has assumed an increasingly important role for managers of wildfire incidents to make strategic decisions. For fire risk assessments and danger rating at very large spatial scales, these models depend on fire weather variables or fire danger indices. Here, we describe a method to simulate fire weather at a national scale that captures the...

  11. A full time-domain approach to spatio-temporal dynamics of semiconductor lasers. II. Spatio-temporal dynamics

    Science.gov (United States)

    Böhringer, Klaus; Hess, Ortwin

    The spatio-temporal dynamics of novel semiconductor lasers is discussed on the basis of a space- and momentum-dependent full time-domain approach. To this means the space-, time-, and momentum-dependent Full-Time Domain Maxwell Semiconductor Bloch equations, derived and discussed in our preceding paper I [K. Böhringer, O. Hess, A full time-domain approach to spatio-temporal dynamics of semiconductor lasers. I. Theoretical formulation], are solved by direct numerical integration. Focussing on the device physics of novel semiconductor lasers that profit, in particular, from recent advances in nanoscience and nanotechnology, we discuss the examples of photonic band edge surface emitting lasers (PBE-SEL) and semiconductor disc lasers (SDLs). It is demonstrated that photonic crystal effects can be obtained for finite crystal structures, and leading to a significant improvement in laser performance such as reduced lasing thresholds. In SDLs, a modern device concept designed to increase the power output of surface-emitters in combination with near-diffraction-limited beam quality, we explore the complex interplay between the intracavity optical fields and the quantum well gain material in SDL structures. Our simulations reveal the dynamical balance between carrier generation due to pumping into high energy states, momentum relaxation of carriers, and stimulated recombination from states near the band edge. Our full time-domain approach is shown to also be an excellent framework for the modelling of the interaction of high-intensity femtosecond and picosecond pulses with semiconductor nanostructures. It is demonstrated that group velocity dispersion, dynamical gain saturation and fast self-phase modulation (SPM) are the main causes for the induced changes and asymmetries in the amplified pulse shape and spectrum of an ultrashort high-intensity pulse. We attest that the time constants of the intraband scattering processes are critical to gain recovery. Moreover, we present

  12. Spatio-temporal Dynamics of Land-use and Land-cover Change: A Multi-agent Simulation Model and Its Application to an Upland Watershed in Central Vietnam

    Science.gov (United States)

    Le, Q.; Vlek, P. L.; Park, S.

    2005-12-01

    Land-use and land-cover change (LUCC) is an essential environmental process that should be monitored and prognosticated to provide a basis for better land management policy. However, LUCC modeling is a challenge due to the complex nature and unexpected behavior of both human drivers and natural constraints. This paper presents a multi-agent-based model to simulate spatio-temporal land-use changes and the interdependent socio-economic dynamics emerging from the complex socio-ecological interactions at micro levels resulting from land-use policy interventions. The model provides land-use scenarios under alternative policy to support decisions on land management for improved rural livelihoods while protecting the environment. In the multi-agent simulation model, the human community is represented by household agents (heterogeneous farming households) with their profiles and decision-making mechanisms about land use. The household profile defines the five asset dimensions of household livelihood (e.g., social, human, financial, natural and physical assets). The land-use decision-making program works by taking inputs from the household profile, perceived spatial environmental attributes, and introduced policies. The decision-making program is a logical procedure that combines a land-use choice model (multi-nominal logistic choices) and anthropological rules. The landscape environment is represented by landscape agents (congruent land patches of 30mx30m) with their state variables and ecological response mechanisms to environmental changes and human interventions. State variables of landscape agents correspond to spatial GIS-raster layers of biophysical, economic, and institutional variables. Ecological mechanisms of landscape agents are represented by internal sub-models of agricultural and forest productivity dynamics, which work in response to the current state, history, and spatial neighbourhood of the landscape agents. A multi-agent based protocol coordinates the

  13. Spatial-temporal dynamics of broadband terahertz Bessel beam propagation

    International Nuclear Information System (INIS)

    Semenova, V A; Kulya, M S; Bespalov, V G

    2016-01-01

    The unique properties of narrowband and broadband terahertz Bessel beams have led to a number of their applications in different fields, for example, for the depth of focusing and resolution enhancement in terahertz imaging. However, broadband terahertz Bessel beams can probably be also used for the diffraction minimization in the short-range broadband terahertz communications. For this purpose, the study of spatial-temporal dynamics of the broadband terahertz Bessel beams is needed. Here we present a simulation-based study of the propagating in non-dispersive medium broadband Bessel beams generated by a conical axicon lens. The algorithm based on scalar diffraction theory was used to obtain the spatial amplitude and phase distributions of the Bessel beam in the frequency range from 0.1 to 3 THz at the distances 10-200 mm from the axicon. Bessel beam field is studied for the different spectral components of the initial pulse. The simulation results show that for the given parameters of the axicon lens one can obtain the Gauss-Bessel beam generation in the spectral range from 0.1 to 3 THz. The length of non-diffraction propagation for a different spectral components was measured, and it was shown that for all spectral components of the initial pulse this length is about 130 mm. (paper)

  14. Identify Dynamic Network Modules with Temporal and Spatial Constraints

    Energy Technology Data Exchange (ETDEWEB)

    Jin, R; McCallen, S; Liu, C; Almaas, E; Zhou, X J

    2007-09-24

    Despite the rapid accumulation of systems-level biological data, understanding the dynamic nature of cellular activity remains a difficult task. The reason is that most biological data are static, or only correspond to snapshots of cellular activity. In this study, we explicitly attempt to detangle the temporal complexity of biological networks by using compilations of time-series gene expression profiling data.We define a dynamic network module to be a set of proteins satisfying two conditions: (1) they form a connected component in the protein-protein interaction (PPI) network; and (2) their expression profiles form certain structures in the temporal domain. We develop the first efficient mining algorithm to discover dynamic modules in a temporal network, as well as frequently occurring dynamic modules across many temporal networks. Using yeast as a model system, we demonstrate that the majority of the identified dynamic modules are functionally homogeneous. Additionally, many of them provide insight into the sequential ordering of molecular events in cellular systems. We further demonstrate that identifying frequent dynamic network modules can significantly increase the signal to noise separation, despite the fact that most dynamic network modules are highly condition-specific. Finally, we note that the applicability of our algorithm is not limited to the study of PPI systems, instead it is generally applicable to the combination of any type of network and time-series data.

  15. PIC Simulation of Laser Plasma Interactions with Temporal Bandwidths

    Science.gov (United States)

    Tsung, Frank; Weaver, J.; Lehmberg, R.

    2015-11-01

    We are performing particle-in-cell simulations using the code OSIRIS to study the effects of laser plasma interactions in the presence of temperal bandwidths under conditions relevant to current and future shock ignition experiments on the NIKE laser. Our simulations show that, for sufficiently large bandwidth, the saturation level, and the distribution of hot electrons, can be effected by the addition of temporal bandwidths (which can be accomplished in experiments using smoothing techniques such as SSD or ISI). We will show that temporal bandwidth along play an important role in the control of LPI's in these lasers and discuss future directions. This work is conducted under the auspices of NRL.

  16. Dynamic CRM occupancy reflects a temporal map of developmental progression.

    Science.gov (United States)

    Wilczyński, Bartek; Furlong, Eileen E M

    2010-06-22

    Development is driven by tightly coordinated spatio-temporal patterns of gene expression, which are initiated through the action of transcription factors (TFs) binding to cis-regulatory modules (CRMs). Although many studies have investigated how spatial patterns arise, precise temporal control of gene expression is less well understood. Here, we show that dynamic changes in the timing of CRM occupancy is a prevalent feature common to all TFs examined in a developmental ChIP time course to date. CRMs exhibit complex binding patterns that cannot be explained by the sequence motifs or expression of the TFs themselves. The temporal changes in TF binding are highly correlated with dynamic patterns of target gene expression, which in turn reflect transitions in cellular function during different stages of development. Thus, it is not only the timing of a TF's expression, but also its temporal occupancy in refined time windows, which determines temporal gene expression. Systematic measurement of dynamic CRM occupancy may therefore serve as a powerful method to decode dynamic changes in gene expression driving developmental progression.

  17. Temporal bone dissection simulator for training pediatric otolaryngology surgeons

    Science.gov (United States)

    Tabrizi, Pooneh R.; Sang, Hongqiang; Talari, Hadi F.; Preciado, Diego; Monfaredi, Reza; Reilly, Brian; Arikatla, Sreekanth; Enquobahrie, Andinet; Cleary, Kevin

    2017-03-01

    Cochlear implantation is the standard of care for infants born with severe hearing loss. Current guidelines approve the surgical placement of implants as early as 12 months of age. Implantation at a younger age poses a greater surgical challenge since the underdeveloped mastoid tip, along with thin calvarial bone, creates less room for surgical navigation and can result in increased surgical risk. We have been developing a temporal bone dissection simulator based on actual clinical cases for training otolaryngology fellows in this delicate procedure. The simulator system is based on pre-procedure CT (Computed Tomography) images from pediatric infant cases (hospital. The simulator includes: (1) simulation engine to provide the virtual reality of the temporal bone surgery environment, (2) a newly developed haptic interface for holding the surgical drill, (3) an Oculus Rift to provide a microscopic-like view of the temporal bone surgery, and (4) user interface to interact with the simulator through the Oculus Rift and the haptic device. To evaluate the system, we have collected 10 representative CT data sets and segmented the key structures: cochlea, round window, facial nerve, and ossicles. The simulator will present these key structures to the user and warn the user if needed by continuously calculating the distances between the tip of surgical drill and the key structures.

  18. Vehicle dynamics modeling and simulation

    CERN Document Server

    Schramm, Dieter; Bardini, Roberto

    2014-01-01

    The authors examine in detail the fundamentals and mathematical descriptions of the dynamics of automobiles. In this context different levels of complexity will be presented, starting with basic single-track models up to complex three-dimensional multi-body models. A particular focus is on the process of establishing mathematical models on the basis of real cars and the validation of simulation results. The methods presented are explained in detail by means of selected application scenarios.

  19. Temporal dynamics of Bose-condensed gases

    Energy Technology Data Exchange (ETDEWEB)

    Trujillo Martinez, Mauricio

    2014-03-19

    We perform a detailed quantum dynamical study of non-equilibrium trapped, interacting Bose-condensed gases. We investigate Josephson oscillations between interacting Bose-Einstein condensates confined in a finite size double-well trap and the non-trivial time evolution of a coherent state placed at the center of a two dimensional optical lattice. For the Josephson oscillations three time scales appear. We find that Josephson junction can sustain multiple undamped oscillations up to a characteristic time scale τ{sub c} without exciting atoms out of the condensates. Beyond the characteristic time scale τ{sub c} the dynamics of the junction are governed by fast, non-condensed particles assisted Josephson tunnelling as well as the collisions between non-condensed particles. In the non-condensed particles dominated regime we observe strong damping of the oscillations due to inelastic collisions, equilibrating the system leading to an effective loss of details of the initial conditions. In addition, we predict that an initially self-trapped BEC state will be destroyed by these fast dynamics. The time evolution of a coherent state released at the center of a two dimensional optical lattice shows a ballistic expansion with a decreasing expansion velocity for increasing two-body interactions strength and particle number. Additionally, we predict that if the two-body interactions strength exceeds a certain value, a forerunner splits up from the expanding coherent state. We also observe that this system, which is prepared far from equilibrium, can evolve to a quasistationary non-equilibrium state.

  20. Effects of dynamic-range compression on temporal acuity

    DEFF Research Database (Denmark)

    Wiinberg, Alan; Jepsen, Morten Løve; Epp, Bastian

    2016-01-01

    Some of the challenges that hearing-aid listeners experience with speech perception in complex acoustic environments may originate from limitations in the temporal processing of sounds. To systematically investigate the influence of hearing impairment and hearing-aid signal processing on temporal...... processing, temporal modulation transfer functions (TMTFs) and “supra-threshold” modulation-depth discrimination (MDD) thresholds were obtained in normal-hearing (NH) and hearing-impaired (HI) listeners with and without wide-dynamic range compression (WDRC). The TMTFs were obtained using tonal carriers of 1...... with the physical compression of the modulation depth due to the WDRC. Indications of reduced temporal resolution in the HI listeners were observed in the TMTF patterns for the 5 kHz carrier. Significantly higher MDD thresholds were found for the HI group relative to the NH group. No relationship was found between...

  1. Temporal nonlinear beam dynamics in infiltrated photonic crystal fibers

    DEFF Research Database (Denmark)

    Bennet, Francis; Rosberg, Christian Romer; Neshev, Dragomir N.

    Liquid-infiltrated photonic crystal fibers (PCFs) offer a new way of studying light propagation in periodic and discrete systems. A wide range of available fiber structures combined with the ease of infiltration opens up a range of novel experimental opportunities for optical detection and bio...... the evolution of the fiber output beam in the few micro or milliseconds after the beam is turned on. The characterization of the temporal behavior of the thermal nonlinear response provides important information about the nonlocality associated with heat diffusion inside the fiber, thus enabling studies of long...... and technological potential of liquid-infiltrated PCFs it is important to understand the temporal dynamics of nonlinear beam propagation in such structures. In this work we consider thermally induced spatial nonlinear effects in infiltrated photonic crystal fibers. We experimentally study the temporal dynamics...

  2. Spatial and temporal dynamics of land use pattern response to ...

    African Journals Online (AJOL)

    Urban settlements account for only two percent of the Earth's land surface. However, over half of the world's population resides in cities (United Nations, 2001). The quantitative evidences presented here showed that there were drastic changes in the temporal and spatial dynamics of land use/land cover. As an overall ...

  3. Temporal acceleration of spatially distributed kinetic Monte Carlo simulations

    International Nuclear Information System (INIS)

    Chatterjee, Abhijit; Vlachos, Dionisios G.

    2006-01-01

    The computational intensity of kinetic Monte Carlo (KMC) simulation is a major impediment in simulating large length and time scales. In recent work, an approximate method for KMC simulation of spatially uniform systems, termed the binomial τ-leap method, was introduced [A. Chatterjee, D.G. Vlachos, M.A. Katsoulakis, Binomial distribution based τ-leap accelerated stochastic simulation, J. Chem. Phys. 122 (2005) 024112], where molecular bundles instead of individual processes are executed over coarse-grained time increments. This temporal coarse-graining can lead to significant computational savings but its generalization to spatially lattice KMC simulation has not been realized yet. Here we extend the binomial τ-leap method to lattice KMC simulations by combining it with spatially adaptive coarse-graining. Absolute stability and computational speed-up analyses for spatial systems along with simulations provide insights into the conditions where accuracy and substantial acceleration of the new spatio-temporal coarse-graining method are ensured. Model systems demonstrate that the r-time increment criterion of Chatterjee et al. obeys the absolute stability limit for values of r up to near 1

  4. Temporal dynamics of the Saccharopolyspora erythraea phosphoproteome.

    Science.gov (United States)

    Licona-Cassani, Cuauhtemoc; Lim, Sooa; Marcellin, Esteban; Nielsen, Lars K

    2014-05-01

    Actinomycetes undergo a dramatic reorganization of metabolic and cellular machinery during a brief period of growth arrest ("metabolic switch") preceding mycelia differentiation and the onset of secondary metabolite biosynthesis. This study explores the role of phosphorylation in coordinating the metabolic switch in the industrial actinomycete Saccharopolyspora erythraea. A total of 109 phosphopeptides from 88 proteins were detected across a 150-h fermentation using open-profile two-dimensional LC-MS proteomics and TiO(2) enrichment. Quantitative analysis of the phosphopeptides and their unphosphorylated cognates was possible for 20 pairs that also displayed constant total protein expression. Enzymes from central carbon metabolism such as putative acetyl-coenzyme A carboxylase, isocitrate lyase, and 2-oxoglutarate dehydrogenase changed dramatically in the degree of phosphorylation during the stationary phase, suggesting metabolic rearrangement for the reutilization of substrates and the production of polyketide precursors. In addition, an enzyme involved in cellular response to environmental stress, trypsin-like serine protease (SACE_6340/NC_009142_6216), decreased in phosphorylation during the growth arrest stage. More important, enzymes related to the regulation of protein synthesis underwent rapid phosphorylation changes during this stage. Whereas the degree of phosphorylation of ribonuclease Rne/Rng (SACE_1406/NC_009142_1388) increased during the metabolic switch, that of two ribosomal proteins, S6 (SACE_7351/NC_009142_7233) and S32 (SACE_6101/NC_009142_5981), dramatically decreased during this stage of the fermentation, supporting the hypothesis that ribosome subpopulations differentially regulate translation before and after the metabolic switch. Overall, we show the great potential of phosphoproteomic studies to explain microbial physiology and specifically provide evidence of dynamic protein phosphorylation events across the developmental cycle of

  5. Temporal Dynamics of the Saccharopolyspora erythraea Phosphoproteome*

    Science.gov (United States)

    Licona-Cassani, Cuauhtemoc; Lim, SooA; Marcellin, Esteban; Nielsen, Lars K.

    2014-01-01

    Actinomycetes undergo a dramatic reorganization of metabolic and cellular machinery during a brief period of growth arrest (“metabolic switch”) preceding mycelia differentiation and the onset of secondary metabolite biosynthesis. This study explores the role of phosphorylation in coordinating the metabolic switch in the industrial actinomycete Saccharopolyspora erythraea. A total of 109 phosphopeptides from 88 proteins were detected across a 150-h fermentation using open-profile two-dimensional LC-MS proteomics and TiO2 enrichment. Quantitative analysis of the phosphopeptides and their unphosphorylated cognates was possible for 20 pairs that also displayed constant total protein expression. Enzymes from central carbon metabolism such as putative acetyl-coenzyme A carboxylase, isocitrate lyase, and 2-oxoglutarate dehydrogenase changed dramatically in the degree of phosphorylation during the stationary phase, suggesting metabolic rearrangement for the reutilization of substrates and the production of polyketide precursors. In addition, an enzyme involved in cellular response to environmental stress, trypsin-like serine protease (SACE_6340/NC_009142_6216), decreased in phosphorylation during the growth arrest stage. More important, enzymes related to the regulation of protein synthesis underwent rapid phosphorylation changes during this stage. Whereas the degree of phosphorylation of ribonuclease Rne/Rng (SACE_1406/NC_009142_1388) increased during the metabolic switch, that of two ribosomal proteins, S6 (SACE_7351/NC_009142_7233) and S32 (SACE_6101/NC_009142_5981), dramatically decreased during this stage of the fermentation, supporting the hypothesis that ribosome subpopulations differentially regulate translation before and after the metabolic switch. Overall, we show the great potential of phosphoproteomic studies to explain microbial physiology and specifically provide evidence of dynamic protein phosphorylation events across the developmental cycle of

  6. Dynamic simulation of LMFBR systems

    International Nuclear Information System (INIS)

    Agrawal, A.K.; Khatib-Rahbar, M.

    1980-01-01

    This review article focuses on the dynamic analysis of liquid-metal-cooled fast breeder reactor systems in the context of protected transients. Following a brief discussion on various design and simulation approaches, a critical review of various models for in-reactor components, intermediate heat exchangers, heat transport systems and the steam generating system is presented. A brief discussion on choice of fuels as well as core and blanket system designs is also included. Numerical considerations for obtaining system-wide steady-state and transient solutions are discussed, and examples of various system transients are presented. Another area of major interest is verification of phenomenological models. Various steps involved in the code and model verification are briefly outlined. The review concludes by posing some further areas of interest in fast reactor dynamics and safety. (author)

  7. Human motion simulation predictive dynamics

    CERN Document Server

    Abdel-Malek, Karim

    2013-01-01

    Simulate realistic human motion in a virtual world with an optimization-based approach to motion prediction. With this approach, motion is governed by human performance measures, such as speed and energy, which act as objective functions to be optimized. Constraints on joint torques and angles are imposed quite easily. Predicting motion in this way allows one to use avatars to study how and why humans move the way they do, given specific scenarios. It also enables avatars to react to infinitely many scenarios with substantial autonomy. With this approach it is possible to predict dynamic motion without having to integrate equations of motion -- rather than solving equations of motion, this approach solves for a continuous time-dependent curve characterizing joint variables (also called joint profiles) for every degree of freedom. Introduces rigorous mathematical methods for digital human modelling and simulation Focuses on understanding and representing spatial relationships (3D) of biomechanics Develops an i...

  8. Dynamic benchmarking of simulation codes

    International Nuclear Information System (INIS)

    Henry, R.E.; Paik, C.Y.; Hauser, G.M.

    1996-01-01

    Computer simulation of nuclear power plant response can be a full-scope control room simulator, an engineering simulator to represent the general behavior of the plant under normal and abnormal conditions, or the modeling of the plant response to conditions that would eventually lead to core damage. In any of these, the underlying foundation for their use in analysing situations, training of vendor/utility personnel, etc. is how well they represent what has been known from industrial experience, large integral experiments and separate effects tests. Typically, simulation codes are benchmarked with some of these; the level of agreement necessary being dependent upon the ultimate use of the simulation tool. However, these analytical models are computer codes, and as a result, the capabilities are continually enhanced, errors are corrected, new situations are imposed on the code that are outside of the original design basis, etc. Consequently, there is a continual need to assure that the benchmarks with important transients are preserved as the computer code evolves. Retention of this benchmarking capability is essential to develop trust in the computer code. Given the evolving world of computer codes, how is this retention of benchmarking capabilities accomplished? For the MAAP4 codes this capability is accomplished through a 'dynamic benchmarking' feature embedded in the source code. In particular, a set of dynamic benchmarks are included in the source code and these are exercised every time the archive codes are upgraded and distributed to the MAAP users. Three different types of dynamic benchmarks are used: plant transients; large integral experiments; and separate effects tests. Each of these is performed in a different manner. The first is accomplished by developing a parameter file for the plant modeled and an input deck to describe the sequence; i.e. the entire MAAP4 code is exercised. The pertinent plant data is included in the source code and the computer

  9. Temporal Variability of Observed and Simulated Hyperspectral Earth Reflectance

    Science.gov (United States)

    Roberts, Yolanda; Pilewskie, Peter; Kindel, Bruce; Feldman, Daniel; Collins, William D.

    2012-01-01

    The Climate Absolute Radiance and Refractivity Observatory (CLARREO) is a climate observation system designed to study Earth's climate variability with unprecedented absolute radiometric accuracy and SI traceability. Observation System Simulation Experiments (OSSEs) were developed using GCM output and MODTRAN to simulate CLARREO reflectance measurements during the 21st century as a design tool for the CLARREO hyperspectral shortwave imager. With OSSE simulations of hyperspectral reflectance, Feldman et al. [2011a,b] found that shortwave reflectance is able to detect changes in climate variables during the 21st century and improve time-to-detection compared to broadband measurements. The OSSE has been a powerful tool in the design of the CLARREO imager and for understanding the effect of climate change on the spectral variability of reflectance, but it is important to evaluate how well the OSSE simulates the Earth's present-day spectral variability. For this evaluation we have used hyperspectral reflectance measurements from the Scanning Imaging Absorption Spectrometer for Atmospheric Cartography (SCIAMACHY), a shortwave spectrometer that was operational between March 2002 and April 2012. To study the spectral variability of SCIAMACHY-measured and OSSE-simulated reflectance, we used principal component analysis (PCA), a spectral decomposition technique that identifies dominant modes of variability in a multivariate data set. Using quantitative comparisons of the OSSE and SCIAMACHY PCs, we have quantified how well the OSSE captures the spectral variability of Earth?s climate system at the beginning of the 21st century relative to SCIAMACHY measurements. These results showed that the OSSE and SCIAMACHY data sets share over 99% of their total variance in 2004. Using the PCs and the temporally distributed reflectance spectra projected onto the PCs (PC scores), we can study the temporal variability of the observed and simulated reflectance spectra. Multivariate time

  10. Nonlinear Spatio-Temporal Dynamics and Chaos in Semiconductors

    Science.gov (United States)

    Schöll, Eckehard

    2005-08-01

    Nonlinear transport phenomena are an increasingly important aspect of modern semiconductor research. This volume deals with complex nonlinear dynamics, pattern formation, and chaotic behavior in such systems. It bridges the gap between two well-established fields: the theory of dynamic systems and nonlinear charge transport in semiconductors. This unified approach helps reveal important electronic transport instabilities. The initial chapters lay a general framework for the theoretical description of nonlinear self-organized spatio-temporal patterns, such as current filaments, field domains, fronts, and analysis of their stability. Later chapters consider important model systems in detail: impact ionization induced impurity breakdown, Hall instabilities, superlattices, and low-dimensional structures. State-of-the-art results include chaos control, spatio-temporal chaos, multistability, pattern selection, activator-inhibitor kinetics, and global coupling, linking fundamental issues to electronic device applications. This book will be of great value to semiconductor physicists and nonlinear scientists alike.

  11. Temporal dynamics of ikaite in experimental sea ice

    OpenAIRE

    S. Rysgaard; F. Wang; R. J. Galley; R. Grimm; D. Notz; M. Lemes; N.-X. Geilfus; A. Chaulk; A. A. Hare; O. Crabeck; B. G. T. Else; K. Campbell; L. L. Sørensen; J. Sievers; T. Papakyriakou

    2014-01-01

    Ikaite (CaCO3 · 6H2O) is a metastable phase of calcium carbonate that normally forms in a cold environment and/or under high pressure. Recently, ikaite crystals have been found in sea ice, and it has been suggested that their precipitation may play an important role in air–sea CO2 exchange in ice-covered seas. Little is known, however, of the spatial and temporal dynamics of ikaite in sea ice. Here we present evidence for highly dynamic ikaite precipitation and dissolution i...

  12. Estimating spatio-temporal dynamics of size-structured populations

    DEFF Research Database (Denmark)

    Kristensen, Kasper; Thygesen, Uffe Høgsbro; Andersen, Ken Haste

    2014-01-01

    with simple stock dynamics, to estimate simultaneously how size distributions and spatial distributions develop in time. We demonstrate the method for a cod population sampled by trawl surveys. Particular attention is paid to correlation between size classes within each trawl haul due to clustering...... of individuals with similar size. The model estimates growth, mortality and reproduction, after which any aspect of size-structure, spatio-temporal population dynamics, as well as the sampling process can be probed. This is illustrated by two applications: 1) tracking the spatial movements of a single cohort...

  13. Iterative analysis of cerebrovascular reactivity dynamic response by temporal decomposition.

    Science.gov (United States)

    van Niftrik, Christiaan Hendrik Bas; Piccirelli, Marco; Bozinov, Oliver; Pangalu, Athina; Fisher, Joseph A; Valavanis, Antonios; Luft, Andreas R; Weller, Michael; Regli, Luca; Fierstra, Jorn

    2017-09-01

    To improve quantitative cerebrovascular reactivity (CVR) measurements and CO 2 arrival times, we present an iterative analysis capable of decomposing different temporal components of the dynamic carbon dioxide- Blood Oxygen-Level Dependent (CO 2 -BOLD) relationship. Decomposition of the dynamic parameters included a redefinition of the voxel-wise CO 2 arrival time, and a separation from the vascular response to a stepwise increase in CO 2 (Delay to signal Plateau - DTP) and a decrease in CO 2 (Delay to signal Baseline -DTB). Twenty-five (normal) datasets, obtained from BOLD MRI combined with a standardized pseudo-square wave CO 2 change, were co-registered to generate reference atlases for the aforementioned dynamic processes to score the voxel-by-voxel deviation probability from normal range. This analysis is further illustrated in two subjects with unilateral carotid artery occlusion using these reference atlases. We have found that our redefined CO 2 arrival time resulted in the best data fit. Additionally, excluding both dynamic BOLD phases (DTP and DTB) resulted in a static CVR, that is maximal response, defined as CVR calculated only over a normocapnic and hypercapnic calibrated plateau. Decomposition and novel iterative modeling of different temporal components of the dynamic CO 2 -BOLD relationship improves quantitative CVR measurements.

  14. A eural etwork Model for Dynamics Simulation

    African Journals Online (AJOL)

    Nafiisah

    Results 5 - 18 ... situations, such as a dynamic environment (e.g., a molecular dynamics (MD) simulation whereby an atom constantly changes its local environment and number ..... of systems including both small clusters and bulk structures. 7.

  15. Reconstruction of tissue dynamics in the compressed breast using multiplexed measurements and temporal basis functions

    Science.gov (United States)

    Boverman, Gregory; Miller, Eric L.; Brooks, Dana H.; Fang, Qianqian; Carp, S. A.; Selb, J. J.; Boas, David A.

    2007-02-01

    In the course of our experiments imaging the compressed breast in conjunction with digital tomosynthesis, we have noted that significant changes in tissue optical properties, on the order of 5%, occur during our imaging protocol. These changes seem to consistent with changes both in total Hemoglobin concentration as well as in oxygen saturation, as was the case for our standalone breast compression study, which made use of reflectance measurements. Simulation experiments show the importance of taking into account the temporal dynamics in the image reconstruction, and demonstrate the possibility of imaging the spatio-temporal dynamics of oxygen saturation and total Hemoglobin in the breast. In the image reconstruction, we make use of spatio-temporal basis functions, specifically a voxel basis for spatial imaging, and a cubic spline basis in time, and we reconstruct the spatio-temporal images using the entire data set simultaneously, making use of both absolute and relative measurements in the cost function. We have modified the sequence of sources used in our imaging acquisition protocol to improve our temporal resolution, and preliminary results are shown for normal subjects.

  16. Envelope detection using temporal magnetization dynamics of resonantly interacting spin-torque oscillator

    Science.gov (United States)

    Nakamura, Y.; Nishikawa, M.; Osawa, H.; Okamoto, Y.; Kanao, T.; Sato, R.

    2018-05-01

    In this article, we propose the detection method of the recorded data pattern by the envelope of the temporal magnetization dynamics of resonantly interacting spin-torque oscillator on the microwave assisted magnetic recording for three-dimensional magnetic recording. We simulate the envelope of the waveform from recorded dots with the staggered magnetization configuration, which are calculated by using a micromagnetic simulation. We study the data detection methods for the envelope and propose a soft-output Viterbi algorithm (SOVA) for partial response (PR) system as a signal processing system for three dimensional magnetic recording.

  17. Synthesizing Dynamic Programming Algorithms from Linear Temporal Logic Formulae

    Science.gov (United States)

    Rosu, Grigore; Havelund, Klaus

    2001-01-01

    The problem of testing a linear temporal logic (LTL) formula on a finite execution trace of events, generated by an executing program, occurs naturally in runtime analysis of software. We present an algorithm which takes an LTL formula and generates an efficient dynamic programming algorithm. The generated algorithm tests whether the LTL formula is satisfied by a finite trace of events given as input. The generated algorithm runs in linear time, its constant depending on the size of the LTL formula. The memory needed is constant, also depending on the size of the formula.

  18. Spatio-temporal Dynamics and Mechanisms of Stress Granule Assembly.

    Directory of Open Access Journals (Sweden)

    Daisuke Ohshima

    2015-06-01

    Full Text Available Stress granules (SGs are non-membranous cytoplasmic aggregates of mRNAs and related proteins, assembled in response to environmental stresses such as heat shock, hypoxia, endoplasmic reticulum (ER stress, chemicals (e.g. arsenite, and viral infections. SGs are hypothesized as a loci of mRNA triage and/or maintenance of proper translation capacity ratio to the pool of mRNAs. In brain ischemia, hippocampal CA3 neurons, which are resilient to ischemia, assemble SGs. In contrast, CA1 neurons, which are vulnerable to ischemia, do not assemble SGs. These results suggest a critical role SG plays in regards to cell fate decisions. Thus SG assembly along with its dynamics should determine the cell fate. However, the process that exactly determines the SG assembly dynamics is largely unknown. In this paper, analyses of experimental data and computer simulations were used to approach this problem. SGs were assembled as a result of applying arsenite to HeLa cells. The number of SGs increased after a short latent period, reached a maximum, then decreased during the application of arsenite. At the same time, the size of SGs grew larger and became localized at the perinuclear region. A minimal mathematical model was constructed, and stochastic simulations were run to test the modeling. Since SGs are discrete entities as there are only several tens of them in a cell, commonly used deterministic simulations could not be employed. The stochastic simulations replicated observed dynamics of SG assembly. In addition, these stochastic simulations predicted a gamma distribution relative to the size of SGs. This same distribution was also found in our experimental data suggesting the existence of multiple fusion steps in the SG assembly. Furthermore, we found that the initial steps in the SG assembly process and microtubules were critical to the dynamics. Thus our experiments and stochastic simulations presented a possible mechanism regulating SG assembly.

  19. Effects of dynamical quarks in UKQCD simulations

    International Nuclear Information System (INIS)

    Allton, Chris

    2002-01-01

    Recent results from the UKQCD Collaboration's dynamical simulations are presented. The main feature of these ensembles is that they have a fixed lattice spacing and volume, but varying sea quark mass from infinite (corresponding to the quenched simulation) down to roughly that of the strange quark mass. The main aim of this work is to uncover dynamical quark effects from these 'matched' ensembles. We obtain some evidence of dynamical quark effects in the static quark potential with less effects in the hadronic spectrum

  20. Impact of Partial Time Delay on Temporal Dynamics of Watts-Strogatz Small-World Neuronal Networks

    Science.gov (United States)

    Yan, Hao; Sun, Xiaojuan

    2017-06-01

    In this paper, we mainly discuss effects of partial time delay on temporal dynamics of Watts-Strogatz (WS) small-world neuronal networks by controlling two parameters. One is the time delay τ and the other is the probability of partial time delay pdelay. Temporal dynamics of WS small-world neuronal networks are discussed with the aid of temporal coherence and mean firing rate. With the obtained simulation results, it is revealed that for small time delay τ, the probability pdelay could weaken temporal coherence and increase mean firing rate of neuronal networks, which indicates that it could improve neuronal firings of the neuronal networks while destroying firing regularity. For large time delay τ, temporal coherence and mean firing rate do not have great changes with respect to pdelay. Time delay τ always has great influence on both temporal coherence and mean firing rate no matter what is the value of pdelay. Moreover, with the analysis of spike trains and histograms of interspike intervals of neurons inside neuronal networks, it is found that the effects of partial time delays on temporal coherence and mean firing rate could be the result of locking between the period of neuronal firing activities and the value of time delay τ. In brief, partial time delay could have great influence on temporal dynamics of the neuronal networks.

  1. Temporal dynamics of ikaite in experimental sea ice

    DEFF Research Database (Denmark)

    Rysgaard, Søren; Wang, F.; Galley, R.J.

    2014-01-01

    Ikaite (CaCO3·6H2O) is a metastable phase of calcium carbonate that normally forms in a cold environment and/or under high pressure. Recently, ikaite crystals have been found in sea ice, and it has been suggested that their precipitation may play an important role in air–sea CO2 exchange in ice......-covered seas. Little is known, however, of the spatial and temporal dynamics of ikaite in sea ice. Here we present evidence for highly dynamic ikaite precipitation and dissolution in sea ice grown at an outdoor pool of the Sea-ice Environmental Research Facility (SERF) in Manitoba, Canada. During...... the experiment, ikaite precipitated in sea ice when temperatures were below −4 C, creating three distinct zones of ikaite concentrations: (1) a millimeter-to-centimeter-thin surface layer containing frost flowers and brine skim with bulk ikaite concentrations of > 2000 μmol kg−1, (2) an internal layer...

  2. Metrics for comparing dynamic earthquake rupture simulations

    Science.gov (United States)

    Barall, Michael; Harris, Ruth A.

    2014-01-01

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

  3. The Temporal Dynamics of Arc Expression Regulate Cognitive Flexibility.

    Science.gov (United States)

    Wall, Mark J; Collins, Dawn R; Chery, Samantha L; Allen, Zachary D; Pastuzyn, Elissa D; George, Arlene J; Nikolova, Viktoriya D; Moy, Sheryl S; Philpot, Benjamin D; Shepherd, Jason D; Müller, Jürgen; Ehlers, Michael D; Mabb, Angela M; Corrêa, Sonia A L

    2018-05-24

    Neuronal activity regulates the transcription and translation of the immediate-early gene Arc/Arg3.1, a key mediator of synaptic plasticity. Proteasome-dependent degradation of Arc tightly limits its temporal expression, yet the significance of this regulation remains unknown. We disrupted the temporal control of Arc degradation by creating an Arc knockin mouse (ArcKR) where the predominant Arc ubiquitination sites were mutated. ArcKR mice had intact spatial learning but showed specific deficits in selecting an optimal strategy during reversal learning. This cognitive inflexibility was coupled to changes in Arc mRNA and protein expression resulting in a reduced threshold to induce mGluR-LTD and enhanced mGluR-LTD amplitude. These findings show that the abnormal persistence of Arc protein limits the dynamic range of Arc signaling pathways specifically during reversal learning. Our work illuminates how the precise temporal control of activity-dependent molecules, such as Arc, regulates synaptic plasticity and is crucial for cognition. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  4. Spatial and Temporal Dynamics in Air Pollution Exposure Assessment

    Science.gov (United States)

    Dias, Daniela; Tchepel, Oxana

    2018-01-01

    Analyzing individual exposure in urban areas offers several challenges where both the individual’s activities and air pollution levels demonstrate a large degree of spatial and temporal dynamics. This review article discusses the concepts, key elements, current developments in assessing personal exposure to urban air pollution (seventy-two studies reviewed) and respective advantages and disadvantages. A new conceptual structure to organize personal exposure assessment methods is proposed according to two classification criteria: (i) spatial-temporal variations of individuals’ activities (point-fixed or trajectory based) and (ii) characterization of air quality (variable or uniform). This review suggests that the spatial and temporal variability of urban air pollution levels in combination with indoor exposures and individual’s time-activity patterns are key elements of personal exposure assessment. In the literature review, the majority of revised studies (44 studies) indicate that the trajectory based with variable air quality approach provides a promising framework for tackling the important question of inter- and intra-variability of individual exposure. However, future quantitative comparison between the different approaches should be performed, and the selection of the most appropriate approach for exposure quantification should take into account the purpose of the health study. This review provides a structured basis for the intercomparing of different methodologies and to make their advantages and limitations more transparent in addressing specific research objectives. PMID:29558426

  5. Molecular dynamics simulation of a phospholipid membrane

    NARCIS (Netherlands)

    Egberts, Egbert; Marrink, Siewert-Jan; Berendsen, Herman J.C.

    We present the results of molecular dynamics (MD) simulations of a phospholipid membrane in water, including full atomic detail. The goal of the simulations was twofold: first we wanted to set up a simulation system which is able to reproduce experimental results and can serve as a model membrane in

  6. Lateralization for dynamic facial expressions in human superior temporal sulcus.

    Science.gov (United States)

    De Winter, François-Laurent; Zhu, Qi; Van den Stock, Jan; Nelissen, Koen; Peeters, Ronald; de Gelder, Beatrice; Vanduffel, Wim; Vandenbulcke, Mathieu

    2015-02-01

    Most face processing studies in humans show stronger activation in the right compared to the left hemisphere. Evidence is largely based on studies with static stimuli focusing on the fusiform face area (FFA). Hence, the pattern of lateralization for dynamic faces is less clear. Furthermore, it is unclear whether this property is common to human and non-human primates due to predisposing processing strategies in the right hemisphere or that alternatively left sided specialization for language in humans could be the driving force behind this phenomenon. We aimed to address both issues by studying lateralization for dynamic facial expressions in monkeys and humans. Therefore, we conducted an event-related fMRI experiment in three macaques and twenty right handed humans. We presented human and monkey dynamic facial expressions (chewing and fear) as well as scrambled versions to both species. We studied lateralization in independently defined face-responsive and face-selective regions by calculating a weighted lateralization index (LIwm) using a bootstrapping method. In order to examine if lateralization in humans is related to language, we performed a separate fMRI experiment in ten human volunteers including a 'speech' expression (one syllable non-word) and its scrambled version. Both within face-responsive and selective regions, we found consistent lateralization for dynamic faces (chewing and fear) versus scrambled versions in the right human posterior superior temporal sulcus (pSTS), but not in FFA nor in ventral temporal cortex. Conversely, in monkeys no consistent pattern of lateralization for dynamic facial expressions was observed. Finally, LIwms based on the contrast between different types of dynamic facial expressions (relative to scrambled versions) revealed left-sided lateralization in human pSTS for speech-related expressions compared to chewing and emotional expressions. To conclude, we found consistent laterality effects in human posterior STS but not

  7. Developing effective automated feedback in temporal bone surgery simulation.

    Science.gov (United States)

    Wijewickrema, Sudanthi; Piromchai, Patorn; Zhou, Yun; Ioannou, Ioanna; Bailey, James; Kennedy, Gregor; O'Leary, Stephen

    2015-06-01

    We aim to test the effectiveness, accuracy, and usefulness of an automated feedback system in facilitating skill acquisition in virtual reality surgery. We evaluate the performance of the feedback system through a randomized controlled trial of 24 students allocated to feedback and nonfeedback groups. The feedback system was based on the Melbourne University temporal bone surgery simulator. The study was conducted at the simulation laboratory of the Royal Victorian Eye and Ear Hospital, Melbourne. The study participants were medical students from the University of Melbourne, who were asked to perform virtual cortical mastoidectomy on the simulator. The extent to which the drilling behavior of the feedback and nonfeedback groups differed was used to evaluate the effectiveness of the system. Its accuracy was determined through a postexperiment observational assessment of recordings made during the experiment by an expert surgeon. Its usability was evaluated using students' self-reports of their impressions of the system. A Friedman's test showed that there was a significant improvement in the drilling performance of the feedback group, χ(2)(1) = 14.450, P feedback (when trainee behavior was detected) 88.6% of the time and appropriate feedback (accurate advice) 84.2% of the time. Participants' opinions about the usefulness of the system were highly positive. The automated feedback system was observed to be effective in improving surgical technique, and the provided feedback was found to be accurate and useful. © American Academy of Otolaryngology—Head and Neck Surgery Foundation 2015.

  8. Spatio-temporal dynamics of security investments in an interdependent risk environment

    Science.gov (United States)

    Shafi, Kamran; Bender, Axel; Zhong, Weicai; Abbass, Hussein A.

    2012-10-01

    In a globalised world where risks spread through contagion, the decision of an entity to invest in securing its premises from stochastic risks no longer depends solely on its own actions but also on the actions of other interacting entities in the system. This phenomenon is commonly seen in many domains including airline, logistics and computer security and is referred to as Interdependent Security (IDS). An IDS game models this decision problem from a game-theoretic perspective and deals with the behavioural dynamics of risk-reduction investments in such settings. This paper enhances this model and investigates the spatio-temporal aspects of the IDS games. The spatio-temporal dynamics are studied using simple replicator dynamics on a variety of network structures and for various security cost tradeoffs that lead to different Nash equilibria in an IDS game. The simulation results show that the neighbourhood configuration has a greater effect on the IDS game dynamics than network structure. An in-depth empirical analysis of game dynamics is carried out on regular graphs, which leads to the articulation of necessary and sufficient conditions for dominance in IDS games under spatial constraints.

  9. A Novel Temporal Bone Simulation Model Using 3D Printing Techniques.

    Science.gov (United States)

    Mowry, Sarah E; Jammal, Hachem; Myer, Charles; Solares, Clementino Arturo; Weinberger, Paul

    2015-09-01

    An inexpensive temporal bone model for use in a temporal bone dissection laboratory setting can be made using a commercially available, consumer-grade 3D printer. Several models for a simulated temporal bone have been described but use commercial-grade printers and materials to produce these models. The goal of this project was to produce a plastic simulated temporal bone on an inexpensive 3D printer that recreates the visual and haptic experience associated with drilling a human temporal bone. Images from a high-resolution CT of a normal temporal bone were converted into stereolithography files via commercially available software, with image conversion and print settings adjusted to achieve optimal print quality. The temporal bone model was printed using acrylonitrile butadiene styrene (ABS) plastic filament on a MakerBot 2x 3D printer. Simulated temporal bones were drilled by seven expert temporal bone surgeons, assessing the fidelity of the model as compared with a human cadaveric temporal bone. Using a four-point scale, the simulated bones were assessed for haptic experience and recreation of the temporal bone anatomy. The created model was felt to be an accurate representation of a human temporal bone. All raters felt strongly this would be a good training model for junior residents or to simulate difficult surgical anatomy. Material cost for each model was $1.92. A realistic, inexpensive, and easily reproducible temporal bone model can be created on a consumer-grade desktop 3D printer.

  10. A Markov model for the temporal dynamics of balanced random networks of finite size

    Science.gov (United States)

    Lagzi, Fereshteh; Rotter, Stefan

    2014-01-01

    The balanced state of recurrent networks of excitatory and inhibitory spiking neurons is characterized by fluctuations of population activity about an attractive fixed point. Numerical simulations show that these dynamics are essentially nonlinear, and the intrinsic noise (self-generated fluctuations) in networks of finite size is state-dependent. Therefore, stochastic differential equations with additive noise of fixed amplitude cannot provide an adequate description of the stochastic dynamics. The noise model should, rather, result from a self-consistent description of the network dynamics. Here, we consider a two-state Markovian neuron model, where spikes correspond to transitions from the active state to the refractory state. Excitatory and inhibitory input to this neuron affects the transition rates between the two states. The corresponding nonlinear dependencies can be identified directly from numerical simulations of networks of leaky integrate-and-fire neurons, discretized at a time resolution in the sub-millisecond range. Deterministic mean-field equations, and a noise component that depends on the dynamic state of the network, are obtained from this model. The resulting stochastic model reflects the behavior observed in numerical simulations quite well, irrespective of the size of the network. In particular, a strong temporal correlation between the two populations, a hallmark of the balanced state in random recurrent networks, are well represented by our model. Numerical simulations of such networks show that a log-normal distribution of short-term spike counts is a property of balanced random networks with fixed in-degree that has not been considered before, and our model shares this statistical property. Furthermore, the reconstruction of the flow from simulated time series suggests that the mean-field dynamics of finite-size networks are essentially of Wilson-Cowan type. We expect that this novel nonlinear stochastic model of the interaction between

  11. Dynamic simulation of hydrogen isotope distillation unit

    International Nuclear Information System (INIS)

    Le Lann, J.M.; Latge, C.; Joulia, X.; Sere-Peyrigain, P.

    1995-01-01

    Dynamic simulation of hydrogen isotope distillation unit involved in the complex environment of a fusion power plant can be a powerful technique in view to analyze the tritium hazard potential. In this paper, issues related to the development of such a dynamic simulator with model formulation and the numerical treatment of the resulting Differential-Algebraic equation (DAE) system are properly adressed. The typical dynamic characteristics of such columns are quantitatively and qualitatively enlighted on case study with very large disturbances. The developed system has proven to be beneficial for understanding the dynamic behaviour and further for developing control schemes. (orig.)

  12. Dynamic simulation of hydrogen isotope distillation unit

    International Nuclear Information System (INIS)

    Le Lann, J.M.; Joulia, X.; Sere-Peyrigain, P.

    1994-01-01

    Dynamic simulation of hydrogen isotope distillation unit involved in the complex environment of a fusion power plant can be a powerful technique in view to analyze the tritium hazard potential. Issues related to the development of such a dynamic simulator with model formulation and the numerical treatment of the resulting Differential-Algebraic equation (DAE) system are properly addressed. The typical dynamic characteristics of such columns are quantitatively and qualitatively enlightened on case study with very large disturbances. The developed system has proven to be beneficial for understanding the dynamic behaviour and further for developing control schemes. (author) 12 refs.; 4 figs

  13. Spatio-temporal dynamics of the tropical rain forest

    Energy Technology Data Exchange (ETDEWEB)

    Chave, J. [CEN Saclay, Gif-sur-Yvette (France). Service de Physique de l' Etat Condense

    2000-07-01

    Mechanisms which drive the dynamics of forest ecosystems are complex, from seedling establishment to pollination, and seed dispersal by animals, running water or wind. These processes are more complex when the ecosystem shelters a large number of species and of vegetative forms, as it is the case in the tropical rainforest. To take them into account, we must develop and use models. I present a review of the fundamental mechanisms for the of a natural forest dynamics - photosynthesis, tree growth, recruitment and mortality - as well as a description of the past and of the present of tropical rainforests. This information is used to develop a spatially-explicit and individual-based forest model. Simplified models are deduced from it, and they serve to address more specific issues, such as the resilience of the forest to climate disturbances, or savanna-forest dynamics. The last topic is related to the spatio-temporal description of tropical plant biodiversity. A detailed introduction to the problem is provided, and models accounting for the maintenance of diversity are compared. These models include non spatial as well a spatial approaches (branching anihilating random walks and voter model with mutation). (orig.)

  14. Temporal dynamics of glyoxalase 1 in secondary neuronal injury.

    Directory of Open Access Journals (Sweden)

    Philipp Pieroh

    Full Text Available BACKGROUND: Enhanced glycolysis leads to elevated levels of the toxic metabolite methylglyoxal which contributes to loss of protein-function, metabolic imbalance and cell death. Neurons were shown being highly susceptible to methylglyoxal toxicity. Glyoxalase 1 as an ubiquitous enzyme reflects the main detoxifying enzyme of methylglyoxal and underlies changes during aging and neurodegeneration. However, little is known about dynamics of Glyoxalase 1 following neuronal lesions so far. METHODS: To determine a possible involvement of Glyoxalase 1 in acute brain injury, we analysed the temporal dynamics of Glyoxalase 1 distribution and expression by immunohistochemistry and Western Blot analysis. Organotypic hippocampal slice cultures were excitotoxically (N-methyl-D-aspartate, 50 µM for 4 hours lesioned in vitro (5 minutes to 72 hours. Additionally, permanent middle cerebral artery occlusion was performed (75 minutes to 60 days. RESULTS: We found (i a predominant localisation of Glyoxalase 1 in endothelial cells in non-lesioned brains (ii a time-dependent up-regulation and re-distribution of Glyoxalase 1 in neurons and astrocytes and (iii a strong increase in Glyoxalase 1 dimers after neuronal injury (24 hours to 72 hours when compared to monomers of the protein. CONCLUSIONS: The high dynamics of Glyoxalase 1 expression and distribution following neuronal injury may indicate a novel role of Glyoxalase 1.

  15. MR-guided dynamic PET reconstruction with the kernel method and spectral temporal basis functions

    Science.gov (United States)

    Novosad, Philip; Reader, Andrew J.

    2016-06-01

    Recent advances in dynamic positron emission tomography (PET) reconstruction have demonstrated that it is possible to achieve markedly improved end-point kinetic parameter maps by incorporating a temporal model of the radiotracer directly into the reconstruction algorithm. In this work we have developed a highly constrained, fully dynamic PET reconstruction algorithm incorporating both spectral analysis temporal basis functions and spatial basis functions derived from the kernel method applied to a co-registered T1-weighted magnetic resonance (MR) image. The dynamic PET image is modelled as a linear combination of spatial and temporal basis functions, and a maximum likelihood estimate for the coefficients can be found using the expectation-maximization (EM) algorithm. Following reconstruction, kinetic fitting using any temporal model of interest can be applied. Based on a BrainWeb T1-weighted MR phantom, we performed a realistic dynamic [18F]FDG simulation study with two noise levels, and investigated the quantitative performance of the proposed reconstruction algorithm, comparing it with reconstructions incorporating either spectral analysis temporal basis functions alone or kernel spatial basis functions alone, as well as with conventional frame-independent reconstruction. Compared to the other reconstruction algorithms, the proposed algorithm achieved superior performance, offering a decrease in spatially averaged pixel-level root-mean-square-error on post-reconstruction kinetic parametric maps in the grey/white matter, as well as in the tumours when they were present on the co-registered MR image. When the tumours were not visible in the MR image, reconstruction with the proposed algorithm performed similarly to reconstruction with spectral temporal basis functions and was superior to both conventional frame-independent reconstruction and frame-independent reconstruction with kernel spatial basis functions. Furthermore, we demonstrate that a joint spectral

  16. molecular dynamics simulations and quantum chemical calculations

    African Journals Online (AJOL)

    ABSTRACT. The molecular dynamic (MD) simulation and quantum chemical calculations for the adsorption of [2-(2-Henicos-10- .... electronic properties of molecule clusters, surfaces and ... The local reactivity was analyzed by determining the.

  17. Induction generator models in dynamic simulation tools

    DEFF Research Database (Denmark)

    Knudsen, Hans; Akhmatov, Vladislav

    1999-01-01

    For AC network with large amount of induction generators (windmills) the paper demonstrates a significant discrepancy in the simulated voltage recovery after fault in weak networks when comparing dynamic and transient stability descriptions and the reasons of discrepancies are explained...

  18. Temporal dynamics of biogeochemical processes at the Norman Landfill site

    Science.gov (United States)

    Arora, Bhavna; Mohanty, Binayak P.; McGuire, Jennifer T.; Cozzarelli, Isabelle M.

    2013-01-01

    The temporal variability observed in redox sensitive species in groundwater can be attributed to coupled hydrological, geochemical, and microbial processes. These controlling processes are typically nonstationary, and distributed across various time scales. Therefore, the purpose of this study is to investigate biogeochemical data sets from a municipal landfill site to identify the dominant modes of variation and determine the physical controls that become significant at different time scales. Data on hydraulic head, specific conductance, δ2H, chloride, sulfate, nitrate, and nonvolatile dissolved organic carbon were collected between 1998 and 2000 at three wells at the Norman Landfill site in Norman, OK. Wavelet analysis on this geochemical data set indicates that variations in concentrations of reactive and conservative solutes are strongly coupled to hydrologic variability (water table elevation and precipitation) at 8 month scales, and to individual eco-hydrogeologic framework (such as seasonality of vegetation, surface-groundwater dynamics) at 16 month scales. Apart from hydrologic variations, temporal variability in sulfate concentrations can be associated with different sources (FeS cycling, recharge events) and sinks (uptake by vegetation) depending on the well location and proximity to the leachate plume. Results suggest that nitrate concentrations show multiscale behavior across temporal scales for different well locations, and dominant variability in dissolved organic carbon for a closed municipal landfill can be larger than 2 years due to its decomposition and changing content. A conceptual framework that explains the variability in chemical concentrations at different time scales as a function of hydrologic processes, site-specific interactions, and/or coupled biogeochemical effects is also presented.

  19. Spatio-temporal correlations in models of collective motion ruled by different dynamical laws.

    Science.gov (United States)

    Cavagna, Andrea; Conti, Daniele; Giardina, Irene; Grigera, Tomas S; Melillo, Stefania; Viale, Massimiliano

    2016-11-15

    Information transfer is an essential factor in determining the robustness of biological systems with distributed control. The most direct way to study the mechanisms ruling information transfer is to experimentally observe the propagation across the system of a signal triggered by some perturbation. However, this method may be inefficient for experiments in the field, as the possibilities to perturb the system are limited and empirical observations must rely on natural events. An alternative approach is to use spatio-temporal correlations to probe the information transfer mechanism directly from the spontaneous fluctuations of the system, without the need to have an actual propagating signal on record. Here we test this method on models of collective behaviour in their deeply ordered phase by using ground truth data provided by numerical simulations in three dimensions. We compare two models characterized by very different dynamical equations and information transfer mechanisms: the classic Vicsek model, describing an overdamped noninertial dynamics and the inertial spin model, characterized by an underdamped inertial dynamics. By using dynamic finite-size scaling, we show that spatio-temporal correlations are able to distinguish unambiguously the diffusive information transfer mechanism of the Vicsek model from the linear mechanism of the inertial spin model.

  20. Visualizing Structure and Dynamics of Disaccharide Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Matthews, J. F.; Beckham, G. T.; Himmel, M. E.; Crowley, M. F.

    2012-01-01

    We examine the effect of several solvent models on the conformational properties and dynamics of disaccharides such as cellobiose and lactose. Significant variation in timescale for large scale conformational transformations are observed. Molecular dynamics simulation provides enough detail to enable insight through visualization of multidimensional data sets. We present a new way to visualize conformational space for disaccharides with Ramachandran plots.

  1. Molecular dynamics simulation of impact test

    International Nuclear Information System (INIS)

    Akahoshi, Y.; Schmauder, S.; Ludwig, M.

    1998-01-01

    This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)

  2. Modular simulation of reefer container dynamics

    DEFF Research Database (Denmark)

    Sørensen, Kresten Kjær; Nielsen, Jens Frederik Dalsgaard; Stoustrup, Jakob

    2014-01-01

    for faults enabling preventive maintenance. In this paper the feasibility of using different simulation methods is assessed with the goal of identifying a fast but accurate method that works well in a multi-rate environment. A modular multi-rate simulation environment for a dynamical system consisting...

  3. Molecular dynamics simulation of impact test

    Energy Technology Data Exchange (ETDEWEB)

    Akahoshi, Y. [Kyushu Inst. of Tech., Kitakyushu, Fukuoka (Japan); Schmauder, S.; Ludwig, M. [Stuttgart Univ. (Germany). Staatliche Materialpruefungsanstalt

    1998-11-01

    This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)

  4. LEADSTO: a Language and Environment for Analysis of Dynamics by SimulaTiOn (extended abstract)

    NARCIS (Netherlands)

    Bosse, T.; Jonker, C.M.; van der Meij, L.; Treur, J.

    2005-01-01

    This paper presents the language and software environment LEADSTO that has been developed to model and simulate dynamic processes in terms of both qualitative and quantitative concepts. The LEADSTO language is a declarative order-sorted temporal language, extended with quantitative means. Dynamic

  5. Simulating forest fuel and fire risk dynamics across landscapes--LANDIS fuel module design

    Science.gov (United States)

    Hong S. He; Bo Z. Shang; Thomas R. Crow; Eric J. Gustafson; Stephen R. Shifley

    2004-01-01

    Understanding fuel dynamics over large spatial (103-106 ha) and temporal scales (101-103 years) is important in comprehensive wildfire management. We present a modeling approach to simulate fuel and fire risk dynamics as well as impacts of alternative fuel treatments. The...

  6. Dynamic Raman imaging system with high spatial and temporal resolution

    Science.gov (United States)

    Wang, Lei; Dai, Yinzhen; He, Hao; Lv, Ruiqi; Zong, Cheng; Ren, Bin

    2017-09-01

    There is an increasing need to study dynamic changing systems with significantly high spatial and temporal resolutions. In this work, we integrated point-scanning, line-scanning, and wide-field Raman imaging techniques into a single system. By using an Electron Multiplying CCD (EMCCD) with a high gain and high frame rate, we significantly reduced the time required for wide-field imaging, making it possible to monitor the electrochemical reactions in situ. The highest frame rate of EMCDD was ˜50 fps, and the Raman images for a specific Raman peak can be obtained by passing the signal from the sample through the Liquid Crystal Tunable Filter. The spatial resolutions of scanning imaging and wide-field imaging with a 100× objective (NA = 0.9) are 0.5 × 0.5 μm2 and 0.36 × 0.36 μm2, respectively. The system was used to study the surface plasmon resonance of Au nanorods, the surface-enhanced Raman scattering signal distribution for Au Nanoparticle aggregates, and dynamic Raman imaging of an electrochemical reacting system.

  7. Learning predictive statistics from temporal sequences: Dynamics and strategies.

    Science.gov (United States)

    Wang, Rui; Shen, Yuan; Tino, Peter; Welchman, Andrew E; Kourtzi, Zoe

    2017-10-01

    Human behavior is guided by our expectations about the future. Often, we make predictions by monitoring how event sequences unfold, even though such sequences may appear incomprehensible. Event structures in the natural environment typically vary in complexity, from simple repetition to complex probabilistic combinations. How do we learn these structures? Here we investigate the dynamics of structure learning by tracking human responses to temporal sequences that change in structure unbeknownst to the participants. Participants were asked to predict the upcoming item following a probabilistic sequence of symbols. Using a Markov process, we created a family of sequences, from simple frequency statistics (e.g., some symbols are more probable than others) to context-based statistics (e.g., symbol probability is contingent on preceding symbols). We demonstrate the dynamics with which individuals adapt to changes in the environment's statistics-that is, they extract the behaviorally relevant structures to make predictions about upcoming events. Further, we show that this structure learning relates to individual decision strategy; faster learning of complex structures relates to selection of the most probable outcome in a given context (maximizing) rather than matching of the exact sequence statistics. Our findings provide evidence for alternate routes to learning of behaviorally relevant statistics that facilitate our ability to predict future events in variable environments.

  8. Dynamic Simulation of AN Helium Refrigerator

    Science.gov (United States)

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

    2008-03-01

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

  9. Parallel Multiscale Algorithms for Astrophysical Fluid Dynamics Simulations

    Science.gov (United States)

    Norman, Michael L.

    1997-01-01

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

  10. Dynamic PET image reconstruction integrating temporal regularization associated with respiratory motion correction for applications in oncology

    Science.gov (United States)

    Merlin, Thibaut; Visvikis, Dimitris; Fernandez, Philippe; Lamare, Frédéric

    2018-02-01

    Respiratory motion reduces both the qualitative and quantitative accuracy of PET images in oncology. This impact is more significant for quantitative applications based on kinetic modeling, where dynamic acquisitions are associated with limited statistics due to the necessity of enhanced temporal resolution. The aim of this study is to address these drawbacks, by combining a respiratory motion correction approach with temporal regularization in a unique reconstruction algorithm for dynamic PET imaging. Elastic transformation parameters for the motion correction are estimated from the non-attenuation-corrected PET images. The derived displacement matrices are subsequently used in a list-mode based OSEM reconstruction algorithm integrating a temporal regularization between the 3D dynamic PET frames, based on temporal basis functions. These functions are simultaneously estimated at each iteration, along with their relative coefficients for each image voxel. Quantitative evaluation has been performed using dynamic FDG PET/CT acquisitions of lung cancer patients acquired on a GE DRX system. The performance of the proposed method is compared with that of a standard multi-frame OSEM reconstruction algorithm. The proposed method achieved substantial improvements in terms of noise reduction while accounting for loss of contrast due to respiratory motion. Results on simulated data showed that the proposed 4D algorithms led to bias reduction values up to 40% in both tumor and blood regions for similar standard deviation levels, in comparison with a standard 3D reconstruction. Patlak parameter estimations on reconstructed images with the proposed reconstruction methods resulted in 30% and 40% bias reduction in the tumor and lung region respectively for the Patlak slope, and a 30% bias reduction for the intercept in the tumor region (a similar Patlak intercept was achieved in the lung area). Incorporation of the respiratory motion correction using an elastic model along with a

  11. Computational plasticity algorithm for particle dynamics simulations

    Science.gov (United States)

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

    2018-01-01

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

  12. Lattice dynamics and molecular dynamics simulation of complex materials

    International Nuclear Information System (INIS)

    Chaplot, S.L.

    1997-01-01

    In this article we briefly review the lattice dynamics and molecular dynamics simulation techniques, as used for complex ionic and molecular solids, and demonstrate a number of applications through examples of our work. These computational studies, along with experiments, have provided microscopic insight into the structure and dynamics, phase transitions and thermodynamical properties of a variety of materials including fullerene, high temperature superconducting oxides and geological minerals as a function of pressure and temperature. The computational techniques also allow the study of the structures and dynamics associated with disorder, defects, surfaces, interfaces etc. (author)

  13. Quality of a fished resource: Assessing spatial and temporal dynamics.

    Directory of Open Access Journals (Sweden)

    Sarah J Teck

    Full Text Available Understanding spatio-temporal variability in the demography of harvested species is essential to improve sustainability, especially if there is large geographic variation in demography. Reproductive patterns commonly vary spatially, which is particularly important for management of "roe"-based fisheries, since profits depend on both the number and reproductive condition of individuals. The red sea urchin, Mesocentrotus franciscanus, is harvested in California for its roe (gonad, which is sold to domestic and international sushi markets. The primary driver of price within this multi-million-dollar industry is gonad quality. A relatively simple measure of the fraction of the body mass that is gonad, the gonadosomatic index (GSI, provides important insight into the ecological and environmental factors associated with variability in reproductive quality, and hence value within the industry. We identified the seasonality of the reproductive cycle and determined whether it varied within a heavily fished region. We found that fishermen were predictable both temporally and spatially in collecting urchins according to the reproductive dynamics of urchins. We demonstrated the use of red sea urchin GSI as a simple, quantitative tool to predict quality, effort, landings, price, and value of the fishery. We found that current management is not effectively realizing some objectives for the southern California fishery, since the reproductive cycle does not match the cycle in northern California, where these management guidelines were originally shaped. Although regulations may not be meeting initial management goals, the scheme may in fact provide conservation benefits by curtailing effort during part of the high-quality fishing season right before spawning.

  14. Simulation of quantum dynamics with integrated photonics

    Science.gov (United States)

    Sansoni, Linda; Sciarrino, Fabio; Mataloni, Paolo; Crespi, Andrea; Ramponi, Roberta; Osellame, Roberto

    2012-12-01

    In recent years, quantum walks have been proposed as promising resources for the simulation of physical quantum systems. In fact it is widely adopted to simulate quantum dynamics. Up to now single particle quantum walks have been experimentally demonstrated by different approaches, while only few experiments involving many-particle quantum walks have been realized. Here we simulate the 2-particle dynamics on a discrete time quantum walk, built on an array of integrated waveguide beam splitters. The polarization independence of the quantum walk circuit allowed us to exploit the polarization entanglement to encode the symmetry of the two-photon wavefunction, thus the bunching-antibunching behavior of non interacting bosons and fermions has been simulated. We have also characterized the possible distinguishability and decoherence effects arising in such a structure. This study is necessary in view of the realization of a quantum simulator based on an integrated optical array built on a large number of beam splitters.

  15. Dynamic large eddy simulation: Stability via realizability

    Science.gov (United States)

    Mokhtarpoor, Reza; Heinz, Stefan

    2017-10-01

    The concept of dynamic large eddy simulation (LES) is highly attractive: such methods can dynamically adjust to changing flow conditions, which is known to be highly beneficial. For example, this avoids the use of empirical, case dependent approximations (like damping functions). Ideally, dynamic LES should be local in physical space (without involving artificial clipping parameters), and it should be stable for a wide range of simulation time steps, Reynolds numbers, and numerical schemes. These properties are not trivial, but dynamic LES suffers from such problems over decades. We address these questions by performing dynamic LES of periodic hill flow including separation at a high Reynolds number Re = 37 000. For the case considered, the main result of our studies is that it is possible to design LES that has the desired properties. It requires physical consistency: a PDF-realizable and stress-realizable LES model, which requires the inclusion of the turbulent kinetic energy in the LES calculation. LES models that do not honor such physical consistency can become unstable. We do not find support for the previous assumption that long-term correlations of negative dynamic model parameters are responsible for instability. Instead, we concluded that instability is caused by the stable spatial organization of significant unphysical states, which are represented by wall-type gradient streaks of the standard deviation of the dynamic model parameter. The applicability of our realizability stabilization to other dynamic models (including the dynamic Smagorinsky model) is discussed.

  16. Sensitivity of air pollution simulations with LOTOS-EUROS to the temporal distribution of anthropogenic emissions

    Science.gov (United States)

    Mues, A.; Kuenen, J.; Hendriks, C.; Manders, A.; Segers, A.; Scholz, Y.; Hueglin, C.; Builtjes, P.; Schaap, M.

    2014-01-01

    In this study the sensitivity of the model performance of the chemistry transport model (CTM) LOTOS-EUROS to the description of the temporal variability of emissions was investigated. Currently the temporal release of anthropogenic emissions is described by European average diurnal, weekly and seasonal time profiles per sector. These default time profiles largely neglect the variation of emission strength with activity patterns, region, species, emission process and meteorology. The three sources dealt with in this study are combustion in energy and transformation industries (SNAP1), nonindustrial combustion (SNAP2) and road transport (SNAP7). First of all, the impact of neglecting the temporal emission profiles for these SNAP categories on simulated concentrations was explored. In a second step, we constructed more detailed emission time profiles for the three categories and quantified their impact on the model performance both separately as well as combined. The performance in comparison to observations for Germany was quantified for the pollutants NO2, SO2 and PM10 and compared to a simulation using the default LOTOS-EUROS emission time profiles. The LOTOS-EUROS simulations were performed for the year 2006 with a temporal resolution of 1 h and a horizontal resolution of approximately 25 × 25km2. In general the largest impact on the model performance was found when neglecting the default time profiles for the three categories. The daily average correlation coefficient for instance decreased by 0.04 (NO2), 0.11 (SO2) and 0.01 (PM10) at German urban background stations compared to the default simulation. A systematic increase in the correlation coefficient is found when using the new time profiles. The size of the increase depends on the source category, component and station. Using national profiles for road transport showed important improvements in the explained variability over the weekdays as well as the diurnal cycle for NO2. The largest impact of the SNAP1

  17. Temporal dynamics of ikaite in experimental sea ice

    Science.gov (United States)

    Rysgaard, S.; Wang, F.; Galley, R. J.; Grimm, R.; Notz, D.; Lemes, M.; Geilfus, N.-X.; Chaulk, A.; Hare, A. A.; Crabeck, O.; Else, B. G. T.; Campbell, K.; Sørensen, L. L.; Sievers, J.; Papakyriakou, T.

    2014-08-01

    Ikaite (CaCO3 · 6H2O) is a metastable phase of calcium carbonate that normally forms in a cold environment and/or under high pressure. Recently, ikaite crystals have been found in sea ice, and it has been suggested that their precipitation may play an important role in air-sea CO2 exchange in ice-covered seas. Little is known, however, of the spatial and temporal dynamics of ikaite in sea ice. Here we present evidence for highly dynamic ikaite precipitation and dissolution in sea ice grown at an outdoor pool of the Sea-ice Environmental Research Facility (SERF) in Manitoba, Canada. During the experiment, ikaite precipitated in sea ice when temperatures were below -4 °C, creating three distinct zones of ikaite concentrations: (1) a millimeter-to-centimeter-thin surface layer containing frost flowers and brine skim with bulk ikaite concentrations of >2000 μmol kg-1, (2) an internal layer with ikaite concentrations of 200-400 μmol kg-1, and (3) a bottom layer with ikaite concentrations of ikaite crystals to dissolve. Manual removal of the snow cover allowed the sea ice to cool and brine salinities to increase, resulting in rapid ikaite precipitation. The observed ikaite concentrations were on the same order of magnitude as modeled by FREZCHEM, which further supports the notion that ikaite concentration in sea ice increases with decreasing temperature. Thus, varying snow conditions may play a key role in ikaite precipitation and dissolution in sea ice. This could have a major implication for CO2 exchange with the atmosphere and ocean that has not been accounted for previously.

  18. Dynamics of Laboratory Simulated Microbursts

    Science.gov (United States)

    Alahyari, Abbas Alexander

    1995-01-01

    A downburst (or microburst) is an intense, localized downdraft of cold air which reaches the Earth and spreads radially outward after it impinges on the ground. Downdrafts are typically induced by rapid evaporation of moisture or melting of hail. The divergent outflow created by a microburst produces strong winds in opposite directions. The sudden changes in the speed and direction of both horizontal and vertical winds within a microburst can create hazardous conditions for aircraft within 1000 ft of the ground, particularly during takeoff and landing. The objective of this investigation was to obtain detailed measurements within a laboratory -simulated version of this flow. The flow was modeled experimentally by releasing a small volume of heavier fluid into a less dense ambient surrounding. The heavier fluid impinged on a horizontal plate which represented the ground. Indices of refraction of the light and heavy fluid were matched to yield clear photographic images. Particle image velocimetry (PIV) was used to obtain detailed maps of the instantaneous velocity fields within horizontal and vertical cross sections through the flow. Laser-induced fluorescence (LIF) was used to determine the local concentration of heavy fluid within the downburst flow at different times. PIV measurements showed that the leading edge of the falling fluid rolled up into a vortex ring which then impacted on the ground and expanded radially outward. After touchdown, the largest horizontal velocities occurred beneath the vortex ring but also extended over some distance upstream of the vortex core. PIV results showed small vertical velocity gradients in the region below the core of the vortex ring. The effects of parameters such as initial release height and release volume shape were investigated. Using appropriate length and time scales, the measured velocities were scaled to and compared with previously studied atmospheric microbursts. The experimental data generally agree well with

  19. Forecasting Temporal Dynamics of Cutaneous Leishmaniasis in Northeast Brazil

    Science.gov (United States)

    Lewnard, Joseph A.; Jirmanus, Lara; Júnior, Nivison Nery; Machado, Paulo R.; Glesby, Marshall J.; Ko, Albert I.; Carvalho, Edgar M.; Schriefer, Albert; Weinberger, Daniel M.

    2014-01-01

    Introduction Cutaneous leishmaniasis (CL) is a vector-borne disease of increasing importance in northeastern Brazil. It is known that sandflies, which spread the causative parasites, have weather-dependent population dynamics. Routinely-gathered weather data may be useful for anticipating disease risk and planning interventions. Methodology/Principal Findings We fit time series models using meteorological covariates to predict CL cases in a rural region of Bahía, Brazil from 1994 to 2004. We used the models to forecast CL cases for the period 2005 to 2008. Models accounting for meteorological predictors reduced mean squared error in one, two, and three month-ahead forecasts by up to 16% relative to forecasts from a null model accounting only for temporal autocorrelation. Significance These outcomes suggest CL risk in northeastern Brazil might be partially dependent on weather. Responses to forecasted CL epidemics may include bolstering clinical capacity and disease surveillance in at-risk areas. Ecological mechanisms by which weather influences CL risk merit future research attention as public health intervention targets. PMID:25356734

  20. Temporal dynamics of top predators interactions in the Barents Sea.

    Science.gov (United States)

    Durant, Joël M; Skern-Mauritzen, Mette; Krasnov, Yuri V; Nikolaeva, Natalia G; Lindstrøm, Ulf; Dolgov, Andrey

    2014-01-01

    The Barents Sea system is often depicted as a simple food web in terms of number of dominant feeding links. The most conspicuous feeding link is between the Northeast Arctic cod Gadus morhua, the world's largest cod stock which is presently at a historical high level, and capelin Mallotus villosus. The system also holds diverse seabird and marine mammal communities. Previous diet studies may suggest that these top predators (cod, bird and sea mammals) compete for food particularly with respect to pelagic fish such as capelin and juvenile herring (Clupea harengus), and krill. In this paper we explored the diet of some Barents Sea top predators (cod, Black-legged kittiwake Rissa tridactyla, Common guillemot Uria aalge, and Minke whale Balaenoptera acutorostrata). We developed a GAM modelling approach to analyse the temporal variation diet composition within and between predators, to explore intra- and inter-specific interactions. The GAM models demonstrated that the seabird diet is temperature dependent while the diet of Minke whale and cod is prey dependent; Minke whale and cod diets depend on the abundance of herring and capelin, respectively. There was significant diet overlap between cod and Minke whale, and between kittiwake and guillemot. In general, the diet overlap between predators increased with changes in herring and krill abundances. The diet overlap models developed in this study may help to identify inter-specific interactions and their dynamics that potentially affect the stocks targeted by fisheries.

  1. Temporal dynamics of access to consciousness in the attentional blink.

    Science.gov (United States)

    Kranczioch, Cornelia; Debener, Stefan; Maye, Alexander; Engel, Andreas K

    2007-09-01

    Presentation of two targets in close temporal succession often results in an impairment of conscious perception for the second stimulus. Previous studies have identified several electrophysiological correlates for this so-called 'attentional blink'. Components of the event-related potential (ERP) such as the N2 and the P3, but also oscillatory brain signals have been shown to distinguish between detected and missed stimuli, and thus, conscious perception. Here we investigate oscillatory responses that specifically relate to conscious stimulus processing together with potential ERP predictors. Our results show that successful target detection is associated with enhanced coherence in the low beta frequency range, but a decrease in alpha coherence before and during target presentation. In addition, we find an inverse relation between the P3 amplitudes associated with the first and second target. We conclude that the resources allocated to first and second target processing are directly mirrored by the P3 component and, moreover, that brain states before and during stimulus presentation, as reflected by oscillatory brain activity, strongly determine the access to consciousness. Thus, becoming aware of a stimulus seems to depend on the dynamic interaction between a number of widely distributed neural processes, rather than on the modulation of one single process or component.

  2. A dynamic neural field model of temporal order judgments.

    Science.gov (United States)

    Hecht, Lauren N; Spencer, John P; Vecera, Shaun P

    2015-12-01

    Temporal ordering of events is biased, or influenced, by perceptual organization-figure-ground organization-and by spatial attention. For example, within a region assigned figural status or at an attended location, onset events are processed earlier (Lester, Hecht, & Vecera, 2009; Shore, Spence, & Klein, 2001), and offset events are processed for longer durations (Hecht & Vecera, 2011; Rolke, Ulrich, & Bausenhart, 2006). Here, we present an extension of a dynamic field model of change detection (Johnson, Spencer, Luck, & Schöner, 2009; Johnson, Spencer, & Schöner, 2009) that accounts for both the onset and offset performance for figural and attended regions. The model posits that neural populations processing the figure are more active, resulting in a peak of activation that quickly builds toward a detection threshold when the onset of a target is presented. This same enhanced activation for some neural populations is maintained when a present target is removed, creating delays in the perception of the target's offset. We discuss the broader implications of this model, including insights regarding how neural activation can be generated in response to the disappearance of information. (c) 2015 APA, all rights reserved).

  3. Temporal dynamics of hippocampal neurogenesis in chronic neurodegeneration

    Science.gov (United States)

    Suzzi, Stefano; Vargas-Caballero, Mariana; Fransen, Nina L.; Al-Malki, Hussain; Cebrian-Silla, Arantxa; Garcia-Verdugo, Jose Manuel; Riecken, Kristoffer; Fehse, Boris; Perry, V. Hugh

    2014-01-01

    The study of neurogenesis during chronic neurodegeneration is crucial in order to understand the intrinsic repair mechanisms of the brain, and key to designing therapeutic strategies. In this study, using an experimental model of progressive chronic neurodegeneration, murine prion disease, we define the temporal dynamics of the generation, maturation and integration of new neurons in the hippocampal dentate gyrus, using dual pulse-chase, multicolour γ-retroviral tracing, transmission electron microscopy and patch-clamp. We found increased neurogenesis during the progression of prion disease, which partially counteracts the effects of chronic neurodegeneration, as evidenced by blocking neurogenesis with cytosine arabinoside, and helps to preserve the hippocampal function. Evidence obtained from human post-mortem samples, of both variant Creutzfeldt-Jakob disease and Alzheimer’s disease patients, also suggests increased neurogenic activity. These results open a new avenue into the exploration of the effects and regulation of neurogenesis during chronic neurodegeneration, and offer a new model to reproduce the changes observed in human neurodegenerative diseases. PMID:24941947

  4. Visualizing Energy on Target: Molecular Dynamics Simulations

    Science.gov (United States)

    2017-12-01

    ARL-TR-8234 ● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics Simulations by DeCarlos E...return it to the originator. ARL-TR-8234● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics...REPORT TYPE Technical Report 3. DATES COVERED (From - To) 1 October 2015–30 September 2016 4. TITLE AND SUBTITLE Visualizing Energy on Target

  5. Dynamic Fracture Simulations of Explosively Loaded Cylinders

    Energy Technology Data Exchange (ETDEWEB)

    Arthur, Carly W. [Univ. of California, Davis, CA (United States). Dept. of Civil and Environmental Engineering; Goto, D. M. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2015-11-30

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

  6. Cyclotron beam dynamic simulations in MATLAB

    International Nuclear Information System (INIS)

    Karamysheva, G.A.; Karamyshev, O.V.; Lepkina, O.E.

    2008-01-01

    MATLAB is useful for beam dynamic simulations in cyclotrons. Programming in an easy-to-use environment permits creation of models in a short space of time. Advanced graphical tools of MATLAB give good visualization features to created models. The beam dynamic modeling results with an example of two different cyclotron designs are presented. Programming with MATLAB opens wide possibilities of the development of the complex program, able to perform complete block of calculations for the design of the accelerators

  7. Development of HTGR plant dynamics simulation code

    International Nuclear Information System (INIS)

    Ohashi, Kazutaka; Tazawa, Yujiro; Mitake, Susumu; Suzuki, Katsuo.

    1987-01-01

    Plant dynamics simulation analysis plays an important role in the design work of nuclear power plant especially in the plant safety analysis, control system analysis, and transient condition analysis. The authors have developed the plant dynamics simulation code named VESPER, which is applicable to the design work of High Temperature Engineering Test Reactor, and have been improving the code corresponding to the design changes made in the subsequent design works. This paper describes the outline of VESPER code and shows its sample calculation results selected from the recent design work. (author)

  8. Dynamic Simulations of Advanced Fuel Cycles

    International Nuclear Information System (INIS)

    Piet, Steven J.; Dixon, Brent W.; Jacobson, Jacob J.; Matthern, Gretchen E.; Shropshire, David E.

    2011-01-01

    Years of performing dynamic simulations of advanced nuclear fuel cycle options provide insights into how they could work and how one might transition from the current once-through fuel cycle. This paper summarizes those insights from the context of the 2005 objectives and goals of the U.S. Advanced Fuel Cycle Initiative (AFCI). Our intent is not to compare options, assess options versus those objectives and goals, nor recommend changes to those objectives and goals. Rather, we organize what we have learned from dynamic simulations in the context of the AFCI objectives for waste management, proliferation resistance, uranium utilization, and economics. Thus, we do not merely describe 'lessons learned' from dynamic simulations but attempt to answer the 'so what' question by using this context. The analyses have been performed using the Verifiable Fuel Cycle Simulation of Nuclear Fuel Cycle Dynamics (VISION). We observe that the 2005 objectives and goals do not address many of the inherently dynamic discriminators among advanced fuel cycle options and transitions thereof.

  9. Multi-material 3D Models for Temporal Bone Surgical Simulation.

    Science.gov (United States)

    Rose, Austin S; Kimbell, Julia S; Webster, Caroline E; Harrysson, Ola L A; Formeister, Eric J; Buchman, Craig A

    2015-07-01

    A simulated, multicolor, multi-material temporal bone model can be created using 3-dimensional (3D) printing that will prove both safe and beneficial in training for actual temporal bone surgical cases. As the process of additive manufacturing, or 3D printing, has become more practical and affordable, a number of applications for the technology in the field of Otolaryngology-Head and Neck Surgery have been considered. One area of promise is temporal bone surgical simulation. Three-dimensional representations of human temporal bones were created from temporal bone computed tomography (CT) scans using biomedical image processing software. Multi-material models were then printed and dissected in a temporal bone laboratory by attending and resident otolaryngologists. A 5-point Likert scale was used to grade the models for their anatomical accuracy and suitability as a simulation of cadaveric and operative temporal bone drilling. The models produced for this study demonstrate significant anatomic detail and a likeness to human cadaver specimens for drilling and dissection. Simulated temporal bones created by this process have potential benefit in surgical training, preoperative simulation for challenging otologic cases, and the standardized testing of temporal bone surgical skills. © The Author(s) 2015.

  10. Towards four-flavour dynamical simulations

    Energy Technology Data Exchange (ETDEWEB)

    Herdoiza, Gregorio [DESY, Zeuthen (Germany). John von Neumann-Institut fuer Computing NIC; Univ. Autonoma de Madrid (Spain). Dept. de Fisica Teorica e Inst. de Fiscia Teorica

    2011-03-15

    The inclusion of physical effects from sea quarks has been one of the main advances in lattice QCD simulations over the last few years. We report on recent studies with four flavours of dynamical quarks and address some of the potential issues arising in this new setup. First results for physical observables in the light, strange and charm sectors are presented together with the status of dedicated simulations to perform the non-perturbative renormalisation in mass-independent schemes. (orig.)

  11. Fast Simulation of Dynamic Ultrasound Images Using the GPU.

    Science.gov (United States)

    Storve, Sigurd; Torp, Hans

    2017-10-01

    Simulated ultrasound data is a valuable tool for development and validation of quantitative image analysis methods in echocardiography. Unfortunately, simulation time can become prohibitive for phantoms consisting of a large number of point scatterers. The COLE algorithm by Gao et al. is a fast convolution-based simulator that trades simulation accuracy for improved speed. We present highly efficient parallelized CPU and GPU implementations of the COLE algorithm with an emphasis on dynamic simulations involving moving point scatterers. We argue that it is crucial to minimize the amount of data transfers from the CPU to achieve good performance on the GPU. We achieve this by storing the complete trajectories of the dynamic point scatterers as spline curves in the GPU memory. This leads to good efficiency when simulating sequences consisting of a large number of frames, such as B-mode and tissue Doppler data for a full cardiac cycle. In addition, we propose a phase-based subsample delay technique that efficiently eliminates flickering artifacts seen in B-mode sequences when COLE is used without enough temporal oversampling. To assess the performance, we used a laptop computer and a desktop computer, each equipped with a multicore Intel CPU and an NVIDIA GPU. Running the simulator on a high-end TITAN X GPU, we observed two orders of magnitude speedup compared to the parallel CPU version, three orders of magnitude speedup compared to simulation times reported by Gao et al. in their paper on COLE, and a speedup of 27000 times compared to the multithreaded version of Field II, using numbers reported in a paper by Jensen. We hope that by releasing the simulator as an open-source project we will encourage its use and further development.

  12. Fluid dynamics theory, computation, and numerical simulation

    CERN Document Server

    Pozrikidis, C

    2001-01-01

    Fluid Dynamics Theory, Computation, and Numerical Simulation is the only available book that extends the classical field of fluid dynamics into the realm of scientific computing in a way that is both comprehensive and accessible to the beginner The theory of fluid dynamics, and the implementation of solution procedures into numerical algorithms, are discussed hand-in-hand and with reference to computer programming This book is an accessible introduction to theoretical and computational fluid dynamics (CFD), written from a modern perspective that unifies theory and numerical practice There are several additions and subject expansions in the Second Edition of Fluid Dynamics, including new Matlab and FORTRAN codes Two distinguishing features of the discourse are solution procedures and algorithms are developed immediately after problem formulations are presented, and numerical methods are introduced on a need-to-know basis and in increasing order of difficulty Matlab codes are presented and discussed for a broad...

  13. Fluid Dynamics Theory, Computation, and Numerical Simulation

    CERN Document Server

    Pozrikidis, Constantine

    2009-01-01

    Fluid Dynamics: Theory, Computation, and Numerical Simulation is the only available book that extends the classical field of fluid dynamics into the realm of scientific computing in a way that is both comprehensive and accessible to the beginner. The theory of fluid dynamics, and the implementation of solution procedures into numerical algorithms, are discussed hand-in-hand and with reference to computer programming. This book is an accessible introduction to theoretical and computational fluid dynamics (CFD), written from a modern perspective that unifies theory and numerical practice. There are several additions and subject expansions in the Second Edition of Fluid Dynamics, including new Matlab and FORTRAN codes. Two distinguishing features of the discourse are: solution procedures and algorithms are developed immediately after problem formulations are presented, and numerical methods are introduced on a need-to-know basis and in increasing order of difficulty. Matlab codes are presented and discussed for ...

  14. Discrimination of Dynamic Tactile Contact by Temporally Precise Event Sensing in Spiking Neuromorphic Networks.

    Science.gov (United States)

    Lee, Wang Wei; Kukreja, Sunil L; Thakor, Nitish V

    2017-01-01

    This paper presents a neuromorphic tactile encoding methodology that utilizes a temporally precise event-based representation of sensory signals. We introduce a novel concept where touch signals are characterized as patterns of millisecond precise binary events to denote pressure changes. This approach is amenable to a sparse signal representation and enables the extraction of relevant features from thousands of sensing elements with sub-millisecond temporal precision. We also proposed measures adopted from computational neuroscience to study the information content within the spiking representations of artificial tactile signals. Implemented on a state-of-the-art 4096 element tactile sensor array with 5.2 kHz sampling frequency, we demonstrate the classification of transient impact events while utilizing 20 times less communication bandwidth compared to frame based representations. Spiking sensor responses to a large library of contact conditions were also synthesized using finite element simulations, illustrating an 8-fold improvement in information content and a 4-fold reduction in classification latency when millisecond-precise temporal structures are available. Our research represents a significant advance, demonstrating that a neuromorphic spatiotemporal representation of touch is well suited to rapid identification of critical contact events, making it suitable for dynamic tactile sensing in robotic and prosthetic applications.

  15. Monte carlo simulation for soot dynamics

    KAUST Repository

    Zhou, Kun

    2012-01-01

    A new Monte Carlo method termed Comb-like frame Monte Carlo is developed to simulate the soot dynamics. Detailed stochastic error analysis is provided. Comb-like frame Monte Carlo is coupled with the gas phase solver Chemkin II to simulate soot formation in a 1-D premixed burner stabilized flame. The simulated soot number density, volume fraction, and particle size distribution all agree well with the measurement available in literature. The origin of the bimodal distribution of particle size distribution is revealed with quantitative proof.

  16. Dynamic modeling and simulation of wind turbines

    International Nuclear Information System (INIS)

    Ghafari Seadat, M.H.; Kheradmand Keysami, M.; Lari, H.R.

    2002-01-01

    Using wind energy for generating electricity in wind turbines is a good way for using renewable energies. It can also help to protect the environment. The main objective of this paper is dynamic modeling by energy method and simulation of a wind turbine aided by computer. In this paper, the equations of motion are extracted for simulating the system of wind turbine and then the behavior of the system become obvious by solving the equations. The turbine is considered with three blade rotor in wind direction, induced generator that is connected to the network and constant revolution for simulation of wind turbine. Every part of the wind turbine should be simulated for simulation of wind turbine. The main parts are blades, gearbox, shafts and generator

  17. Object Oriented Modelling and Dynamical Simulation

    DEFF Research Database (Denmark)

    Wagner, Falko Jens; Poulsen, Mikael Zebbelin

    1998-01-01

    This report with appendix describes the work done in master project at DTU.The goal of the project was to develop a concept for simulation of dynamical systems based on object oriented methods.The result was a library of C++-classes, for use when both building componentbased models and when...

  18. Molecular dynamics simulations and quantum chemical calculations ...

    African Journals Online (AJOL)

    Molecular dynamic simulation results indicate that the imidazoline derivative molecules uses the imidazoline ring to effectively adsorb on the surface of iron, with the alkyl hydrophobic tail forming an n shape (canopy like covering) at geometry optimization and at 353 K. The n shape canopy like covering to a large extent may ...

  19. Generator dynamics in aeroelastic analysis and simulations

    Energy Technology Data Exchange (ETDEWEB)

    Larsen, T.J.; Hansen, M.H.; Iov, F.

    2003-05-01

    This report contains a description of a dynamic model for a doubly-fed induction generator implemented in the aeroelastic code HAWC. The model has physical input parameters (resistance, reactance etc.) and input variables (stator and rotor voltage and rotor speed). The model can be used to simulate the generator torque as well as the rotor and stator currents, active and reactive power. A perturbation method has been used to reduce the original generator model equations to a set of equations which can be solved with the same time steps as a typical aeroelastic code. The method is used to separate the fast transients of the model from the slow variations and deduce a reduced order expression for the slow part. Dynamic effects of the first order terms in the model as well as the influence on drive train eigenfrequencies and damping has been investigated. Load response during time simulation of wind turbine response have been compared to simulations with a linear static generator model originally implemented i HAWC. A 2 MW turbine has been modelled in the aeroelastic code HAWC. When using the new dynamic generator model there is an interesting coupling between the generator dynamics and a global turbine vibration mode at 4.5 Hz, which only occurs when a dynamic formulation of the generator equations is applied. This frequency can especially be seen in the electrical power of the generator and the rotational speed of the generator, but also as torque variations in the drive train. (au)

  20. Temporal dynamics in microbial soil communities at anthrax carcass sites.

    Science.gov (United States)

    Valseth, Karoline; Nesbø, Camilla L; Easterday, W Ryan; Turner, Wendy C; Olsen, Jaran S; Stenseth, Nils Chr; Haverkamp, Thomas H A

    2017-09-26

    Anthrax is a globally distributed disease affecting primarily herbivorous mammals. It is caused by the soil-dwelling and spore-forming bacterium Bacillus anthracis. The dormant B. anthracis spores become vegetative after ingestion by grazing mammals. After killing the host, B. anthracis cells return to the soil where they sporulate, completing the lifecycle of the bacterium. Here we present the first study describing temporal microbial soil community changes in Etosha National Park, Namibia, after decomposition of two plains zebra (Equus quagga) anthrax carcasses. To circumvent state-associated-challenges (i.e. vegetative cells/spores) we monitored B. anthracis throughout the period using cultivation, qPCR and shotgun metagenomic sequencing. The combined results suggest that abundance estimation of spore-forming bacteria in their natural habitat by DNA-based approaches alone is insufficient due to poor recovery of DNA from spores. However, our combined approached allowed us to follow B. anthracis population dynamics (vegetative cells and spores) in the soil, along with closely related organisms from the B. cereus group, despite their high sequence similarity. Vegetative B. anthracis abundance peaked early in the time-series and then dropped when cells either sporulated or died. The time-series revealed that after carcass deposition, the typical semi-arid soil community (e.g. Frankiales and Rhizobiales species) becomes temporarily dominated by the orders Bacillales and Pseudomonadales, known to contain plant growth-promoting species. Our work indicates that complementing DNA based approaches with cultivation may give a more complete picture of the ecology of spore forming pathogens. Furthermore, the results suggests that the increased vegetation biomass production found at carcass sites is due to both added nutrients and the proliferation of microbial taxa that can be beneficial for plant growth. Thus, future B. anthracis transmission events at carcass sites may be

  1. Dynamic encoding of speech sequence probability in human temporal cortex.

    Science.gov (United States)

    Leonard, Matthew K; Bouchard, Kristofer E; Tang, Claire; Chang, Edward F

    2015-05-06

    Sensory processing involves identification of stimulus features, but also integration with the surrounding sensory and cognitive context. Previous work in animals and humans has shown fine-scale sensitivity to context in the form of learned knowledge about the statistics of the sensory environment, including relative probabilities of discrete units in a stream of sequential auditory input. These statistics are a defining characteristic of one of the most important sequential signals humans encounter: speech. For speech, extensive exposure to a language tunes listeners to the statistics of sound sequences. To address how speech sequence statistics are neurally encoded, we used high-resolution direct cortical recordings from human lateral superior temporal cortex as subjects listened to words and nonwords with varying transition probabilities between sound segments. In addition to their sensitivity to acoustic features (including contextual features, such as coarticulation), we found that neural responses dynamically encoded the language-level probability of both preceding and upcoming speech sounds. Transition probability first negatively modulated neural responses, followed by positive modulation of neural responses, consistent with coordinated predictive and retrospective recognition processes, respectively. Furthermore, transition probability encoding was different for real English words compared with nonwords, providing evidence for online interactions with high-order linguistic knowledge. These results demonstrate that sensory processing of deeply learned stimuli involves integrating physical stimulus features with their contextual sequential structure. Despite not being consciously aware of phoneme sequence statistics, listeners use this information to process spoken input and to link low-level acoustic representations with linguistic information about word identity and meaning. Copyright © 2015 the authors 0270-6474/15/357203-12$15.00/0.

  2. Temporal dynamics of blue and green virtual water trade networks

    Science.gov (United States)

    Konar, M.; Dalin, C.; Hanasaki, N.; Rinaldo, A.; Rodriguez-Iturbe, I.

    2012-12-01

    Global food security increasingly relies on the trade of food commodities. Freshwater resources are essential to agricultural production and are thus embodied in the trade of food commodities, referred to as "virtual water trade." Agricultural production predominantly relies on rainwater (i.e., "green water"), though irrigation (i.e., "blue water") does play an important role. These different sources of water have distinctly different opportunity costs, which may be reflected in the way these resources are traded. Thus, the temporal dynamics of the virtual water trade networks from these distinct water sources require characterization. We find that 42 × 109 m3 blue and 310 × 109 m3 green water was traded in 1986, growing to 78 × 109 m3 blue and 594 × 109 m3 green water traded in 2008. Three nations dominate the export of green water resources: the USA, Argentina, and Brazil. As a country increases its export trade partners it tends to export relatively more blue water. However, as a country increases its import trade partners it does not preferentially import water from a specific source. The amount of virtual water that a country imports by increasing its import trade partners has been decreasing over time, with the exception of the soy trade. Both blue and green virtual water networks are efficient: 119 × 109 m3 blue and 105 × 109 m3 green water were saved in 2008. Importantly, trade has been increasingly saving water over time, due to the intensification of crop trade on more water-efficient links.

  3. Dynamic aspects of dislocation motion: atomistic simulations

    International Nuclear Information System (INIS)

    Bitzek, Erik; Gumbsch, Peter

    2005-01-01

    Atomistic simulations of accelerating edge and screw dislocations were carried out to study the dynamics of dislocations in a face centered cubic metal. Using two different embedded atom potentials for nickel and a simple slab geometry, the Peierls stress, the effective mass, the line tension and the drag coefficient were determined. A dislocation intersecting an array of voids is used to study dynamic effects in dislocation-obstacle interactions. A pronounced effect caused by inertial overshooting is found. A dynamic line tension model is developed which reproduces the simulation results. The model can be used to easily estimate the magnitude of inertial effects in the interaction of dislocations with localized obstacles for different obstacle strengths, -spacings and temperatures

  4. Kinetics from Replica Exchange Molecular Dynamics Simulations.

    Science.gov (United States)

    Stelzl, Lukas S; Hummer, Gerhard

    2017-08-08

    Transitions between metastable states govern many fundamental processes in physics, chemistry and biology, from nucleation events in phase transitions to the folding of proteins. The free energy surfaces underlying these processes can be obtained from simulations using enhanced sampling methods. However, their altered dynamics makes kinetic and mechanistic information difficult or impossible to extract. Here, we show that, with replica exchange molecular dynamics (REMD), one can not only sample equilibrium properties but also extract kinetic information. For systems that strictly obey first-order kinetics, the procedure to extract rates is rigorous. For actual molecular systems whose long-time dynamics are captured by kinetic rate models, accurate rate coefficients can be determined from the statistics of the transitions between the metastable states at each replica temperature. We demonstrate the practical applicability of the procedure by constructing master equation (Markov state) models of peptide and RNA folding from REMD simulations.

  5. A review of simulation platforms in surgery of the temporal bone.

    Science.gov (United States)

    Bhutta, M F

    2016-10-01

    Surgery of the temporal bone is a high-risk activity in an anatomically complex area. Simulation enables rehearsal of such surgery. The traditional simulation platform is the cadaveric temporal bone, but in recent years other simulation platforms have been created, including plastic and virtual reality platforms. To undertake a review of simulation platforms for temporal bone surgery, specifically assessing their educational value in terms of validity and in enabling transition to surgery. Systematic qualitative review. Search of the Pubmed, CINAHL, BEI and ERIC databases. Assessment of reported outcomes in terms of educational value. A total of 49 articles were included, covering cadaveric, animal, plastic and virtual simulation platforms. Cadaveric simulation is highly rated as an educational tool, but there may be a ceiling effect on educational outcomes after drilling 8-10 temporal bones. Animal models show significant anatomical variation from man. Plastic temporal bone models offer much potential, but at present lack sufficient anatomical or haptic validity. Similarly, virtual reality platforms lack sufficient anatomical or haptic validity, but with technological improvements they are advancing rapidly. At present, cadaveric simulation remains the best platform for training in temporal bone surgery. Technological advances enabling improved materials or modelling mean that in the future plastic or virtual platforms may become comparable to cadaveric platforms, and also offer additional functionality including patient-specific simulation from CT data. © 2015 John Wiley & Sons Ltd.

  6. Probing Cellular Dynamics with Mesoscopic Simulations

    DEFF Research Database (Denmark)

    Shillcock, Julian C.

    2010-01-01

    Cellular processes span a huge range of length and time scales from the molecular to the near-macroscopic. Understanding how effects on one scale influence, and are themselves influenced by, those on lower and higher scales is a critical issue for the construction of models in Systems Biology....... Advances in computing hardware and software now allow explicit simulation of some aspects of cellular dynamics close to the molecular scale. Vesicle fusion is one example of such a process. Experiments, however, typically probe cellular behavior from the molecular scale up to microns. Standard particle...... soon be coupled to Mass Action models allowing the parameters in such models to be continuously tuned according to the finer resolution simulation. This will help realize the goal of a computational cellular simulation that is able to capture the dynamics of membrane-associated processes...

  7. Computer simulation of population dynamics inside the urban environment

    Science.gov (United States)

    Andreev, A. S.; Inovenkov, I. N.; Echkina, E. Yu.; Nefedov, V. V.; Ponomarenko, L. S.; Tikhomirov, V. V.

    2017-12-01

    In this paper using a mathematical model of the so-called “space-dynamic” approach we investigate the problem of development and temporal dynamics of different urban population groups. For simplicity we consider an interaction of only two population groups inside a single urban area with axial symmetry. This problem can be described qualitatively by a system of two non-stationary nonlinear differential equations of the diffusion type with boundary conditions of the third type. The results of numerical simulations show that with a suitable choice of the diffusion coefficients and interaction functions between different population groups we can receive different scenarios of population dynamics: from complete displacement of one population group by another (originally more “aggressive”) to the “peaceful” situation of co-existence of them together.

  8. GROSS- GAMMA RAY OBSERVATORY ATTITUDE DYNAMICS SIMULATOR

    Science.gov (United States)

    Garrick, J.

    1994-01-01

    The Gamma Ray Observatory (GRO) spacecraft will constitute a major advance in gamma ray astronomy by offering the first opportunity for comprehensive observations in the range of 0.1 to 30,000 megaelectronvolts (MeV). The Gamma Ray Observatory Attitude Dynamics Simulator, GROSS, is designed to simulate this mission. The GRO Dynamics Simulator consists of three separate programs: the Standalone Profile Program; the Simulator Program, which contains the Simulation Control Input/Output (SCIO) Subsystem, the Truth Model (TM) Subsystem, and the Onboard Computer (OBC) Subsystem; and the Postprocessor Program. The Standalone Profile Program models the environment of the spacecraft and generates a profile data set for use by the simulator. This data set contains items such as individual external torques; GRO spacecraft, Tracking and Data Relay Satellite (TDRS), and solar and lunar ephemerides; and star data. The Standalone Profile Program is run before a simulation. The SCIO subsystem is the executive driver for the simulator. It accepts user input, initializes parameters, controls simulation, and generates output data files and simulation status display. The TM subsystem models the spacecraft dynamics, sensors, and actuators. It accepts ephemerides, star data, and environmental torques from the Standalone Profile Program. With these and actuator commands from the OBC subsystem, the TM subsystem propagates the current state of the spacecraft and generates sensor data for use by the OBC and SCIO subsystems. The OBC subsystem uses sensor data from the TM subsystem, a Kalman filter (for attitude determination), and control laws to compute actuator commands to the TM subsystem. The OBC subsystem also provides output data to the SCIO subsystem for output to the analysts. The Postprocessor Program is run after simulation is completed. It generates printer and CRT plots and tabular reports of the simulated data at the direction of the user. GROSS is written in FORTRAN 77 and

  9. Engineering dynamics from the Lagrangian to simulation

    CERN Document Server

    Gans, Roger F

    2013-01-01

    This engineering dynamics textbook is aimed at beginning graduate students in mechanical engineering and other related engineering disciplines who need training in dynamics as applied to engineering mechanisms. It introduces the formal mathematical development of Lagrangian mechanics (and its corollaries), while solving numerous engineering applications. The author’s goal is to instill an understanding of the basic physics required for engineering dynamics, while providing a recipe (algorithm) for the simulation of engineering mechanisms such as robots. The book is reasonably self-contained so that the practicing engineer interested in this area can also make use of it. This book is made accessible to the widest possible audience by numerous, solved examples and diagrams that apply the principles to real engineering applications. • Provides an applied textbook for intermediate/advanced engineering dynamics courses; • Discusses Lagrangian mechanics in the context of numerous engineering applications...

  10. Dynamics and Thermodynamics of Transthyretin Association from Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Cedrix J. Dongmo Foumthuim

    2018-01-01

    Full Text Available Molecular dynamics simulations are used in this work to probe the structural stability and the dynamics of engineered mutants of transthyretin (TTR, i.e., the double mutant F87M/L110M (MT-TTR and the triple mutant F87M/L110M/S117E (3M-TTR, in relation to wild-type. Free energy analysis from end-point simulations and statistical effective energy functions are used to analyze trajectories, revealing that mutations do not have major impact on protein structure but rather on protein association, shifting the equilibria towards dissociated species. The result is confirmed by the analysis of 3M-TTR which shows dissociation within the first 10 ns of the simulation, indicating that contacts are lost at the dimer-dimer interface, whereas dimers (formed by monomers which pair to form two extended β-sheets appear fairly stable. Overall the simulations provide a detailed view of the dynamics and thermodynamics of wild-type and mutant transthyretins and a rationale of the observed effects.

  11. Sensitivity of air pollution simulations with LOTOS-EUROS to temporal distribution of anthropogenic emissions

    Science.gov (United States)

    Mues, A.; Kuenen, J.; Hendriks, C.; Manders, A.; Segers, A.; Scholz, Y.; Hueglin, C.; Builtjes, P.; Schaap, M.

    2013-07-01

    In this study the sensitivity of the model performance of the chemistry transport model (CTM) LOTOS-EUROS to the description of the temporal variability of emissions was investigated. Currently the temporal release of anthropogenic emissions is described by European average diurnal, weekly and seasonal time profiles per sector. These default time profiles largely neglect the variation of emission strength with activity patterns, region, species, emission process and meteorology. The three sources dealt with in this study are combustion in energy and transformation industries (SNAP1), non-industrial combustion (SNAP2) and road transport (SNAP7). First the impact of neglecting the temporal emission profiles for these SNAP categories on simulated concentrations was explored. In a~second step, we constructed more detailed emission time profiles for the three categories and quantified their impact on the model performance separately as well as combined. The performance in comparison to observations for Germany was quantified for the pollutants NO2, SO2 and PM10 and compared to a simulation using the default LOTOS-EUROS emission time profiles. In general the largest impact on the model performance was found when neglecting the default time profiles for the three categories. The daily average correlation coefficient for instance decreased by 0.04 (NO2), 0.11 (SO2) and 0.01 (PM10) at German urban background stations compared to the default simulation. A systematic increase of the correlation coefficient is found when using the new time profiles. The size of the increase depends on the source category, the component and station. Using national profiles for road transport showed important improvements of the explained variability over the weekdays as well as the diurnal cycle for NO2. The largest impact of the SNAP1 and 2 profiles were found for SO2. When using all new time profiles simultaneously in one simulation the daily average correlation coefficient increased by 0

  12. How Well Do Students in Secondary School Understand Temporal Development of Dynamical Systems?

    Science.gov (United States)

    Forjan, Matej; Grubelnik, Vladimir

    2015-01-01

    Despite difficulties understanding the dynamics of complex systems only simple dynamical systems without feedback connections have been taught in secondary school physics. Consequently, students do not have opportunities to develop intuition of temporal development of systems, whose dynamics are conditioned by the influence of feedback processes.…

  13. Dynamic Simulator for Nuclear Power Plants (DSNP)

    International Nuclear Information System (INIS)

    Saphier, D.

    1976-01-01

    A new simulation language DSNP (Dynamic Simulator for Nuclear Power Plants) is being developed. It is a simple block oriented simulation language with an extensive library of component and auxiliary modules. Each module is a self-contained unit of a part of a physical component to be found in nuclear power plants. Each module will be available in four levels of sophistication, the fourth being a user supplied model. A module can be included in the simulation by a single statement. The precompiler translates DSNP statements into FORTRAN statements, takes care of the module parameters and the intermodular communication blocks, prepares proper data files and I/0 statements and searches the various libraries for the appropriate component modules. The documentation is computerized and all the necessary information for a particular module can be retrieved by a special document generator. The DSNP will be a flexible tool which will allow dynamic simulations to be performed on a large variety of nuclear power plants or specific components of these plants

  14. Dynamic bounds coupled with Monte Carlo simulations

    Energy Technology Data Exchange (ETDEWEB)

    Rajabalinejad, M., E-mail: M.Rajabalinejad@tudelft.n [Faculty of Civil Engineering, Delft University of Technology, Delft (Netherlands); Meester, L.E. [Delft Institute of Applied Mathematics, Delft University of Technology, Delft (Netherlands); Gelder, P.H.A.J.M. van; Vrijling, J.K. [Faculty of Civil Engineering, Delft University of Technology, Delft (Netherlands)

    2011-02-15

    For the reliability analysis of engineering structures a variety of methods is known, of which Monte Carlo (MC) simulation is widely considered to be among the most robust and most generally applicable. To reduce simulation cost of the MC method, variance reduction methods are applied. This paper describes a method to reduce the simulation cost even further, while retaining the accuracy of Monte Carlo, by taking into account widely present monotonicity. For models exhibiting monotonic (decreasing or increasing) behavior, dynamic bounds (DB) are defined, which in a coupled Monte Carlo simulation are updated dynamically, resulting in a failure probability estimate, as well as a strict (non-probabilistic) upper and lower bounds. Accurate results are obtained at a much lower cost than an equivalent ordinary Monte Carlo simulation. In a two-dimensional and a four-dimensional numerical example, the cost reduction factors are 130 and 9, respectively, where the relative error is smaller than 5%. At higher accuracy levels, this factor increases, though this effect is expected to be smaller with increasing dimension. To show the application of DB method to real world problems, it is applied to a complex finite element model of a flood wall in New Orleans.

  15. Temporally Dynamic, Spatially Static, Cobble Bedforms In Reversing Subtidal Currents

    Science.gov (United States)

    Abdulkade, Akirat; Carling, Paul; Zong, Quanli; Leyland, Julian; Thompson, Charlie

    2016-04-01

    Cobble bedforms, transverse to the reversing tidal currents, are exposed at extreme low-water Spring tides on an inter-tidal bedrock shelf in the macro-tidal Severn Estuary, UK. Near-bed flow velocities during Spring tides can exceed 1.5m/s, with water depths varying from zero to in excess of 10m. During neap tides the bedforms are not exposed, and sediment is expected to be of limited mobility. When exposed, the bedform geometry tends to be asymmetric; orientated down estuary with the ebb current. During Spring tides, vigorous bedload transport of gravel (including large cobbles) occurs during both flood and ebb over the crests and yet, despite this temporal dynamism, the bedforms remain spatially static over long time periods or show weak down-estuary migration. Stasis implies that the tidal bedload transport vectors are essentially in balance. Near-bed shear stress and bed roughness values vary systematically with the Spring-tide current speeds and the predicted grain-size of the bed load using the Shields criterion is in accord with observed coarser grain-sizes in transport. These hydrodynamic data, delimited by estimates of the threshold of motion, and integrated over either flood or ebb tides are being used to explain the apparent stability of the bedforms. The bulk hydraulic data are supplemented by particle tracer studies and laser-scanning of bed configurations between tides. The high-energy environment results in two forms of armouring. Pronounced steep imbrication of platy-cobbles visible on the exposed up-estuary side of dunes is probably disrupted during flood tides leading to rapid reworking of the toe deposits facing up-estuary. In contrast, some crest and leeside locations have been stable for prolonged periods such that closely-fitted fabrics result; these portions of the bedforms are static and effectively are 'armour-plated'. Ebb-tide deposits of finer, ephemeral sandy-units occur on the down estuary side of the bedforms. Sandy-units (although

  16. Parallelization of quantum molecular dynamics simulation code

    International Nuclear Information System (INIS)

    Kato, Kaori; Kunugi, Tomoaki; Shibahara, Masahiko; Kotake, Susumu

    1998-02-01

    A quantum molecular dynamics simulation code has been developed for the analysis of the thermalization of photon energies in the molecule or materials in Kansai Research Establishment. The simulation code is parallelized for both Scalar massively parallel computer (Intel Paragon XP/S75) and Vector parallel computer (Fujitsu VPP300/12). Scalable speed-up has been obtained with a distribution to processor units by division of particle group in both parallel computers. As a result of distribution to processor units not only by particle group but also by the particles calculation that is constructed with fine calculations, highly parallelization performance is achieved in Intel Paragon XP/S75. (author)

  17. Lipid Configurations from Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Pezeshkian, Weria; Khandelia, Himanshu; Marsh, Derek

    2018-01-01

    of dihedral angles in palmitoyl-oleoyl phosphatidylcholine from molecular dynamics simulations of hydrated fluid bilayer membranes. We compare results from the widely used lipid force field of Berger et al. with those from the most recent C36 release of the CHARMM force field for lipids. Only the CHARMM force......The extent to which current force fields faithfully reproduce conformational properties of lipids in bilayer membranes, and whether these reflect the structural principles established for phospholipids in bilayer crystals, are central to biomembrane simulations. We determine the distribution...

  18. Description of the grout system dynamic simulation

    International Nuclear Information System (INIS)

    Zimmerman, B.D.

    1993-07-01

    The grout system dynamic computer simulation was created to allow investigation of the ability of the grouting system to meet established milestones, for various assumed system configurations and parameters. The simulation simulates the movement of tank waste through the system versus time, from initial storage tanks, through feed tanks and the grout plant, then finally to a grout vault. The simulation properly accounts for the following (1) time required to perform various actions or processes, (2) delays involved in gaining regulatory approval, (3) random system component failures, (4) limitations on equipment capacities, (5) available parallel components, and (6) different possible strategies for vault filling. The user is allowed to set a variety of system parameters for each simulation run. Currently, the output of a run primarily consists of a plot of projected grouting campaigns completed versus time, for comparison with milestones. Other outputs involving any model component can also be quickly created or deleted as desired. In particular, sensitivity runs where the effect of varying a model parameter (flow rates, delay times, number of feed tanks available, etc.) on the ability of the system to meet milestones can be made easily. The grout system simulation was implemented using the ITHINK* simulation language for Macintosh** computers

  19. Modelling temporal and spatial dynamics of benthic fauna in North-West-European shelf seas

    Science.gov (United States)

    Lessin, Gennadi; Bruggeman, Jorn; Artioli, Yuri; Butenschön, Momme; Blackford, Jerry

    2017-04-01

    Benthic zones of shallow shelf seas receive high amounts of organic material. Physical processes such as resuspension, as well as complex transformations mediated by diverse faunal and microbial communities, define fate of this material, which can be returned to the water column, reworked within sediments or ultimately buried. In recent years, numerical models of various complexity and serving different goals have been developed and applied in order to better understand and predict dynamics of benthic processes. ERSEM includes explicit parameterisations of several groups of benthic biota, which makes it particularly applicable for studies of benthic biodiversity, biological interactions within sediments and benthic-pelagic coupling. To assess model skill in reproducing temporal (inter-annual and seasonal) dynamics of major benthic macrofaunal groups, 1D model simulation results were compared with data from the Western Channel Observatory (WCO) benthic survey. The benthic model was forced with organic matter deposition rates inferred from observed phytoplankton abundance and model parameters were subsequently recalibrated. Based on model results and WCO data comparison, deposit-feeders exert clear seasonal variability, while for suspension-feeders inter-annual variability is more pronounced. Spatial distribution of benthic fauna was investigated using results of a full-scale NEMO-ERSEM hindcast simulation of the North-West European Shelf Seas area, covering the period of 1981-2014. Results suggest close relationship between spatial distribution of biomass of benthic faunal functional groups in relation to bathymetry, hydrodynamic conditions and organic matter supply. Our work highlights that it is feasible to construct, implement and validate models that explicitly include functional groups of benthic macrofauna. Moreover, the modelling approach delivers detailed information on benthic biogeochemistry and food-web at spatial and temporal scales that are unavailable

  20. Hydration dynamics in water clusters via quantum molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Turi, László, E-mail: turi@chem.elte.hu [Department of Physical Chemistry, Eötvös Loránd University, Budapest 112, P. O. Box 32, H-1518 (Hungary)

    2014-05-28

    We have investigated the hydration dynamics in size selected water clusters with n = 66, 104, 200, 500, and 1000 water molecules using molecular dynamics simulations. To study the most fundamental aspects of relaxation phenomena in clusters, we choose one of the simplest, still realistic, quantum mechanically treated test solute, an excess electron. The project focuses on the time evolution of the clusters following two processes, electron attachment to neutral equilibrated water clusters and electron detachment from an equilibrated water cluster anion. The relaxation dynamics is significantly different in the two processes, most notably restoring the equilibrium final state is less effective after electron attachment. Nevertheless, in both scenarios only minor cluster size dependence is observed. Significantly different relaxation patterns characterize electron detachment for interior and surface state clusters, interior state clusters relaxing significantly faster. This observation may indicate a potential way to distinguish surface state and interior state water cluster anion isomers experimentally. A comparison of equilibrium and non-equilibrium trajectories suggests that linear response theory breaks down for electron attachment at 200 K, but the results converge to reasonable agreement at higher temperatures. Relaxation following electron detachment clearly belongs to the linear regime. Cluster relaxation was also investigated using two different computational models, one preferring cavity type interior states for the excess electron in bulk water, while the other simulating non-cavity structure. While the cavity model predicts appearance of several different hydrated electron isomers in agreement with experiment, the non-cavity model locates only cluster anions with interior excess electron distribution. The present simulations show that surface isomers computed with the cavity predicting potential show similar dynamical behavior to the interior clusters of

  1. A dynamic texture based approach to recognition of facial actions and their temporal models

    NARCIS (Netherlands)

    Koelstra, Sander; Pantic, Maja; Patras, Ioannis (Yannis)

    2010-01-01

    In this work, we propose a dynamic texture-based approach to the recognition of facial Action Units (AUs, atomic facial gestures) and their temporal models (i.e., sequences of temporal segments: neutral, onset, apex, and offset) in near-frontal-view face videos. Two approaches to modeling the

  2. Dislocation dynamics simulations in a cylinder

    International Nuclear Information System (INIS)

    Weinberger, Christopher R; Aubry, Sylvie; Cai, Wei; Lee, Seok-Woo

    2009-01-01

    In this work we describe how to perform dislocation dynamics simulations in a cylindrical geometry. An algorithm for computing the image stress is given in detail including methods for handling the singularity. Additional remesh rules address the problems of the cylindrical geometry and the required self consistency with mobility laws. Numerical studies benchmark the accuracy of the algorithms and the importance of handling the singularity correctly.

  3. Temporal and spatial dynamics of mineral levels of forage, soil and ...

    African Journals Online (AJOL)

    Temporal and spatial dynamics of mineral levels of forage, soil and cattle blood ... In the plain lands, local variations occurred for soil phosphorus and magnesium. ... Rangeland improvement and supplementation strategies are suggested to ...

  4. A Language and Environment for Analysis of Dynamics by SimulaTiOn

    NARCIS (Netherlands)

    Bosse, T.; Jonker, C.M.; van der Meij, L.; Treur, J.

    2007-01-01

    This article presents the language and software environment LEADSTO that has been developed to model and simulate dynamic processes in terms of both qualitative and quantitative concepts. The LEADSTO language is a declarative order-sorted temporal language, extended with quantitative notions like

  5. LEADSTO: a Language and Environment for Analysis of Dynamics by SimulaTiOn

    NARCIS (Netherlands)

    Bosse, T.; Jonker, C.M.; van der Meij, L.; Treur, J.

    2005-01-01

    This paper presents the language and software environment LEADSTO that has been developed to model and simulate the dynamics of Multi-Agent Systems (MAS) in terms of both qualitative and quantitative concepts. The LEADSTO language is a declarative order-sorted temporal language, extended with

  6. Assessment of skills using a virtual reality temporal bone surgery simulator.

    Science.gov (United States)

    Linke, R; Leichtle, A; Sheikh, F; Schmidt, C; Frenzel, H; Graefe, H; Wollenberg, B; Meyer, J E

    2013-08-01

    Surgery on the temporal bone is technically challenging due to its complex anatomy. Precise anatomical dissection of the human temporal bone is essential and is fundamental for middle ear surgery. We assessed the possible application of a virtual reality temporal bone surgery simulator to the education of ear surgeons. Seventeen ENT physicians with different levels of surgical training and 20 medical students performed an antrotomy with a computer-based virtual temporal bone surgery simulator. The ease, accuracy and timing of the simulated temporal bone surgery were assessed using the automatic assessment software provided by the simulator device and additionally with a modified Final Product Analysis Scale. Trained ENT surgeons, physicians without temporal bone surgical training and medical students were all able to perform the antrotomy. However, the highly trained ENT surgeons were able to complete the surgery in approximately half the time, with better handling and accuracy as assessed by the significant reduction in injury to important middle ear structures. Trained ENT surgeons achieved significantly higher scores using both dissection analysis methods. Surprisingly, there were no significant differences in the results between medical students and physicians without experience in ear surgery. The virtual temporal bone training system can stratify users of known levels of experience. This system can be used not only to improve the surgical skills of trained ENT surgeons for more successful and injury-free surgeries, but also to train inexperienced physicians/medical students in developing their surgical skills for the ear.

  7. A molecular dynamics simulation code ISIS

    International Nuclear Information System (INIS)

    Kambayashi, Shaw

    1992-06-01

    Computer simulation based on the molecular dynamics (MD) method has become an important tool complementary to experiments and theoretical calculations in a wide range of scientific fields such as physics, chemistry, biology, and so on. In the MD method, the Newtonian equations-of-motion of classical particles are integrated numerically to reproduce a phase-space trajectory of the system. In the 1980's, several new techniques have been developed for simulation at constant-temperature and/or constant-pressure in convenient to compare result of computer simulation with experimental results. We first summarize the MD method for both microcanonical and canonical simulations. Then, we present and overview of a newly developed ISIS (Isokinetic Simulation of Soft-spheres) code and its performance on various computers including vector processors. The ISIS code has a capability to make a MD simulation under constant-temperature condition by using the isokinetic constraint method. The equations-of-motion is integrated by a very accurate fifth-order finite differential algorithm. The bookkeeping method is also utilized to reduce the computational time. Furthermore, the ISIS code is well adopted for vector processing: Speedup ratio ranged from 16 to 24 times is obtained on a VP2600/10 vector processor. (author)

  8. A molecular dynamics simulation study of chloroform

    Science.gov (United States)

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

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

  9. Simulating coronal condensation dynamics in 3D

    Science.gov (United States)

    Moschou, S. P.; Keppens, R.; Xia, C.; Fang, X.

    2015-12-01

    We present numerical simulations in 3D settings where coronal rain phenomena take place in a magnetic configuration of a quadrupolar arcade system. Our simulation is a magnetohydrodynamic simulation including anisotropic thermal conduction, optically thin radiative losses, and parametrised heating as main thermodynamical features to construct a realistic arcade configuration from chromospheric to coronal heights. The plasma evaporation from chromospheric and transition region heights eventually causes localised runaway condensation events and we witness the formation of plasma blobs due to thermal instability, that evolve dynamically in the heated arcade part and move gradually downwards due to interchange type dynamics. Unlike earlier 2.5D simulations, in this case there is no large scale prominence formation observed, but a continuous coronal rain develops which shows clear indications of Rayleigh-Taylor or interchange instability, that causes the denser plasma located above the transition region to fall down, as the system moves towards a more stable state. Linear stability analysis is used in the non-linear regime for gaining insight and giving a prediction of the system's evolution. After the plasma blobs descend through interchange, they follow the magnetic field topology more closely in the lower coronal regions, where they are guided by the magnetic dips.

  10. Dynamic simulator for PEFC propulsion plant

    Energy Technology Data Exchange (ETDEWEB)

    Hiraide, Masataka; Kaneda, Eiichi; Sato, Takao [Mitsui Engineering & Shipbuilding Co., Ltd., Tokyo (Japan)] [and others

    1996-12-31

    This report covers part of a joint study on a PEFC propulsion system for surface ships, summarized in a presentation to this Seminar, entitled {open_quote}Study on a Polymer Electrolyte Fuel Cell (PEFC) Propulsion System for Surface Ships{close_quotes}, and which envisages application to a 1,500 DWT cargo vessel. The work presented here focuses on a simulation study on PEFC propulsion plant performance, and particularly on the system response to changes in load. Using a dynamic simulator composed of system components including fuel cell, various simulations were executed, to examine the performance of the system as a whole and of the individual system components under quick and large load changes such as occasioned by maneuvering operations and by racing when the propeller emerges above water in heavy sea.

  11. Fish and phytoplankton exhibit contrasting temporal species abundance patterns in a dynamic north temperate lake.

    Directory of Open Access Journals (Sweden)

    Gretchen J A Hansen

    Full Text Available Temporal patterns of species abundance, although less well-studied than spatial patterns, provide valuable insight to the processes governing community assembly. We compared temporal abundance distributions of two communities, phytoplankton and fish, in a north temperate lake. We used both 17 years of observed relative abundance data as well as resampled data from Monte Carlo simulations to account for the possible effects of non-detection of rare species. Similar to what has been found in other communities, phytoplankton and fish species that appeared more frequently were generally more abundant than rare species. However, neither community exhibited two distinct groups of "core" (common occurrence and high abundance and "occasional" (rare occurrence and low abundance species. Both observed and resampled data show that the phytoplankton community was dominated by occasional species appearing in only one year that exhibited large variation in their abundances, while the fish community was dominated by core species occurring in all 17 years at high abundances. We hypothesize that the life-history traits that enable phytoplankton to persist in highly dynamic environments may result in communities dominated by occasional species capable of reaching high abundances when conditions allow. Conversely, longer turnover times and broad environmental tolerances of fish may result in communities dominated by core species structured primarily by competitive interactions.

  12. Fish and Phytoplankton Exhibit Contrasting Temporal Species Abundance Patterns in a Dynamic North Temperate Lake

    Science.gov (United States)

    Hansen, Gretchen J. A.; Carey, Cayelan C.

    2015-01-01

    Temporal patterns of species abundance, although less well-studied than spatial patterns, provide valuable insight to the processes governing community assembly. We compared temporal abundance distributions of two communities, phytoplankton and fish, in a north temperate lake. We used both 17 years of observed relative abundance data as well as resampled data from Monte Carlo simulations to account for the possible effects of non-detection of rare species. Similar to what has been found in other communities, phytoplankton and fish species that appeared more frequently were generally more abundant than rare species. However, neither community exhibited two distinct groups of “core” (common occurrence and high abundance) and “occasional” (rare occurrence and low abundance) species. Both observed and resampled data show that the phytoplankton community was dominated by occasional species appearing in only one year that exhibited large variation in their abundances, while the fish community was dominated by core species occurring in all 17 years at high abundances. We hypothesize that the life-history traits that enable phytoplankton to persist in highly dynamic environments may result in communities dominated by occasional species capable of reaching high abundances when conditions allow. Conversely, longer turnover times and broad environmental tolerances of fish may result in communities dominated by core species structured primarily by competitive interactions. PMID:25651399

  13. Pre-operative simulation of pediatric mastoid surgery with 3D-printed temporal bone models.

    Science.gov (United States)

    Rose, Austin S; Webster, Caroline E; Harrysson, Ola L A; Formeister, Eric J; Rawal, Rounak B; Iseli, Claire E

    2015-05-01

    As the process of additive manufacturing, or three-dimensional (3D) printing, has become more practical and affordable, a number of applications for the technology in the field of pediatric otolaryngology have been considered. One area of promise is temporal bone surgical simulation. Having previously developed a model for temporal bone surgical training using 3D printing, we sought to produce a patient-specific model for pre-operative simulation in pediatric otologic surgery. Our hypothesis was that the creation and pre-operative dissection of such a model was possible, and would demonstrate potential benefits in cases of abnormal temporal bone anatomy. In the case presented, an 11-year-old boy underwent a planned canal-wall-down (CWD) tympano-mastoidectomy for recurrent cholesteatoma preceded by a pre-operative surgical simulation using 3D-printed models of the temporal bone. The models were based on the child's pre-operative clinical CT scan and printed using multiple materials to simulate both bone and soft tissue structures. To help confirm the models as accurate representations of the child's anatomy, distances between various anatomic landmarks were measured and compared to the temporal bone CT scan and the 3D model. The simulation allowed the surgical team to appreciate the child's unusual temporal bone anatomy as well as any challenges that might arise in the safety of the temporal bone laboratory, prior to actual surgery in the operating room (OR). There was minimal variability, in terms of absolute distance (mm) and relative distance (%), in measurements between anatomic landmarks obtained from the patient intra-operatively, the pre-operative CT scan and the 3D-printed models. Accurate 3D temporal bone models can be rapidly produced based on clinical CT scans for pre-operative simulation of specific challenging otologic cases in children, potentially reducing medical errors and improving patient safety. Copyright © 2015 Elsevier Ireland Ltd. All rights

  14. Dynamic simulation of an electrorheological fluid

    International Nuclear Information System (INIS)

    Bonnecaze, R.T.; Brady, J.F.

    1992-01-01

    A molecular-dynamics-like method is presented for the simulation of a suspension of dielectric particles in a nonconductive solvent forming an electrorheological fluid. The method accurately accounts for both hydrodynamic and electrostatic interparticle interactions from dilute volume fractions to closest packing for simultaneous shear and electric fields. The hydrodynamic interactions and rheology are determined with the Stokesian dynamics methodology, while the electrostatic interactions, in particular, the conservative electrostatic interparticle forces, are determined from the electrostatic energy of the suspension. The energy of the suspension is computed from the induced particle dipoles by a method previously developed [R. T. Bonnecaze and J. F. Brady, Proc. R. Soc. London, Ser. A 430, 285 (1990)]. Using the simulation, the dynamics can be directly correlated to the observed macroscopic rheology of the suspension for a range of the so-called Mason number, Ma, the ratio of viscous to electrostatic forces. The simulation is specifically applied to a monolayer of spherical particles of areal fraction 0.4 with a particle-to-fluid dielectric constant ratio of 4 for Ma=10 -4 to ∞. The effective viscosity of the suspension increases as Ma -1 or with the square of the electric field for small Ma and has a plateau value at large Ma, as is observed experimentally. This rheological behavior can be interpreted as Bingham plastic-like with a dynamic yield stress. The first normal stress difference is negative, and its magnitude increases as Ma -1 at small Ma with a large Ma plateau value of zero. In addition to the time averages of the rheology, the time traces of the viscosities are presented along with selected ''snapshots'' of the suspension microstructure

  15. Community ecology in 3D: Tensor decomposition reveals spatio-temporal dynamics of large ecological communities

    DEFF Research Database (Denmark)

    Frelat, Romain; Lindegren, Martin; Dencker, Tim Spaanheden

    2017-01-01

    it to multiple dimensions. This extension allows for the synchronized study of multiple ecological variables measured repeatedly in time and space. We applied this comprehensive approach to explore the spatio-temporal dynamics of 65 demersal fish species in the North Sea, a marine ecosystem strongly altered...... by human activities and climate change. Our case study demonstrates how tensor decomposition can successfully (i) characterize the main spatio-temporal patterns and trends in species abundances, (ii) identify sub-communities of species that share similar spatial distribution and temporal dynamics, and (iii...

  16. In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.

    Science.gov (United States)

    Yoo, Jejoong; Aksimentiev, Aleksei

    2013-12-10

    The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects.

  17. Evaluating the Effect of Virtual Reality Temporal Bone Simulation on Mastoidectomy Performance: A Meta-analysis.

    Science.gov (United States)

    Lui, Justin T; Hoy, Monica Y

    2017-06-01

    Background The increasing prevalence of virtual reality simulation in temporal bone surgery warrants an investigation to assess training effectiveness. Objectives To determine if temporal bone simulator use improves mastoidectomy performance. Data Sources Ovid Medline, Embase, and PubMed databases were systematically searched per the PRISMA guidelines. Review Methods Inclusion criteria were peer-reviewed publications that utilized quantitative data of mastoidectomy performance following the use of a temporal bone simulator. The search was restricted to human studies published in English. Studies were excluded if they were in non-peer-reviewed format, were descriptive in nature, or failed to provide surgical performance outcomes. Meta-analysis calculations were then performed. Results A meta-analysis based on the random-effects model revealed an improvement in overall mastoidectomy performance following training on the temporal bone simulator. A standardized mean difference of 0.87 (95% CI, 0.38-1.35) was generated in the setting of a heterogeneous study population ( I 2 = 64.3%, P virtual reality simulation temporal bone surgery studies, meta-analysis calculations demonstrate an improvement in trainee mastoidectomy performance with virtual simulation training.

  18. Graph regularized nonnegative matrix factorization for temporal link prediction in dynamic networks

    Science.gov (United States)

    Ma, Xiaoke; Sun, Penggang; Wang, Yu

    2018-04-01

    Many networks derived from society and nature are temporal and incomplete. The temporal link prediction problem in networks is to predict links at time T + 1 based on a given temporal network from time 1 to T, which is essential to important applications. The current algorithms either predict the temporal links by collapsing the dynamic networks or collapsing features derived from each network, which are criticized for ignoring the connection among slices. to overcome the issue, we propose a novel graph regularized nonnegative matrix factorization algorithm (GrNMF) for the temporal link prediction problem without collapsing the dynamic networks. To obtain the feature for each network from 1 to t, GrNMF factorizes the matrix associated with networks by setting the rest networks as regularization, which provides a better way to characterize the topological information of temporal links. Then, the GrNMF algorithm collapses the feature matrices to predict temporal links. Compared with state-of-the-art methods, the proposed algorithm exhibits significantly improved accuracy by avoiding the collapse of temporal networks. Experimental results of a number of artificial and real temporal networks illustrate that the proposed method is not only more accurate but also more robust than state-of-the-art approaches.

  19. Computer simulation of confined liquid crystal dynamics

    International Nuclear Information System (INIS)

    Webster, R.E.

    2001-11-01

    Results are presented from a series of simulations undertaken to determine whether dynamic processes observed in device-scale liquid crystal cells confined between aligning substrates can be simulated in a molecular system using parallel molecular dynamics of the Gay-Berne model. In a nematic cell, on removal of an aligning field, initial near-surface director relaxation can induce flow, termed 'backflow' in the liquid. This, in turn, can cause director rotation, termed 'orientational kickback', in the centre of the cell. Simulations are performed of the relaxation in nematic systems confined between substrates with a common alignment on removal of an aligning field. Results show /that relaxation timescales of medium sized systems are accessible. Following this, simulations are performed of relaxation in hybrid aligned nematic systems, where each surface induces a different alignment. Flow patterns associated with director reorientation are observed. The damped oscillatory nature of the relaxation process suggests that the behaviour of these systems is dominated by orientational elastic forces and that the observed director motion and flow do not correspond to the macroscopic processes of backflow and kickback. Chevron structures can occur in confined smectic cells which develop two domains of equal and opposite layer tilt on cooling. Layer lilting is thought to be caused by a need to reconcile a mismatch between bulk and surface smectic layer spacing. Here, simulations are performed of the formation of structures in confined smectic systems where layer tilt is induced by an imposed surface pretilt. Results show that bookshelf, chevron and tilled layer structures are observable in a confined Gay-Berne system. The formation and stability of the chevron structure are shown to be influenced by surface slip. (author)

  20. Computer simulation of confined liquid crystal dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Webster, R.E

    2001-11-01

    Results are presented from a series of simulations undertaken to determine whether dynamic processes observed in device-scale liquid crystal cells confined between aligning substrates can be simulated in a molecular system using parallel molecular dynamics of the Gay-Berne model. In a nematic cell, on removal of an aligning field, initial near-surface director relaxation can induce flow, termed 'backflow' in the liquid. This, in turn, can cause director rotation, termed 'orientational kickback', in the centre of the cell. Simulations are performed of the relaxation in nematic systems confined between substrates with a common alignment on removal of an aligning field. Results show /that relaxation timescales of medium sized systems are accessible. Following this, simulations are performed of relaxation in hybrid aligned nematic systems, where each surface induces a different alignment. Flow patterns associated with director reorientation are observed. The damped oscillatory nature of the relaxation process suggests that the behaviour of these systems is dominated by orientational elastic forces and that the observed director motion and flow do not correspond to the macroscopic processes of backflow and kickback. Chevron structures can occur in confined smectic cells which develop two domains of equal and opposite layer tilt on cooling. Layer lilting is thought to be caused by a need to reconcile a mismatch between bulk and surface smectic layer spacing. Here, simulations are performed of the formation of structures in confined smectic systems where layer tilt is induced by an imposed surface pretilt. Results show that bookshelf, chevron and tilled layer structures are observable in a confined Gay-Berne system. The formation and stability of the chevron structure are shown to be influenced by surface slip. (author)

  1. Dynamic interactions between hydrogeological and exposure parameters in daily dose prediction under uncertainty and temporal variability

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Vikas, E-mail: vikas.kumar@urv.cat [Department of Chemical Engineering, Rovira i Virgili University, Tarragona 43007 (Spain); Barros, Felipe P.J. de [Sonny Astani Department of Civil and Environmental Engineering, University of Southern California, Los Angeles 90089, CA (United States); Schuhmacher, Marta [Department of Chemical Engineering, Rovira i Virgili University, Tarragona 43007 (Spain); Fernàndez-Garcia, Daniel; Sanchez-Vila, Xavier [Hydrogeology Group, Department of Geotechnical Engineering and Geosciences, University Politècnica de Catalunya-BarcelonaTech, Barcelona 08034 (Spain)

    2013-12-15

    Highlights: • Dynamic parametric interaction in daily dose prediction under uncertainty. • Importance of temporal dynamics associated with the dose. • Different dose experienced by different population cohorts as a function of time. • Relevance of uncertainty reduction in the input parameters shows temporal dynamism. -- Abstract: We study the time dependent interaction between hydrogeological and exposure parameters in daily dose predictions due to exposure of humans to groundwater contamination. Dose predictions are treated stochastically to account for an incomplete hydrogeological and geochemical field characterization, and an incomplete knowledge of the physiological response. We used a nested Monte Carlo framework to account for uncertainty and variability arising from both hydrogeological and exposure variables. Our interest is in the temporal dynamics of the total dose and their effects on parametric uncertainty reduction. We illustrate the approach to a HCH (lindane) pollution problem at the Ebro River, Spain. The temporal distribution of lindane in the river water can have a strong impact in the evaluation of risk. The total dose displays a non-linear effect on different population cohorts, indicating the need to account for population variability. We then expand the concept of Comparative Information Yield Curves developed earlier (see de Barros et al. [29]) to evaluate parametric uncertainty reduction under temporally variable exposure dose. Results show that the importance of parametric uncertainty reduction varies according to the temporal dynamics of the lindane plume. The approach could be used for any chemical to aid decision makers to better allocate resources towards reducing uncertainty.

  2. HTTR plant dynamic simulation using a hybrid computer

    International Nuclear Information System (INIS)

    Shimazaki, Junya; Suzuki, Katsuo; Nabeshima, Kunihiko; Watanabe, Koichi; Shinohara, Yoshikuni; Nakagawa, Shigeaki.

    1990-01-01

    A plant dynamic simulation of High-Temperature Engineering Test Reactor has been made using a new-type hybrid computer. This report describes a dynamic simulation model of HTTR, a hybrid simulation method for SIMSTAR and some results obtained from dynamics analysis of HTTR simulation. It concludes that the hybrid plant simulation is useful for on-line simulation on account of its capability of computation at high speed, compared with that of all digital computer simulation. With sufficient accuracy, 40 times faster computation than real time was reached only by changing an analog time scale for HTTR simulation. (author)

  3. A dynamic appearance descriptor approach to facial actions temporal modeling

    NARCIS (Netherlands)

    Jiang, Bihan; Valstar, Michel; Martinez, Brais; Pantic, Maja

    Both the configuration and the dynamics of facial expressions are crucial for the interpretation of human facial behavior. Yet to date, the vast majority of reported efforts in the field either do not take the dynamics of facial expressions into account, or focus only on prototypic facial

  4. Temporal dynamics of figure-ground segregation in human vision.

    Science.gov (United States)

    Neri, Peter; Levi, Dennis M

    2007-01-01

    The segregation of figure from ground is arguably one of the most fundamental operations in human vision. Neural signals reflecting this operation appear in cortex as early as 50 ms and as late as 300 ms after presentation of a visual stimulus, but it is not known when these signals are used by the brain to construct the percepts of figure and ground. We used psychophysical reverse correlation to identify the temporal window for figure-ground signals in human perception and found it to lie within the range of 100-160 ms. Figure enhancement within this narrow temporal window was transient rather than sustained as may be expected from measurements in single neurons. These psychophysical results prompt and guide further electrophysiological studies.

  5. Spatio-temporal patterns of soil erosion and suspended sediment dynamics in the Mekong River Basin.

    Science.gov (United States)

    Suif, Zuliziana; Fleifle, Amr; Yoshimura, Chihiro; Saavedra, Oliver

    2016-10-15

    Understanding of the distribution patterns of sediment erosion, concentration and transport in river basins is critically important as sediment plays a major role in river basin hydrophysical and ecological processes. In this study, we proposed an integrated framework for the assessment of sediment dynamics, including soil erosion (SE), suspended sediment load (SSL) and suspended sediment concentration (SSC), and applied this framework to the Mekong River Basin. The Revised Universal Soil Loss Equation (RUSLE) model was adopted with a geographic information system to assess SE and was coupled with a sediment accumulation and a routing scheme to simulate SSL. This framework also analyzed Landsat imagery captured between 1987 and 2000 together with ground observations to interpolate spatio-temporal patterns of SSC. The simulated SSL results from 1987 to 2000 showed the relative root mean square error of 41% and coefficient of determination (R(2)) of 0.89. The polynomial relationship of the near infrared exoatmospheric reflectance and the band 4 wavelength (760-900nm) to the observed SSC at 9 sites demonstrated the good agreement (overall relative RMSE=5.2%, R(2)=0.87). The result found that the severe SE occurs in the upper (China and Lao PDR) and lower (western part of Vietnam) regions. The SSC in the rainy season (June-November) showed increasing and decreasing trends longitudinally in the upper (China and Lao PDR) and lower regions (Cambodia), respectively, while the longitudinal profile of SSL showed a fluctuating trend along the river in the early rainy season. Overall, the results described the unique spatio-temporal patterns of SE, SSL and SSC in the Mekong River Basin. Thus, the proposed integrated framework is useful for elucidating complex process of sediment generation and transport in the land and river systems of large river basins. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Generator dynamics in aeroelastic analysis and simulations

    DEFF Research Database (Denmark)

    Larsen, Torben J.; Hansen, Morten Hartvig; Iov, F.

    2003-01-01

    This report contains a description of a dynamic model for a doubly-fed induction generator. The model has physical input parameters (voltage, resistance, reactance etc.) and can be used to calculate rotor and stator currents, hence active and reactivepower. A perturbation method has been used...... to reduce the original generator model equations to a set of equations which can be solved with the same time steps as a typical aeroelastic code. The method is used to separate the fast transients of the modelfrom the slow variations and deduce a reduced order expression for the slow part. Dynamic effects...... of the first order terms in the model as well as the influence on drive train eigenfrequencies and damping has been investigated. Load response during timesimulation of wind turbine response have been compared to simulations with a traditional static generator model based entirely on the slip angle. A 2 MW...

  7. Traffic flow dynamics data, models and simulation

    CERN Document Server

    Treiber, Martin

    2013-01-01

    This textbook provides a comprehensive and instructive coverage of vehicular traffic flow dynamics and modeling. It makes this fascinating interdisciplinary topic, which to date was only documented in parts by specialized monographs, accessible to a broad readership. Numerous figures and problems with solutions help the reader to quickly understand and practice the presented concepts. This book is targeted at students of physics and traffic engineering and, more generally, also at students and professionals in computer science, mathematics, and interdisciplinary topics. It also offers material for project work in programming and simulation at college and university level. The main part, after presenting different categories of traffic data, is devoted to a mathematical description of the dynamics of traffic flow, covering macroscopic models which describe traffic in terms of density, as well as microscopic many-particle models in which each particle corresponds to a vehicle and its driver. Focus chapters on ...

  8. Good experiences with interactive temporal bone surgical simulator

    DEFF Research Database (Denmark)

    Andersen, Steven A W; Mikkelsen, Peter Trier; Noe, Karsten Ostergaard

    2014-01-01

    time. In a multilingual user interface the integrated tutor function provides stepwise instructions during drilling through an intuitive, volumetric approach. A censor function draws on metrics derived from the simulator to provide instant and summary feedback for the user. The VES can be downloaded...

  9. Temporal dynamics of a subtropical urban forest in San Juan, Puerto Rico, 2001-2010

    Science.gov (United States)

    J. M. Tucker Lima; C. L. Staudhammer; T. J. Brandeis; F. J. Escobedo; W. Zipperer

    2013-01-01

    Several studies report urban tree growth and mortality rates as well as species composition, structural dynamics, and other characteristics of urban forests in mostly temperate, inland urban areas. Temporal dynamics of urban forests in subtropical and tropical forest regions are, until now, little explored and represent a new and important direction for study and...

  10. Evaluation of a haptics-based virtual reality temporal bone simulator for anatomy and surgery training.

    Science.gov (United States)

    Fang, Te-Yung; Wang, Pa-Chun; Liu, Chih-Hsien; Su, Mu-Chun; Yeh, Shih-Ching

    2014-02-01

    Virtual reality simulation training may improve knowledge of anatomy and surgical skills. We evaluated a 3-dimensional, haptic, virtual reality temporal bone simulator for dissection training. The subjects were 7 otolaryngology residents (3 training sessions each) and 7 medical students (1 training session each). The virtual reality temporal bone simulation station included a computer with software that was linked to a force-feedback hand stylus, and the system recorded performance and collisions with vital anatomic structures. Subjects performed virtual reality dissections and completed questionnaires after the training sessions. Residents and students had favorable responses to most questions of the technology acceptance model (TAM) questionnaire. The average TAM scores were above neutral for residents and medical students in all domains, and the average TAM score for residents was significantly higher for the usefulness domain and lower for the playful domain than students. The average satisfaction questionnaire for residents showed that residents had greater overall satisfaction with cadaver temporal bone dissection training than training with the virtual reality simulator or plastic temporal bone. For medical students, the average comprehension score was significantly increased from before to after training for all anatomic structures. Medical students had significantly more collisions with the dura than residents. The residents had similar mean performance scores after the first and third training sessions for all dissection procedures. The virtual reality temporal bone simulator provided satisfactory training for otolaryngology residents and medical students. Copyright © 2013. Published by Elsevier Ireland Ltd.

  11. Parallel beam dynamics simulation of linear accelerators

    International Nuclear Information System (INIS)

    Qiang, Ji; Ryne, Robert D.

    2002-01-01

    In this paper we describe parallel particle-in-cell methods for the large scale simulation of beam dynamics in linear accelerators. These techniques have been implemented in the IMPACT (Integrated Map and Particle Accelerator Tracking) code. IMPACT is being used to study the behavior of intense charged particle beams and as a tool for the design of next-generation linear accelerators. As examples, we present applications of the code to the study of emittance exchange in high intensity beams and to the study of beam transport in a proposed accelerator for the development of accelerator-driven waste transmutation technologies

  12. Viscosity calculations at molecular dynamics simulations

    International Nuclear Information System (INIS)

    Kirova, E M; Norman, G E

    2015-01-01

    Viscosity and diffusion are chosen as an example to demonstrate the universality of diagnostics methods in the molecular dynamics method. To emphasize the universality, three diverse systems are investigated, which differ from each other drastically: liquids with embedded atom method and pairwise interatomic interaction potentials and dusty plasma with a unique multiparametric interparticle interaction potential. Both the Einstein-Helfand and Green-Kubo relations are used. Such a particular process as glass transition is analysed at the simulation of the aluminium melt. The effect of the dust particle charge fluctuation is considered. The results are compared with the experimental data. (paper)

  13. Motion Tree Delineates Hierarchical Structure of Protein Dynamics Observed in Molecular Dynamics Simulation.

    Directory of Open Access Journals (Sweden)

    Kei Moritsugu

    Full Text Available Molecular dynamics (MD simulations of proteins provide important information to understand their functional mechanisms, which are, however, likely to be hidden behind their complicated motions with a wide range of spatial and temporal scales. A straightforward and intuitive analysis of protein dynamics observed in MD simulation trajectories is therefore of growing significance with the large increase in both the simulation time and system size. In this study, we propose a novel description of protein motions based on the hierarchical clustering of fluctuations in the inter-atomic distances calculated from an MD trajectory, which constructs a single tree diagram, named a "Motion Tree", to determine a set of rigid-domain pairs hierarchically along with associated inter-domain fluctuations. The method was first applied to the MD trajectory of substrate-free adenylate kinase to clarify the usefulness of the Motion Tree, which illustrated a clear-cut dynamics picture of the inter-domain motions involving the ATP/AMP lid and the core domain together with the associated amplitudes and correlations. The comparison of two Motion Trees calculated from MD simulations of ligand-free and -bound glutamine binding proteins clarified changes in inherent dynamics upon ligand binding appeared in both large domains and a small loop that stabilized ligand molecule. Another application to a huge protein, a multidrug ATP binding cassette (ABC transporter, captured significant increases of fluctuations upon binding a drug molecule observed in both large scale inter-subunit motions and a motion localized at a transmembrane helix, which may be a trigger to the subsequent structural change from inward-open to outward-open states to transport the drug molecule. These applications demonstrated the capabilities of Motion Trees to provide an at-a-glance view of various sizes of functional motions inherent in the complicated MD trajectory.

  14. Visualizing functional motions of membrane transporters with molecular dynamics simulations.

    Science.gov (United States)

    Shaikh, Saher A; Li, Jing; Enkavi, Giray; Wen, Po-Chao; Huang, Zhijian; Tajkhorshid, Emad

    2013-01-29

    Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.

  15. Parallel Monte Carlo simulation of aerosol dynamics

    KAUST Repository

    Zhou, K.

    2014-01-01

    A highly efficient Monte Carlo (MC) algorithm is developed for the numerical simulation of aerosol dynamics, that is, nucleation, surface growth, and coagulation. Nucleation and surface growth are handled with deterministic means, while coagulation is simulated with a stochastic method (Marcus-Lushnikov stochastic process). Operator splitting techniques are used to synthesize the deterministic and stochastic parts in the algorithm. The algorithm is parallelized using the Message Passing Interface (MPI). The parallel computing efficiency is investigated through numerical examples. Near 60% parallel efficiency is achieved for the maximum testing case with 3.7 million MC particles running on 93 parallel computing nodes. The algorithm is verified through simulating various testing cases and comparing the simulation results with available analytical and/or other numerical solutions. Generally, it is found that only small number (hundreds or thousands) of MC particles is necessary to accurately predict the aerosol particle number density, volume fraction, and so forth, that is, low order moments of the Particle Size Distribution (PSD) function. Accurately predicting the high order moments of the PSD needs to dramatically increase the number of MC particles. 2014 Kun Zhou et al.

  16. Measuring and modeling the temporal dynamics of nitrogen balance in an experimental-scale paddy field

    Science.gov (United States)

    Tseng, C.; Lin, Y.

    2013-12-01

    Nitrogen balance involves many mechanisms and plays an important role to maintain the function of nature. Fertilizer application in agriculture activity is usually seen as a common and significant nitrogen input to environment. Improper fertilizer application on paddy field can result in great amount of various types of nitrogen losses. Hence, it is essential to understand and quantify the nitrogen dynamics in paddy field for fertilizer management and pollution control. In this study, we develop a model which considers major transformation processes of nitrogen (e.g. volatilization, nitrification, denitrification and plant uptake). In addition, we measured different types of nitrogen in plants, soil and water at plant growth stages in an experimental-scale paddy field in Taiwan. The measurement includes total nitrogen in plants and soil, and ammonium-N (NH4+-N), nitrate-N (NO3--N) and organic nitrogen in water. The measured data were used to calibrate the model parameters and validate the model for nitrogen balance simulation. The results showed that the model can accurately estimate the temporal dynamics of nitrogen balance in paddy field during the whole growth stage. This model might be helpful and useful for future fertilizer management and pollution control in paddy field.

  17. Use of soil moisture dynamics and patterns at different spatio-temporal scales for the investigation of subsurface flow processes

    Directory of Open Access Journals (Sweden)

    T. Blume

    2009-07-01

    Full Text Available Spatial patterns as well as temporal dynamics of soil moisture have a major influence on runoff generation. The investigation of these dynamics and patterns can thus yield valuable information on hydrological processes, especially in data scarce or previously ungauged catchments. The combination of spatially scarce but temporally high resolution soil moisture profiles with episodic and thus temporally scarce moisture profiles at additional locations provides information on spatial as well as temporal patterns of soil moisture at the hillslope transect scale. This approach is better suited to difficult terrain (dense forest, steep slopes than geophysical techniques and at the same time less cost-intensive than a high resolution grid of continuously measuring sensors. Rainfall simulation experiments with dye tracers while continuously monitoring soil moisture response allows for visualization of flow processes in the unsaturated zone at these locations. Data was analyzed at different spacio-temporal scales using various graphical methods, such as space-time colour maps (for the event and plot scale and binary indicator maps (for the long-term and hillslope scale. Annual dynamics of soil moisture and decimeter-scale variability were also investigated. The proposed approach proved to be successful in the investigation of flow processes in the unsaturated zone and showed the importance of preferential flow in the Malalcahuello Catchment, a data-scarce catchment in the Andes of Southern Chile. Fast response times of stream flow indicate that preferential flow observed at the plot scale might also be of importance at the hillslope or catchment scale. Flow patterns were highly variable in space but persistent in time. The most likely explanation for preferential flow in this catchment is a combination of hydrophobicity, small scale heterogeneity in rainfall due to redistribution in the canopy and strong gradients in unsaturated conductivities leading to

  18. Spatio-temporal cell dynamics in tumour spheroid irradiation

    International Nuclear Information System (INIS)

    Kempf, H.; Bleicher, M.; Meyer-Hermann, M.; Kempf, H.; Bleicher, M.; Kempf, H.; Meyer-Hermann, M.

    2010-01-01

    Multicellular tumour spheroids are realistic in vitro systems in radiation research that integrate cell-cell interaction and cell cycle control by factors in the medium. The dynamic reaction inside a tumour spheroid triggered by radiation is not well understood. Of special interest is the amount of cell cycle synchronization which could be triggered by irradiation, since this would allow follow-up irradiations to exploit the increased sensitivity of certain cell cycle phases. In order to investigate these questions we need to support irradiation experiments with mathematical models. In this article a new model is introduced combining the dynamics of tumour growth and irradiation treatments. The tumour spheroid growth is modelled using an agent-based Delaunay/Voronoi hybrid model in which the cells are represented by weighted dynamic vertices. Cell properties like full cell cycle dynamics are included. In order to be able to distinguish between different cell reactions in response to irradiation quality we introduce a probabilistic model for damage dynamics. The overall cell survival from this model is in agreement with predictions from the linear-quadratic model. Our model can describe the growth of avascular tumour spheroids in agreement to experimental results. Using the probabilistic model for irradiation damage dynamics the classic 'four Rs' of radiotherapy can be studied in silico. We found a pronounced reactivation of the tumour spheroid in response to irradiation. A majority of the surviving cells is synchronized in their cell cycle progression after irradiation. The cell synchronization could be actively triggered and should be exploited in an advanced fractionation scheme. Thus it has been demonstrated that our model could be used to understand the dynamics of tumour growth after irradiation and to propose optimized fractionation schemes in cooperation with experimental investigations. (authors)

  19. Dynamic characteristics of nanoindentation using atomistic simulation

    International Nuclear Information System (INIS)

    Fang, Te-Hua; Chang, Wen-Yang; Huang, Jian-Jin

    2009-01-01

    Atomistic simulations are used to investigate how the nanoindentation mechanism influences dislocation nucleation under molecular dynamic behavior on the aluminum (0 0 1) surface. The characteristics of molecular dynamics in terms of various nucleation criteria are explored, including various molecular models, a multi-step load/unload cycle, deformation mechanism of atoms, tilt angle of the indenter, and slip vectors. Simulation results show that both the plastic energy and the adhesive force increase with increasing nanoindentation depths. The maximum forces for all indentation depths decrease with increasing multi-step load/unload cycle time. Dislocation nucleation, gliding, and interaction occur along Shockley partials on (1 1 1) slip planes. The indentation force applied along the normal direction, a tilt angle of 0 o , is smaller than the force component that acts on the surface atoms. The corresponding slip vector of the atoms in the (1 1 1) plane has low-energy sessile stair-rod dislocations in the pyramid of intrinsic stacking faults.

  20. Dynamic characteristics of nanoindentation using atomistic simulation

    Energy Technology Data Exchange (ETDEWEB)

    Fang, Te-Hua, E-mail: fang.tehua@msa.hinet.net [Institute of Mechanical and Electromechanical Engineering, National Formosa University, Yunlin 632, Taiwan (China); Chang, Wen-Yang [Microsystems Technology Center, Industrial Technology Research Institute, Tainan 709, Taiwan (China); Huang, Jian-Jin [Institute of Mechanical and Electromechanical Engineering, National Formosa University, Yunlin 632, Taiwan (China)

    2009-06-15

    Atomistic simulations are used to investigate how the nanoindentation mechanism influences dislocation nucleation under molecular dynamic behavior on the aluminum (0 0 1) surface. The characteristics of molecular dynamics in terms of various nucleation criteria are explored, including various molecular models, a multi-step load/unload cycle, deformation mechanism of atoms, tilt angle of the indenter, and slip vectors. Simulation results show that both the plastic energy and the adhesive force increase with increasing nanoindentation depths. The maximum forces for all indentation depths decrease with increasing multi-step load/unload cycle time. Dislocation nucleation, gliding, and interaction occur along Shockley partials on (1 1 1) slip planes. The indentation force applied along the normal direction, a tilt angle of 0{sup o}, is smaller than the force component that acts on the surface atoms. The corresponding slip vector of the atoms in the (1 1 1) plane has low-energy sessile stair-rod dislocations in the pyramid of intrinsic stacking faults.

  1. Choosing the speed of dynamic mental simulations.

    Science.gov (United States)

    Makin, Alexis D J

    2017-01-01

    The brain continuously maintains a current representation of its immediate surroundings. Perceptual representations are often updated when the world changes, e.g., when we notice an object move. However, we can also update representations internally, without incoming signals from the senses. In other words, we can run internal simulations of dynamic events. This ability is evident during mental object rotation. These uncontroversial observations lead to an obvious question that nevertheless remains to be answered: How does the brain control the speed of dynamic mental simulations? Is there a central rate controller or pacemaker module in the brain that can be temporarily coupled to sensory maps? We can refer to this as the common rate control theory. Alternatively, the primitive intelligence within each map could tune into the speed of recent changes and use this information to keep going after stimuli disappear. We can call this the separate rate control theory. Preliminary evidence from prediction motion experiments supports common rate control, although local predictive mechanisms may cover short gaps of cognitive timing literature. Indirect neuroimaging evidence suggests rate control is a function of the core timing system in the dorsal striatum. © 2017 Elsevier B.V. All rights reserved.

  2. Modeling initial contact dynamics during ambulation with dynamic simulation.

    Science.gov (United States)

    Meyer, Andrew R; Wang, Mei; Smith, Peter A; Harris, Gerald F

    2007-04-01

    Ankle-foot orthoses are frequently used interventions to correct pathological gait. Their effects on the kinematics and kinetics of the proximal joints are of great interest when prescribing ankle-foot orthoses to specific patient groups. Mathematical Dynamic Model (MADYMO) is developed to simulate motor vehicle crash situations and analyze tissue injuries of the occupants based multibody dynamic theories. Joint kinetics output from an inverse model were perturbed and input to the forward model to examine the effects of changes in the internal sagittal ankle moment on knee and hip kinematics following heel strike. Increasing the internal ankle moment (augmentation, equivalent to gastroc-soleus contraction) produced less pronounced changes in kinematic results at the hip, knee and ankle than decreasing the moment (attenuation, equivalent to gastroc-soleus relaxation). Altering the internal ankle moment produced two distinctly different kinematic curve morphologies at the hip. Decreased internal ankle moments increased hip flexion, peaking at roughly 8% of the gait cycle. Increasing internal ankle moments decreased hip flexion to a lesser degree, and approached normal at the same point in the gait cycle. Increasing the internal ankle moment produced relatively small, well-behaved extension-biased kinematic results at the knee. Decreasing the internal ankle moment produced more substantial changes in knee kinematics towards flexion that increased with perturbation magnitude. Curve morphologies were similar to those at the hip. Immediately following heel strike, kinematic results at the ankle showed movement in the direction of the internal moment perturbation. Increased internal moments resulted in kinematic patterns that rapidly approach normal after initial differences. When the internal ankle moment was decreased, differences from normal were much greater and did not rapidly decrease. This study shows that MADYMO can be successfully applied to accomplish forward

  3. Photodynamics of oxybenzone sunscreen: Nonadiabatic dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Li, Chun-Xiang; Guo, Wei-Wei; Xie, Bin-Bin; Cui, Ganglong, E-mail: ganglong.cui@bnu.edu.cn [Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875 (China)

    2016-08-21

    Herein we have used combined static electronic structure calculations and “on-the-fly” global-switching trajectory surface-hopping dynamics simulations to explore the photochemical mechanism of oxybenzone sunscreen. We have first employed the multi-configurational CASSCF method to optimize minima, conical intersections, and minimum-energy reaction paths related to excited-state intramolecular proton transfer (ESIPT) and excited-state decays in the {sup 1}ππ{sup ∗}, {sup 1}nπ{sup ∗}, and S{sub 0} states (energies are refined at the higher MS-CASPT2 level). According to the mapped potential energy profiles, we have identified two ultrafast excited-state deactivation pathways for the initially populated {sup 1}ππ{sup ∗} system. The first is the diabatic ESIPT process along the {sup 1}ππ{sup ∗} potential energy profile. The generated {sup 1}ππ{sup ∗} keto species then decays to the S{sub 0} state via the keto {sup 1}ππ{sup ∗}/gs conical intersection. The second is internal conversion to the dark {sup 1}nπ{sup ∗} state near the {sup 1}ππ{sup ∗} /{sup 1}nπ{sup ∗} crossing point in the course of the diabatic {sup 1}ππ{sup ∗} ESIPT process. Our following dynamics simulations have shown that the ESIPT and {sup 1}ππ{sup ∗} → S{sub 0} internal conversion times are 104 and 286 fs, respectively. Finally, our present work demonstrates that in addition to the ESIPT process and the {sup 1}ππ{sup ∗} → S{sub 0} internal conversion in the keto region, the {sup 1}ππ{sup ∗} → {sup 1}nπ{sup ∗} internal conversion in the enol region plays as well an important role for the excited-state relaxation dynamics of oxybenzone.

  4. Simulation of Molten Salt Reactor dynamics

    International Nuclear Information System (INIS)

    Krepel, J.; Rohde, U.; Grundmann, U.

    2005-01-01

    Dynamics of the Molten Salt Reactor - one of the 'Generation IV' concepts - was studied in this paper. The graphite-moderated channel type MSR was selected for the numerical simulation of the reactor with liquid fuel. The MSR dynamics is very specific because of two physical peculiarities of the liquid fueled reactor: the delayed neutrons precursors are drifted by the fuel flow and the fission energy is immediately released directly into the coolant. Presently, there are not many accessible numerical codes appropriate for the MSR simulation, therefore the DYN3D-MSR code was developed based on the FZR in-house code DYN3D. It allows calculating of full 3D transient neutronics in combination with parallel channel type thermal-hydraulics. By means of DYN3D-MSR, several transients typical for the liquid fuel system were analyzed. Those transients were initiated by reactivity insertion, by overcooling of fuel at the core inlet, by the fuel pump start-up or coast-down, or by the blockage of selected fuel channels. In these considered transients, the response of the MSR is characterized by the immediate change of the fuel temperature with changing power and fast negative temperature feedback to the power. The response through the graphite temperature is slower. Furthermore, for big MSR cores fueled with U233 the graphite feedback coefficient can be positive. In this case the addition of erbium to the graphite can ensure the inherent safety features. The DYN3D-MSR code has been shown to be an effective tool for MSR dynamics studies. (author)

  5. Dynamics simulations for engineering macromolecular interactions

    Science.gov (United States)

    Robinson-Mosher, Avi; Shinar, Tamar; Silver, Pamela A.; Way, Jeffrey

    2013-01-01

    The predictable engineering of well-behaved transcriptional circuits is a central goal of synthetic biology. The artificial attachment of promoters to transcription factor genes usually results in noisy or chaotic behaviors, and such systems are unlikely to be useful in practical applications. Natural transcriptional regulation relies extensively on protein-protein interactions to insure tightly controlled behavior, but such tight control has been elusive in engineered systems. To help engineer protein-protein interactions, we have developed a molecular dynamics simulation framework that simplifies features of proteins moving by constrained Brownian motion, with the goal of performing long simulations. The behavior of a simulated protein system is determined by summation of forces that include a Brownian force, a drag force, excluded volume constraints, relative position constraints, and binding constraints that relate to experimentally determined on-rates and off-rates for chosen protein elements in a system. Proteins are abstracted as spheres. Binding surfaces are defined radially within a protein. Peptide linkers are abstracted as small protein-like spheres with rigid connections. To address whether our framework could generate useful predictions, we simulated the behavior of an engineered fusion protein consisting of two 20 000 Da proteins attached by flexible glycine/serine-type linkers. The two protein elements remained closely associated, as if constrained by a random walk in three dimensions of the peptide linker, as opposed to showing a distribution of distances expected if movement were dominated by Brownian motion of the protein domains only. We also simulated the behavior of fluorescent proteins tethered by a linker of varying length, compared the predicted Förster resonance energy transfer with previous experimental observations, and obtained a good correspondence. Finally, we simulated the binding behavior of a fusion of two ligands that could

  6. Face and content validation of a virtual reality temporal bone simulator.

    Science.gov (United States)

    Arora, Asit; Khemani, Sam; Tolley, Neil; Singh, Arvind; Budge, James; Varela, David A Diaz Voss; Francis, Howard W; Darzi, Ara; Bhatti, Nasir I

    2012-03-01

    To validate the VOXEL-MAN TempoSurg simulator for temporal bone dissection. Prospective international study. Otolaryngology departments of 2 academic health care institutions in the United Kingdom and United States. Eighty-five subjects were recruited consisting of an experienced and referent group. Participants performed a standardized familiarization session and temporal bone dissection task. Realism, training effectiveness, and global impressions were evaluated across 21 domains using a 5-point Likert-type scale. A score of 4 was the minimum threshold for acceptability. The experienced group comprised 25 otolaryngology trainers who had performed 150 mastoid operations. The referent group comprised 60 trainees (mean otolaryngology experience of 2.9 years). Familiarization took longer in the experienced group (P = .01). User-friendliness was positively rated (mean score 4.1). Seventy percent of participants rated anatomical appearance as acceptable. Trainers rated drill ergonomics worse than did trainees (P = .01). Simulation temporal bone training scored highly (mean score 4.3). Surgical anatomy, drill navigation, and hand-eye coordination accounted for this. Trainees were more likely to recommend temporal bone simulation to a colleague than were trainers (P = .01). Transferability of skills to the operating room was undecided (mean score 3.5). Realism of the VOXEL-MAN virtual reality temporal bone simulator is suboptimal in its current version. Nonetheless, it represents a useful adjunct to existing training methods and is particularly beneficial for novice surgeons before performing cadaveric temporal bone dissection. Improvements in realism, specifically drill ergonomics and visual-spatial perception during deeper temporal bone dissection, are warranted.

  7. Spatial and temporal infiltration dynamics during managed aquifer recharge.

    Science.gov (United States)

    Racz, Andrew J; Fisher, Andrew T; Schmidt, Calla M; Lockwood, Brian S; Los Huertos, Marc

    2012-01-01

    Natural groundwater recharge is inherently difficult to quantify and predict, largely because it comprises a series of processes that are spatially distributed and temporally variable. Infiltration ponds used for managed aquifer recharge (MAR) provide an opportunity to quantify recharge processes across multiple scales under semi-controlled conditions. We instrumented a 3-ha MAR infiltration pond to measure and compare infiltration patterns determined using whole-pond and point-specific methods. Whole-pond infiltration was determined by closing a transient water budget (accounting for inputs, outputs, and changes in storage), whereas point-specific infiltration rates were determined using heat as a tracer and time series analysis at eight locations in the base of the pond. Whole-pond infiltration, normalized for wetted area, rose rapidly to more than 1.0 m/d at the start of MAR operations (increasing as pond stage rose), was sustained at high rates for the next 40 d, and then decreased to less than 0.1 m/d by the end of the recharge season. Point-specific infiltration rates indicated high spatial and temporal variability, with the mean of measured values generally being lower than rates indicated by whole-pond calculations. Colocated measurements of head gradients within saturated soils below the pond were combined with infiltration rates to calculate soil hydraulic conductivity. Observations indicate a brief period of increasing saturated hydraulic conductivity, followed by a decrease of one to two orders of magnitude during the next 50 to 75 d. Locations indicating the most rapid infiltration shifted laterally during MAR operation, and we suggest that infiltration may function as a "variable source area" processes, conceptually similar to catchment runoff. © 2011, The Author(s). Ground Water © 2011, National Ground Water Association.

  8. Dynamic imaging in mild traumatic brain injury: support for the theory of medial temporal vulnerability.

    Science.gov (United States)

    Umile, Eric M; Sandel, M Elizabeth; Alavi, Abass; Terry, Charles M; Plotkin, Rosette C

    2002-11-01

    To determine whether patients with mild traumatic brain injury (TBI) and persistent postconcussive symptoms have evidence of temporal lobe injury on dynamic imaging. Case series. An academic medical center. Twenty patients with a clinical diagnosis of mild TBI and persistent postconcussive symptoms were referred for neuropsychologic evaluation and dynamic imaging. Fifteen (75%) had normal magnetic resonance imaging (MRI) and/or computed tomography (CT) scans at the time of injury. Neuropsychologic testing, positron-emission tomography (PET), and single-photon emission-computed tomography (SPECT). Temporal lobe findings on static imaging (MRI, CT) and dynamic imaging (PET, SPECT); neuropsychologic test findings on measures of verbal and visual memory. Testing documented neurobehavioral deficits in 19 patients (95%). Dynamic imaging documented abnormal findings in 18 patients (90%). Fifteen patients (75%) had temporal lobe abnormalities on PET and SPECT (primarily in medial temporal regions); abnormal findings were bilateral in 10 patients (50%) and unilateral in 5 (25%). Six patients (30%) had frontal abnormalities, and 8 (40%) had nonfrontotemporal abnormalities. Correlations between neuropsychologic testing and dynamic imaging could be established but not consistently across the whole group. Patients with mild TBI and persistent postconcussive symptoms have a high incidence of temporal lobe injury (presumably involving the hippocampus and related structures), which may explain the frequent finding of memory disorders in this population. The abnormal temporal lobe findings on PET and SPECT in humans may be analogous to the neuropathologic evidence of medial temporal injury provided by animal studies after mild TBI. Copyright 2002 by the American Congress of Rehabilitation Medicine and the American Academy of Physical Medicine and Rehabilitation

  9. Spatio-temporal dynamics of a pulsed microwave argon plasma: ignition and afterglow

    International Nuclear Information System (INIS)

    Carbone, Emile; Sadeghi, Nader; Vos, Erik; Hübner, Simon; Van Veldhuizen, Eddie; Van Dijk, Jan; Nijdam, Sander; Kroesen, Gerrit

    2015-01-01

    In this paper, a detailed investigation of the spatio-temporal dynamics of a pulsed microwave plasma is presented. The plasma is ignited inside a dielectric tube in a repetitively pulsed regime at pressures ranging from 1 up to 100 mbar with pulse repetition frequencies from 200 Hz up to 500 kHz. Various diagnostic techniques are employed to obtain the main plasma parameters both spatially and with high temporal resolution. Thomson scattering is used to obtain the electron density and mean electron energy at fixed positions in the dielectric tube. The temporal evolution of the two resonant and two metastable argon 4s states are measured by laser diode absorption spectroscopy. Nanosecond time-resolved imaging of the discharge allows us to follow the spatio-temporal evolution of the discharge with high temporal and spatial resolution. Finally, the temporal evolution of argon 4p and higher states is measured by optical emission spectroscopy. The combination of these various diagnostics techniques gives deeper insight on the plasma dynamics during pulsed microwave plasma operation from low to high pressure regimes. The effects of the pulse repetition frequency on the plasma ignition dynamics are discussed and the plasma-off time is found to be the relevant parameter for the observed ignition modes. Depending on the delay between two plasma pulses, the dynamics of the ionization front are found to be changing dramatically. This is also reflected in the dynamics of the electron density and temperature and argon line emission from the plasma. On the other hand, the (quasi) steady state properties of the plasma are found to depend only weakly on the pulse repetition frequency and the afterglow kinetics present an uniform spatio-temporal behavior. However, compared to continuous operation, the time-averaged metastable and resonant state 4s densities are found to be significantly larger around a few kHz pulsing frequency. (paper)

  10. Spatio-temporal dynamics of cod nursery areas in the Baltic Sea

    Science.gov (United States)

    Hinrichsen, H.-H.; von Dewitz, B.; Lehmann, A.; Bergström, U.; Hüssy, K.

    2017-06-01

    In this study the drift of eastern Baltic cod larvae and juveniles spawned within the historical eastern Baltic cod spawning grounds was investigated by detailed drift model simulations for the years 1971-2010, to examine the spatio-temporal dynamics of environmental suitability in the nursery areas of juvenile cod settlement. The results of the long-term model scenario runs, where juvenile cod were treated as simulated passively drifting particles, enabled us to find strong indications for long-term variations of settlement and potentially the reproduction success of the historically important eastern Baltic cod nursery grounds. Only low proportions of juveniles hatched in the Arkona Basin and in the Gotland Basin were able to settle in their respective spawning ground. Ocean currents were either unfavorable for the juveniles to reach suitable habitats or transported the juveniles to nursery grounds of neighboring subdivisions. Juveniles which hatched in the Bornholm Basin were most widely dispersed and showed the highest settlement probability, while the second highest settlement probability and horizontal dispersal was observed for juveniles originating from the Gdansk Deep. In a long-term perspective, wind-driven transport of larvae/juveniles positively affected the settlement success predominately in the Bornholm Basin and in the Bay of Gdansk. The Bornholm Basin has the potential to contribute on average 54% and the Bay of Gdansk 11% to the production of juveniles in the Baltic Sea. Furthermore, transport of juveniles surviving to the age of settlement with origin in the Bornholm Basin contributed on average 13 and 11% to the total settlement in the Arkona Basin and in the Gdansk Deep, respectively. The time-series of the simulated occupied juvenile cod habitat in the Bornholm Basin and in the Gdansk Deep showed a similar declining trend as the Fulton's K condition factor of demersal 1-group cod, which may confirm the importance of oxygen-dependent habitat

  11. Urbanization Changes the Temporal Dynamics of Nutrients and Water Chemistry

    Science.gov (United States)

    Steele, M.; Badgley, B.

    2017-12-01

    Recent studies find that urban development alters the seasonal dynamics of nutrient concentrations, where the highest concentrations of nitrogen occurred during the winter in urban watersheds, rather than the summer. However, the effects of urbanization on the seasonal concentrations of other nutrients and chemical components is unknown. Therefore, to determine how urbanization changes the seasonal dynamics, once a week we measured concentrations of dissolved organic carbon (DOC), nutrients (NO3, DON, TN, PO4), base cations (Ca, Mg, Na, K), anions (F, Cl, SO4), pH, sediment, temperature, conductivity, and dissolved oxygen (DO) of nine urban, agricultural, and minimally developed watersheds in southwest Virginia, USA. We found that urbanization disrupted the seasonal dynamics of all metrics, except DON, PO4, Ca, sediment, and DO, where some shifted to high concentrations during the winter (Cl, conductivity), highs during late winter or spring (DOC, Na), a season low (TN, SO4, NO3) or high (NH4) during the summer, or remained more constant throughout the year compared to the reference watersheds (Mg, K, pH). The complex changes in seasonal dynamics coincide with a decoupling of common correlations between constituents; for example, DO and NO3 are negatively correlated in reference watersheds (NO3 increases, DO decreases), but positively correlated in urban watersheds. These results suggest that as watersheds become more intensely developed, the influence of natural drivers like temperature and vegetation become steadily overcome by the influence of urban drivers like deicing salts and wastewater leakage, which exert increasing control of seasonal water quality and aquatic habitat.

  12. Molecular dynamic simulation study of molten cesium

    Directory of Open Access Journals (Sweden)

    Yeganegi Saeid

    2017-01-01

    Full Text Available Molecular dynamics simulations were performed to study thermodynamics and structural properties of expanded caesium fluid. Internal pressure, radial distribution functions (RDFs, coordination numbers and diffusion coefficients have been calculated at temperature range 700–1600 K and pressure range 100–800 bar. We used the internal pressure to predict the metal–non-metal transition occurrence region. RDFs were calculated at wide ranges of temperature and pressure. The coordination numbers decrease and positions of the first peak of RDFs slightly increase as the temperature increases and pressure decreases. The calculated self-diffusion coefficients at various temperatures and pressures show no distinct boundary between Cs metallic fluid and its expanded fluid where it continuously increases with temperature.

  13. Temporal dynamics and leaf trait variability in Neotropical dry forests

    Science.gov (United States)

    Hesketh, Michael Sean

    This thesis explores the variability of leaf traits resulting from changes in season, ecosystem successional stage, and site characteristics. In chapter two, I present a review of the use of remote sensing analysis for the evaluation of Neotropical dry forests. Here, I stress the conclusion, drawn from studies on land cover characterization, biodiversity assessment, and evaluation of forest structural characteristics, that addressing temporal variability in spectral properties is an essential element in the monitoring of these ecosystems. Chapter three describes the effect of wet-dry seasonality on spectral classification of tree and liana species. Highly accurate classification (> 80%) was possible using data from either the wet or dry season. However, this accuracy decreased by a factor of ten when data from the wet season was classified using an algorithm trained on the dry, or vice versa. I also address the potential creation of a spectral taxonomy of species, but found that any clustering based on spectral properties resulted in markedly different arrangements in the wet and dry seasons. In chapter 4, I address the variation present in both physical and spectral leaf traits according to changes in forest successional stage at dry forest sites in Mexico and Costa Rica. I found significant differences in leaf traits between successional stages, but more strongly so in Costa Rica. This variability deceased the accuracy of spectral classification of tree species by a factor of four when classifying data using an algorithm trained on a different successional stage. Chapter 5 shows the influence of seasonality and succession on trait variability in Mexico. Differences in leaf traits between successional stages were found to be greater during the dry season, but were sufficient in both seasons to negatively influence spectral classification of tree species. Throughout this thesis, I show clear and unambiguous evidence of the variability of key physical and spectral

  14. Annual and diurnal african biomass burning temporal dynamics

    Directory of Open Access Journals (Sweden)

    G. Roberts

    2009-05-01

    Full Text Available Africa is the single largest continental source of biomass burning emissions. Here we conduct the first analysis of one full year of geostationary active fire detections and fire radiative power data recorded over Africa at 15-min temporal interval and a 3 km sub-satellite spatial resolution by the Spinning Enhanced Visible and Infrared Imager (SEVIRI imaging radiometer onboard the Meteosat-8 satellite. We use these data to provide new insights into the rates and totals of open biomass burning over Africa, particularly into the extremely strong seasonal and diurnal cycles that exist across the continent. We estimate peak daily biomass combustion totals to be 9 and 6 million tonnes of fuel per day in the northern and southern hemispheres respectively, and total fuel consumption between February 2004 and January 2005 is estimated to be at least 855 million tonnes. Analysis is carried out with regard to fire pixel temporal persistence, and we note that the majority of African fires are detected only once in consecutive 15 min imaging slots. An investigation of the variability of the diurnal fire cycle is carried out with respect to 20 different land cover types, and whilst differences are noted between land covers, the fire diurnal cycle characteristics for most land cover type are very similar in both African hemispheres. We compare the Fire Radiative Power (FRP derived biomass combustion estimates to burned-areas, both at the scale of individual fires and over the entire continent at a 1-degree scale. Fuel consumption estimates are found to be less than 2 kg/m2 for all land cover types noted to be subject to significant fire activity, and for savanna grasslands where literature values are commonly reported the FRP-derived median fuel consumption estimate of 300 g/m2 is well within commonly quoted values. Meteosat-derived FRP data of the type presented here is now available freely to interested users continuously and in near

  15. Temporal dynamics of all-optical switching in Photonic Crystal Cavity

    DEFF Research Database (Denmark)

    Colman, Pierre; Heuck, Mikkel; Yu, Yi

    2014-01-01

    The temporal dynamics of all-optical switching has been investigated in a Photonic Crystal Cavity with a 150fs-40aJ/pulse resolution. This allowed observing for the first time effects like pulse reshaping, pulse delay and intra-cavity Four-Wave-Mixing.......The temporal dynamics of all-optical switching has been investigated in a Photonic Crystal Cavity with a 150fs-40aJ/pulse resolution. This allowed observing for the first time effects like pulse reshaping, pulse delay and intra-cavity Four-Wave-Mixing....

  16. Traffic flow dynamics. Data, models and simulation

    Energy Technology Data Exchange (ETDEWEB)

    Treiber, Martin [Technische Univ. Dresden (Germany). Inst. fuer Wirtschaft und Verkehr; Kesting, Arne [TomTom Development Germany GmbH, Berlin (Germany)

    2013-07-01

    First comprehensive textbook of this fascinating interdisciplinary topic which explains advances in a way that it is easily accessible to engineering, physics and math students. Presents practical applications of traffic theory such as driving behavior, stability analysis, stop-and-go waves, and travel time estimation. Presents the topic in a novel and systematic way by addressing both microscopic and macroscopic models with a focus on traffic instabilities. Revised and extended edition of the German textbook ''Verkehrsdynamik und -simulation''. This textbook provides a comprehensive and instructive coverage of vehicular traffic flow dynamics and modeling. It makes this fascinating interdisciplinary topic, which to date was only documented in parts by specialized monographs, accessible to a broad readership. Numerous figures and problems with solutions help the reader to quickly understand and practice the presented concepts. This book is targeted at students of physics and traffic engineering and, more generally, also at students and professionals in computer science, mathematics, and interdisciplinary topics. It also offers material for project work in programming and simulation at college and university level. The main part, after presenting different categories of traffic data, is devoted to a mathematical description of the dynamics of traffic flow, covering macroscopic models which describe traffic in terms of density, as well as microscopic many-particle models in which each particle corresponds to a vehicle and its driver. Focus chapters on traffic instabilities and model calibration/validation present these topics in a novel and systematic way. Finally, the theoretical framework is shown at work in selected applications such as traffic-state and travel-time estimation, intelligent transportation systems, traffic operations management, and a detailed physics-based model for fuel consumption and emissions.

  17. A data model for simulation models relying on spatio-temporal urban data

    OpenAIRE

    Langlois , G ,; Tourre , Vincent; Servières , Myriam; Gervais , G ,; Gesquière , Gilles

    2016-01-01

    International audience; To understand the complexity of modern cities and anticipate their expansion, experts from various fields conceive simulation models that can be very different. Those simulation models work with a variety of data with their own organization. Furthermore, because the urban objects are studied in the context of the evolution of a city or urban area, they carry temporal and spatial information. In this paper, we present the base classes of a common data model robust and f...

  18. STABILITY AND DYNAMICS OF SPATIO-TEMPORAL STRUCTURES

    Energy Technology Data Exchange (ETDEWEB)

    Hermann Riecke

    2005-10-21

    This document constitutes the final report for the grant. It provides a complete list of publications and presentations that arose from the project as well as a brief description of the highlights of the research results. The research funded by this grant has provided insights into the spontaneous formation of structures of increasing complexity in systems driven far from thermodynamic equilibrium. A classic example of such a system is thermally driven convection in a horizontal fluid layer. Highlights of the research are: (1) explanation of the localized traveling wave pulses observed in binary-mixture convection, (2) explanation of the localized waves in electroconvection, (3) introduction of a new diagnostics for spatially and temporally chaotic states, which is based on the statistics of defect trajectories, (4) prediction of complex states in thermally driven convection in rotating systems. Additional contributions provided insight into the localization mechanism for oscillons, the prediction of a new localization mechanism for traveling waves based on a resonant periodic forcing, and an analysis of the stability of quasi-periodic patterns.

  19. Classical molecular dynamics simulation of nuclear fuels

    International Nuclear Information System (INIS)

    Devanathan, R.; Krack, M.; Bertolus, M.

    2015-01-01

    Molecular dynamics simulation using forces calculated from empirical potentials, commonly called classical molecular dynamics, is well suited to study primary damage production by irradiation, defect interactions with fission gas atoms, gas bubble nucleation, grain boundary effects on defect and gas bubble evolution in nuclear fuel, and the resulting changes in thermomechanical properties. This enables one to obtain insights into fundamental mechanisms governing the behaviour of nuclear fuel, as well as parameters that can be used as inputs for mesoscale models. The interaction potentials used for the force calculations are generated by fitting properties of interest to experimental data and electronic structure calculations (see Chapter 12). We present here the different types of potentials currently available for UO 2 and illustrations of applications to the description of the behaviour of this material under irradiation. The results obtained from the present generation of potentials for UO 2 are qualitatively similar, but quantitatively different. There is a need to refine these existing potentials to provide a better representation of the performance of polycrystalline fuel under a variety of operating conditions, develop models that are equipped to handle deviations from stoichiometry, and validate the models and assumptions used. (authors)

  20. Brownian dynamics simulations of insulin microspheres formation

    Science.gov (United States)

    Li, Wei; Chakrabarti, Amit; Gunton, James

    2010-03-01

    Recent experiments have indicated a novel, aqueous process of microsphere insulin fabrication based on controlled phase separation of protein from water-soluble polymers. We investigate the insulin microsphere crystal formation from insulin-PEG-water systems via 3D Brownian Dynamics simulations. We use the two component Asakura-Oosawa model to simulate the kinetics of this colloid polymer mixture. We first perform a deep quench below the liquid-crystal boundary that leads to fractal formation. We next heat the system to obtain a break-up of the fractal clusters and subsequently cool the system to obtain a spherical aggregation of droplets with a relatively narrow size distribution. We analyze the structure factor S(q) to identify the cluster dimension. S(q) crosses over from a power law q dependence of 1.8 (in agreement with DLCA) to 4 as q increases, which shows the evolution from fractal to spherical clusters. By studying the bond-order parameters, we find the phase transition from liquid-like droplets to crystals which exhibit local HCP and FCC order. This work is supported by grants from the NSF and Mathers Foundation.

  1. An Investigation on Temporal Aspects in the Audio-Haptic Simulation of Footsteps

    DEFF Research Database (Denmark)

    Turchet, Luca; Serafin, Stefania

    2011-01-01

    In this paper, we present an experiment whose goal is to assess the role of temporal aspects in sonically and haptically simulating the act of walking on a bump or a hole. In particular, we investigated whether the timing between heel and toe and the timing between footsteps affected perception...

  2. MDAnalysis: a toolkit for the analysis of molecular dynamics simulations.

    Science.gov (United States)

    Michaud-Agrawal, Naveen; Denning, Elizabeth J; Woolf, Thomas B; Beckstein, Oliver

    2011-07-30

    MDAnalysis is an object-oriented library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. It is written in the Python language with some performance-critical code in C. It uses the powerful NumPy package to expose trajectory data as fast and efficient NumPy arrays. It has been tested on systems of millions of particles. Many common file formats of simulation packages including CHARMM, Gromacs, Amber, and NAMD and the Protein Data Bank format can be read and written. Atoms can be selected with a syntax similar to CHARMM's powerful selection commands. MDAnalysis enables both novice and experienced programmers to rapidly write their own analytical tools and access data stored in trajectories in an easily accessible manner that facilitates interactive explorative analysis. MDAnalysis has been tested on and works for most Unix-based platforms such as Linux and Mac OS X. It is freely available under the GNU General Public License from http://mdanalysis.googlecode.com. Copyright © 2011 Wiley Periodicals, Inc.

  3. In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation.

    Science.gov (United States)

    Gray, Alan; Harlen, Oliver G; Harris, Sarah A; Khalid, Syma; Leung, Yuk Ming; Lonsdale, Richard; Mulholland, Adrian J; Pearson, Arwen R; Read, Daniel J; Richardson, Robin A

    2015-01-01

    Despite huge advances in the computational techniques available for simulating biomolecules at the quantum-mechanical, atomistic and coarse-grained levels, there is still a widespread perception amongst the experimental community that these calculations are highly specialist and are not generally applicable by researchers outside the theoretical community. In this article, the successes and limitations of biomolecular simulation and the further developments that are likely in the near future are discussed. A brief overview is also provided of the experimental biophysical methods that are commonly used to probe biomolecular structure and dynamics, and the accuracy of the information that can be obtained from each is compared with that from modelling. It is concluded that progress towards an accurate spatial and temporal model of biomacromolecules requires a combination of all of these biophysical techniques, both experimental and computational.

  4. Dynamic Response and Simulations of Nanoparticle-Enhanced Composites

    National Research Council Canada - National Science Library

    Mantena, P. R; Al-Ostaz, Ahmed; Cheng, Alexander H

    2007-01-01

    ...) molecular dynamics simulations of nanoparticle-enhanced composites and fly- ash based foams that are being considered for the future generation naval structures or retrofitting of existing ones...

  5. Simulating CubeSat Structure Deployment Dynamics, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — There is high value in simulating the nonlinear dynamics of stowing, deploying, and performance of deployable space structures, especially given the profound...

  6. Transition Dynamics of a Dentate Gyrus-CA3 Neuronal Network during Temporal Lobe Epilepsy

    Directory of Open Access Journals (Sweden)

    Liyuan Zhang

    2017-07-01

    Full Text Available In temporal lobe epilepsy (TLE, the variation of chemical receptor expression underlies the basis of neural network activity shifts, resulting in neuronal hyperexcitability and epileptiform discharges. However, dynamical mechanisms involved in the transitions of TLE are not fully understood, because of the neuronal diversity and the indeterminacy of network connection. Hence, based on Hodgkin–Huxley (HH type neurons and Pinsky–Rinzel (PR type neurons coupling with glutamatergic and GABAergic synaptic connections respectively, we propose a computational framework which contains dentate gyrus (DG region and CA3 region. By regulating the concentration range of N-methyl-D-aspartate-type glutamate receptor (NMDAR, we demonstrate the pyramidal neuron can generate transitions from interictal to seizure discharges. This suggests that enhanced endogenous activity of NMDAR contributes to excitability in pyramidal neuron. Moreover, we conclude that excitatory discharges in CA3 region vary considerably on account of the excitatory currents produced by the excitatory pyramidal neuron. Interestingly, by changing the backprojection connection, we find that glutamatergic type backprojection can promote the dominant frequency of firings and further motivate excitatory counterpropagation from CA3 region to DG region. However, GABAergic type backprojection can reduce firing rate and block morbid counterpropagation, which may be factored into the terminations of TLE. In addition, neuronal diversity dominated network shows weak correlation with different backprojections. Our modeling and simulation studies provide new insights into the mechanisms of seizures generation and connectionism in local hippocampus, along with the synaptic mechanisms of this disease.

  7. Transition Dynamics of a Dentate Gyrus-CA3 Neuronal Network during Temporal Lobe Epilepsy.

    Science.gov (United States)

    Zhang, Liyuan; Fan, Denggui; Wang, Qingyun

    2017-01-01

    In temporal lobe epilepsy (TLE), the variation of chemical receptor expression underlies the basis of neural network activity shifts, resulting in neuronal hyperexcitability and epileptiform discharges. However, dynamical mechanisms involved in the transitions of TLE are not fully understood, because of the neuronal diversity and the indeterminacy of network connection. Hence, based on Hodgkin-Huxley (HH) type neurons and Pinsky-Rinzel (PR) type neurons coupling with glutamatergic and GABAergic synaptic connections respectively, we propose a computational framework which contains dentate gyrus (DG) region and CA3 region. By regulating the concentration range of N-methyl-D-aspartate-type glutamate receptor (NMDAR), we demonstrate the pyramidal neuron can generate transitions from interictal to seizure discharges. This suggests that enhanced endogenous activity of NMDAR contributes to excitability in pyramidal neuron. Moreover, we conclude that excitatory discharges in CA3 region vary considerably on account of the excitatory currents produced by the excitatory pyramidal neuron. Interestingly, by changing the backprojection connection, we find that glutamatergic type backprojection can promote the dominant frequency of firings and further motivate excitatory counterpropagation from CA3 region to DG region. However, GABAergic type backprojection can reduce firing rate and block morbid counterpropagation, which may be factored into the terminations of TLE. In addition, neuronal diversity dominated network shows weak correlation with different backprojections. Our modeling and simulation studies provide new insights into the mechanisms of seizures generation and connectionism in local hippocampus, along with the synaptic mechanisms of this disease.

  8. Practical considerations for high spatial and temporal resolution dynamic transmission electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Armstrong, Michael R. [Materials Science and Technology Division, Chemistry and Materials Science Directorate, Lawrence Livermore National Laboratory, P.O. Box 808, L-356, Livermore, CA 94550 (United States)], E-mail: armstrong30@llnl.gov; Boyden, Ken [Materials Science and Technology Division, Chemistry and Materials Science Directorate, Lawrence Livermore National Laboratory, P.O. Box 808, L-356, Livermore, CA 94550 (United States); Browning, Nigel D. [Materials Science and Technology Division, Chemistry and Materials Science Directorate, Lawrence Livermore National Laboratory, P.O. Box 808, L-356, Livermore, CA 94550 (United States); Department of Chemical Engineering and Materials Science, University of California-Davis, One Shields Avenue, Davis, CA 95616 (United States); Campbell, Geoffrey H.; Colvin, Jeffrey D.; De Hope, William J.; Frank, Alan M. [Materials Science and Technology Division, Chemistry and Materials Science Directorate, Lawrence Livermore National Laboratory, P.O. Box 808, L-356, Livermore, CA 94550 (United States); Gibson, David J.; Hartemann, Fred [N Division, Physics and Advanced Technologies Directorate, Lawrence Livermore National Laboratory, P.O. Box 808, L-280, Livermore, CA 94550 (United States); Kim, Judy S. [Materials Science and Technology Division, Chemistry and Materials Science Directorate, Lawrence Livermore National Laboratory, P.O. Box 808, L-356, Livermore, CA 94550 (United States); Department of Chemical Engineering and Materials Science, University of California-Davis, One Shields Avenue, Davis, CA 95616 (United States); King, Wayne E.; La Grange, Thomas B.; Pyke, Ben J.; Reed, Bryan W.; Shuttlesworth, Richard M.; Stuart, Brent C.; Torralva, Ben R. [Materials Science and Technology Division, Chemistry and Materials Science Directorate, Lawrence Livermore National Laboratory, P.O. Box 808, L-356, Livermore, CA 94550 (United States)

    2007-04-15

    Although recent years have seen significant advances in the spatial resolution possible in the transmission electron microscope (TEM), the temporal resolution of most microscopes is limited to video rate at best. This lack of temporal resolution means that our understanding of dynamic processes in materials is extremely limited. High temporal resolution in the TEM can be achieved, however, by replacing the normal thermionic or field emission source with a photoemission source. In this case the temporal resolution is limited only by the ability to create a short pulse of photoexcited electrons in the source, and this can be as short as a few femtoseconds. The operation of the photo-emission source and the control of the subsequent pulse of electrons (containing as many as 5x10{sup 7} electrons) create significant challenges for a standard microscope column that is designed to operate with a single electron in the column at any one time. In this paper, the generation and control of electron pulses in the TEM to obtain a temporal resolution <10{sup -6} s will be described and the effect of the pulse duration and current density on the spatial resolution of the instrument will be examined. The potential of these levels of temporal and spatial resolution for the study of dynamic materials processes will also be discussed.

  9. Practical considerations for high spatial and temporal resolution dynamic transmission electron microscopy

    International Nuclear Information System (INIS)

    Armstrong, Michael R.; Boyden, Ken; Browning, Nigel D.; Campbell, Geoffrey H.; Colvin, Jeffrey D.; De Hope, William J.; Frank, Alan M.; Gibson, David J.; Hartemann, Fred; Kim, Judy S.; King, Wayne E.; La Grange, Thomas B.; Pyke, Ben J.; Reed, Bryan W.; Shuttlesworth, Richard M.; Stuart, Brent C.; Torralva, Ben R.

    2007-01-01

    Although recent years have seen significant advances in the spatial resolution possible in the transmission electron microscope (TEM), the temporal resolution of most microscopes is limited to video rate at best. This lack of temporal resolution means that our understanding of dynamic processes in materials is extremely limited. High temporal resolution in the TEM can be achieved, however, by replacing the normal thermionic or field emission source with a photoemission source. In this case the temporal resolution is limited only by the ability to create a short pulse of photoexcited electrons in the source, and this can be as short as a few femtoseconds. The operation of the photo-emission source and the control of the subsequent pulse of electrons (containing as many as 5x10 7 electrons) create significant challenges for a standard microscope column that is designed to operate with a single electron in the column at any one time. In this paper, the generation and control of electron pulses in the TEM to obtain a temporal resolution -6 s will be described and the effect of the pulse duration and current density on the spatial resolution of the instrument will be examined. The potential of these levels of temporal and spatial resolution for the study of dynamic materials processes will also be discussed

  10. Temporal Expectations Guide Dynamic Prioritization in Visual Working Memory through Attenuated α Oscillations.

    Science.gov (United States)

    van Ede, Freek; Niklaus, Marcel; Nobre, Anna C

    2017-01-11

    Although working memory is generally considered a highly dynamic mnemonic store, popular laboratory tasks used to understand its psychological and neural mechanisms (such as change detection and continuous reproduction) often remain relatively "static," involving the retention of a set number of items throughout a shared delay interval. In the current study, we investigated visual working memory in a more dynamic setting, and assessed the following: (1) whether internally guided temporal expectations can dynamically and reversibly prioritize individual mnemonic items at specific times at which they are deemed most relevant; and (2) the neural substrates that support such dynamic prioritization. Participants encoded two differently colored oriented bars into visual working memory to retrieve the orientation of one bar with a precision judgment when subsequently probed. To test for the flexible temporal control to access and retrieve remembered items, we manipulated the probability for each of the two bars to be probed over time, and recorded EEG in healthy human volunteers. Temporal expectations had a profound influence on working memory performance, leading to faster access times as well as more accurate orientation reproductions for items that were probed at expected times. Furthermore, this dynamic prioritization was associated with the temporally specific attenuation of contralateral α (8-14 Hz) oscillations that, moreover, predicted working memory access times on a trial-by-trial basis. We conclude that attentional prioritization in working memory can be dynamically steered by internally guided temporal expectations, and is supported by the attenuation of α oscillations in task-relevant sensory brain areas. In dynamic, everyday-like, environments, flexible goal-directed behavior requires that mental representations that are kept in an active (working memory) store are dynamic, too. We investigated working memory in a more dynamic setting than is conventional

  11. The interplay between perceptual organization and object recognition: Temporal dynamics and neuropsychology

    OpenAIRE

    Torfs, Katrien

    2012-01-01

    The ease and efficiency with which we perceive objects in daily life masks the complexity of the processes involved. The main goal of my doctoral research was to enhance our understanding of the complex interplay between perceptual organization and object recognition. To this end, we investigated the dynamic interplay between different component processes of object recognition, and their temporal dynamics. In the first part of this thesis, I present three behavioral studies focusing on the ro...

  12. The Temporal Signature of Memories: Identification of a General Mechanism for Dynamic Memory Replay in Humans

    Science.gov (United States)

    Michelmann, Sebastian; Bowman, Howard; Hanslmayr, Simon

    2016-01-01

    Reinstatement of dynamic memories requires the replay of neural patterns that unfold over time in a similar manner as during perception. However, little is known about the mechanisms that guide such a temporally structured replay in humans, because previous studies used either unsuitable methods or paradigms to address this question. Here, we overcome these limitations by developing a new analysis method to detect the replay of temporal patterns in a paradigm that requires participants to mentally replay short sound or video clips. We show that memory reinstatement is accompanied by a decrease of low-frequency (8 Hz) power, which carries a temporal phase signature of the replayed stimulus. These replay effects were evident in the visual as well as in the auditory domain and were localized to sensory-specific regions. These results suggest low-frequency phase to be a domain-general mechanism that orchestrates dynamic memory replay in humans. PMID:27494601

  13. The Temporal Signature of Memories: Identification of a General Mechanism for Dynamic Memory Replay in Humans.

    Directory of Open Access Journals (Sweden)

    Sebastian Michelmann

    2016-08-01

    Full Text Available Reinstatement of dynamic memories requires the replay of neural patterns that unfold over time in a similar manner as during perception. However, little is known about the mechanisms that guide such a temporally structured replay in humans, because previous studies used either unsuitable methods or paradigms to address this question. Here, we overcome these limitations by developing a new analysis method to detect the replay of temporal patterns in a paradigm that requires participants to mentally replay short sound or video clips. We show that memory reinstatement is accompanied by a decrease of low-frequency (8 Hz power, which carries a temporal phase signature of the replayed stimulus. These replay effects were evident in the visual as well as in the auditory domain and were localized to sensory-specific regions. These results suggest low-frequency phase to be a domain-general mechanism that orchestrates dynamic memory replay in humans.

  14. Brazilian Amazon Roads and Parks: Temporal & Spatial Deforestation Dynamics

    Science.gov (United States)

    Pfaff, A.; Robalino, J.

    2011-12-01

    Heterogeneous Forest Impacts of Transport Infrastructure: spatial frontier dynamics & impacts of Brazilian Amazon road changes Prior research on road impacts has almost completely ignored heterogeneity of impacts and as a result both empirically understated potential impact and missed policy potential. We note von Thunen's model suggests not only heterogeneity with distance from market but also specifically road impacts rising then falling with distance ('non-monoThunicity') Endogenous development and partial adjustment dynamics support this for the short run. Causal effects result from studying Brazilian Amazon deforestation (1976-87, 2000-04) using matching for short-run responses to lagged new roads changes (1968-75, 1985-00). We show the critical role of prior development, proxied by 1968 and 1985 road distances, for which exact matching addresses development trends and transforms impact estimates. Splitting the sample on this measure finds confirmation of the nonmonotonic predictions: new road impacts are relatively low if a prior road was close, such that prior transport access and endogenous development dynamics compete with the new road for influence, but also if a prior road was far, since first-decade adjustment in pristine areas is limited; yet in between these bounds, investments immediately raise deforestation significantly. This pattern helps to explain lower estimates within research on a single average impact. It suggests potential for REDD if a country chooses to shift its spatial transport networks. Protected Areas & Brazilian Amazon Deforestation: modeling and testing the impacts of varied PA strategies We model and then estimate the impacts of multiple types of protected areas upon 2000 - 2004 deforestation in the Brazilian Amazon. Our modeling starts with federal versus state objectives and predicts differences in both choice and implementation of each PA strategy that we examine. Our empirical examination brings not only breakdowns sufficient

  15. Graphics Processing Unit-Enhanced Genetic Algorithms for Solving the Temporal Dynamics of Gene Regulatory Networks.

    Science.gov (United States)

    García-Calvo, Raúl; Guisado, J L; Diaz-Del-Rio, Fernando; Córdoba, Antonio; Jiménez-Morales, Francisco

    2018-01-01

    Understanding the regulation of gene expression is one of the key problems in current biology. A promising method for that purpose is the determination of the temporal dynamics between known initial and ending network states, by using simple acting rules. The huge amount of rule combinations and the nonlinear inherent nature of the problem make genetic algorithms an excellent candidate for finding optimal solutions. As this is a computationally intensive problem that needs long runtimes in conventional architectures for realistic network sizes, it is fundamental to accelerate this task. In this article, we study how to develop efficient parallel implementations of this method for the fine-grained parallel architecture of graphics processing units (GPUs) using the compute unified device architecture (CUDA) platform. An exhaustive and methodical study of various parallel genetic algorithm schemes-master-slave, island, cellular, and hybrid models, and various individual selection methods (roulette, elitist)-is carried out for this problem. Several procedures that optimize the use of the GPU's resources are presented. We conclude that the implementation that produces better results (both from the performance and the genetic algorithm fitness perspectives) is simulating a few thousands of individuals grouped in a few islands using elitist selection. This model comprises 2 mighty factors for discovering the best solutions: finding good individuals in a short number of generations, and introducing genetic diversity via a relatively frequent and numerous migration. As a result, we have even found the optimal solution for the analyzed gene regulatory network (GRN). In addition, a comparative study of the performance obtained by the different parallel implementations on GPU versus a sequential application on CPU is carried out. In our tests, a multifold speedup was obtained for our optimized parallel implementation of the method on medium class GPU over an equivalent

  16. Graphics Processing Unit–Enhanced Genetic Algorithms for Solving the Temporal Dynamics of Gene Regulatory Networks

    Science.gov (United States)

    García-Calvo, Raúl; Guisado, JL; Diaz-del-Rio, Fernando; Córdoba, Antonio; Jiménez-Morales, Francisco

    2018-01-01

    Understanding the regulation of gene expression is one of the key problems in current biology. A promising method for that purpose is the determination of the temporal dynamics between known initial and ending network states, by using simple acting rules. The huge amount of rule combinations and the nonlinear inherent nature of the problem make genetic algorithms an excellent candidate for finding optimal solutions. As this is a computationally intensive problem that needs long runtimes in conventional architectures for realistic network sizes, it is fundamental to accelerate this task. In this article, we study how to develop efficient parallel implementations of this method for the fine-grained parallel architecture of graphics processing units (GPUs) using the compute unified device architecture (CUDA) platform. An exhaustive and methodical study of various parallel genetic algorithm schemes—master-slave, island, cellular, and hybrid models, and various individual selection methods (roulette, elitist)—is carried out for this problem. Several procedures that optimize the use of the GPU’s resources are presented. We conclude that the implementation that produces better results (both from the performance and the genetic algorithm fitness perspectives) is simulating a few thousands of individuals grouped in a few islands using elitist selection. This model comprises 2 mighty factors for discovering the best solutions: finding good individuals in a short number of generations, and introducing genetic diversity via a relatively frequent and numerous migration. As a result, we have even found the optimal solution for the analyzed gene regulatory network (GRN). In addition, a comparative study of the performance obtained by the different parallel implementations on GPU versus a sequential application on CPU is carried out. In our tests, a multifold speedup was obtained for our optimized parallel implementation of the method on medium class GPU over an equivalent

  17. A Model of the Temporal Dynamics of Knowledge Brokerage in Sustainable Development

    Science.gov (United States)

    Hukkinen, Janne I.

    2016-01-01

    I develop a conceptual model of the temporal dynamics of knowledge brokerage for sustainable development. Brokerage refers to efforts to make research and policymaking more accessible to each other. The model enables unbiased and systematic consideration of knowledge brokerage as part of policy evolution. The model is theoretically grounded in…

  18. Temporal dynamics of motor cortex excitability during perception of natural emotional scenes

    NARCIS (Netherlands)

    Borgomaneri, Sara; Gazzola, Valeria; Avenanti, Alessio

    2014-01-01

    Although it is widely assumed that emotions prime the body for action, the effects of visual perception of natural emotional scenes on the temporal dynamics of the human motor system have scarcely been investigated. Here, we used single-pulse transcranial magnetic stimulation (TMS) to assess motor

  19. The Temporal Dynamics of Spoken Word Recognition in Adverse Listening Conditions

    Science.gov (United States)

    Brouwer, Susanne; Bradlow, Ann R.

    2016-01-01

    This study examined the temporal dynamics of spoken word recognition in noise and background speech. In two visual-world experiments, English participants listened to target words while looking at four pictures on the screen: a target (e.g. "candle"), an onset competitor (e.g. "candy"), a rhyme competitor (e.g.…

  20. An assessment of the temporal dynamics of moral decisions

    Directory of Open Access Journals (Sweden)

    Gregory J. Koop

    2013-09-01

    Full Text Available In the domain of moral decision making, models in which emotion and deliberation constitute competing dual-systems have become increasingly popular. Currently, the favored explanation of this interaction is what Evans (2008 termed a ``default-interventionist'' (DI process where moral decisions are the result of a prepotent emotional response, which can be overridden with substantial deliberative effort. Although this ``emotion-then-deliberation'' sequence is often assumed, existing methods have lacked the requisite process resolution to clearly depict the nature of this interaction. The present work utilized continuous mouse tracking, or response dynamics, to develop and test predictions of these DI models of moral decision making. Study 1 utilized previously published moral dilemmas to validate the method for use with such complex stimuli. Although the data replicated typical choice and RT patterns, the process metrics provided by the response trajectories did not demonstrate the online preference reversals predicted by DI models. Study 2 utilized more rigorously constructed stimuli and an alternative presentation format to provide the strongest possible test of DI predictions, but again failed to show the predicted reversals. In summary, neither experiment provided data in accordance with the predictions of popular DI dual-systems models, which suggests that researchers should consider models allowing for concurrent activation of deliberative and emotional systems, or reconceptualize moral decisions within the typical multiattribute decision framework.

  1. Temporal dynamics of reward anticipation in the human brain.

    Science.gov (United States)

    Zhang, Yuanyuan; Li, Qi; Wang, Zhao; Liu, Xun; Zheng, Ya

    2017-09-01

    Reward anticipation is a complex process including cue evaluation, motor preparation, and feedback anticipation. The present study investigated whether these psychological processes were dissociable on neural dynamics in terms of incentive valence and approach motivation. We recorded EEG when participants were performing a monetary incentive delay task, and found a cue-P3 during the cue-evaluation stage, a contingent negative variation (CNV) during the motor-preparation stage, and a stimulus-preceding negativity (SPN) during the feedback-anticipation stage. Critically, both the cue-P3 and SPN exhibited an enhanced sensitivity to gain versus loss anticipation, which was not observed for the CNV. Moreover, both the cue-P3 and SPN, instead of the CNV, for gain anticipation selectively predicted the participants' approach motivation as measured in a following effort expenditure for rewards task, particularly when reward uncertainty was maximal. Together, these results indicate that reward anticipation consists of several sub-stages, each with distinct functional significance, thus providing implications for neuropsychiatric diseases characterized by dysfunction in anticipatory reward processing. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. An American termite in Paris: temporal colony dynamics.

    Science.gov (United States)

    Baudouin, Guillaume; Dedeine, Franck; Bech, Nicolas; Bankhead-Dronnet, Stéphanie; Dupont, Simon; Bagnères, Anne-Geneviève

    2017-12-01

    Termites of the genus Reticulitermes are widespread invaders, particularly in urban habitats. Their cryptic and subterranean lifestyle makes them difficult to detect, and we know little about their colony dynamics over time. In this study we examined the persistence of Reticulitermes flavipes (Kollar) colonies in the city of Paris over a period of 15 years. The aim was (1) to define the boundaries of colonies sampled within the same four areas over two sampling periods, (2) to determine whether the colonies identified during the first sampling period persisted to the second sampling period, and (3) to compare the results obtained when colonies were delineated using a standard population genetic approach versus a Bayesian clustering method that combined both spatial and genetic information. Herein, colony delineations were inferred from genetic differences at nine microsatellite loci and one mitochondrial locus. Four of the 18 identified colonies did not show significant differences in their genotype distributions between the two sampling periods. While allelic richness was low, making it hard to reliably distinguish colony family type, most colonies appeared to retain the same breeding structure over time. These large and expansive colonies showed an important ability to fuse (39% were mixed-family colonies), contained hundreds of reproductives and displayed evidence of isolation-by-distance, suggesting budding dispersal. These traits, which favor colony persistence over time, present a challenge for pest control efforts, which apply treatment locally. The other colonies showed significant differences, but we cannot exclude the possibility that their genotype distributions simply changed over time.

  3. Estimation of numerical uncertainty in computational fluid dynamics simulations of a passively controlled wave energy converter

    DEFF Research Database (Denmark)

    Wang, Weizhi; Wu, Minghao; Palm, Johannes

    2018-01-01

    for almost linear incident waves. First, we show that the computational fluid dynamics simulations have acceptable agreement to experimental data. We then present a verification and validation study focusing on the solution verification covering spatial and temporal discretization, iterative and domain......The wave loads and the resulting motions of floating wave energy converters are traditionally computed using linear radiation–diffraction methods. Yet for certain cases such as survival conditions, phase control and wave energy converters operating in the resonance region, more complete...... dynamics simulations have largely been overlooked in the wave energy sector. In this article, we apply formal verification and validation techniques to computational fluid dynamics simulations of a passively controlled point absorber. The phase control causes the motion response to be highly nonlinear even...

  4. Simulation of burning plasma dynamics in ITER

    International Nuclear Information System (INIS)

    Wang, J.F.; Amano, T.; Ogawa, Y.; Inoue, N.

    1996-02-01

    Dynamics of burning plasma for various transient situations in ITER plasma has been simulated with a 1.5-dimensional up-down asymmetry Tokamak Transport Simulation Code (TTSC). We have mainly paid attention to intrinsic plasma transport processes such as the confinement improvement and the change of plasma profiles. It is shown that a large excursion of the fusion power takes place with a small improvement of the plasma confinement; e.g., an increase of the global energy confinement by a factor of 1.22 yields the fusion power excursion of ∼ 30% within a few seconds. Any feedback control of fueling D-T gas is difficult to respond to this short time scale of fusion power transient. The effect of the plasma profile on the fusion power excursion has been studied, by changing the particle transport denoted by the inward pinch parameter C V . It is found that the fusion power excursion is mild and slow, and the feedback control is quite effective in suppressing the fusion power excursion and in shortening the duration time of power transient in this case. The change in the pumping efficiency has also been studied and a large excursion of the fusion power has not been observed, because of the decrease in the fuel density itself in the case of the increase in the pumping efficiency, and the helium ash accumulation in the case of the decrease in the pumping efficiency. Finally it is shown that the MHD sawteeth activity leads to the fusion power fluctuation of ± 20%, although it is helpful for the helium ash exhaust. (author)

  5. Computer simulation of dynamic processes on accelerators

    International Nuclear Information System (INIS)

    Kol'ga, V.V.

    1979-01-01

    The problems of computer numerical investigation of motion of accelerated particles in accelerators and storages, an effect of different accelerator systems on the motion, determination of optimal characteristics of accelerated charged particle beams are considered. Various simulation representations are discussed which describe the accelerated particle dynamics, such as the enlarged particle method, the representation where a great number of discrete particle is substituted for a field of continuously distributed space charge, the method based on determination of averaged beam characteristics. The procedure is described of numerical studies involving the basic problems, viz. calculation of closed orbits, establishment of stability regions, investigation of resonance propagation determination of the phase stability region, evaluation of the space charge effect the problem of beam extraction. It is shown that most of such problems are reduced to solution of the Cauchy problem using a computer. The ballistic method which is applied to solution of the boundary value problem of beam extraction is considered. It is shown that introduction into the equation under study of additional members with the small positive regularization parameter is a general idea of the methods for regularization of noncorrect problems [ru

  6. Annual Report 1999 Environmental Dynamics and Simulation

    Energy Technology Data Exchange (ETDEWEB)

    NS Foster-Mills

    2000-06-28

    This annual report describes selected 1999 research accomplishments for the Environmental Dynamics and Simulation (ED and S) directorate, one of six research organizations in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL). These accomplishments are representative of the different lines of research underway in the ED and S directorate. EMSL is one of US Department of Energy's (DOE) national scientific user facilities and is the centerpiece of DOE's commitment to providing world-class experimental, theoretical, and computational capabilities for solving the nation's environmental problems. Capabilities in the EMSL include over 100 major instrument systems for use by the resident research staff, their collaborators, and users of the EMSL. These capabilities are used to address the fundamental science that will be the basis for finding solutions to national environmental issues such as cleaning up contamianted areas at DOE sites across the country and developing green technologies that will reduce or eliminate future pollution production. The capabilities are also used to further the understanding of global climate change and environmental issues relevant to energy production and use and health effects resulting from exposure to contaminated environments.

  7. Spatio-temporal reconstruction of brain dynamics from EEG with a Markov prior

    DEFF Research Database (Denmark)

    Hansen, Sofie Therese; Hansen, Lars Kai

    2016-01-01

    the functional dynamics of the brain. Solving the inverse problem of EEG is however highly ill-posed as there are many more potential locations of the EEG generators than EEG measurement points. Several well-known properties of brain dynamics can be exploited to alleviate this problem. More short ranging......Electroencephalography (EEG) can capture brain dynamics in high temporal resolution. By projecting the scalp EEG signal back to its origin in the brain also high spatial resolution can be achieved. Source localized EEG therefore has potential to be a very powerful tool for understanding...

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

    Energy Technology Data Exchange (ETDEWEB)

    Concepcion, Ricky James [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Elliott, Ryan Thomas [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-12-01

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

  9. System Design Description Salt Well Liquid Pumping Dynamic Simulation

    International Nuclear Information System (INIS)

    HARMSEN, R.W.

    1999-01-01

    The Salt Well Liquid (SWL) Pumping Dynamic Simulation used by the single-shell tank (SST) Interim Stabilization Project is described. A graphical dynamic simulation predicts SWL removal from 29 SSTs using an exponential function and unique time constant for each SST. Increasing quarterly efficiencies are applied to adjust the pumping rates during fiscal year 2000

  10. Spatial and Temporal Dynamics and Value of Nature-Based Recreation, Estimated via Social Media.

    Science.gov (United States)

    Sonter, Laura J; Watson, Keri B; Wood, Spencer A; Ricketts, Taylor H

    2016-01-01

    Conserved lands provide multiple ecosystem services, including opportunities for nature-based recreation. Managing this service requires understanding the landscape attributes underpinning its provision, and how changes in land management affect its contribution to human wellbeing over time. However, evidence from both spatially explicit and temporally dynamic analyses is scarce, often due to data limitations. In this study, we investigated nature-based recreation within conserved lands in Vermont, USA. We used geotagged photographs uploaded to the photo-sharing website Flickr to quantify visits by in-state and out-of-state visitors, and we multiplied visits by mean trip expenditures to show that conserved lands contributed US $1.8 billion (US $0.18-20.2 at 95% confidence) to Vermont's tourism industry between 2007 and 2014. We found eight landscape attributes explained the pattern of visits to conserved lands; visits were higher in larger conserved lands, with less forest cover, greater trail density and more opportunities for snow sports. Some of these attributes differed from those found in other locations, but all aligned with our understanding of recreation in Vermont. We also found that using temporally static models to inform conservation decisions may have perverse outcomes for nature-based recreation. For example, static models suggest conserved land with less forest cover receive more visits, but temporally dynamic models suggest clearing forests decreases, rather than increases, visits to these sites. Our results illustrate the importance of understanding both the spatial and temporal dynamics of ecosystem services for conservation decision-making.

  11. Portraying Temporal Dynamics of Urban Spatial Divisions with Mobile Phone Positioning Data: A Complex Network Approach

    Directory of Open Access Journals (Sweden)

    Meng Zhou

    2016-12-01

    Full Text Available Spatial structure is a fundamental characteristic of cities that influences the urban functioning to a large extent. While administrative partitioning is generally done in the form of static spatial division, understanding a more temporally dynamic structure of the urban space would benefit urban planning and management immensely. This study makes use of a large-scale mobile phone positioning dataset to characterize the diurnal dynamics of the interaction-based urban spatial structure. To extract the temporally vibrant structure, spatial interaction networks at different times are constructed based on the movement connections of individuals between geographical units. Complex network community detection technique is applied to identify the spatial divisions as well as to quantify their temporal dynamics. Empirical analysis is conducted using data containing all user positions on a typical weekday in Shenzhen, China. Results are compared with official zoning and planned structure and indicate a certain degree of expansion in urban central areas and fragmentation in industrial suburban areas. A high level of variability in spatial divisions at different times of day is detected with some distinct temporal features. Peak and pre-/post-peak hours witness the most prominent fluctuation in spatial division indicating significant change in the characteristics of movements and activities during these periods of time. Findings of this study demonstrate great potential of large-scale mobility data in supporting intelligent spatial decision making and providing valuable knowledge to the urban planning sectors.

  12. Modeling Temporal Behavior in Large Networks: A Dynamic Mixed-Membership Model

    Energy Technology Data Exchange (ETDEWEB)

    Rossi, R; Gallagher, B; Neville, J; Henderson, K

    2011-11-11

    Given a large time-evolving network, how can we model and characterize the temporal behaviors of individual nodes (and network states)? How can we model the behavioral transition patterns of nodes? We propose a temporal behavior model that captures the 'roles' of nodes in the graph and how they evolve over time. The proposed dynamic behavioral mixed-membership model (DBMM) is scalable, fully automatic (no user-defined parameters), non-parametric/data-driven (no specific functional form or parameterization), interpretable (identifies explainable patterns), and flexible (applicable to dynamic and streaming networks). Moreover, the interpretable behavioral roles are generalizable, computationally efficient, and natively supports attributes. We applied our model for (a) identifying patterns and trends of nodes and network states based on the temporal behavior, (b) predicting future structural changes, and (c) detecting unusual temporal behavior transitions. We use eight large real-world datasets from different time-evolving settings (dynamic and streaming). In particular, we model the evolving mixed-memberships and the corresponding behavioral transitions of Twitter, Facebook, IP-Traces, Email (University), Internet AS, Enron, Reality, and IMDB. The experiments demonstrate the scalability, flexibility, and effectiveness of our model for identifying interesting patterns, detecting unusual structural transitions, and predicting the future structural changes of the network and individual nodes.

  13. A dynamic texture-based approach to recognition of facial actions and their temporal models.

    Science.gov (United States)

    Koelstra, Sander; Pantic, Maja; Patras, Ioannis

    2010-11-01

    In this work, we propose a dynamic texture-based approach to the recognition of facial Action Units (AUs, atomic facial gestures) and their temporal models (i.e., sequences of temporal segments: neutral, onset, apex, and offset) in near-frontal-view face videos. Two approaches to modeling the dynamics and the appearance in the face region of an input video are compared: an extended version of Motion History Images and a novel method based on Nonrigid Registration using Free-Form Deformations (FFDs). The extracted motion representation is used to derive motion orientation histogram descriptors in both the spatial and temporal domain. Per AU, a combination of discriminative, frame-based GentleBoost ensemble learners and dynamic, generative Hidden Markov Models detects the presence of the AU in question and its temporal segments in an input image sequence. When tested for recognition of all 27 lower and upper face AUs, occurring alone or in combination in 264 sequences from the MMI facial expression database, the proposed method achieved an average event recognition accuracy of 89.2 percent for the MHI method and 94.3 percent for the FFD method. The generalization performance of the FFD method has been tested using the Cohn-Kanade database. Finally, we also explored the performance on spontaneous expressions in the Sensitive Artificial Listener data set.

  14. A Temporal Domain Decomposition Algorithmic Scheme for Large-Scale Dynamic Traffic Assignment

    Directory of Open Access Journals (Sweden)

    Eric J. Nava

    2012-03-01

    This paper presents a temporal decomposition scheme for large spatial- and temporal-scale dynamic traffic assignment, in which the entire analysis period is divided into Epochs. Vehicle assignment is performed sequentially in each Epoch, thus improving the model scalability and confining the peak run-time memory requirement regardless of the total analysis period. A proposed self-turning scheme adaptively searches for the run-time-optimal Epoch setting during iterations regardless of the characteristics of the modeled network. Extensive numerical experiments confirm the promising performance of the proposed algorithmic schemes.

  15. Dual Quaternion Variational Integrator for Rigid Body Dynamic Simulation

    OpenAIRE

    Xu, Jiafeng; Halse, Karl Henning

    2016-01-01

    In rigid body dynamic simulations, often the algorithm is required to deal with general situations where both reference point and inertia matrix are arbitrarily de- fined. We introduce a novel Lie group variational integrator using dual quaternion for simulating rigid body dynamics in all six degrees of freedom. Dual quaternion is used to represent rigid body kinematics and one-step Lie group method is used to derive dynamic equations. The combination of these two becomes the first Lie group ...

  16. A note on simulation and dynamical hierarchies

    Energy Technology Data Exchange (ETDEWEB)

    Rasmussen, S.; Barrett, C.L. [Los Alamos National Lab., NM (United States)]|[Santa Fe Institute, Sante Fe, NM (United States); Baas, N.A. [Trondheim Univ. (Norway). Dept. of Mathematical Sciences; Olesen, M.W. [Los Alamos National Lab., NM (United States)

    1996-02-22

    This paper summarizes some of the problems associated with the generation of higher order emergent structures in formal dynamical systems as well as some of the formal properties of dynamical systems capable of generating higher order structures.

  17. Characterization and Simulation of Transient Vibrations Using Band Limited Temporal Moments

    Directory of Open Access Journals (Sweden)

    David O. Smallwood

    1994-01-01

    Full Text Available A method is described to characterize shocks (transient time histories in terms of the Fourier energy spectrum and the temporal moments of the shock passed through a contiguous set of band pass filters. The product model is then used to generate of a random process as simulations that in the mean will have the same energy and moments as the characterization of the transient event.

  18. Surface Dynamic Process Simulation with the Use of Cellular Automata

    International Nuclear Information System (INIS)

    Adamska-Szatko, M.; Bala, J.

    2010-01-01

    Cellular automata are known for many applications, especially for physical and biological simulations. Universal cellular automata can be used for modelling complex natural phenomena. The paper presents simulation of surface dynamic process. Simulation uses 2-dimensional cellular automata algorithm. Modelling and visualisation were created by in-house developed software with standard OpenGL graphic library. (authors)

  19. High tech supply chain simulation based on dynamical systems model

    NARCIS (Netherlands)

    Yuan, X.; Ashayeri, J.

    2013-01-01

    During the last 45 years, system dynamics as a continuous type of simulation has been used for simulating various problems, ranging from economic to engineering and managerial when limited (historical) information is available. Control theory is another alternative for continuous simulation that

  20. Application of the maximum entropy method to dynamical fermion simulations

    Science.gov (United States)

    Clowser, Jonathan

    This thesis presents results for spectral functions extracted from imaginary-time correlation functions obtained from Monte Carlo simulations using the Maximum Entropy Method (MEM). The advantages this method are (i) no a priori assumptions or parametrisations of the spectral function are needed, (ii) a unique solution exists and (iii) the statistical significance of the resulting image can be quantitatively analysed. The Gross Neveu model in d = 3 spacetime dimensions (GNM3) is a particularly interesting model to study with the MEM because at T = 0 it has a broken phase with a rich spectrum of mesonic bound states and a symmetric phase where there are resonances. Results for the elementary fermion, the Goldstone boson (pion), the sigma, the massive pseudoscalar meson and the symmetric phase resonances are presented. UKQCD Nf = 2 dynamical QCD data is also studied with MEM. Results are compared to those found from the quenched approximation, where the effects of quark loops in the QCD vacuum are neglected, to search for sea-quark effects in the extracted spectral functions. Information has been extract from the difficult axial spatial and scalar as well as the pseudoscalar, vector and axial temporal channels. An estimate for the non-singlet scalar mass in the chiral limit is given which is in agreement with the experimental value of Mao = 985 MeV.

  1. Estimating spatio-temporal dynamics of stream total phosphate concentration by soft computing techniques.

    Science.gov (United States)

    Chang, Fi-John; Chen, Pin-An; Chang, Li-Chiu; Tsai, Yu-Hsuan

    2016-08-15

    This study attempts to model the spatio-temporal dynamics of total phosphate (TP) concentrations along a river for effective hydro-environmental management. We propose a systematical modeling scheme (SMS), which is an ingenious modeling process equipped with a dynamic neural network and three refined statistical methods, for reliably predicting the TP concentrations along a river simultaneously. Two different types of artificial neural network (BPNN-static neural network; NARX network-dynamic neural network) are constructed in modeling the dynamic system. The Dahan River in Taiwan is used as a study case, where ten-year seasonal water quality data collected at seven monitoring stations along the river are used for model training and validation. Results demonstrate that the NARX network can suitably capture the important dynamic features and remarkably outperforms the BPNN model, and the SMS can effectively identify key input factors, suitably overcome data scarcity, significantly increase model reliability, satisfactorily estimate site-specific TP concentration at seven monitoring stations simultaneously, and adequately reconstruct seasonal TP data into a monthly scale. The proposed SMS can reliably model the dynamic spatio-temporal water pollution variation in a river system for missing, hazardous or costly data of interest. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Real time simulation method for fast breeder reactors dynamics

    International Nuclear Information System (INIS)

    Miki, Tetsushi; Mineo, Yoshiyuki; Ogino, Takamichi; Kishida, Koji; Furuichi, Kenji.

    1985-01-01

    The development of multi-purpose real time simulator models with suitable plant dynamics was made; these models can be used not only in training operators but also in designing control systems, operation sequences and many other items which must be studied for the development of new type reactors. The prototype fast breeder reactor ''Monju'' is taken as an example. Analysis is made on various factors affecting the accuracy and computer load of its dynamic simulation. A method is presented which determines the optimum number of nodes in distributed systems and time steps. The oscillations due to the numerical instability are observed in the dynamic simulation of evaporators with a small number of nodes, and a method to cancel these oscillations is proposed. It has been verified through the development of plant dynamics simulation codes that these methods can provide efficient real time dynamics models of fast breeder reactors. (author)

  3. Face processing regions are sensitive to distinct aspects of temporal sequence in facial dynamics.

    Science.gov (United States)

    Reinl, Maren; Bartels, Andreas

    2014-11-15

    Facial movement conveys important information for social interactions, yet its neural processing is poorly understood. Computational models propose that shape- and temporal sequence sensitive mechanisms interact in processing dynamic faces. While face processing regions are known to respond to facial movement, their sensitivity to particular temporal sequences has barely been studied. Here we used fMRI to examine the sensitivity of human face-processing regions to two aspects of directionality in facial movement trajectories. We presented genuine movie recordings of increasing and decreasing fear expressions, each of which were played in natural or reversed frame order. This two-by-two factorial design matched low-level visual properties, static content and motion energy within each factor, emotion-direction (increasing or decreasing emotion) and timeline (natural versus artificial). The results showed sensitivity for emotion-direction in FFA, which was timeline-dependent as it only occurred within the natural frame order, and sensitivity to timeline in the STS, which was emotion-direction-dependent as it only occurred for decreased fear. The occipital face area (OFA) was sensitive to the factor timeline. These findings reveal interacting temporal sequence sensitive mechanisms that are responsive to both ecological meaning and to prototypical unfolding of facial dynamics. These mechanisms are temporally directional, provide socially relevant information regarding emotional state or naturalness of behavior, and agree with predictions from modeling and predictive coding theory. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  4. Laminar and Temporal Expression Dynamics of Coding and Noncoding RNAs in the Mouse Neocortex

    Directory of Open Access Journals (Sweden)

    Sofia Fertuzinhos

    2014-03-01

    Full Text Available The hallmark of the cerebral neocortex is its organization into six layers, each containing a characteristic set of cell types and synaptic connections. The transcriptional events involved in laminar development and function still remain elusive. Here, we employed deep sequencing of mRNA and small RNA species to gain insights into transcriptional differences among layers and their temporal dynamics during postnatal development of the mouse primary somatosensory neocortex. We identify a number of coding and noncoding transcripts with specific spatiotemporal expression and splicing patterns. We also identify signature trajectories and gene coexpression networks associated with distinct biological processes and transcriptional overlap between these processes. Finally, we provide data that allow the study of potential miRNA and mRNA interactions. Overall, this study provides an integrated view of the laminar and temporal expression dynamics of coding and noncoding transcripts in the mouse neocortex and a resource for studies of neurodevelopment and transcriptome.

  5. Ensemble simulations with discrete classical dynamics

    DEFF Research Database (Denmark)

    Toxværd, Søren

    2013-01-01

    For discrete classical Molecular dynamics (MD) obtained by the "Verlet" algorithm (VA) with the time increment $h$ there exist a shadow Hamiltonian $\\tilde{H}$ with energy $\\tilde{E}(h)$, for which the discrete particle positions lie on the analytic trajectories for $\\tilde{H}$. $\\tilde......{E}(h)$ is employed to determine the relation with the corresponding energy, $E$ for the analytic dynamics with $h=0$ and the zero-order estimate $E_0(h)$ of the energy for discrete dynamics, appearing in the literature for MD with VA. We derive a corresponding time reversible VA algorithm for canonical dynamics...

  6. Spatial and temporal dynamics of the microbial community in the Hanford unconfined aquifer

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Xueju; McKinley, James P.; Resch, Charles T.; Kaluzny, Rachael M.; Lauber, C.; Fredrickson, Jim K.; Knight, Robbie C.; Konopka, Allan

    2012-03-29

    Pyrosequencing analysis of 16S rRNA genes was used to study temporal dynamics of groundwater Bacteria and Archaea over 10 months within 3 well clusters separated by ~30 m and located 250 m from the Columbia River on the Hanford Site, WA. Each cluster contained 3 wells screened at different depths ranging from 10 to 17 m that differed in hydraulic conductivities. Representative samples were selected for analyses of prokaryotic 16S and eukaryotic 18S rRNA gene copy numbers. Temporal changes in community composition occurred in all 9 wells over the 10 month sampling period. However, there were particularly strong effects near the top of the water table when the seasonal rise in the Columbia River caused river water intrusion at the top of the aquifer. The occurrence and disappearance of some microbial assemblages (such as Actinobacteria ACK-M1) were correlated to river water intrusion. This seasonal impact on microbial community structure was greater in the shallow saturated zone than deeper in the aquifer. Spatial and temporal patterns for several 16S rRNA gene operational taxonomic units associated with particular physiological functions (e.g.methane oxidizers and metal reducers) suggests dynamic changes in fluxes of electron donors and acceptors over an annual cycle. In addition, temporal dynamics in eukaryotic 18S rRNA gene copies and the dominance of protozoa in 18S clone libraries suggest that bacterial community dynamics could be affected not only by the physical and chemical environment, but also by top-down biological control.

  7. Kinematics and dynamics analysis of a novel serial-parallel dynamic simulator

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Bo; Zhang, Lian Dong; Yu, Jingjing [Parallel Robot and Mechatronic System Laboratory of Hebei Province, Yanshan University, Qinhuangdao, Hebei (China)

    2016-11-15

    A serial-parallel dynamics simulator based on serial-parallel manipulator is proposed. According to the dynamics simulator motion requirement, the proposed serial-parallel dynamics simulator formed by 3-RRS (active revolute joint-revolute joint-spherical joint) and 3-SPR (Spherical joint-active prismatic joint-revolute joint) PMs adopts the outer and inner layout. By integrating the kinematics, constraint and coupling information of the 3-RRS and 3-SPR PMs into the serial-parallel manipulator, the inverse Jacobian matrix, velocity, and acceleration of the serial-parallel dynamics simulator are studied. Based on the principle of virtual work and the kinematics model, the inverse dynamic model is established. Finally, the workspace of the (3-RRS)+(3-SPR) dynamics simulator is constructed.

  8. Kinematics and dynamics analysis of a novel serial-parallel dynamic simulator

    International Nuclear Information System (INIS)

    Hu, Bo; Zhang, Lian Dong; Yu, Jingjing

    2016-01-01

    A serial-parallel dynamics simulator based on serial-parallel manipulator is proposed. According to the dynamics simulator motion requirement, the proposed serial-parallel dynamics simulator formed by 3-RRS (active revolute joint-revolute joint-spherical joint) and 3-SPR (Spherical joint-active prismatic joint-revolute joint) PMs adopts the outer and inner layout. By integrating the kinematics, constraint and coupling information of the 3-RRS and 3-SPR PMs into the serial-parallel manipulator, the inverse Jacobian matrix, velocity, and acceleration of the serial-parallel dynamics simulator are studied. Based on the principle of virtual work and the kinematics model, the inverse dynamic model is established. Finally, the workspace of the (3-RRS)+(3-SPR) dynamics simulator is constructed

  9. Integrating Future Land Use Scenarios to Evaluate the Spatio-Temporal Dynamics of Landscape Ecological Security

    Directory of Open Access Journals (Sweden)

    Yi Lu

    2016-11-01

    Full Text Available Urban ecological security is the basic principle of national ecological security. However, analyses of the spatial and temporal dynamics of ecological security remain limited, especially those that consider different scenarios of urban development. In this study, an integrated method is proposed that combines the Conversion of Land Use and its Effects (CLUE-S model with the Pressure–State–Response (P-S-R framework to assess landscape ecological security (LES in Huangshan City, China under two scenarios. Our results suggest the following conclusions: (1 the spatial and temporal dynamics of ecological security are closely related to the urbanization process; (2 although the average values of landscape ecological security are similar under different scenarios, the areas of relatively high security levels vary considerably; and (3 spatial heterogeneity in ecological security exists between different districts and counties, and the city center and its vicinity may face relatively serious declines in ecological security in the future. Overall, the proposed method not only illustrates the spatio-temporal dynamics of landscape ecological security under different scenarios but also reveals the anthropogenic effects on ecosystems by differentiating between causes, effects, and human responses at the landscape scale. This information is of great significance to decision-makers for future urban planning and management.

  10. Development Of Dynamic Probabilistic Safety Assessment: The Accident Dynamic Simulator (ADS) Tool

    International Nuclear Information System (INIS)

    Chang, Y.H.; Mosleh, A.; Dang, V.N.

    2003-01-01

    The development of a dynamic methodology for Probabilistic Safety Assessment (PSA) addresses the complex interactions between the behaviour of technical systems and personnel response in the evolution of accident scenarios. This paper introduces the discrete dynamic event tree, a framework for dynamic PSA, and its implementation in the Accident Dynamic Simulator (ADS) tool. Dynamic event tree tools generate and quantify accident scenarios through coupled simulation models of the plant physical processes, its automatic systems, the equipment reliability, and the human response. The current research on the framework, the ADS tool, and on Human Reliability Analysis issues within dynamic PSA, is discussed. (author)

  11. Development Of Dynamic Probabilistic Safety Assessment: The Accident Dynamic Simulator (ADS) Tool

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Y.H.; Mosleh, A.; Dang, V.N

    2003-03-01

    The development of a dynamic methodology for Probabilistic Safety Assessment (PSA) addresses the complex interactions between the behaviour of technical systems and personnel response in the evolution of accident scenarios. This paper introduces the discrete dynamic event tree, a framework for dynamic PSA, and its implementation in the Accident Dynamic Simulator (ADS) tool. Dynamic event tree tools generate and quantify accident scenarios through coupled simulation models of the plant physical processes, its automatic systems, the equipment reliability, and the human response. The current research on the framework, the ADS tool, and on Human Reliability Analysis issues within dynamic PSA, is discussed. (author)

  12. Dynamic fault simulation of wind turbines using commercial simulation tools

    DEFF Research Database (Denmark)

    Lund, Torsten; Eek, Jarle; Uski, Sanna

    2005-01-01

    This paper compares the commercial simulation tools: PSCAD/EMTDC, PowerFactory, SIMPOW and PSS/E for analysing fault sequences defined in the Danish grid code requirements for wind turbines connected to a voltage level below 100 kV. Both symmetrical and unsymmetrical faults are analysed. The devi......This paper compares the commercial simulation tools: PSCAD/EMTDC, PowerFactory, SIMPOW and PSS/E for analysing fault sequences defined in the Danish grid code requirements for wind turbines connected to a voltage level below 100 kV. Both symmetrical and unsymmetrical faults are analysed....... The deviations and the reasons for the deviations between the tools are stated. The simulation models are imple-mented using the built-in library components of the simulation tools with exception of the mechanical drive-train model, which had to be user-modeled in PowerFactory and PSS/E....

  13. Integration of temporal and spatial properties of dynamic connectivity networks for automatic diagnosis of brain disease.

    Science.gov (United States)

    Jie, Biao; Liu, Mingxia; Shen, Dinggang

    2018-07-01

    Functional connectivity networks (FCNs) using resting-state functional magnetic resonance imaging (rs-fMRI) have been applied to the analysis and diagnosis of brain disease, such as Alzheimer's disease (AD) and its prodrome, i.e., mild cognitive impairment (MCI). Different from conventional studies focusing on static descriptions on functional connectivity (FC) between brain regions in rs-fMRI, recent studies have resorted to dynamic connectivity networks (DCNs) to characterize the dynamic changes of FC, since dynamic changes of FC may indicate changes in macroscopic neural activity patterns in cognitive and behavioral aspects. However, most of the existing studies only investigate the temporal properties of DCNs (e.g., temporal variability of FC between specific brain regions), ignoring the important spatial properties of the network (e.g., spatial variability of FC associated with a specific brain region). Also, emerging evidence on FCNs has suggested that, besides temporal variability, there is significant spatial variability of activity foci over time. Hence, integrating both temporal and spatial properties of DCNs can intuitively promote the performance of connectivity-network-based learning methods. In this paper, we first define a new measure to characterize the spatial variability of DCNs, and then propose a novel learning framework to integrate both temporal and spatial variabilities of DCNs for automatic brain disease diagnosis. Specifically, we first construct DCNs from the rs-fMRI time series at successive non-overlapping time windows. Then, we characterize the spatial variability of a specific brain region by computing the correlation of functional sequences (i.e., the changing profile of FC between a pair of brain regions within all time windows) associated with this region. Furthermore, we extract both temporal variabilities and spatial variabilities from DCNs as features, and integrate them for classification by using manifold regularized multi

  14. Effects of high spatial and temporal resolution Earth observations on simulated hydrometeorological variables in a cropland (southwestern France

    Directory of Open Access Journals (Sweden)

    J. Etchanchu

    2017-11-01

    Full Text Available Agricultural landscapes are often constituted by a patchwork of crop fields whose seasonal evolution is dependent on specific crop rotation patterns and phenologies. This temporal and spatial heterogeneity affects surface hydrometeorological processes and must be taken into account in simulations of land surface and distributed hydrological models. The Sentinel-2 mission allows for the monitoring of land cover and vegetation dynamics at unprecedented spatial resolutions and revisit frequencies (20 m and 5 days, respectively that are fully compatible with such heterogeneous agricultural landscapes. Here, we evaluate the impact of Sentinel-2-like remote sensing data on the simulation of surface water and energy fluxes via the Interactions between the Surface Biosphere Atmosphere (ISBA land surface model included in the EXternalized SURface (SURFEX modeling platform. The study focuses on the effect of the leaf area index (LAI spatial and temporal variability on these fluxes. We compare the use of the LAI climatology from ECOCLIMAP-II, used by default in SURFEX-ISBA, and time series of LAI derived from the high-resolution Formosat-2 satellite data (8 m. The study area is an agricultural zone in southwestern France covering 576 km2 (24 km  ×  24 km. An innovative plot-scale approach is used, in which each computational unit has a homogeneous vegetation type. Evaluation of the simulations quality is done by comparing model outputs with in situ eddy covariance measurements of latent heat flux (LE. Our results show that the use of LAI derived from high-resolution remote sensing significantly improves simulated evapotranspiration with respect to ECOCLIMAP-II, especially when the surface is covered with summer crops. The comparison with in situ measurements shows an improvement of roughly 0.3 in the correlation coefficient and a decrease of around 30 % of the root mean square error (RMSE in the simulated evapotranspiration. This

  15. Simulations of the temporal and spatial resolution for a compact time-resolved electron diffractometer

    Science.gov (United States)

    Robinson, Matthew S.; Lane, Paul D.; Wann, Derek A.

    2016-02-01

    A novel compact electron gun for use in time-resolved gas electron diffraction experiments has recently been designed and commissioned. In this paper we present and discuss the extensive simulations that were performed to underpin the design in terms of the spatial and temporal qualities of the pulsed electron beam created by the ionisation of a gold photocathode using a femtosecond laser. The response of the electron pulses to a solenoid lens used to focus the electron beam has also been studied. The simulated results show that focussing the electron beam affects the overall spatial and temporal resolution of the experiment in a variety of ways, and that factors that improve the resolution of one parameter can often have a negative effect on the other. A balance must, therefore, be achieved between spatial and temporal resolution. The optimal experimental time resolution for the apparatus is predicted to be 416 fs for studies of gas-phase species, while the predicted spatial resolution of better than 2 nm-1 compares well with traditional time-averaged electron diffraction set-ups.

  16. Rare event simulation for dynamic fault trees

    NARCIS (Netherlands)

    Ruijters, Enno Jozef Johannes; Reijsbergen, D.P.; de Boer, Pieter-Tjerk; Stoelinga, Mariëlle Ida Antoinette

    2017-01-01

    Fault trees (FT) are a popular industrial method for reliability engineering, for which Monte Carlo simulation is an important technique to estimate common dependability metrics, such as the system reliability and availability. A severe drawback of Monte Carlo simulation is that the number of

  17. Rare Event Simulation for Dynamic Fault Trees

    NARCIS (Netherlands)

    Ruijters, Enno Jozef Johannes; Reijsbergen, D.P.; de Boer, Pieter-Tjerk; Stoelinga, Mariëlle Ida Antoinette; Tonetta, Stefano; Schoitsch, Erwin; Bitsch, Friedemann

    2017-01-01

    Fault trees (FT) are a popular industrial method for reliability engineering, for which Monte Carlo simulation is an important technique to estimate common dependability metrics, such as the system reliability and availability. A severe drawback of Monte Carlo simulation is that the number of

  18. Dynamic bounds coupled with Monte Carlo simulations

    NARCIS (Netherlands)

    Rajabali Nejad, Mohammadreza; Meester, L.E.; van Gelder, P.H.A.J.M.; Vrijling, J.K.

    2011-01-01

    For the reliability analysis of engineering structures a variety of methods is known, of which Monte Carlo (MC) simulation is widely considered to be among the most robust and most generally applicable. To reduce simulation cost of the MC method, variance reduction methods are applied. This paper

  19. Monitoring, analyzing and simulating of spatial-temporal changes of landscape pattern over mining area

    Science.gov (United States)

    Liu, Pei; Han, Ruimei; Wang, Shuangting

    2014-11-01

    According to the merits of remotely sensed data in depicting regional land cover and Land changes, multi- objective information processing is employed to remote sensing images to analyze and simulate land cover in mining areas. In this paper, multi-temporal remotely sensed data were selected to monitor the pattern, distri- bution and trend of LUCC and predict its impacts on ecological environment and human settlement in mining area. The monitor, analysis and simulation of LUCC in this coal mining areas are divided into five steps. The are information integration of optical and SAR data, LULC types extraction with SVM classifier, LULC trends simulation with CA Markov model, landscape temporal changes monitoring and analysis with confusion matrixes and landscape indices. The results demonstrate that the improved data fusion algorithm could make full use of information extracted from optical and SAR data; SVM classifier has an efficient and stable ability to obtain land cover maps, which could provide a good basis for both land cover change analysis and trend simulation; CA Markov model is able to predict LULC trends with good performance, and it is an effective way to integrate remotely sensed data with spatial-temporal model for analysis of land use / cover change and corresponding environmental impacts in mining area. Confusion matrixes are combined with landscape indices to evaluation and analysis show that, there was a sustained downward trend in agricultural land and bare land, but a continues growth trend tendency in water body, forest and other lands, and building area showing a wave like change, first increased and then decreased; mining landscape has undergone a from small to large and large to small process of fragmentation, agricultural land is the strongest influenced landscape type in this area, and human activities are the primary cause, so the problem should be pay more attentions by government and other organizations.

  20. Dynamic PET reconstruction using temporal patch-based low rank penalty for ROI-based brain kinetic analysis

    International Nuclear Information System (INIS)

    Kim, Kyungsang; Ye, Jong Chul; Son, Young Don; Cho, Zang Hee; Bresler, Yoram; Ra, Jong Beom

    2015-01-01

    Dynamic positron emission tomography (PET) is widely used to measure changes in the bio-distribution of radiopharmaceuticals within particular organs of interest over time. However, to retain sufficient temporal resolution, the number of photon counts in each time frame must be limited. Therefore, conventional reconstruction algorithms such as the ordered subset expectation maximization (OSEM) produce noisy reconstruction images, thus degrading the quality of the extracted time activity curves (TACs). To address this issue, many advanced reconstruction algorithms have been developed using various spatio-temporal regularizations. In this paper, we extend earlier results and develop a novel temporal regularization, which exploits the self-similarity of patches that are collected in dynamic images. The main contribution of this paper is to demonstrate that the correlation of patches can be exploited using a low-rank constraint that is insensitive to global intensity variations. The resulting optimization framework is, however, non-Lipschitz and non-convex due to the Poisson log-likelihood and low-rank penalty terms. Direct application of the conventional Poisson image deconvolution by an augmented Lagrangian (PIDAL) algorithm is, however, problematic due to its large memory requirements, which prevents its parallelization. Thus, we propose a novel optimization framework using the concave-convex procedure (CCCP) by exploiting the Legendre–Fenchel transform, which is computationally efficient and parallelizable. In computer simulation and a real in vivo experiment using a high-resolution research tomograph (HRRT) scanner, we confirm that the proposed algorithm can improve image quality while also extracting more accurate region of interests (ROI) based kinetic parameters. Furthermore, we show that the total reconstruction time for HRRT PET is significantly accelerated using our GPU implementation, which makes the algorithm very practical in clinical environments

  1. A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations

    KAUST Repository

    Neumann, Philipp; Tchipev, Nikola

    2012-01-01

    We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm

  2. Unified Nonlinear Flight Dynamics and Aeroelastic Simulator Tool, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — ZONA Technology, Inc. (ZONA) proposes a R&D effort to develop a Unified Nonlinear Flight Dynamics and Aeroelastic Simulator (UNFDAS) Tool that will combine...

  3. The effects of spatial and temporal heterogeneity on the population dynamics of four animal species in a Danish landscape

    Directory of Open Access Journals (Sweden)

    Forchhammer Mads C

    2009-06-01

    Full Text Available Abstract Background Variation in carrying capacity and population return rates is generally ignored in traditional studies of population dynamics. Variation is hard to study in the field because of difficulties controlling the environment in order to obtain statistical replicates, and because of the scale and expense of experimenting on populations. There may also be ethical issues. To circumvent these problems we used detailed simulations of the simultaneous behaviours of interacting animals in an accurate facsimile of a real Danish landscape. The models incorporate as much as possible of the behaviour and ecology of skylarks Alauda arvensis, voles Microtus agrestis, a ground beetle Bembidion lampros and a linyphiid spider Erigone atra. This allows us to quantify and evaluate the importance of spatial and temporal heterogeneity on the population dynamics of the four species. Results Both spatial and temporal heterogeneity affected the relationship between population growth rate and population density in all four species. Spatial heterogeneity accounted for 23–30% of the variance in population growth rate after accounting for the effects of density, reflecting big differences in local carrying capacity associated with the landscape features important to individual species. Temporal heterogeneity accounted for 3–13% of the variance in vole, skylark and spider, but 43% in beetles. The associated temporal variation in carrying capacity would be problematic in traditional analyses of density dependence. Return rates were less than one in all species and essentially invariant in skylarks, spiders and beetles. Return rates varied over the landscape in voles, being slower where there were larger fluctuations in local population sizes. Conclusion Our analyses estimated the traditional parameters of carrying capacities and return rates, but these are now seen as varying continuously over the landscape depending on habitat quality and the mechanisms

  4. Differentiating levels of surgical experience on a virtual reality temporal bone simulator.

    Science.gov (United States)

    Zhao, Yi C; Kennedy, Gregor; Hall, Richard; O'Leary, Stephen

    2010-11-01

    Virtual reality simulation is increasingly being incorporated into surgical training and may have a role in temporal bone surgical education. Here we test whether metrics generated by a virtual reality surgical simulation can differentiate between three levels of experience, namely novices, otolaryngology residents, and experienced qualified surgeons. Cohort study. Royal Victorian Eye and Ear Hospital. Twenty-seven participants were recruited. There were 12 experts, six residents, and nine novices. After orientation, participants were asked to perform a modified radical mastoidectomy on the simulator. Comparisons of time taken, injury to structures, and forces exerted were made between the groups to determine which specific metrics would discriminate experience levels. Experts completed the simulated task in significantly shorter time than the other two groups (experts 22 minutes, residents 36 minutes, and novices 46 minutes; P = 0.001). Novices exerted significantly higher average forces when dissecting close to vital structures compared with experts (0.24 Newton [N] vs 0.13 N, P = 0.002). Novices were also more likely to injure structures such as dura compared to experts (23 injuries vs 3 injuries, P = 0.001). Compared with residents, the experts modulated their force between initial cortex dissection and dissection close to vital structures. Using the combination of these metrics, we were able to correctly classify the participants' level of experience 90 percent of the time. This preliminary study shows that measurements of performance obtained from within a virtual reality simulator can differentiate between levels of users' experience. These results suggest that simulator training may have a role in temporal bone training beyond foundational training. Copyright © 2010 American Academy of Otolaryngology–Head and Neck Surgery Foundation. Published by Mosby, Inc. All rights reserved.

  5. In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation

    Energy Technology Data Exchange (ETDEWEB)

    Gray, Alan [The University of Edinburgh, Edinburgh EH9 3JZ, Scotland (United Kingdom); Harlen, Oliver G. [University of Leeds, Leeds LS2 9JT (United Kingdom); Harris, Sarah A., E-mail: s.a.harris@leeds.ac.uk [University of Leeds, Leeds LS2 9JT (United Kingdom); University of Leeds, Leeds LS2 9JT (United Kingdom); Khalid, Syma; Leung, Yuk Ming [University of Southampton, Southampton SO17 1BJ (United Kingdom); Lonsdale, Richard [Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany); Philipps-Universität Marburg, Hans-Meerwein Strasse, 35032 Marburg (Germany); Mulholland, Adrian J. [University of Bristol, Bristol BS8 1TS (United Kingdom); Pearson, Arwen R. [University of Leeds, Leeds LS2 9JT (United Kingdom); University of Hamburg, Hamburg (Germany); Read, Daniel J.; Richardson, Robin A. [University of Leeds, Leeds LS2 9JT (United Kingdom); The University of Edinburgh, Edinburgh EH9 3JZ, Scotland (United Kingdom)

    2015-01-01

    The current computational techniques available for biomolecular simulation are described, and the successes and limitations of each with reference to the experimental biophysical methods that they complement are presented. Despite huge advances in the computational techniques available for simulating biomolecules at the quantum-mechanical, atomistic and coarse-grained levels, there is still a widespread perception amongst the experimental community that these calculations are highly specialist and are not generally applicable by researchers outside the theoretical community. In this article, the successes and limitations of biomolecular simulation and the further developments that are likely in the near future are discussed. A brief overview is also provided of the experimental biophysical methods that are commonly used to probe biomolecular structure and dynamics, and the accuracy of the information that can be obtained from each is compared with that from modelling. It is concluded that progress towards an accurate spatial and temporal model of biomacromolecules requires a combination of all of these biophysical techniques, both experimental and computational.

  6. [Interdependence of plankton spatial distribution and plancton biomass temporal oscillations: mathematical simulation].

    Science.gov (United States)

    Medvedinskiĭ, A B; Tikhonova, I A; Li, B L; Malchow, H

    2003-01-01

    The dynamics of aquatic biological communities in a patchy environment is of great interest in respect to interrelations between phenomena at various spatial and time scales. To study the complex plankton dynamics in relation to variations of such a biologically essential parameter as the fish predation rate, we use a simple reaction-diffusion model of trophic interactions between phytoplankton, zooplankton, and fish. We suggest that plankton is distributed between two habitats one of which is fish-free due to hydrological inhomogeneity, while the other is fish-populated. We show that temporal variations in the fish predation rate do not violate the strong correspondence between the character of spatial distribution of plankton and changes of plankton biomass in time: regular temporal oscillations of plankton biomass correspond to large-scale plankton patches, while chaotic oscillations correspond to small-scale plankton patterns. As in the case of the constant fish predation rate, the chaotic plankton dynamics is characterized by coexistence of the chaotic attractor and limit cycle.

  7. Molecular dynamics simulation of ribosome jam

    KAUST Repository

    Matsumoto, Shigenori; Takagi, Fumiko; Shimada, Takashi; Ito, Nobuyasu

    2011-01-01

    We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We

  8. The Temporal Derivative of Expected Utility: A Neural Mechanism for Dynamic Decision-making

    Science.gov (United States)

    Zhang, Xian; Hirsch, Joy

    2012-01-01

    Real world tasks involving moving targets, such as driving a vehicle, are performed based on continuous decisions thought to depend upon the temporal derivative of the expected utility (∂V/∂t), where the expected utility (V) is the effective value of a future reward. However, those neural mechanisms that underlie dynamic decision-making are not well understood. This study investigates human neural correlates of both V and ∂V/∂t using fMRI and a novel experimental paradigm based on a pursuit-evasion game optimized to isolate components of dynamic decision processes. Our behavioral data show that players of the pursuit-evasion game adopt an exponential discounting function, supporting the expected utility theory. The continuous functions of V and ∂V/∂t were derived from the behavioral data and applied as regressors in fMRI analysis, enabling temporal resolution that exceeded the sampling rate of image acquisition, hyper-temporal resolution, by taking advantage of numerous trials that provide rich and independent manipulation of those variables. V and ∂V/∂t were each associated with distinct neural activity. Specifically, ∂V/∂t was associated with anterior and posterior cingulate cortices, superior parietal lobule, and ventral pallidum, whereas V was primarily associated with supplementary motor, pre and post central gyri, cerebellum, and thalamus. The association between the ∂V/∂t and brain regions previously related to decision-making is consistent with the primary role of the temporal derivative of expected utility in dynamic decision-making. PMID:22963852

  9. The temporal derivative of expected utility: a neural mechanism for dynamic decision-making.

    Science.gov (United States)

    Zhang, Xian; Hirsch, Joy

    2013-01-15

    Real world tasks involving moving targets, such as driving a vehicle, are performed based on continuous decisions thought to depend upon the temporal derivative of the expected utility (∂V/∂t), where the expected utility (V) is the effective value of a future reward. However, the neural mechanisms that underlie dynamic decision-making are not well understood. This study investigates human neural correlates of both V and ∂V/∂t using fMRI and a novel experimental paradigm based on a pursuit-evasion game optimized to isolate components of dynamic decision processes. Our behavioral data show that players of the pursuit-evasion game adopt an exponential discounting function, supporting the expected utility theory. The continuous functions of V and ∂V/∂t were derived from the behavioral data and applied as regressors in fMRI analysis, enabling temporal resolution that exceeded the sampling rate of image acquisition, hyper-temporal resolution, by taking advantage of numerous trials that provide rich and independent manipulation of those variables. V and ∂V/∂t were each associated with distinct neural activity. Specifically, ∂V/∂t was associated with anterior and posterior cingulate cortices, superior parietal lobule, and ventral pallidum, whereas V was primarily associated with supplementary motor, pre and post central gyri, cerebellum, and thalamus. The association between the ∂V/∂t and brain regions previously related to decision-making is consistent with the primary role of the temporal derivative of expected utility in dynamic decision-making. Copyright © 2012 Elsevier Inc. All rights reserved.

  10. Spatial and Temporal Dynamics and Value of Nature-Based Recreation, Estimated via Social Media

    Science.gov (United States)

    Watson, Keri B.; Wood, Spencer A.; Ricketts, Taylor H.

    2016-01-01

    Conserved lands provide multiple ecosystem services, including opportunities for nature-based recreation. Managing this service requires understanding the landscape attributes underpinning its provision, and how changes in land management affect its contribution to human wellbeing over time. However, evidence from both spatially explicit and temporally dynamic analyses is scarce, often due to data limitations. In this study, we investigated nature-based recreation within conserved lands in Vermont, USA. We used geotagged photographs uploaded to the photo-sharing website Flickr to quantify visits by in-state and out-of-state visitors, and we multiplied visits by mean trip expenditures to show that conserved lands contributed US $1.8 billion (US $0.18–20.2 at 95% confidence) to Vermont’s tourism industry between 2007 and 2014. We found eight landscape attributes explained the pattern of visits to conserved lands; visits were higher in larger conserved lands, with less forest cover, greater trail density and more opportunities for snow sports. Some of these attributes differed from those found in other locations, but all aligned with our understanding of recreation in Vermont. We also found that using temporally static models to inform conservation decisions may have perverse outcomes for nature-based recreation. For example, static models suggest conserved land with less forest cover receive more visits, but temporally dynamic models suggest clearing forests decreases, rather than increases, visits to these sites. Our results illustrate the importance of understanding both the spatial and temporal dynamics of ecosystem services for conservation decision-making. PMID:27611325

  11. Dynamic spatial organization of the occipito-temporal word form area for second language processing.

    Science.gov (United States)

    Gao, Yue; Sun, Yafeng; Lu, Chunming; Ding, Guosheng; Guo, Taomei; Malins, Jeffrey G; Booth, James R; Peng, Danling; Liu, Li

    2017-08-01

    Despite the left occipito-temporal region having shown consistent activation in visual word form processing across numerous studies in different languages, the mechanisms by which word forms of second languages are processed in this region remain unclear. To examine this more closely, 16 Chinese-English and 14 English-Chinese late bilinguals were recruited to perform lexical decision tasks to visually presented words in both their native and second languages (L1 and L2) during functional magnetic resonance imaging scanning. Here we demonstrate that visual word form processing for L1 versus L2 engaged different spatial areas of the left occipito-temporal region. Namely, the spatial organization of the visual word form processing in the left occipito-temporal region is more medial and posterior for L2 than L1 processing in Chinese-English bilinguals, whereas activation is more lateral and anterior for L2 in English-Chinese bilinguals. In addition, for Chinese-English bilinguals, more lateral recruitment of the occipito-temporal region was correlated with higher L2 proficiency, suggesting higher L2 proficiency is associated with greater involvement of L1-preferred mechanisms. For English-Chinese bilinguals, higher L2 proficiency was correlated with more lateral and anterior activation of the occipito-temporal region, suggesting higher L2 proficiency is associated with greater involvement of L2-preferred mechanisms. Taken together, our results indicate that L1 and L2 recruit spatially different areas of the occipito-temporal region in visual word processing when the two scripts belong to different writing systems, and that the spatial organization of this region for L2 visual word processing is dynamically modulated by L2 proficiency. Specifically, proficiency in L2 in Chinese-English is associated with assimilation to the native language mechanisms, whereas L2 in English-Chinese is associated with accommodation to second language mechanisms. Copyright © 2017

  12. Bursts and heavy tails in temporal and sequential dynamics of foraging decisions.

    Directory of Open Access Journals (Sweden)

    Kanghoon Jung

    2014-08-01

    Full Text Available A fundamental understanding of behavior requires predicting when and what an individual will choose. However, the actual temporal and sequential dynamics of successive choices made among multiple alternatives remain unclear. In the current study, we tested the hypothesis that there is a general bursting property in both the timing and sequential patterns of foraging decisions. We conducted a foraging experiment in which rats chose among four different foods over a continuous two-week time period. Regarding when choices were made, we found bursts of rapidly occurring actions, separated by time-varying inactive periods, partially based on a circadian rhythm. Regarding what was chosen, we found sequential dynamics in affective choices characterized by two key features: (a a highly biased choice distribution; and (b preferential attachment, in which the animals were more likely to choose what they had previously chosen. To capture the temporal dynamics, we propose a dual-state model consisting of active and inactive states. We also introduce a satiation-attainment process for bursty activity, and a non-homogeneous Poisson process for longer inactivity between bursts. For the sequential dynamics, we propose a dual-control model consisting of goal-directed and habit systems, based on outcome valuation and choice history, respectively. This study provides insights into how the bursty nature of behavior emerges from the interaction of different underlying systems, leading to heavy tails in the distribution of behavior over time and choices.

  13. Bursts and Heavy Tails in Temporal and Sequential Dynamics of Foraging Decisions

    Science.gov (United States)

    Jung, Kanghoon; Jang, Hyeran; Kralik, Jerald D.; Jeong, Jaeseung

    2014-01-01

    A fundamental understanding of behavior requires predicting when and what an individual will choose. However, the actual temporal and sequential dynamics of successive choices made among multiple alternatives remain unclear. In the current study, we tested the hypothesis that there is a general bursting property in both the timing and sequential patterns of foraging decisions. We conducted a foraging experiment in which rats chose among four different foods over a continuous two-week time period. Regarding when choices were made, we found bursts of rapidly occurring actions, separated by time-varying inactive periods, partially based on a circadian rhythm. Regarding what was chosen, we found sequential dynamics in affective choices characterized by two key features: (a) a highly biased choice distribution; and (b) preferential attachment, in which the animals were more likely to choose what they had previously chosen. To capture the temporal dynamics, we propose a dual-state model consisting of active and inactive states. We also introduce a satiation-attainment process for bursty activity, and a non-homogeneous Poisson process for longer inactivity between bursts. For the sequential dynamics, we propose a dual-control model consisting of goal-directed and habit systems, based on outcome valuation and choice history, respectively. This study provides insights into how the bursty nature of behavior emerges from the interaction of different underlying systems, leading to heavy tails in the distribution of behavior over time and choices. PMID:25122498

  14. INFORMATION MINING OF SPATIO-TEMPORAL EVOLUTION OF LAKES BASED ON MULTIPLE DYNAMIC MEASUREMENTS

    Directory of Open Access Journals (Sweden)

    W. Feng

    2017-09-01

    Full Text Available Lakes are important water resources and integral parts of the natural ecosystem, and it is of great significance to study the evolution of lakes. The area of each lake increased and decreased at the same time in natural condition, only but the net change of lakes’ area is the result of the bidirectional evolution of lakes. In this paper, considering the effects of net fragmentation, net attenuation, swap change and spatial invariant part in lake evolution, a comprehensive evaluation indexes of lake dynamic evolution were defined,. Such degree contains three levels of measurement: 1 the swap dynamic degree (SDD reflects the space activity of lakes in the study period. 2 the attenuation dynamic degree (ADD reflects the net attenuation of lakes into non-lake areas. 3 the fragmentation dynamic degree (FDD reflects the trend of lakes to be divided and broken into smaller lakes. Three levels of dynamic measurement constitute the three-dimensional "Swap - attenuation – fragmentation" dynamic evolution measurement system of lakes. To show its effectiveness, the dynamic measurement was applied to lakes in Jianghan Plain, the middle Yangtze region of China for a more detailed analysis of lakes from 1984 to 2014. In combination with spatial-temporal location characteristics of lakes, the hidden information in lake evolution in the past 30 years can be revealed.

  15. Parallel Monte Carlo simulation of aerosol dynamics

    KAUST Repository

    Zhou, K.; He, Z.; Xiao, M.; Zhang, Z.

    2014-01-01

    is simulated with a stochastic method (Marcus-Lushnikov stochastic process). Operator splitting techniques are used to synthesize the deterministic and stochastic parts in the algorithm. The algorithm is parallelized using the Message Passing Interface (MPI

  16. A general science-based framework for dynamical spatio-temporal models

    Science.gov (United States)

    Wikle, C.K.; Hooten, M.B.

    2010-01-01

    Spatio-temporal statistical models are increasingly being used across a wide variety of scientific disciplines to describe and predict spatially-explicit processes that evolve over time. Correspondingly, in recent years there has been a significant amount of research on new statistical methodology for such models. Although descriptive models that approach the problem from the second-order (covariance) perspective are important, and innovative work is being done in this regard, many real-world processes are dynamic, and it can be more efficient in some cases to characterize the associated spatio-temporal dependence by the use of dynamical models. The chief challenge with the specification of such dynamical models has been related to the curse of dimensionality. Even in fairly simple linear, first-order Markovian, Gaussian error settings, statistical models are often over parameterized. Hierarchical models have proven invaluable in their ability to deal to some extent with this issue by allowing dependency among groups of parameters. In addition, this framework has allowed for the specification of science based parameterizations (and associated prior distributions) in which classes of deterministic dynamical models (e. g., partial differential equations (PDEs), integro-difference equations (IDEs), matrix models, and agent-based models) are used to guide specific parameterizations. Most of the focus for the application of such models in statistics has been in the linear case. The problems mentioned above with linear dynamic models are compounded in the case of nonlinear models. In this sense, the need for coherent and sensible model parameterizations is not only helpful, it is essential. Here, we present an overview of a framework for incorporating scientific information to motivate dynamical spatio-temporal models. First, we illustrate the methodology with the linear case. We then develop a general nonlinear spatio-temporal framework that we call general quadratic

  17. Simulation of spatial and temporal properties of aftershocks by means of the fiber bundle model

    Science.gov (United States)

    Monterrubio-Velasco, Marisol; Zúñiga, F. R.; Márquez-Ramírez, Victor Hugo; Figueroa-Soto, Angel

    2017-11-01

    The rupture processes of any heterogeneous material constitute a complex physical problem. Earthquake aftershocks show temporal and spatial behaviors which are consequence of the heterogeneous stress distribution and multiple rupturing following the main shock. This process is difficult to model deterministically due to the number of parameters and physical conditions, which are largely unknown. In order to shed light on the minimum requirements for the generation of aftershock clusters, in this study, we perform a simulation of the main features of such a complex process by means of a fiber bundle (FB) type model. The FB model has been widely used to analyze the fracture process in heterogeneous materials. It is a simple but powerful tool that allows modeling the main characteristics of a medium such as the brittle shallow crust of the earth. In this work, we incorporate spatial properties, such as the Coulomb stress change pattern, which help simulate observed characteristics of aftershock sequences. In particular, we introduce a parameter ( P) that controls the probability of spatial distribution of initial loads. Also, we use a "conservation" parameter ( π), which accounts for the load dissipation of the system, and demonstrate its influence on the simulated spatio-temporal patterns. Based on numerical results, we find that P has to be in the range 0.06 sequences. This means that the system requires a small difference in the spatial distribution of initial stress, and a very particular fraction of load transfer in order to generate realistic aftershocks.

  18. Selection of Activities in Dynamic Business Process Simulation

    Directory of Open Access Journals (Sweden)

    Toma Rusinaitė

    2016-06-01

    Full Text Available Maintaining dynamicity of business processes is one of the core issues of today's business as it enables businesses to adapt to constantly changing environment. Upon changing the processes, it is vital to assess possible impact, which is achieved by using simulation of dynamic processes. In order to implement dynamicity in business processes, it is necessary to have an ability to change components of the process (a set of activities, a content of activity, a set of activity sequences, a set of rules, performers and resources or dynamically select them during execution. This problem attracted attention of researches over the past few years; however, there is no proposed solution, which ensures the business process (BP dynamicity. This paper proposes and specifies dynamic business process (DBP simulation model, which satisfies all of the formulated DBP requirements.

  19. Spatial and temporal dynamics of deep percolation, lag time and recharge in an irrigated semi-arid region

    Science.gov (United States)

    Nazarieh, F.; Ansari, H.; Ziaei, A. N.; Izady, A.; Davari, K.; Brunner, P.

    2018-05-01

    The time required for deep percolating water to reach the water table can be considerable in areas with a thick vadose zone. Sustainable groundwater management, therefore, has to consider the spatial and temporal dynamics of groundwater recharge. The key parameters that control the lag time have been widely examined in soil physics using small-scale lysimeters and modeling studies. However, only a small number of studies have analyzed how deep-percolation rates affect groundwater recharge dynamics over large spatial scales. This study examined how the parameters influencing lag time affect groundwater recharge in a semi-arid catchment under irrigation (in northeastern Iran) using a numerical modeling approach. Flow simulations were performed by the MODFLOW-NWT code with the Vadose-Zone Flow (UZF) Package. Calibration of the groundwater model was based on data from 48 observation wells. Flow simulations showed that lag times vary from 1 to more than 100 months. A sensitivity analysis demonstrated that during drought conditions, the lag time was highly sensitive to the rate of deep percolation. The study illustrated two critical points: (1) the importance of providing estimates of the lag time as a basis for sustainable groundwater management, and (2) lag time not only depends on factors such as soil hydraulic conductivity or vadose zone depth but also depends on the deep-percolation rates and the antecedent soil-moisture condition. Therefore, estimates of the lag time have to be associated with specific percolation rates, in addition to depth to groundwater and soil properties.

  20. Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and Markov modeling.

    Science.gov (United States)

    Yi, Zheng; Lindner, Benjamin; Prinz, Jan-Hendrik; Noé, Frank; Smith, Jeremy C

    2013-11-07

    Neutron scattering experiments directly probe the dynamics of complex molecules on the sub pico- to microsecond time scales. However, the assignment of the relaxations seen experimentally to specific structural rearrangements is difficult, since many of the underlying dynamical processes may exist on similar timescales. In an accompanying article, we present a theoretical approach to the analysis of molecular dynamics simulations with a Markov State Model (MSM) that permits the direct identification of structural transitions leading to each contributing relaxation process. Here, we demonstrate the use of the method by applying it to the configurational dynamics of the well-characterized alanine dipeptide. A practical procedure for deriving the MSM from an MD is introduced. The result is a 9-state MSM in the space of the backbone dihedral angles and the side-chain methyl group. The agreement between the quasielastic spectrum calculated directly from the atomic trajectories and that derived from the Markov state model is excellent. The dependence on the wavevector of the individual Markov processes is described. The procedure means that it is now practicable to interpret quasielastic scattering spectra in terms of well-defined intramolecular transitions with minimal a priori assumptions as to the nature of the dynamics taking place.

  1. Simulation of capillary flow with a dynamic contact angle

    NARCIS (Netherlands)

    van Mourik, S; Veldman, AEP; Dreyer, ME

    2005-01-01

    A number of theoretical and empirical dynamic contact angle (DCA) models have been tested in a numerical simulation of liquid reorientation in microgravity for which experimental validation data are available. It is observed that the DCA can have a large influence on liquid dynamics in microgravity.

  2. Simulating market dynamics : Interactions between consumer psychology and social networks

    NARCIS (Netherlands)

    Janssen, M.A; Jager, W.

    2003-01-01

    Markets can show different types of dynamics, from quiet markets dominated by one or a few products, to markets with continual penetration of new and reintroduced products. in a previous article we explored the dynamics of markets from a psychological perspective using a multi-agent simulation

  3. Energy conservation in molecular dynamics simulations of classical systems

    DEFF Research Database (Denmark)

    Toxværd, Søren; Heilmann, Ole; Dyre, J. C.

    2012-01-01

    Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete “Verlet” algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence...

  4. Temporal dynamics and transcriptional control using single-cell gene expression analysis.

    Science.gov (United States)

    Kouno, Tsukasa; de Hoon, Michiel; Mar, Jessica C; Tomaru, Yasuhiro; Kawano, Mitsuoki; Carninci, Piero; Suzuki, Harukazu; Hayashizaki, Yoshihide; Shin, Jay W

    2013-01-01

    Changes in environmental conditions lead to expression variation that manifest at the level of gene regulatory networks. Despite a strong understanding of the role noise plays in synthetic biological systems, it remains unclear how propagation of expression heterogeneity in an endogenous regulatory network is distributed and utilized by cells transitioning through a key developmental event. Here we investigate the temporal dynamics of a single-cell transcriptional network of 45 transcription factors in THP-1 human myeloid monocytic leukemia cells undergoing differentiation to macrophages. We systematically measure temporal regulation of expression and variation by profiling 120 single cells at eight distinct time points, and infer highly controlled regulatory modules through which signaling operates with stochastic effects. This reveals dynamic and specific rewiring as a cellular strategy for differentiation. The integration of both positive and negative co-expression networks further identifies the proto-oncogene MYB as a network hinge to modulate both the pro- and anti-differentiation pathways. Compared to averaged cell populations, temporal single-cell expression profiling provides a much more powerful technique to probe for mechanistic insights underlying cellular differentiation. We believe that our approach will form the basis of novel strategies to study the regulation of transcription at a single-cell level.

  5. Temporal variability in phosphorus transfers: classifying concentration–discharge event dynamics

    Directory of Open Access Journals (Sweden)

    P. Haygarth

    2004-01-01

    Full Text Available The importance of temporal variability in relationships between phosphorus (P concentration (Cp and discharge (Q is linked to a simple means of classifying the circumstances of Cp–Q relationships in terms of functional types of response. New experimental data at the upstream interface of grassland soil and catchment systems at a range of scales (lysimeters to headwaters in England and Australia are used to demonstrate the potential of such an approach. Three types of event are defined as Types 1–3, depending on whether the relative change in Q exceeds the relative change in Cp (Type 1, whether Cp and Q are positively inter-related (Type 2 and whether Cp varies yet Q is unchanged (Type 3. The classification helps to characterise circumstances that can be explained mechanistically in relation to (i the scale of the study (with a tendency towards Type 1 in small scale lysimeters, (ii the form of P with a tendency for Type 1 for soluble (i.e., p–Q relationships that can be developed further to contribute to future models of P transfer and delivery from slope to stream. Studies that evaluate the temporal dynamics of the transfer of P are currently grossly under-represented in comparison with models based on static/spatial factors. Keywords: phosphorus, concentration, discharge, lysimeters, temporal dynamics, overland flow

  6. Dynamic evolving spiking neural networks for on-line spatio- and spectro-temporal pattern recognition.

    Science.gov (United States)

    Kasabov, Nikola; Dhoble, Kshitij; Nuntalid, Nuttapod; Indiveri, Giacomo

    2013-05-01

    On-line learning and recognition of spatio- and spectro-temporal data (SSTD) is a very challenging task and an important one for the future development of autonomous machine learning systems with broad applications. Models based on spiking neural networks (SNN) have already proved their potential in capturing spatial and temporal data. One class of them, the evolving SNN (eSNN), uses a one-pass rank-order learning mechanism and a strategy to evolve a new spiking neuron and new connections to learn new patterns from incoming data. So far these networks have been mainly used for fast image and speech frame-based recognition. Alternative spike-time learning methods, such as Spike-Timing Dependent Plasticity (STDP) and its variant Spike Driven Synaptic Plasticity (SDSP), can also be used to learn spatio-temporal representations, but they usually require many iterations in an unsupervised or semi-supervised mode of learning. This paper introduces a new class of eSNN, dynamic eSNN, that utilise both rank-order learning and dynamic synapses to learn SSTD in a fast, on-line mode. The paper also introduces a new model called deSNN, that utilises rank-order learning and SDSP spike-time learning in unsupervised, supervised, or semi-supervised modes. The SDSP learning is used to evolve dynamically the network changing connection weights that capture spatio-temporal spike data clusters both during training and during recall. The new deSNN model is first illustrated on simple examples and then applied on two case study applications: (1) moving object recognition using address-event representation (AER) with data collected using a silicon retina device; (2) EEG SSTD recognition for brain-computer interfaces. The deSNN models resulted in a superior performance in terms of accuracy and speed when compared with other SNN models that use either rank-order or STDP learning. The reason is that the deSNN makes use of both the information contained in the order of the first input spikes

  7. Towards understanding temporal and spatial dynamics of seagrass landscapes using time-series remote sensing

    Science.gov (United States)

    Lyons, Mitchell B.; Roelfsema, Chris M.; Phinn, Stuart R.

    2013-03-01

    The spatial and temporal dynamics of seagrasses have been well studied at the leaf to patch scales, however, the link to large spatial extent landscape and population dynamics is still unresolved in seagrass ecology. Traditional remote sensing approaches have lacked the temporal resolution and consistency to appropriately address this issue. This study uses two high temporal resolution time-series of thematic seagrass cover maps to examine the spatial and temporal dynamics of seagrass at both an inter- and intra-annual time scales, one of the first globally to do so at this scale. Previous work by the authors developed an object-based approach to map seagrass cover level distribution from a long term archive of Landsat TM and ETM+ images on the Eastern Banks (≈200 km2), Moreton Bay, Australia. In this work a range of trend and time-series analysis methods are demonstrated for a time-series of 23 annual maps from 1988 to 2010 and a time-series of 16 monthly maps during 2008-2010. Significant new insight was presented regarding the inter- and intra-annual dynamics of seagrass persistence over time, seagrass cover level variability, seagrass cover level trajectory, and change in area of seagrass and cover levels over time. Overall we found that there was no significant decline in total seagrass area on the Eastern Banks, but there was a significant decline in seagrass cover level condition. A case study of two smaller communities within the Eastern Banks that experienced a decline in both overall seagrass area and condition are examined in detail, highlighting possible differences in environmental and process drivers. We demonstrate how trend and time-series analysis enabled seagrass distribution to be appropriately assessed in context of its spatial and temporal history and provides the ability to not only quantify change, but also describe the type of change. We also demonstrate the potential use of time-series analysis products to investigate seagrass growth and

  8. Insights into soil carbon dynamics across climatic and geologic gradients from temporally-resolved radiocarbon measurements

    Science.gov (United States)

    van der Voort, T. S.; Hagedorn, F.; Mannu, U.; Walthert, L.; McIntyre, C.; Eglinton, T. I.

    2016-12-01

    Soil carbon constitutes the largest terrestrial reservoir of organic carbon, and therefore quantifying soil organic matter dynamics (carbon turnover, stocks and fluxes) across spatial gradients is essential for an understanding of the carbon cycle and the impacts of global change. In particular, links between soil carbon dynamics and different climatic and compositional factors remains poorly understood. Radiocarbon constitutes a powerful tool for unraveling soil carbon dynamics. Temporally-resolved radiocarbon measurements, which take advantage of "bomb-radiocarbon"-driven changes in atmospheric 14C, enable further constraints to be placed on C turnover times. These in turn can yield more precise flux estimates for both upper and deeper soil horizons. This project combines bulk radiocarbon measurements on a suite of soil profiles spanning strong climatic (MAT 1.3-9.2°C, MAP 600 to 2100 mm m-2y-1) and geologic gradients with a more in-depth approach for a subset of locations. For this subset, temporal and carbon-fraction specific radiocarbon data has been acquired for both topsoil and deeper soils. These well-studied sites are part of the Long-Term Forest Ecosystem Research (LWF) program of the Swiss Federal Institute for Forest, Snow and Landscape research (WSL). Resulting temporally-resolved turnover estimates are coupled to carbon stocks, fluxes across this wide range of forest ecosystems and are examined in the context of environmental drivers (temperature, precipitation, primary production and soil moisture) as well as composition (sand, silt and clay content). Statistical analysis on the region-scale - correlating radiocarbon signature with climatic variables such as temperature, precipitation, primary production and elevation - indicates that composition rather than climate is a key driver of ­­Δ14C signatures. Estimates of carbon turnover, stocks and fluxes derived from temporally-resolved measurements highlight the pivotal role of soil moisture as a

  9. A Process for Comparing Dynamics of Distributed Space Systems Simulations

    Science.gov (United States)

    Cures, Edwin Z.; Jackson, Albert A.; Morris, Jeffery C.

    2009-01-01

    The paper describes a process that was developed for comparing the primary orbital dynamics behavior between space systems distributed simulations. This process is used to characterize and understand the fundamental fidelities and compatibilities of the modeling of orbital dynamics between spacecraft simulations. This is required for high-latency distributed simulations such as NASA s Integrated Mission Simulation and must be understood when reporting results from simulation executions. This paper presents 10 principal comparison tests along with their rationale and examples of the results. The Integrated Mission Simulation (IMSim) (formerly know as the Distributed Space Exploration Simulation (DSES)) is a NASA research and development project focusing on the technologies and processes that are related to the collaborative simulation of complex space systems involved in the exploration of our solar system. Currently, the NASA centers that are actively participating in the IMSim project are the Ames Research Center, the Jet Propulsion Laboratory (JPL), the Johnson Space Center (JSC), the Kennedy Space Center, the Langley Research Center and the Marshall Space Flight Center. In concept, each center participating in IMSim has its own set of simulation models and environment(s). These simulation tools are used to build the various simulation products that are used for scientific investigation, engineering analysis, system design, training, planning, operations and more. Working individually, these production simulations provide important data to various NASA projects.

  10. The Temporal Dynamics of Visual Search: Evidence for Parallel Processing in Feature and Conjunction Searches

    Science.gov (United States)

    McElree, Brian; Carrasco, Marisa

    2012-01-01

    Feature and conjunction searches have been argued to delineate parallel and serial operations in visual processing. The authors evaluated this claim by examining the temporal dynamics of the detection of features and conjunctions. The 1st experiment used a reaction time (RT) task to replicate standard mean RT patterns and to examine the shapes of the RT distributions. The 2nd experiment used the response-signal speed–accuracy trade-off (SAT) procedure to measure discrimination (asymptotic detection accuracy) and detection speed (processing dynamics). Set size affected discrimination in both feature and conjunction searches but affected detection speed only in the latter. Fits of models to the SAT data that included a serial component overpredicted the magnitude of the observed dynamics differences. The authors concluded that both features and conjunctions are detected in parallel. Implications for the role of attention in visual processing are discussed. PMID:10641310

  11. Simulating the evolution of industries using a dynamic behavioural model

    OpenAIRE

    Kunc, Martin

    2004-01-01

    Investment decisions determine that not only the evolution of industries is hard to forecast with certainty but also industries may have different dynamic behaviour and evolutionary paths. In this paper we present a behavioural framework to simulate the evolution of industries. Two factors determine the dynamic behaviour of an industry: managerial decision-making and the interconnected set of resources. Managerial decision-making significantly affects the dynamic behaviour of firms. Bounded r...

  12. Investigating fine-scale spatio-temporal predator-prey patterns in dynamic marine ecosystems: a functional data analysis approach

    NARCIS (Netherlands)

    Embling, C.B.; Illian, J.; Armstrong, E.; van der Kooij, J.; Sharples, J.; Camphuysen, K.C.J.; Scott, B.E.

    2012-01-01

    1. Spatial management of marine ecosystems requires detailed knowledge of spatio-temporal mechanisms linking physical and biological processes. Tidal currents, the main driver of ecosystem dynamics in temperate coastal ecosystems, influence predator foraging ecology by affecting prey distribution

  13. Computational fluid dynamics (CFD) simulation of hot air flow ...

    African Journals Online (AJOL)

    Computational Fluid Dynamics simulation of air flow distribution, air velocity and pressure field pattern as it will affect moisture transient in a cabinet tray dryer is performed using SolidWorks Flow Simulation (SWFS) 2014 SP 4.0 program. The model used for the drying process in this experiment was designed with Solid ...

  14. Molecular dynamics simulations of ballistic He penetration into W fuzz

    NARCIS (Netherlands)

    Klaver, T. P. C.; Nordlund, K.; Morgan, T. W.; Westerhof, E.; Thijsse, B. J.; van de Sanden, M. C. M.

    2016-01-01

    Results are presented of large-scale Molecular Dynamics simulations of low-energy He bombardment of W nanorods, or so-called ‘fuzz’ structures. The goal of these simulations is to see if ballistic He penetration through W fuzz offers a more realistic scenario for how He moves through fuzz layers

  15. Experiences on dynamic simulation software in chemical engineering education

    DEFF Research Database (Denmark)

    Komulainen, Tiina M.; Enemark-rasmussen, Rasmus; Sin, Gürkan

    2012-01-01

    Commercial process simulators are increasing interest in the chemical engineer education. In this paper, the use of commercial dynamic simulation software, D-SPICE® and K-Spice®, for three different chemical engineering courses is described and discussed. The courses cover the following topics...

  16. Dynamic wind turbine models in power system simulation tool

    DEFF Research Database (Denmark)

    Hansen, A.; Jauch, Clemens; Soerensen, P.

    The present report describes the dynamic wind turbine models implemented in the power system simulation tool DIgSILENT. The developed models are a part of the results of a national research project, whose overall objective is to create a model database in different simulation tools. The report...

  17. Innovative tools for real-time simulation of dynamic systems

    NARCIS (Netherlands)

    Palli, Gianluca; Carloni, Raffaella; Melchiorri, Claudio

    2008-01-01

    In this paper, we present a software architecture, based on RTAI-Linux, for the real-time simulation of dynamic systems and for the rapid prototyping of digital controllers. Our aim is to simplify the testing phase of digital controllers by providing the real-time simulation of the plant with the

  18. Molecular Dynamics Simulations of Kinetic Models for Chiral Dominance in Soft Condensed Matter

    DEFF Research Database (Denmark)

    Toxvaerd, Søren

    2001-01-01

    Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality......Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality...

  19. Fluid dynamics theory, computation, and numerical simulation

    CERN Document Server

    Pozrikidis, C

    2017-01-01

    This book provides an accessible introduction to the basic theory of fluid mechanics and computational fluid dynamics (CFD) from a modern perspective that unifies theory and numerical computation. Methods of scientific computing are introduced alongside with theoretical analysis and MATLAB® codes are presented and discussed for a broad range of topics: from interfacial shapes in hydrostatics, to vortex dynamics, to viscous flow, to turbulent flow, to panel methods for flow past airfoils. The third edition includes new topics, additional examples, solved and unsolved problems, and revised images. It adds more computational algorithms and MATLAB programs. It also incorporates discussion of the latest version of the fluid dynamics software library FDLIB, which is freely available online. FDLIB offers an extensive range of computer codes that demonstrate the implementation of elementary and advanced algorithms and provide an invaluable resource for research, teaching, classroom instruction, and self-study. This ...

  20. Effects of the Temporal Variability of Evapotranspiration on Hydrologic Simulation in Central Florida

    Science.gov (United States)

    O'Reilly, Andrew M.

    2007-01-01

    The transient response of a hydrologic system can be of concern to water-resource managers, because it is often extreme relatively short-lived events, such as floods or droughts, that profoundly influence the management of the resource. The water available to a hydrologic system for stream flow and aquifer recharge is determined by the difference of precipitation and evapotranspiration (ET). As such, temporal variations in precipitation and ET determine the degree of influence each has on the transient response of the hydrologic system. Meteorological, ET, and hydrologic data collected from 1993 to 2003 and spanning 1- to 3 2/3 -year periods were used to develop a hydrologic model for each of five sites in central Florida. The sensitivities of simulated water levels and flows to simple approximations of ET were quantified and the adequacy of each ET approximation was assessed. ET was approximated by computing potential ET, using the Hargreaves and Priestley-Taylor equations, and applying vegetation coefficients to adjust the potential ET values to actual ET. The Hargreaves and Priestley-Taylor ET approximations were used in the calibrated hydrologic models while leaving all other model characteristics and parameter values unchanged. Two primary factors that influence how the temporal variability of ET affects hydrologic simulation in central Florida were identified: (1) stochastic character of precipitation and ET and (2) the ability of the local hydrologic system to attenuate variability in input stresses. Differences in the stochastic character of precipitation and ET, both the central location and spread of the data, result in substantial influence of precipitation on the quantity and timing of water available to the hydrologic system and a relatively small influence of ET. The temporal variability of ET was considerably less than that of precipitation at each site over a wide range of time scales (from daily to annual). However, when precipitation and ET are of

  1. Simulation-Based Dynamic Passenger Flow Assignment Modelling for a Schedule-Based Transit Network

    Directory of Open Access Journals (Sweden)

    Xiangming Yao

    2017-01-01

    Full Text Available The online operation management and the offline policy evaluation in complex transit networks require an effective dynamic traffic assignment (DTA method that can capture the temporal-spatial nature of traffic flows. The objective of this work is to propose a simulation-based dynamic passenger assignment framework and models for such applications in the context of schedule-based rail transit systems. In the simulation framework, travellers are regarded as individual agents who are able to obtain complete information on the current traffic conditions. A combined route selection model integrated with pretrip route selection and entrip route switch is established for achieving the dynamic network flow equilibrium status. The train agent is operated strictly with the timetable and its capacity limitation is considered. A continuous time-driven simulator based on the proposed framework and models is developed, whose performance is illustrated through a large-scale network of Beijing subway. The results indicate that more than 0.8 million individual passengers and thousands of trains can be simulated simultaneously at a speed ten times faster than real time. This study provides an efficient approach to analyze the dynamic demand-supply relationship for large schedule-based transit networks.

  2. Gamma ray observatory dynamics simulator in Ada (GRODY)

    International Nuclear Information System (INIS)

    1990-09-01

    This experiment involved the parallel development of dynamics simulators for the Gamma Ray Observatory in both FORTRAN and Ada for the purpose of evaluating the applicability of Ada to the NASA/Goddard Space Flight Center's flight dynamics environment. The experiment successfully demonstrated that Ada is a viable, valuable technology for use in this environment. In addition to building a simulator, the Ada team evaluated training approaches, developed an Ada methodology appropriate to the flight dynamics environment, and established a baseline for evaluating future Ada projects

  3. Hierarchical Conformational Analysis of Native Lysozyme Based on Sub-Millisecond Molecular Dynamics Simulations.

    Directory of Open Access Journals (Sweden)

    Kai Wang

    Full Text Available Hierarchical organization of free energy landscape (FEL for native globular proteins has been widely accepted by the biophysics community. However, FEL of native proteins is usually projected onto one or a few dimensions. Here we generated collectively 0.2 milli-second molecular dynamics simulation trajectories in explicit solvent for hen egg white lysozyme (HEWL, and carried out detailed conformational analysis based on backbone torsional degrees of freedom (DOF. Our results demonstrated that at micro-second and coarser temporal resolutions, FEL of HEWL exhibits hub-like topology with crystal structures occupying the dominant structural ensemble that serves as the hub of conformational transitions. However, at 100 ns and finer temporal resolutions, conformational substates of HEWL exhibit network-like topology, crystal structures are associated with kinetic traps that are important but not dominant ensembles. Backbone torsional state transitions on time scales ranging from nanoseconds to beyond microseconds were found to be associated with various types of molecular interactions. Even at nanoseconds temporal resolution, the number of conformational substates that are of statistical significance is quite limited. These observations suggest that detailed analysis of conformational substates at multiple temporal resolutions is both important and feasible. Transition state ensembles among various conformational substates at microsecond temporal resolution were observed to be considerably disordered. Life times of these transition state ensembles are found to be nearly independent of the time scales of the participating torsional DOFs.

  4. Topology in dynamical lattice QCD simulations

    Energy Technology Data Exchange (ETDEWEB)

    Gruber, Florian

    2012-08-20

    Lattice simulations of Quantum Chromodynamics (QCD), the quantum field theory which describes the interaction between quarks and gluons, have reached a point were contact to experimental data can be made. The underlying mechanisms, like chiral symmetry breaking or the confinement of quarks, are however still not understood. This thesis focuses on topological structures in the QCD vacuum. Those are not only mathematically interesting but also closely related to chiral symmetry and confinement. We consider methods to identify these objects in lattice QCD simulations. Based on this, we explore the structures resulting from different discretizations and investigate the effect of a very strong electromagnetic field on the QCD vacuum.

  5. Topology in dynamical lattice QCD simulations

    International Nuclear Information System (INIS)

    Gruber, Florian

    2012-01-01

    Lattice simulations of Quantum Chromodynamics (QCD), the quantum field theory which describes the interaction between quarks and gluons, have reached a point were contact to experimental data can be made. The underlying mechanisms, like chiral symmetry breaking or the confinement of quarks, are however still not understood. This thesis focuses on topological structures in the QCD vacuum. Those are not only mathematically interesting but also closely related to chiral symmetry and confinement. We consider methods to identify these objects in lattice QCD simulations. Based on this, we explore the structures resulting from different discretizations and investigate the effect of a very strong electromagnetic field on the QCD vacuum.

  6. Molecular dynamics simulations of RNA motifs

    Czech Academy of Sciences Publication Activity Database

    Csaszar, K.; Špačková, Naďa; Šponer, Jiří; Leontis, N. B.

    2002-01-01

    Roč. 223, - (2002), s. 154 ISSN 0065-7727. [Annual Meeting of the American Chemistry Society /223./. 07.04.2002-11.04.2002, Orlando ] Institutional research plan: CEZ:AV0Z5004920 Keywords : molecular dynamics * RNA * hydration Subject RIV: BO - Biophysics

  7. Dynamic modeling and simulation of power transformer maintenance costs

    Directory of Open Access Journals (Sweden)

    Ristić Olga

    2016-01-01

    Full Text Available The paper presents the dynamic model of maintenance costs of the power transformer functional components. Reliability is modeled combining the exponential and Weibull's distribution. The simulation was performed with the aim of corrective maintenance and installation of the continuous monitoring system of the most critical components. Simulation Dynamic System (SDS method and VENSIM PLE software was used to simulate the cost. In this way, significant savings in maintenance costs will be achieved with a small initial investment. [Projekat Ministarstva nauke Republike Srbije, br. III 41025 i br. OI 171007

  8. AceCloud: Molecular Dynamics Simulations in the Cloud.

    Science.gov (United States)

    Harvey, M J; De Fabritiis, G

    2015-05-26

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

  9. A dynamic simulation of the Hanford site grout facility

    International Nuclear Information System (INIS)

    Zimmerman, B.D.; Klimper, S.C.; Williamson, G.F.

    1992-01-01

    Computer-based dynamic simulation can be a powerful, low-cost tool for investigating questions concerning timing, throughput capability, and ability of engineering facilities and systems to meet established milestones. The simulation project described herein was undertaken to develop a dynamic simulation model of the Hanford site grout facility and its associated systems at the US Department of Energy's (DOE's) Hanford site in Washington State. The model allows assessment of the effects of engineering design and operation trade-offs and of variable programmatic constraints, such as regulatory review, on the ability of the grout system to meet milestones established by DOE for low-level waste disposal

  10. Dynamic Biological Functioning Important for Simulating and Stabilizing Ocean Biogeochemistry

    Science.gov (United States)

    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.

  11. Approximation of quantum observables by molecular dynamics simulations

    KAUST Repository

    Sandberg, Mattias

    2016-01-01

    In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.

  12. Approximation of quantum observables by molecular dynamics simulations

    KAUST Repository

    Sandberg, Mattias

    2016-01-06

    In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.

  13. Computer simulation of multiple dynamic photorefractive gratings

    DEFF Research Database (Denmark)

    Buchhave, Preben

    1998-01-01

    The benefits of a direct visualization of space-charge grating buildup are described. The visualization is carried out by a simple repetitive computer program, which simulates the basic processes in the band-transport model and displays the result graphically or in the form of numerical data. The...

  14. Dynamic simulation of steam generator failures

    Energy Technology Data Exchange (ETDEWEB)

    Meister, G [Institut fuer Nukleare Sicherheitsforschung, Kernforschungsanlage Juelich GmbH, Juelich (Germany)

    1988-07-01

    A computer program will be described which is capable to simulate severe transients in a gas heated steam generator. Such transients may arise in the safety analysis of accidents resulting from failures in the heat removal system of an HTGR power plant. Important failure modes which have to be considered are ruptures of one or more steam generator tubes leading to water or steam ejection into the primary system or anomalous operating conditions which my cause damage due to excessive thermal stress. Examples are the complete dryout as a consequence of feedwater interrupt in connection with continuing gas heating and the reflooding of the secondary channel with cold feedwater after dryout. The steam generator program which is capable to simulate accidents of this type is written as a module which can be implemented into a program system fur the simulation of the total heat rejection system. It based on an advanced mathematical model for the two phase flow taking deviations from thermal equilibrium into account. Mass, energy and momentum balances for the primary and secondary fluid and the heat diffusion equations for the heat exchanging wall form a system of coupled differential equations which is solved numerically by an algorithm which is stiffly stable and suppresses effectively oscillations of numerical origin. Results of the simulation of transients of the type mentioned above will be presented and discussed. (author)

  15. Dynamic simulation of steam generator failures

    International Nuclear Information System (INIS)

    Meister, G.

    1988-01-01

    A computer program will be described which is capable to simulate severe transients in a gas heated steam generator. Such transients may arise in the safety analysis of accidents resulting from failures in the heat removal system of an HTGR power plant. Important failure modes which have to be considered are ruptures of one or more steam generator tubes leading to water or steam ejection into the primary system or anomalous operating conditions which my cause damage due to excessive thermal stress. Examples are the complete dryout as a consequence of feedwater interrupt in connection with continuing gas heating and the reflooding of the secondary channel with cold feedwater after dryout. The steam generator program which is capable to simulate accidents of this type is written as a module which can be implemented into a program system fur the simulation of the total heat rejection system. It based on an advanced mathematical model for the two phase flow taking deviations from thermal equilibrium into account. Mass, energy and momentum balances for the primary and secondary fluid and the heat diffusion equations for the heat exchanging wall form a system of coupled differential equations which is solved numerically by an algorithm which is stiffly stable and suppresses effectively oscillations of numerical origin. Results of the simulation of transients of the type mentioned above will be presented and discussed. (author)

  16. Analytical system dynamics modeling and simulation

    CERN Document Server

    Fabien, Brian C

    2008-01-01

    This book offering a modeling technique based on Lagrange's energy method includes 125 worked examples. Using this technique enables one to model and simulate systems as diverse as a six-link, closed-loop mechanism or a transistor power amplifier.

  17. Dynamic Interactions for Network Visualization and Simulation

    Science.gov (United States)

    2009-03-01

    projects.htm, Site accessed January 5, 2009. 12. John S. Weir, Major, USAF, Mediated User-Simulator Interactive Command with Visualization ( MUSIC -V). Master’s...Computing Sciences in Colleges, December 2005). 14. Enrique Campos -Nanez, “nscript user manual,” Department of System Engineer- ing University of

  18. Distributed dynamic simulations of networked control and building performance applications.

    Science.gov (United States)

    Yahiaoui, Azzedine

    2018-02-01

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

  19. MODELLING AND SIMULATION OF A NEUROPHYSIOLOGICAL EXPERIMENT BY SPATIO-TEMPORAL POINT PROCESSES

    Directory of Open Access Journals (Sweden)

    Viktor Beneš

    2011-05-01

    Full Text Available We present a stochastic model of an experimentmonitoring the spiking activity of a place cell of hippocampus of an experimental animal moving in an arena. Doubly stochastic spatio-temporal point process is used to model and quantify overdispersion. Stochastic intensity is modelled by a Lévy based random field while the animal path is simplified to a discrete random walk. In a simulation study first a method suggested previously is used. Then it is shown that a solution of the filtering problem yields the desired inference to the random intensity. Two approaches are suggested and the new one based on finite point process density is applied. Using Markov chain Monte Carlo we obtain numerical results from the simulated model. The methodology is discussed.

  20. Spatial and temporal dynamics of multidimensional well-being, livelihoods and ecosystem services in coastal Bangladesh

    Science.gov (United States)

    Adams, Helen; Adger, W. Neil; Ahmad, Sate; Ahmed, Ali; Begum, Dilruba; Lázár, Attila N.; Matthews, Zoe; Rahman, Mohammed Mofizur; Streatfield, Peter Kim

    2016-01-01

    Populations in resource dependent economies gain well-being from the natural environment, in highly spatially and temporally variable patterns. To collect information on this, we designed and implemented a 1586-household quantitative survey in the southwest coastal zone of Bangladesh. Data were collected on material, subjective and health dimensions of well-being in the context of natural resource use, particularly agriculture, aquaculture, mangroves and fisheries. The questionnaire included questions on factors that mediate poverty outcomes: mobility and remittances; loans and micro-credit; environmental perceptions; shocks; and women’s empowerment. The data are stratified by social-ecological system to take into account spatial dynamics and the survey was repeated with the same respondents three times within a year to incorporate seasonal dynamics. The dataset includes blood pressure measurements and height and weight of men, women and children. In addition, the household listing includes basic data on livelihoods and income for approximately 10,000 households. The dataset facilitates interdisciplinary research on spatial and temporal dynamics of well-being in the context of natural resource dependence in low income countries. PMID:27824340

  1. A comprehensive model of audiovisual perception: both percept and temporal dynamics.

    Directory of Open Access Journals (Sweden)

    Patricia Besson

    Full Text Available The sparse information captured by the sensory systems is used by the brain to apprehend the environment, for example, to spatially locate the source of audiovisual stimuli. This is an ill-posed inverse problem whose inherent uncertainty can be solved by jointly processing the information, as well as introducing constraints during this process, on the way this multisensory information is handled. This process and its result--the percept--depend on the contextual conditions perception takes place in. To date, perception has been investigated and modeled on the basis of either one of two of its dimensions: the percept or the temporal dynamics of the process. Here, we extend our previously proposed audiovisual perception model to predict both these dimensions to capture the phenomenon as a whole. Starting from a behavioral analysis, we use a data-driven approach to elicit a bayesian network which infers the different percepts and dynamics of the process. Context-specific independence analyses enable us to use the model's structure to directly explore how different contexts affect the way subjects handle the same available information. Hence, we establish that, while the percepts yielded by a unisensory stimulus or by the non-fusion of multisensory stimuli may be similar, they result from different processes, as shown by their differing temporal dynamics. Moreover, our model predicts the impact of bottom-up (stimulus driven factors as well as of top-down factors (induced by instruction manipulation on both the perception process and the percept itself.

  2. Femtosecond laser spectroscopy of spins: Magnetization dynamics in thin magnetic films with spatio-temporal resolution

    International Nuclear Information System (INIS)

    Carpene, E.; Mancini, E.; Dallera, C.; Puppin, E.; De Silvestri, S.

    2010-01-01

    Based on the Magneto-Optical Kerr Effect (MOKE), we have developed an experimental set-up that allows us to fully characterize the magnetization dynamics in thin magnetic films by measuring all three real space components of the magnetization vector M. By means of the pump-probe technique it is possible to extract the time dependence of each individual projection with sub-picosecond resolution. This method has been exploited to investigate the temporal evolution of the magnetization (modulus and orientation) induced by an ultrashort laser pulse in thin epitaxial iron films. According to our results, we deduced that the initial, sub-picosecond demagnetization is established at the electronic level through electron-magnon excitations. The subsequent dynamics is characterized by a precessional motion on the 100 ps time scale, around an effective, time-dependent magnetic field. Following the full dynamics of M, the temporal evolution of the magneto-crystalline anisotropy constant can be unambiguously determined, providing the experimental evidence that the precession is triggered by the rapid, optically-induced misalignment between the magnetization vector and the effective magnetic field. These results suggest a possible pathway toward the ultrarapid switching of the magnetization.

  3. Method to investigate temporal dynamics of ganglion and other retinal cells in the living human eye

    Science.gov (United States)

    Kurokawa, Kazuhiro; Liu, Zhuolin; Crowell, James; Zhang, Furu; Miller, Donald T.

    2018-02-01

    The inner retina is critical for visual processing, but much remains unknown about its neural circuitry and vulnerability to disease. A major bottleneck has been our inability to observe the structure and function of the cells composing these retinal layers in the living human eye. Here, we present a noninvasive method to observe both structural and functional information. Adaptive optics optical coherence tomography (AO-OCT) is used to resolve the inner retinal cells in all three dimensions and novel post processing algorithms are applied to extract structure and physiology down to the cellular level. AO-OCT captured the 3D mosaic of individual ganglion cell somas, retinal nerve fiber bundles of micron caliber, and microglial cells, all in exquisite detail. Time correlation analysis of the AO-OCT videos revealed notable temporal differences between the principal layers of the inner retina. The GC layer was more dynamic than the nerve fiber and inner plexiform layers. At the cellular level, we applied a customized correlation method to individual GCL somas, and found a mean time constant of activity of 0.57 s and spread of +/-0.1 s suggesting a range of physiological dynamics even in the same cell type. Extending our method to slower dynamics (from minutes to one year), time-lapse imaging and temporal speckle contrast revealed appendage and soma motion of resting microglial cells at the retinal surface.

  4. Dynamics of temporally localized states in passively mode-locked semiconductor lasers

    Science.gov (United States)

    Schelte, C.; Javaloyes, J.; Gurevich, S. V.

    2018-05-01

    We study the emergence and the stability of temporally localized structures in the output of a semiconductor laser passively mode locked by a saturable absorber in the long-cavity regime. For large yet realistic values of the linewidth enhancement factor, we disclose the existence of secondary dynamical instabilities where the pulses develop regular and subsequent irregular temporal oscillations. By a detailed bifurcation analysis we show that additional solution branches that consist of multipulse (molecules) solutions exist. We demonstrate that the various solution curves for the single and multipeak pulses can splice and intersect each other via transcritical bifurcations, leading to a complex web of solutions. Our analysis is based on a generic model of mode locking that consists of a time-delayed dynamical system, but also on a much more numerically efficient, yet approximate, partial differential equation. We compare the results of the bifurcation analysis of both models in order to assess up to which point the two approaches are equivalent. We conclude our analysis by the study of the influence of group velocity dispersion, which is only possible in the framework of the partial differential equation model, and we show that it may have a profound impact on the dynamics of the localized states.

  5. Stability of molecular dynamics simulations of classical systems

    DEFF Research Database (Denmark)

    Toxværd, Søren

    2012-01-01

    The existence of a shadow Hamiltonian for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics....... The investigation is based on the stability of the shadow energy, obtained by including the first term in the asymptotic expansion, and on the exact solution of discrete dynamics for a single harmonic mode. The exact solution of discrete dynamics for a harmonic potential with frequency ω gives a criterion...... for the limit of stability h ⩽ 2/ω. Simulations of the Lennard-Jones system and the viscous Kob-Andersen system show that one can use the limit of stability of the shadow energy or the stability criterion for a harmonic mode on the spectrum of instantaneous frequencies to determine the limit of stability of MD...

  6. Molecular dynamics simulation of a chemical reaction

    International Nuclear Information System (INIS)

    Gorecki, J.; Gryko, J.

    1988-06-01

    Molecular dynamics is used to study the chemical reaction A+A→B+B. It is shown that the reaction rate constant follows the Arrhenius law both for Lennard-Jones and hard sphere interaction potentials between substrate particles. A. For the denser systems the reaction rate is proportional to the value of the radial distribution function at the contact point of two hard spheres. 10 refs, 4 figs

  7. An Agent Model of Temporal Dynamics in Relapse and Recurrence in Depression

    NARCIS (Netherlands)

    Aziz, A.A.; Klein, M.C.A.; Treur, J.

    2009-01-01

    This paper presents a dynamic agent model of recurrences of a depression for an individual. Based on several personal characteristics and a representation of events (i.e. life events or daily hassles) the agent model can simulate whether a human agent that recovered from a depression will fall into

  8. An Urban Cellular Automata Model for Simulating Dynamic States on a Local Scale

    Directory of Open Access Journals (Sweden)

    Jenni Partanen

    2016-12-01

    Full Text Available In complex systems, flexibility and adaptability to changes are crucial to the systems’ dynamic stability and evolution. Such resilience requires that the system is able to respond to disturbances by self-organizing, which implies a certain level of entropy within the system. Dynamic states (static, cyclical/periodic, complex, and chaotic reflect this generative capacity, and correlate with the level of entropy. For planning complex cities, we need to develop methods to guide such autonomous progress in an optimal manner. A classical apparatus, cellular automaton (CA, provides such a tool. Applications of CA help us to study temporal dynamics in self-organizing urban systems. By exploring the dynamic states of the model’s dynamics resulting from different border conditions it is possible to discover favorable set(s of rules conductive to the self-organizing dynamics and enable the system’s recovery at the time of crises. Level of entropy is a relevant measurement for evaluation of these dynamic states. The 2-D urban cellular automaton model studied here is based on the microeconomic principle that similar urban activities are attracted to each other, especially in certain self-organizing areas, and that the local dynamics of these enclaves affect the dynamics of the urban region by channeling flows of information, goods and people. The results of the modeling experiment indicate that the border conditions have a major impact on the model’s dynamics generating various dynamic states of the system. Most importantly, it seemed that the model could simulate a favorable, complex dynamic state with medium entropy level which may refer to the continuous self-organization of the system. The model provides a tool for exploring and understanding the effects of boundary conditions in the planning process as various scenarios are tested: resulting dynamics of the system can be explored with such “planning rules” prior to decisions, helping to

  9. Embodiment of intersubjective time: relational dynamics as attractors in the temporal coordination of interpersonal behaviors and experiences.

    Science.gov (United States)

    Laroche, Julien; Berardi, Anna Maria; Brangier, Eric

    2014-01-01

    This paper addresses the issue of "being together," and more specifically the issue of "being together in time." We provide with an integrative framework that is inspired by phenomenology, the enactive approach and dynamical systems theories. To do so, we first define embodiment as a living and lived phenomenon that emerges from agent-world coupling. We then show that embodiment is essentially dynamical and therefore we describe experiential, behavioral and brain dynamics. Both lived temporality and the temporality of the living appear to be complex, multiscale phenomena. Next we discuss embodied dynamics in the context of interpersonal interactions, and briefly review the empirical literature on between-persons temporal coordination. Overall, we propose that being together in time emerges from the relational dynamics of embodied interactions and their flexible co-regulation.

  10. Chain networking revealed by molecular dynamics simulation

    Science.gov (United States)

    Zheng, Yexin; Tsige, Mesfin; Wang, Shi-Qing

    Based on Kremer-Grest model for entangled polymer melts, we demonstrate how the response of a polymer glass depends critically on the chain length. After quenching two melts of very different chain lengths (350 beads per chain and 30 beads per chain) into deeply glassy states, we subject them to uniaxial extension. Our MD simulations show that the glass of long chains undergoes stable necking after yielding whereas the system of short chains is unable to neck and breaks up after strain localization. During ductile extension of the polymer glass made of long chain significant chain tension builds up in the load-bearing strands (LBSs). Further analysis is expected to reveal evidence of activation of the primary structure during post-yield extension. These results lend support to the recent molecular model 1 and are the simulations to demonstrate the role of chain networking. This work is supported, in part, by a NSF Grant (DMR-EAGER-1444859)

  11. Electrical Dynamic Simulation Activities in Forsmark NPP

    International Nuclear Information System (INIS)

    Lamell, Per

    2015-01-01

    The original power system analysis was done in the seventies in former ASEA AB software. For approximate twenty years no major new studies was done because of limited numbers of renewal projects. In the end of the nineties the plant started to update the selectivity planning and study of the loading of the safety bus-bars. The simulation and start of the development of simulation models was done in a tool named Simpow. Simpow was also an ASEA/ABB AB software developed from the program used in the seventies. To continue to work with Simpow was a decision made after doing an extensive review of on the marked available commercially software. Also at that time we start to do our first attempt building electrical simulation models of unit 1 and 2 according to the original documentation. The development of models for the unit 1, 2 and 3 became more intensive some years after the millennium. Partly because of event July 25, 2006 and also because of the renewal of unit 1 and 2 and had subsequently been initiated for unit 3 also. Today we have initiated a conversion of our models to a new program called PowerFactory. That due to the withdrawal of support and development on SIMPOW a couple of years ago. To development relevance, accuracy and detail, models are an important issue for FKA (Forsmark Kraftgrupp AB). The model is initially created according to the plant documentation and also including requested information from the original supplier. Continued development and updates of the model is done according to the data received from the contractors via the demands according to requirements in our technical documents on different electrical components in renewal projects. The development of the model is driven by known weaknesses, depending of the type of studies and necessary data related to events. An important part that will be described is to have a verified simulation tool and validated models. An example is that the models have been validated by making start and

  12. The absence or temporal offset of visual feedback does not influence adaptation to novel movement dynamics.

    Science.gov (United States)

    McKenna, Erin; Bray, Laurence C Jayet; Zhou, Weiwei; Joiner, Wilsaan M

    2017-10-01

    Delays in transmitting and processing sensory information require correctly associating delayed feedback to issued motor commands for accurate error compensation. The flexibility of this alignment between motor signals and feedback has been demonstrated for movement recalibration to visual manipulations, but the alignment dependence for adapting movement dynamics is largely unknown. Here we examined the effect of visual feedback manipulations on force-field adaptation. Three subject groups used a manipulandum while experiencing a lag in the corresponding cursor motion (0, 75, or 150 ms). When the offset was applied at the start of the session (continuous condition), adaptation was not significantly different between groups. However, these similarities may be due to acclimation to the offset before motor adaptation. We tested additional subjects who experienced the same delays concurrent with the introduction of the perturbation (abrupt condition). In this case adaptation was statistically indistinguishable from the continuous condition, indicating that acclimation to feedback delay was not a factor. In addition, end-point errors were not significantly different across the delay or onset conditions, but end-point correction (e.g., deceleration duration) was influenced by the temporal offset. As an additional control, we tested a group of subjects who performed without visual feedback and found comparable movement adaptation results. These results suggest that visual feedback manipulation (absence or temporal misalignment) does not affect adaptation to novel dynamics, independent of both acclimation and perceptual awareness. These findings could have implications for modeling how the motor system adjusts to errors despite concurrent delays in sensory feedback information. NEW & NOTEWORTHY A temporal offset between movement and distorted visual feedback (e.g., visuomotor rotation) influences the subsequent motor recalibration, but the effects of this offset for

  13. From Brain-Environment Connections to Temporal Dynamics and Social Interaction: Principles of Human Brain Function.

    Science.gov (United States)

    Hari, Riitta

    2017-06-07

    Experimental data about brain function accumulate faster than does our understanding of how the brain works. To tackle some general principles at the grain level of behavior, I start from the omnipresent brain-environment connection that forces regularities of the physical world to shape the brain. Based on top-down processing, added by sparse sensory information, people are able to form individual "caricature worlds," which are similar enough to be shared among other people and which allow quick and purposeful reactions to abrupt changes. Temporal dynamics and social interaction in natural environments serve as further essential organizing principles of human brain function. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Nonlinear mirror mode dynamics: Simulations and modeling

    Czech Academy of Sciences Publication Activity Database

    Califano, F.; Hellinger, Petr; Kuznetsov, E.; Passot, T.; Sulem, P. L.; Trávníček, Pavel

    2008-01-01

    Roč. 113, - (2008), A08219/1-A08219/20 ISSN 0148-0227 R&D Projects: GA AV ČR IAA300420702; GA AV ČR IAA300420602 Grant - others:PECS(CZ) 98024 Institutional research plan: CEZ:AV0Z30420517 Keywords : mirror instability * nonlinear evolution * numerical simulations * magnetic holes * mirror structures * kinetic plasma instabilities Subject RIV: BL - Plasma and Gas Discharge Physics Impact factor: 3.147, year: 2008

  15. Molecular dynamics simulation of propagating cracks

    Science.gov (United States)

    Mullins, M.

    1982-01-01

    Steady state crack propagation is investigated numerically using a model consisting of 236 free atoms in two (010) planes of bcc alpha iron. The continuum region is modeled using the finite element method with 175 nodes and 288 elements. The model shows clear (010) plane fracture to the edge of the discrete region at moderate loads. Analysis of the results obtained indicates that models of this type can provide realistic simulation of steady state crack propagation.

  16. Computer Simulation of Turbulent Reactive Gas Dynamics

    Directory of Open Access Journals (Sweden)

    Bjørn H. Hjertager

    1984-10-01

    Full Text Available A simulation procedure capable of handling transient compressible flows involving combustion is presented. The method uses the velocity components and pressure as primary flow variables. The differential equations governing the flow are discretized by integration over control volumes. The integration is performed by application of up-wind differencing in a staggered grid system. The solution procedure is an extension of the SIMPLE-algorithm accounting for compressibility effects.

  17. Monte Carlo simulated dynamical magnetization of single-chain magnets

    Energy Technology Data Exchange (ETDEWEB)

    Li, Jun; Liu, Bang-Gui, E-mail: bgliu@iphy.ac.cn

    2015-03-15

    Here, a dynamical Monte-Carlo (DMC) method is used to study temperature-dependent dynamical magnetization of famous Mn{sub 2}Ni system as typical example of single-chain magnets with strong magnetic anisotropy. Simulated magnetization curves are in good agreement with experimental results under typical temperatures and sweeping rates, and simulated coercive fields as functions of temperature are also consistent with experimental curves. Further analysis indicates that the magnetization reversal is determined by both thermal-activated effects and quantum spin tunnelings. These can help explore basic properties and applications of such important magnetic systems. - Highlights: • Monte Carlo simulated magnetization curves are in good agreement with experimental results. • Simulated coercive fields as functions of temperature are consistent with experimental results. • The magnetization reversal is understood in terms of the Monte Carlo simulations.

  18. Stereochemical errors and their implications for molecular dynamics simulations

    Directory of Open Access Journals (Sweden)

    Freddolino Peter L

    2011-05-01

    Full Text Available Abstract Background Biological molecules are often asymmetric with respect to stereochemistry, and correct stereochemistry is essential to their function. Molecular dynamics simulations of biomolecules have increasingly become an integral part of biophysical research. However, stereochemical errors in biomolecular structures can have a dramatic impact on the results of simulations. Results Here we illustrate the effects that chirality and peptide bond configuration flips may have on the secondary structure of proteins throughout a simulation. We also analyze the most common sources of stereochemical errors in biomolecular structures and present software tools to identify, correct, and prevent stereochemical errors in molecular dynamics simulations of biomolecules. Conclusions Use of the tools presented here should become a standard step in the preparation of biomolecular simulations and in the generation of predicted structural models for proteins and nucleic acids.

  19. Autonomous dynamic decision making in a nuclear fuel cycle simulator

    International Nuclear Information System (INIS)

    Pelakauskas, Martynas; Auzans, Aris; Schneider, Erich A.; Tkaczyk, Alan H.

    2013-01-01

    Highlights: • Objective criteria based decision making in a nuclear fuel cycle simulator. • Simulation driven by an evolving performance metric. • Implementation of the model in a nuclear fuel cycle simulator. • Verification of dynamic decision making based on uranium price evolution. -- Abstract: Growing energy demand and the push to move toward carbon-free ways of electricity generation have renewed the world's interest in nuclear energy. Due to the high technical and economic uncertainties related to nuclear energy, simulation tools have become a necessity in order to plan and evaluate possible nuclear fuel cycles (NFCs). Most of the NFC simulators today work by running the simulation with a user-defined set of facility build orders and preferences. While this allows for a simple way to change the simulation conditions, it may not always lead to optimal results and strongly relies on the user defining the correct parameters. This study looks into the possibility of using the expected cost of electricity (CoE) as the driving build decision variable instead of relying on user-defined build orders. This is a first step toward a more general decision making strategy in dynamic fuel cycle simulation. For this purpose, additional modules were implemented in an NFC simulator, VEGAS, with the consumption dependent price of uranium as a time-varying NFC cost component that drives the cost competitiveness of available NFC options. The model was demonstrated to verify the correct operation of a CoE-driven NFC simulator

  20. Internal cycling, not external loading, decides the nutrient limitation in eutrophic lake: A dynamic model with temporal Bayesian hierarchical inference.

    Science.gov (United States)

    Wu, Zhen; Liu, Yong; Liang, Zhongyao; Wu, Sifeng; Guo, Huaicheng

    2017-06-01

    Lake eutrophication is associated with excessive anthropogenic nutrients (mainly nitrogen (N) and phosphorus (P)) and unobserved internal nutrient cycling. Despite the advances in understanding the role of external loadings, the contribution of internal nutrient cycling is still an open question. A dynamic mass-balance model was developed to simulate and measure the contributions of internal cycling and external loading. It was based on the temporal Bayesian Hierarchical Framework (BHM), where we explored the seasonal patterns in the dynamics of nutrient cycling processes and the limitation of N and P on phytoplankton growth in hyper-eutrophic Lake Dianchi, China. The dynamic patterns of the five state variables (Chla, TP, ammonia, nitrate and organic N) were simulated based on the model. Five parameters (algae growth rate, sediment exchange rate of N and P, nitrification rate and denitrification rate) were estimated based on BHM. The model provided a good fit to observations. Our model results highlighted the role of internal cycling of N and P in Lake Dianchi. The internal cycling processes contributed more than external loading to the N and P changes in the water column. Further insights into the nutrient limitation analysis indicated that the sediment exchange of P determined the P limitation. Allowing for the contribution of denitrification to N removal, N was the more limiting nutrient in most of the time, however, P was the more important nutrient for eutrophication management. For Lake Dianchi, it would not be possible to recover solely by reducing the external watershed nutrient load; the mechanisms of internal cycling should also be considered as an approach to inhibit the release of sediments and to enhance denitrification. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. GRODY - GAMMA RAY OBSERVATORY DYNAMICS SIMULATOR IN ADA

    Science.gov (United States)

    Stark, M.

    1994-01-01

    Analysts use a dynamics simulator to test the attitude control system algorithms used by a satellite. The simulator must simulate the hardware, dynamics, and environment of the particular spacecraft and provide user services which enable the analyst to conduct experiments. Researchers at Goddard's Flight Dynamics Division developed GRODY alongside GROSS (GSC-13147), a FORTRAN simulator which performs the same functions, in a case study to assess the feasibility and effectiveness of the Ada programming language for flight dynamics software development. They used popular object-oriented design techniques to link the simulator's design with its function. GRODY is designed for analysts familiar with spacecraft attitude analysis. The program supports maneuver planning as well as analytical testing and evaluation of the attitude determination and control system used on board the Gamma Ray Observatory (GRO) satellite. GRODY simulates the GRO on-board computer and Control Processor Electronics. The analyst/user sets up and controls the simulation. GRODY allows the analyst to check and update parameter values and ground commands, obtain simulation status displays, interrupt the simulation, analyze previous runs, and obtain printed output of simulation runs. The video terminal screen display allows visibility of command sequences, full-screen display and modification of parameters using input fields, and verification of all input data. Data input available for modification includes alignment and performance parameters for all attitude hardware, simulation control parameters which determine simulation scheduling and simulator output, initial conditions, and on-board computer commands. GRODY generates eight types of output: simulation results data set, analysis report, parameter report, simulation report, status display, plots, diagnostic output (which helps the user trace any problems that have occurred during a simulation), and a permanent log of all runs and errors. The

  2. Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D., E-mail: sergei.ivanov@uni-rostock.de; Kühn, Oliver [Institute of Physics, Rostock University, Universitätsplatz 3, 18055 Rostock (Germany)

    2015-06-28

    Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom.

  3. Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations

    International Nuclear Information System (INIS)

    Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D.; Kühn, Oliver

    2015-01-01

    Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom

  4. Molecular dynamics simulation of ribosome jam

    KAUST Repository

    Matsumoto, Shigenori

    2011-09-01

    We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We estimated the influence of the temperature and concentration of molecules on the hopping probability used in the ASEP model. Our model can also treat environmental effects on the translation process that cannot be explained by such cellular automaton models. © 2010 Elsevier B.V. All rights reserved.

  5. First-principles electron dynamics control simulation of diamond under femtosecond laser pulse train irradiation

    International Nuclear Information System (INIS)

    Wang Cong; Jiang Lan; Wang Feng; Li Xin; Yuan Yanping; Xiao Hai; Tsai, Hai-Lung; Lu Yongfeng

    2012-01-01

    A real-time and real-space time-dependent density functional is applied to simulate the nonlinear electron-photon interactions during shaped femtosecond laser pulse train ablation of diamond. Effects of the key pulse train parameters such as the pulse separation, spatial/temporal pulse energy distribution and pulse number per train on the electron excitation and energy absorption are discussed. The calculations show that photon-electron interactions and transient localized electron dynamics can be controlled including photon absorption, electron excitation, electron density, and free electron distribution by the ultrafast laser pulse train. (paper)

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

    Science.gov (United States)

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

    2009-06-01

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

  7. Computational fluid dynamics for sport simulation

    CERN Document Server

    2009-01-01

    All over the world sport plays a prominent role in society: as a leisure activity for many, as an ingredient of culture, as a business and as a matter of national prestige in such major events as the World Cup in soccer or the Olympic Games. Hence, it is not surprising that science has entered the realm of sports, and, in particular, that computer simulation has become highly relevant in recent years. This is explored in this book by choosing five different sports as examples, demonstrating that computational science and engineering (CSE) can make essential contributions to research on sports topics on both the fundamental level and, eventually, by supporting athletes’ performance.

  8. Modelling, simulation and applications of longitudinal train dynamics

    Science.gov (United States)

    Cole, Colin; Spiryagin, Maksym; Wu, Qing; Sun, Yan Quan

    2017-10-01

    Significant developments in longitudinal train simulation and an overview of the approaches to train models and modelling vehicle force inputs are firstly presented. The most important modelling task, that of the wagon connection, consisting of energy absorption devices such as draft gears and buffers, draw gear stiffness, coupler slack and structural stiffness is then presented. Detailed attention is given to the modelling approaches for friction wedge damped and polymer draft gears. A significant issue in longitudinal train dynamics is the modelling and calculation of the input forces - the co-dimensional problem. The need to push traction performances higher has led to research and improvement in the accuracy of traction modelling which is discussed. A co-simulation method that combines longitudinal train simulation, locomotive traction control and locomotive vehicle dynamics is presented. The modelling of other forces, braking propulsion resistance, curve drag and grade forces are also discussed. As extensions to conventional longitudinal train dynamics, lateral forces and coupler impacts are examined in regards to interaction with wagon lateral and vertical dynamics. Various applications of longitudinal train dynamics are then presented. As an alternative to the tradition single wagon mass approach to longitudinal train dynamics, an example incorporating fully detailed wagon dynamics is presented for a crash analysis problem. Further applications of starting traction, air braking, distributed power, energy analysis and tippler operation are also presented.

  9. Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input.

    Science.gov (United States)

    Armstrong, Alacia; Valverde, Angel; Ramond, Jean-Baptiste; Makhalanyane, Thulani P; Jansson, Janet K; Hopkins, David W; Aspray, Thomas J; Seely, Mary; Trindade, Marla I; Cowan, Don A

    2016-09-29

    The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO 2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall.

  10. Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input

    Energy Technology Data Exchange (ETDEWEB)

    Armstrong, Alacia; Valverde, Angel; Ramond, Jean-Baptiste; Makhalanyane, Thulani P.; Jansson, Janet K.; Hopkins, David W.; Aspray, Thomas J.; Seely, Mary; Trindade, Marla I.; Cowan, Don A.

    2016-09-29

    The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall.

  11. Quantitative Evaluation of Temporal Regularizers in Compressed Sensing Dynamic Contrast Enhanced MRI of the Breast

    Directory of Open Access Journals (Sweden)

    Dong Wang

    2017-01-01

    Full Text Available Purpose. Dynamic contrast enhanced magnetic resonance imaging (DCE-MRI is used in cancer imaging to probe tumor vascular properties. Compressed sensing (CS theory makes it possible to recover MR images from randomly undersampled k-space data using nonlinear recovery schemes. The purpose of this paper is to quantitatively evaluate common temporal sparsity-promoting regularizers for CS DCE-MRI of the breast. Methods. We considered five ubiquitous temporal regularizers on 4.5x retrospectively undersampled Cartesian in vivo breast DCE-MRI data: Fourier transform (FT, Haar wavelet transform (WT, total variation (TV, second-order total generalized variation (TGVα2, and nuclear norm (NN. We measured the signal-to-error ratio (SER of the reconstructed images, the error in tumor mean, and concordance correlation coefficients (CCCs of the derived pharmacokinetic parameters Ktrans (volume transfer constant and ve (extravascular-extracellular volume fraction across a population of random sampling schemes. Results. NN produced the lowest image error (SER: 29.1, while TV/TGVα2 produced the most accurate Ktrans (CCC: 0.974/0.974 and ve (CCC: 0.916/0.917. WT produced the highest image error (SER: 21.8, while FT produced the least accurate Ktrans (CCC: 0.842 and ve (CCC: 0.799. Conclusion. TV/TGVα2 should be used as temporal constraints for CS DCE-MRI of the breast.

  12. Emergent dynamics of spatio-temporal chaos in a heterogeneous excitable medium.

    Science.gov (United States)

    Bittihn, Philip; Berg, Sebastian; Parlitz, Ulrich; Luther, Stefan

    2017-09-01

    Self-organized activation patterns in excitable media such as spiral waves and spatio-temporal chaos underlie dangerous cardiac arrhythmias. While the interaction of single spiral waves with different types of heterogeneity has been studied extensively, the effect of heterogeneity on fully developed spatio-temporal chaos remains poorly understood. We investigate how the complexity and stability properties of spatio-temporal chaos in the Bär-Eiswirth model of excitable media depend on the heterogeneity of the underlying medium. We employ different measures characterizing the chaoticity of the system and find that the spatial arrangement of multiple discrete lower excitability regions has a strong impact on the complexity of the dynamics. Varying the number, shape, and spatial arrangement of the heterogeneities, we observe strong emergent effects ranging from increases in chaoticity to the complete cessation of chaos, contrasting the expectation from the homogeneous behavior. The implications of our findings for the development and treatment of arrhythmias in the heterogeneous cardiac muscle are discussed.

  13. Temporal Microbial Community Dynamics in Microbial Electrolysis Cells – Influence of Acetate and Propionate Concentration

    KAUST Repository

    Rao, Hari Ananda

    2017-07-20

    Microbial electrolysis cells (MECs) are widely considered as a next generation wastewater treatment system. However, fundamental insight on the temporal dynamics of microbial communities associated with MEC performance under different organic types with varied loading concentrations is still unknown, nevertheless this knowledge is essential for optimizing this technology for real-scale applications. Here, the temporal dynamics of anodic microbial communities associated with MEC performance was examined at low (0.5 g COD/L) and high (4 g COD/L) concentrations of acetate or propionate, which are important intermediates of fermentation of municipal wastewaters and sludge. The results showed that acetate-fed reactors exhibited higher performance in terms of maximum current density (I: 4.25 ± 0.23 A/m), coulombic efficiency (CE: 95 ± 8%), and substrate degradation rate (98.8 ± 1.2%) than propionate-fed reactors (I: 2.7 ± 0.28 A/m; CE: 68 ± 9.5%; substrate degradation rate: 84 ± 13%) irrespective of the concentrations tested. Despite of the repeated sampling of the anodic biofilm over time, the high-concentration reactors demonstrated lower and stable performance in terms of current density (I: 1.1 ± 0.14 to 4.2 ± 0.21 A/m), coulombic efficiency (CE: 44 ± 4.1 to 103 ± 7.2%) and substrate degradation rate (64.9 ± 6.3 to 99.7 ± 0.5%), while the low-concentration reactors produced higher and dynamic performance (I: 1.1 ± 0.12 to 4.6 ± 0.1 A/m; CE: 52 ± 2.5 to 105 ± 2.7%; substrate degradation rate: 87.2 ± 0.2 to 99.9 ± 0.06%) with the different substrates tested. Correlating reactor\\'s performance with temporal dynamics of microbial communities showed that relatively similar anodic microbial community composition but with varying relative abundances was observed in all the reactors despite differences in the substrate and concentrations tested. Particularly, Geobacter was the predominant bacteria on the anode biofilm of all MECs over time suggesting its

  14. Spatio-Temporal Simulation and Analysis of Regional Ecological Security Based on Lstm

    Science.gov (United States)

    Gong, C.; Qi, L.; Heming, L.; Karimian, H.; Yuqin, M.

    2017-10-01

    Region is a complicated system, where human, nature and society interact and influence. Quantitative modeling and simulation of ecology in the region are the key to realize the strategy of regional sustainable development. Traditional machine learning methods have made some achievements in the modeling of regional ecosystems, but it is difficult to determine the learning characteristics and to realize spatio-temporal simulation. Deep learning does not need prior identification of training characteristics, have excellent feature learning ability, can improve the accuracy of model prediction, so the use of deep learning model has a significant advantage. Therefore, we use net primary productivity (NPP), atmospheric optical depth (AOD), moderate-resolution imaging spectrometer (MODIS), Normalized Difference Vegetation Index (NDVI), landcover and population data, and use LSTM to do spatio-temporal simulation. We conduct spatial analysis and driving force analysis. The conclusions are as follows: the ecological deficit of northwestern Henan and urban communities such as Zhengzhou is higher. The reason of former lies in the weak land productivity of the Loess Plateau, the irrational crop cultivation mode. The latter lies in the high consumption of resources in the large urban agglomeration; The positive trend of Henan ecological development from 2013 is mainly due to the effective environmental protection policy in the 12th five-year plan; The main driver of the sustained ecological deficit growth of Henan in 2004-2013 is high-speed urbanization, increasing population and goods consumption. This article provides relevant basic scientific support and reference for the regional ecological scientific management and construction.

  15. SPATIO-TEMPORAL SIMULATION AND ANALYSIS OF REGIONAL ECOLOGICAL SECURITY BASED ON LSTM

    Directory of Open Access Journals (Sweden)

    C. Gong

    2017-10-01

    Full Text Available Region is a complicated system, where human, nature and society interact and influence. Quantitative modeling and simulation of ecology in the region are the key to realize the strategy of regional sustainable development. Traditional machine learning methods have made some achievements in the modeling of regional ecosystems, but it is difficult to determine the learning characteristics and to realize spatio-temporal simulation. Deep learning does not need prior identification of training characteristics, have excellent feature learning ability, can improve the accuracy of model prediction, so the use of deep learning model has a significant advantage. Therefore, we use net primary productivity (NPP, atmospheric optical depth (AOD, moderate-resolution imaging spectrometer (MODIS, Normalized Difference Vegetation Index (NDVI, landcover and population data, and use LSTM to do spatio-temporal simulation. We conduct spatial analysis and driving force analysis. The conclusions are as follows: the ecological deficit of northwestern Henan and urban communities such as Zhengzhou is higher. The reason of former lies in the weak land productivity of the Loess Plateau, the irrational crop cultivation mode. The latter lies in the high consumption of resources in the large urban agglomeration; The positive trend of Henan ecological development from 2013 is mainly due to the effective environmental protection policy in the 12th five-year plan; The main driver of the sustained ecological deficit growth of Henan in 2004-2013 is high-speed urbanization, increasing population and goods consumption. This article provides relevant basic scientific support and reference for the regional ecological scientific management and construction.

  16. Evaluating complementary networks of restoration plantings for landscape-scale occurrence of temporally dynamic species.

    Science.gov (United States)

    Ikin, Karen; Tulloch, Ayesha; Gibbons, Philip; Ansell, Dean; Seddon, Julian; Lindenmayer, David

    2016-10-01

    Multibillion dollar investments in land restoration make it critical that conservation goals are achieved cost-effectively. Approaches developed for systematic conservation planning offer opportunities to evaluate landscape-scale, temporally dynamic biodiversity outcomes from restoration and improve on traditional approaches that focus on the most species-rich plantings. We investigated whether it is possible to apply a complementarity-based approach to evaluate the extent to which an existing network of restoration plantings meets representation targets. Using a case study of woodland birds of conservation concern in southeastern Australia, we compared complementarity-based selections of plantings based on temporally dynamic species occurrences with selections based on static species occurrences and selections based on ranking plantings by species richness. The dynamic complementarity approach, which incorporated species occurrences over 5 years, resulted in higher species occurrences and proportion of targets met compared with the static complementarity approach, in which species occurrences were taken at a single point in time. For equivalent cost, the dynamic complementarity approach also always resulted in higher average minimum percent occurrence of species maintained through time and a higher proportion of the bird community meeting representation targets compared with the species-richness approach. Plantings selected under the complementarity approaches represented the full range of planting attributes, whereas those selected under the species-richness approach were larger in size. Our results suggest that future restoration policy should not attempt to achieve all conservation goals within individual plantings, but should instead capitalize on restoration opportunities as they arise to achieve collective value of multiple plantings across the landscape. Networks of restoration plantings with complementary attributes of age, size, vegetation structure, and

  17. Partial multicanonical algorithm for molecular dynamics and Monte Carlo simulations.

    Science.gov (United States)

    Okumura, Hisashi

    2008-09-28

    Partial multicanonical algorithm is proposed for molecular dynamics and Monte Carlo simulations. The partial multicanonical simulation samples a wide range of a part of the potential-energy terms, which is necessary to sample the conformational space widely, whereas a wide range of total potential energy is sampled in the multicanonical algorithm. Thus, one can concentrate the effort to determine the weight factor only on the important energy terms in the partial multicanonical simulation. The partial multicanonical, multicanonical, and canonical molecular dynamics algorithms were applied to an alanine dipeptide in explicit water solvent. The canonical simulation sampled the states of P(II), C(5), alpha(R), and alpha(P). The multicanonical simulation covered the alpha(L) state as well as these states. The partial multicanonical simulation also sampled the C(7) (ax) state in addition to the states that were sampled by the multicanonical simulation. In the partial multicanonical simulation, furthermore, backbone dihedral angles phi and psi rotated more frequently than those in the multicanonical and canonical simulations. These results mean that the partial multicanonical algorithm has a higher sampling efficiency than the multicanonical and canonical algorithms.

  18. Nonparametric evaluation of dynamic disease risk: a spatio-temporal kernel approach.

    Directory of Open Access Journals (Sweden)

    Zhijie Zhang

    Full Text Available Quantifying the distributions of disease risk in space and time jointly is a key element for understanding spatio-temporal phenomena while also having the potential to enhance our understanding of epidemiologic trajectories. However, most studies to date have neglected time dimension and focus instead on the "average" spatial pattern of disease risk, thereby masking time trajectories of disease risk. In this study we propose a new idea titled "spatio-temporal kernel density estimation (stKDE" that employs hybrid kernel (i.e., weight functions to evaluate the spatio-temporal disease risks. This approach not only can make full use of sample data but also "borrows" information in a particular manner from neighboring points both in space and time via appropriate choice of kernel functions. Monte Carlo simulations show that the proposed method performs substantially better than the traditional (i.e., frequency-based kernel density estimation (trKDE which has been used in applied settings while two illustrative examples demonstrate that the proposed approach can yield superior results compared to the popular trKDE approach. In addition, there exist various possibilities for improving and extending this method.

  19. Somatic growth dynamics of West Atlantic hawksbill sea turtles: a spatio-temporal perspective

    Science.gov (United States)

    Bjorndal, Karen A.; Chaloupka, Milani; Saba, Vincent S.; Diez, Carlos E.; van Dam, Robert P.; Krueger, Barry H.; Horrocks, Julia A.; Santos, Armando J.B.; Bellini, Cláudio; Marcovaldi, Maria A.G.; Nava, Mabel; Willis, Sue; Godley, Brendan J.; Gore, Shannon; Hawkes, Lucy A.; McGowan, Andrew; Witt, Matthew J.; Stringell, Thomas B.; Sanghera, Amdeep; Richardson, Peter B.; Broderick, Annette C.; Phillips, Quinton; Calosso, Marta C.; Claydon, John A.B.; Blumenthal, Janice; Moncada, Felix; Nodarse, Gonzalo; Medina, Yosvani; Dunbar, Stephen G.; Wood, Lawrence D.; Lagueux, Cynthia J.; Campbell, Cathi L.; Meylan, Anne B.; Meylan, Peter A.; Burns Perez, Virginia R.; Coleman, Robin A.; Strindberg, Samantha; Guzmán-H, Vicente; Hart, Kristen M.; Cherkiss, Michael S.; Hillis-Starr, Zandy; Lundgren, Ian; Boulon, Ralf H.; Connett, Stephen; Outerbridge, Mark E.; Bolten, Alan B.

    2016-01-01

    Somatic growth dynamics are an integrated response to environmental conditions. Hawksbill sea turtles (Eretmochelys imbricata) are long-lived, major consumers in coral reef habitats that move over broad geographic areas (hundreds to thousands of kilometers). We evaluated spatio-temporal effects on hawksbill growth dynamics over a 33-yr period and 24 study sites throughout the West Atlantic and explored relationships between growth dynamics and climate indices. We compiled the largest ever data set on somatic growth rates for hawksbills – 3541 growth increments from 1980 to 2013. Using generalized additive mixed model analyses, we evaluated 10 covariates, including spatial and temporal variation, that could affect growth rates. Growth rates throughout the region responded similarly over space and time. The lack of a spatial effect or spatio-temporal interaction and the very strong temporal effect reveal that growth rates in West Atlantic hawksbills are likely driven by region-wide forces. Between 1997 and 2013, mean growth rates declined significantly and steadily by 18%. Regional climate indices have significant relationships with annual growth rates with 0- or 1-yr lags: positive with the Multivariate El Niño Southern Oscillation Index (correlation = 0.99) and negative with Caribbean sea surface temperature (correlation = −0.85). Declines in growth rates between 1997 and 2013 throughout the West Atlantic most likely resulted from warming waters through indirect negative effects on foraging resources of hawksbills. These climatic influences are complex. With increasing temperatures, trajectories of decline of coral cover and availability in reef habitats of major prey species of hawksbills are not parallel. Knowledge of how choice of foraging habitats, prey selection, and prey abundance are affected by warming water temperatures is needed to understand how climate change will affect productivity of consumers that live in association with coral reefs. Main

  20. Near equilibrium dynamics and one-dimensional spatial—temporal structures of polar active liquid crystals

    International Nuclear Information System (INIS)

    Yang Xiao-Gang; Wang Qi; Forest, M. Gregory

    2014-01-01

    We systematically explore near equilibrium, flow-driven, and flow-activity coupled dynamics of polar active liquid crystals using a continuum model. Firstly, we re-derive the hydrodynamic model to ensure the thermodynamic laws are obeyed and elastic stresses and forces are consistently accounted. We then carry out a linear stability analysis about constant steady states to study near equilibrium dynamics around the steady states, revealing long-wave instability inherent in this model system and how active parameters in the model affect the instability. We then study model predictions for one-dimensional (1D) spatial—temporal structures of active liquid crystals in a channel subject to physical boundary conditions. We discuss the model prediction in two selected regimes, one is the viscous stress dominated regime, also known as the flow-driven regime, while the other is the full regime, in which all active mechanisms are included. In the viscous stress dominated regime, the polarity vector is driven by the prescribed flow field. Dynamics depend sensitively on the physical boundary condition and the type of the driven flow field. Bulk-dominated temporal periodic states and spatially homogeneous states are possible under weak anchoring conditions while spatially inhomogeneous states exist under strong anchoring conditions. In the full model, flow-orientation interaction generates a host of planar as well as out-of-plane spatial—temporal structures related to the spontaneous flows due to the molecular self-propelled motion. These results provide contact with the recent literature on active nematic suspensions. In addition, symmetry breaking patterns emerge as the additional active viscous stress due to the polarity vector is included in the force balance. The inertia effect is found to limit the long-time survival of spatial structures to those with small wave numbers, i.e., an asymptotic coarsening to long wave structures. A rich set of mechanisms for generating

  1. DYNSIR; A dynamic simulator for the chemical process

    International Nuclear Information System (INIS)

    Park, Hyun Soo; Yoo, Jae Hyung; Byeon, Kee Hoh; Park, Jeong Hwa; Park, Seong Won

    1990-03-01

    A program code for dynamic simulation of arbitrary chemical process, called DYNSIR, is developed. The code can simulate rather arbitrary arrangements of individual chemical processing units whose models are described by ordinary differential equations. The code structure to handle input/output, memory and data management, numerical interactive or predetermined changes in parameter values during the simulation. Individual model is easy to maintain since the modular approach is used. The integration routine is highly effective because of the development of algorithm for modular integration method using the cubic spline. DYNSIR's data structures are not the index but the pointer structure. This pointer structure allows the dynamic memory allocation for the memory management. The dynamic memory allocation methods is to minimize the amount of memories and to overcome the limitation of the number of variables to be used. Finally, it includes various functions, such as the input preprocessor, the effective error processing, and plotting and reporting routines. (author)

  2. Molecular dynamics simulation of laser shock phenomena

    Energy Technology Data Exchange (ETDEWEB)

    Fukumoto, Ichirou [Japan Atomic Energy Research Inst., Kansai Research Establishment, Advanced Photon Research Center, Neyagawa, Osaka (Japan).

    2001-10-01

    Recently, ultrashort-pulse lasers with high peak power have been developed, and their application to materials processing is expected as a tool of precision microfabrication. When a high power laser irradiates, a shock wave propagates into the material and dislocations are generated. In this paper, laser shock phenomena of the metal were analyzed using the modified molecular dynamics method, which has been developed by Ohmura and Fukumoto. The main results obtained are summarized as follows: (1) The shock wave induced by the Gaussian beam irradiation propagates radially from the surface to the interior. (2) A lot of dislocations are generated at the solid-liquid interface by the propagation of a shock wave. (3) Some dislocations are moved instantaneously with the velocity of the longitudinal wave when the shock wave passes, and their velocity is not larger than the transverse velocity after the shock wave has passed. (author)

  3. A Compact Synchronous Cellular Model of Nonlinear Calcium Dynamics: Simulation and FPGA Synthesis Results.

    Science.gov (United States)

    Soleimani, Hamid; Drakakis, Emmanuel M

    2017-06-01

    Recent studies have demonstrated that calcium is a widespread intracellular ion that controls a wide range of temporal dynamics in the mammalian body. The simulation and validation of such studies using experimental data would benefit from a fast large scale simulation and modelling tool. This paper presents a compact and fully reconfigurable cellular calcium model capable of mimicking Hopf bifurcation phenomenon and various nonlinear responses of the biological calcium dynamics. The proposed cellular model is synthesized on a digital platform for a single unit and a network model. Hardware synthesis, physical implementation on FPGA, and theoretical analysis confirm that the proposed cellular model can mimic the biological calcium behaviors with considerably low hardware overhead. The approach has the potential to speed up large-scale simulations of slow intracellular dynamics by sharing more cellular units in real-time. To this end, various networks constructed by pipelining 10 k to 40 k cellular calcium units are compared with an equivalent simulation run on a standard PC workstation. Results show that the cellular hardware model is, on average, 83 times faster than the CPU version.

  4. Fluid consumption and taste novelty determines transcription temporal dynamics in the gustatory cortex.

    Science.gov (United States)

    Inberg, Sharon; Jacob, Eyal; Elkobi, Alina; Edry, Efrat; Rappaport, Akiva; Simpson, T Ian; Armstrong, J Douglas; Shomron, Noam; Pasmanik-Chor, Metsada; Rosenblum, Kobi

    2016-02-09

    Novel taste memories, critical for animal survival, are consolidated to form long term memories which are dependent on translation regulation in the gustatory cortex (GC) hours following acquisition. However, the role of transcription regulation in the process is unknown. Here, we report that transcription in the GC is necessary for taste learning in rats, and that drinking and its consequences, as well as the novel taste experience, affect transcription in the GC during taste memory consolidation. We show differential effects of learning on temporal dynamics in set of genes in the GC, including Arc/Arg3.1, known to regulate the homeostasis of excitatory synapses. We demonstrate that in taste learning, transcription programs were activated following the physiological responses (i.e., fluid consumption following a water restriction regime, reward, arousal of the animal, etc.) and the specific information about a given taste (i.e., taste novelty). Moreover, the cortical differential prolonged kinetics of mRNA following novel versus familiar taste learning may represent additional novelty related molecular response, where not only the total amount, but also the temporal dynamics of transcription is modulated by sensory experience of novel information.

  5. Amygdala temporal dynamics: temperamental differences in the timing of amygdala response to familiar and novel faces

    Directory of Open Access Journals (Sweden)

    Shelton Richard C

    2009-12-01

    Full Text Available Abstract Background Inhibited temperament - the predisposition to respond to new people, places or things with wariness or avoidance behaviors - is associated with increased risk for social anxiety disorder and major depression. Although the magnitude of the amygdala's response to novelty has been identified as a neural substrate of inhibited temperament, there may also be differences in temporal dynamics (latency, duration, and peak. We hypothesized that persons with inhibited temperament would have faster responses to novel relative to familiar neutral faces compared to persons with uninhibited temperament. We used event-related functional magnetic resonance imaging to measure the temporal dynamics of the blood oxygen level dependent (BOLD response to both novel and familiar neutral faces in participants with inhibited or uninhibited temperament. Results Inhibited participants had faster amygdala responses to novel compared with familiar faces, and both longer and greater amygdala response to all faces. There were no differences in peak response. Conclusion Faster amygdala response to novelty may reflect a computational bias that leads to greater neophobic responses and represents a mechanism for the development of social anxiety.

  6. Left or right? Lateralizing temporal lobe epilepsy by dynamic amygdala fMRI.

    Science.gov (United States)

    Ives-Deliperi, Victoria; Butler, James Thomas; Jokeit, Hennric

    2017-05-01

    In this case series, the findings of 85 functional MRI studies employing a dynamic fearful face paradigm are reported. Previous findings have shown the paradigm to generate bilateral amygdala activations in healthy subjects and unilateral activations in patients with MTLE, in the contralateral hemisphere to seizure origin. Such findings suggest ipsilateral limbic pathology and offer collateral evidence in lateralizing MTLE. The series includes 60 patients with TLE, 12 patients with extra-temporal lobe epilepsy, and 13 healthy controls. Functional MRI studies using a 1.5T scanner were conducted over a three-year period at a single epilepsy center and individual results were compared with EEG findings. In the cohort of unilateral TLE patients, lateralized activations of the amygdala were concordant with EEG findings in 76% of patients (77% lTLE, 74% rTLE). The differences in the mean lateralized indices of the lTLE, rTLE, and healthy control groups were all statistically significant. Lateralized amygdala activations were concordant with EEG findings in only 31% of the 12 patients with extra-temporal lobe epilepsy and bilateral amygdala activations were generated in all but one of the healthy control subjects. This case series further endorses the utility of the dynamic fearful face functional MRI paradigm using the widely available 1.5T as an adjunctive investigation to lateralize TLE. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Temporal dynamics of categorization: Forgetting as the basis of abstraction and generalization

    Directory of Open Access Journals (Sweden)

    Haley eVlach

    2014-09-01

    Full Text Available Historically, models of categorization have focused on how learners track frequencies and co-occurrence information to abstract relevant category features for generalization. The current study takes a different approach by examining how the temporal dynamics of categorization affect abstraction and generalization. In the learning phase of the experiment, all relevant category features were presented an equal number of times across category exemplars. However, the relevant features were presented on one of two learning schedules: massed or interleaved. At a series of immediate and delayed tests, learners were asked to generalize to novel exemplars that contained massed features, interleaved features, or all novel features. The results of this experiment revealed that, at an immediate test, learners more readily generalized based upon features presented on a massed schedule. Conversely, at a delayed test, learners more readily generalized based upon features presented on an interleaved schedule, until information was no longer readily retrievable from memory. These findings suggest that forgetting and retrieval processes engendered by the temporal dynamics of learning are used as a basis of abstraction, implicating forgetting as a central mechanism of generalization.

  8. Spatial and temporal dynamics of the genetic organization of small mammal populations

    International Nuclear Information System (INIS)

    Smith, M.H.; Manlove, M.N.; Joule, J.

    1978-01-01

    A functional population is a group of organisms and their offspring that contributes to a common gene pool within a certain area and time period. It is also the unit of evolution and should be viewed both in quantitative and qualitative terms. Selection, drift, dispersal, and mutation can alter the composition of populations. Spatial heterogeneity in allele frequencies argues for a conceptual model that has a series of relatively small populations semi-isolated from one another. Because of the relatively high levels of genetic variability characteristic of most mammalian species, significant amounts of gene flow between these spatially subdivided populations must occur when longer time periods are considered. Fluctuations in the genetic structure of populations seem to be important in altering the fitness of the individuals within the populations. The interaction of populations through gene flow is important in changing the levels of intrapopulational genetic variability. Populations can be characterized as existing on a continuum from relatively stable to unstable numbers and by other associated changes in their characteristics. Temporal changes in allele frequency occur in a variety of mammals. Conceptually, a species can be viewed as a series of dynamic populations that vary in numbers and quality in both a spatial and temporal context even over short distances and time periods. Short term changes in the quality of individuals in a population can be important in altering the short term dynamics of a population

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

    Science.gov (United States)

    Chen, Jundong

    2018-03-01

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

  10. Influence of fluvial environments on sediment archiving processes and temporal pollutant dynamics (Upper Loire River, France).

    Science.gov (United States)

    Dhivert, E; Grosbois, C; Rodrigues, S; Desmet, M

    2015-02-01

    Floodplains are often cored to build long-term pollutant trends at the basin scale. To highlight the influences of depositional environments on archiving processes, aggradation rates, archived trace element signals and vertical redistribution processes, two floodplain cores were sampled near in two different environments of the Upper Loire River (France): (i) a river bank ridge and (ii) a paleochannel connected by its downstream end. The base of the river bank core is composed of sandy sediments from the end of the Little Ice Age (late 18th century). This composition corresponds to a proximal floodplain aggradation (sediments that settled in the distal floodplain. In this distal floodplain environment, the aggradation rate depends on the topography and connection degree to the river channel. The temporal dynamics of anthropogenic trace element enrichments recorded in the distal floodplain are initially synchronous and present similar levels. Although the river bank core shows general temporal trends, the paleochannel core has a better resolution for short-time variations of trace element signals. After local water depth regulation began in the early 1930s, differences of connection degree were enhanced between the two cores. Therefore, large trace element signal divergences are recorded across the floodplain. The paleochannel core shows important temporal variations of enrichment levels from the 1930s to the coring date. However, the river bank core has no significant temporal variations of trace element enrichments and lower contamination levels because of a lower deposition of contaminated sediments and a pedogenetic trace elements redistribution. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Exploring spatial-temporal dynamics of fire regime features in mainland Spain

    Science.gov (United States)

    Jiménez-Ruano, Adrián; Rodrigues Mimbrero, Marcos; de la Riva Fernández, Juan

    2017-10-01

    This paper explores spatial-temporal dynamics in fire regime features, such as fire frequency, burnt area, large fires and natural- and human-caused fires, as an essential part of fire regime characterization. Changes in fire features are analysed at different spatial - regional and provincial/NUTS3 - levels, together with summer and winter temporal scales, using historical fire data from Spain for the period 1974-2013. Temporal shifts in fire features are investigated by means of change point detection procedures - Pettitt test, AMOC (at most one change), PELT (pruned exact linear time) and BinSeg (binary segmentation) - at a regional level to identify changes in the time series of the features. A trend analysis was conducted using the Mann-Kendall and Sen's slope tests at both the regional and NUTS3 level. Finally, we applied a principal component analysis (PCA) and varimax rotation to trend outputs - mainly Sen's slope values - to summarize overall temporal behaviour and to explore potential links in the evolution of fire features. Our results suggest that most fire features show remarkable shifts between the late 1980s and the first half of the 1990s. Mann-Kendall outputs revealed negative trends in the Mediterranean region. Results from Sen's slope suggest high spatial and intra-annual variability across the study area. Fire activity related to human sources seems to be experiencing an overall decrease in the northwestern provinces, particularly pronounced during summer. Similarly, the Hinterland and the Mediterranean coast are gradually becoming less fire affected. Finally, PCA enabled trends to be synthesized into four main components: winter fire frequency (PC1), summer burnt area (PC2), large fires (PC3) and natural fires (PC4).

  12. Exploring spatial–temporal dynamics of fire regime features in mainland Spain

    Directory of Open Access Journals (Sweden)

    A. Jiménez-Ruano

    2017-10-01

    Full Text Available This paper explores spatial–temporal dynamics in fire regime features, such as fire frequency, burnt area, large fires and natural- and human-caused fires, as an essential part of fire regime characterization. Changes in fire features are analysed at different spatial – regional and provincial/NUTS3 – levels, together with summer and winter temporal scales, using historical fire data from Spain for the period 1974–2013. Temporal shifts in fire features are investigated by means of change point detection procedures – Pettitt test, AMOC (at most one change, PELT (pruned exact linear time and BinSeg (binary segmentation – at a regional level to identify changes in the time series of the features. A trend analysis was conducted using the Mann–Kendall and Sen's slope tests at both the regional and NUTS3 level. Finally, we applied a principal component analysis (PCA and varimax rotation to trend outputs – mainly Sen's slope values – to summarize overall temporal behaviour and to explore potential links in the evolution of fire features. Our results suggest that most fire features show remarkable shifts between the late 1980s and the first half of the 1990s. Mann–Kendall outputs revealed negative trends in the Mediterranean region. Results from Sen's slope suggest high spatial and intra-annual variability across the study area. Fire activity related to human sources seems to be experiencing an overall decrease in the northwestern provinces, particularly pronounced during summer. Similarly, the Hinterland and the Mediterranean coast are gradually becoming less fire affected. Finally, PCA enabled trends to be synthesized into four main components: winter fire frequency (PC1, summer burnt area (PC2, large fires (PC3 and natural fires (PC4.

  13. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics

    DEFF Research Database (Denmark)

    Papaleo, Elena

    2015-01-01

    that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome...... with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties...... simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations....

  14. Molecular Dynamic Simulations of Nanostructured Ceramic Materials on Parallel Computers

    International Nuclear Information System (INIS)

    Vashishta, Priya; Kalia, Rajiv

    2005-01-01

    Large-scale molecular-dynamics (MD) simulations have been performed to gain insight into: (1) sintering, structure, and mechanical behavior of nanophase SiC and SiO2; (2) effects of dynamic charge transfers on the sintering of nanophase TiO2; (3) high-pressure structural transformation in bulk SiC and GaAs nanocrystals; (4) nanoindentation in Si3N4; and (5) lattice mismatched InAs/GaAs nanomesas. In addition, we have designed a multiscale simulation approach that seamlessly embeds MD and quantum-mechanical (QM) simulations in a continuum simulation. The above research activities have involved strong interactions with researchers at various universities, government laboratories, and industries. 33 papers have been published and 22 talks have been given based on the work described in this report

  15. Molecular Dynamics Simulations of displacement cascades in metallic systems

    International Nuclear Information System (INIS)

    Doan, N.V.; Tietze, H.

    1995-01-01

    We use Molecular Dynamics Computer Simulations to investigate defect production induced by energetic displacement cascades up to 10 keV in pure metals (Cu, Ni) and in ordered intermetallic alloys NiAl, Ni 3 Al. Various model potentials were employed to describe the many-body nature of the interactions: the RGL (Rosato-Guillope-Legrand) model was used in pure Cu and Ni simulations; the modified version of the Vitek, Ackland and Cserti potentials (due to Gao, Bacon and Ackland) in Ni 3 Al and the EAM potentials of Foiles and Daw modified by Rubini and Ballone in NiAl, Ni 3 Al were used in alloy simulations. Atomic mixing and disordering were studied into details owing to imaging techniques and determined at different phases of the cascades. Some mixing mechanisms were identified. Our results were compared with existing data and those obtained by similar Molecular Dynamics Simulations available in the literature. (orig.)

  16. Temporal dynamics of distinct CA1 cell populations during unconscious state induced by ketamine.

    Directory of Open Access Journals (Sweden)

    Hui Kuang

    2010-12-01

    Full Text Available Ketamine is a widely used dissociative anesthetic which can induce some psychotic-like symptoms and memory deficits in some patients during the post-operative period. To understand its effects on neural population dynamics in the brain, we employed large-scale in vivo ensemble recording techniques to monitor the activity patterns of simultaneously recorded hippocampal CA1 pyramidal cells and various interneurons during several conscious and unconscious states such as awake rest, running, slow wave sleep, and ketamine-induced anesthesia. Our analyses reveal that ketamine induces distinct oscillatory dynamics not only in pyramidal cells but also in at least seven different types of CA1 interneurons including putative basket cells, chandelier cells, bistratified cells, and O-LM cells. These emergent unique oscillatory dynamics may very well reflect the intrinsic temporal relationships within the CA1 circuit. It is conceivable that systematic characterization of network dynamics may eventually lead to better understanding of how ketamine induces unconsciousness and consequently alters the conscious mind.

  17. Stochastic Simulation of Cardiac Ventricular Myocyte Calcium Dynamics and Waves

    OpenAIRE

    Tuan, Hoang-Trong Minh; Williams, George S. B.; Chikando, Aristide C.; Sobie, Eric A.; Lederer, W. Jonathan; Jafri, M. Saleet

    2011-01-01

    A three dimensional model of calcium dynamics in the rat ventricular myocyte was developed to study the mechanism of calcium homeostasis and pathological calcium dynamics during calcium overload. The model contains 20,000 calcium release units (CRUs) each containing 49 ryanodine receptors. The model simulates calcium sparks with a realistic spontaneous calcium spark rate. It suggests that in addition to the calcium spark-based leak, there is an invisible calcium leak caused by the stochastic ...

  18. The simulation research for the dynamic performance of integrated PWR

    International Nuclear Information System (INIS)

    Yuan Jiandong; Xia Guoqing; Fu Mingyu

    2005-01-01

    The mathematical model of the reactor core of integrated PWR has been studied and simplified properly. With the lumped parameter method, authors have established the mathematical model of the reactor core, including the neutron dynamic equation, the feedback reactivities model and the thermo-hydraulic model of the reactor. Based on the above equations and models, the incremental transfer functions of the reactor core model have been built. By simulation experimentation, authors have compared the dynamic characteristics of the integrated PWR with the traditional dispersed PWR. The simulation results show that the mathematical models and equations are correct. (authors)

  19. Coalescence of silver unidimensional structures by molecular dynamics simulation

    International Nuclear Information System (INIS)

    Perez A, M.; Gutierrez W, C.E.; Mondragon, G.; Arenas, J.

    2007-01-01

    The study of nanoparticles coalescence and silver nano rods phenomena by means of molecular dynamics simulation under the thermodynamic laws is reported. In this work we focus ourselves to see the conditions under which the one can be given one dimension growth of silver nano rods for the coalescence phenomenon among two nano rods or one nano rod and one particle; what allows us to study those structural, dynamic and morphological properties of the silver nano rods to different thermodynamic conditions. The simulations are carried out using the Sutton-Chen potentials of interaction of many bodies that allow to obtain appropriate results with the real physical systems. (Author)

  20. Beam dynamics simulation in the X-ray Compton source

    Energy Technology Data Exchange (ETDEWEB)

    Gladkikh, P.; Karnaukhov, I.; Telegin, Yu.; Shcherbakov, A. E-mail: shcherbakov@kipt.kharkov.ua; Zelinsky, A

    2002-05-01

    At the National Science Center 'Kharkov Institute of Physics and Technology' the X-ray source based on Compton scattering has been developed. The computer code for simulation of electron beam dynamics with taking into account the Compton scattering effect based on Monte Carlo method is described in this report. The first results of computer simulation of beam dynamics with electron-photon interaction, parameters of electron and photon beams are presented. Calculations were carried out with the lattice of synchrotron light source SRS-800 Ukrainian Synchrotron Center.

  1. Beam dynamics simulation in the X-ray Compton source

    International Nuclear Information System (INIS)

    Gladkikh, P.; Karnaukhov, I.; Telegin, Yu.; Shcherbakov, A.; Zelinsky, A.

    2002-01-01

    At the National Science Center 'Kharkov Institute of Physics and Technology' the X-ray source based on Compton scattering has been developed. The computer code for simulation of electron beam dynamics with taking into account the Compton scattering effect based on Monte Carlo method is described in this report. The first results of computer simulation of beam dynamics with electron-photon interaction, parameters of electron and photon beams are presented. Calculations were carried out with the lattice of synchrotron light source SRS-800 Ukrainian Synchrotron Center

  2. Beam dynamics simulation in the X-ray Compton source

    CERN Document Server

    Gladkikh, P; Telegin, Yu P; Shcherbakov, A; Zelinsky, A

    2002-01-01

    At the National Science Center 'Kharkov Institute of Physics and Technology' the X-ray source based on Compton scattering has been developed. The computer code for simulation of electron beam dynamics with taking into account the Compton scattering effect based on Monte Carlo method is described in this report. The first results of computer simulation of beam dynamics with electron-photon interaction, parameters of electron and photon beams are presented. Calculations were carried out with the lattice of synchrotron light source SRS-800 Ukrainian Synchrotron Center.

  3. Dynamic modeling, simulation and control of energy generation

    CERN Document Server

    Vepa, Ranjan

    2013-01-01

    This book addresses the core issues involved in the dynamic modeling, simulation and control of a selection of energy systems such as gas turbines, wind turbines, fuel cells and batteries. The principles of modeling and control could be applied to other non-convention methods of energy generation such as solar energy and wave energy.A central feature of Dynamic Modeling, Simulation and Control of Energy Generation is that it brings together diverse topics in thermodynamics, fluid mechanics, heat transfer, electro-chemistry, electrical networks and electrical machines and focuses on their appli

  4. Lessons Learned From Dynamic Simulations of Advanced Fuel Cycles

    International Nuclear Information System (INIS)

    Piet, Steven J.; Dixon, Brent W.; Jacobson, Jacob J.; Matthern, Gretchen E.; Shropshire, David E.

    2009-01-01

    Years of performing dynamic simulations of advanced nuclear fuel cycle options provide insights into how they could work and how one might transition from the current once-through fuel cycle. This paper summarizes those insights from the context of the 2005 objectives and goals of the Advanced Fuel Cycle Initiative (AFCI). Our intent is not to compare options, assess options versus those objectives and goals, nor recommend changes to those objectives and goals. Rather, we organize what we have learned from dynamic simulations in the context of the AFCI objectives for waste management, proliferation resistance, uranium utilization, and economics. Thus, we do not merely describe 'lessons learned' from dynamic simulations but attempt to answer the 'so what' question by using this context. The analyses have been performed using the Verifiable Fuel Cycle Simulation of Nuclear Fuel Cycle Dynamics (VISION). We observe that the 2005 objectives and goals do not address many of the inherently dynamic discriminators among advanced fuel cycle options and transitions thereof

  5. Dynamic simulation of the NET In-Vessel Handling Unit

    International Nuclear Information System (INIS)

    Reim, J.

    1991-01-01

    During the conceptual design phase of the Next European Torus (NET) a large remote maintenance transporter system, the In-Vessel Handling Unit (IVHU), is being developed. It consists of an articulated boom with four rotational joints, which is mounted on a carrier outside the vessel. This boom will be able to carry master-slave manipulators or special work units. The engineering design is supported by dynamic computations. Main topics of the dynamic simulation are the evaluation of IVHU performance, selection and optimisation of the actuator design and of the control algorithms. This simulation task requires full three-dimensional modelling regarding structural elasticity and non-linear actuator dynamics. The Multibody dynamics of the transporter system are modelled with a commerical analysis package. Elastic links and a precise dynamic actuator model are introduced by applied forces, spring elements and differential equations. The actuator model comprises electric motors, gears and linear control algorithms. Non-linear effects which have an influence on control stability and accuracy are taken into account. Most important effects are backlash and static friction. The simulations concentrate on test and optimisation of the control layout and performance studies for critical remote handling tasks. Simulations for control layout and critical remote maintenance tasks correspond to the design objectives of the transporter system. (orig.)

  6. Molecular dynamics simulations reveal the conformational dynamics of Arabidopsis thaliana BRI1 and BAK1 receptor-like kinases.

    Science.gov (United States)

    Moffett, Alexander S; Bender, Kyle W; Huber, Steven C; Shukla, Diwakar

    2017-07-28

    The structural motifs responsible for activation and regulation of eukaryotic protein kinases in animals have been studied extensively in recent years, and a coherent picture of their activation mechanisms has begun to emerge. In contrast, non-animal eukaryotic protein kinases are not as well understood from a structural perspective, representing a large knowledge gap. To this end, we investigated the conformational dynamics of two key Arabidopsis thaliana receptor-like kinases, brassinosteroid-insensitive 1 (BRI1) and BRI1-associated kinase 1 (BAK1), through extensive molecular dynamics simulations of their fully phosphorylated kinase domains. Molecular dynamics simulations calculate the motion of each atom in a protein based on classical approximations of interatomic forces, giving researchers insight into protein function at unparalleled spatial and temporal resolutions. We found that in an otherwise "active" BAK1 the αC helix is highly disordered, a hallmark of deactivation, whereas the BRI1 αC helix is moderately disordered and displays swinging behavior similar to numerous animal kinases. An analysis of all known sequences in the A. thaliana kinome found that αC helix disorder may be a common feature of plant kinases. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  7. Dynamic Garment Simulation based on Hybrid Bounding Volume Hierarchy

    Directory of Open Access Journals (Sweden)

    Zhu Dongyong

    2016-12-01

    Full Text Available In order to solve the computing speed and efficiency problem of existing dynamic clothing simulation, this paper presents a dynamic garment simulation based on a hybrid bounding volume hierarchy. It firstly uses MCASG graph theory to do the primary segmentation for a given three-dimensional human body model. And then it applies K-means cluster to do the secondary segmentation to collect the human body’s upper arms, lower arms, upper legs, lower legs, trunk, hip and woman’s chest as the elementary units of dynamic clothing simulation. According to different shapes of these elementary units, it chooses the closest and most efficient hybrid bounding box to specify these units, such as cylinder bounding box and elliptic cylinder bounding box. During the process of constructing these bounding boxes, it uses the least squares method and slices of the human body to get the related parameters. This approach makes it possible to use the least amount of bounding boxes to create close collision detection regions for the appearance of the human body. A spring-mass model based on a triangular mesh of the clothing model is finally constructed for dynamic simulation. The simulation result shows the feasibility and superiority of the method described.

  8. Agent-based modeling of autophagy reveals emergent regulatory behavior of spatio-temporal autophagy dynamics.

    Science.gov (United States)

    Börlin, Christoph S; Lang, Verena; Hamacher-Brady, Anne; Brady, Nathan R

    2014-09-10

    Autophagy is a vesicle-mediated pathway for lysosomal degradation, essential under basal and stressed conditions. Various cellular components, including specific proteins, protein aggregates, organelles and intracellular pathogens, are targets for autophagic degradation. Thereby, autophagy controls numerous vital physiological and pathophysiological functions, including cell signaling, differentiation, turnover of cellular components and pathogen defense. Moreover, autophagy enables the cell to recycle cellular components to metabolic substrates, thereby permitting prolonged survival under low nutrient conditions. Due to the multi-faceted roles for autophagy in maintaining cellular and organismal homeostasis and responding to diverse stresses, malfunction of autophagy contributes to both chronic and acute pathologies. We applied a systems biology approach to improve the understanding of this complex cellular process of autophagy. All autophagy pathway vesicle activities, i.e. creation, movement, fusion and degradation, are highly dynamic, temporally and spatially, and under various forms of regulation. We therefore developed an agent-based model (ABM) to represent individual components of the autophagy pathway, subcellular vesicle dynamics and metabolic feedback with the cellular environment, thereby providing a framework to investigate spatio-temporal aspects of autophagy regulation and dynamic behavior. The rules defining our ABM were derived from literature and from high-resolution images of autophagy markers under basal and activated conditions. Key model parameters were fit with an iterative method using a genetic algorithm and a predefined fitness function. From this approach, we found that accurate prediction of spatio-temporal behavior required increasing model complexity by implementing functional integration of autophagy with the cellular nutrient state. The resulting model is able to reproduce short-term autophagic flux measurements (up to 3

  9. Numerical methodologies for investigation of moderate-velocity flow using a hybrid computational fluid dynamics - molecular dynamics simulation approach

    International Nuclear Information System (INIS)

    Ko, Soon Heum; Kim, Na Yong; Nikitopoulos, Dimitris E.; Moldovan, Dorel; Jha, Shantenu

    2014-01-01

    Numerical approaches are presented to minimize the statistical errors inherently present due to finite sampling and the presence of thermal fluctuations in the molecular region of a hybrid computational fluid dynamics (CFD) - molecular dynamics (MD) flow solution. Near the fluid-solid interface the hybrid CFD-MD simulation approach provides a more accurate solution, especially in the presence of significant molecular-level phenomena, than the traditional continuum-based simulation techniques. It also involves less computational cost than the pure particle-based MD. Despite these advantages the hybrid CFD-MD methodology has been applied mostly in flow studies at high velocities, mainly because of the higher statistical errors associated with low velocities. As an alternative to the costly increase of the size of the MD region to decrease statistical errors, we investigate a few numerical approaches that reduce sampling noise of the solution at moderate-velocities. These methods are based on sampling of multiple simulation replicas and linear regression of multiple spatial/temporal samples. We discuss the advantages and disadvantages of each technique in the perspective of solution accuracy and computational cost.

  10. Temporal resolution criterion for correctly simulating relativistic electron motion in a high-intensity laser field

    Energy Technology Data Exchange (ETDEWEB)

    Arefiev, Alexey V. [Institute for Fusion Studies, The University of Texas, Austin, Texas 78712 (United States); Cochran, Ginevra E.; Schumacher, Douglass W. [Physics Department, The Ohio State University, Columbus, Ohio 43210 (United States); Robinson, Alexander P. L. [Central Laser Facility, STFC Rutherford-Appleton Laboratory, Didcot OX11 0QX (United Kingdom); Chen, Guangye [Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

    2015-01-15

    Particle-in-cell codes are now standard tools for studying ultra-intense laser-plasma interactions. Motivated by direct laser acceleration of electrons in sub-critical plasmas, we examine temporal resolution requirements that must be satisfied to accurately calculate electron dynamics in strong laser fields. Using the motion of a single electron in a perfect plane electromagnetic wave as a test problem, we show surprising deterioration of the numerical accuracy with increasing wave amplitude a{sub 0} for a given time-step. We go on to show analytically that the time-step must be significantly less than λ/ca{sub 0} to achieve good accuracy. We thus propose adaptive electron sub-cycling as an efficient remedy.

  11. High-fidelity haptic and visual rendering for patient-specific simulation of temporal bone surgery.

    Science.gov (United States)

    Chan, Sonny; Li, Peter; Locketz, Garrett; Salisbury, Kenneth; Blevins, Nikolas H

    2016-12-01

    Medical imaging techniques provide a wealth of information for surgical preparation, but it is still often the case that surgeons are examining three-dimensional pre-operative image data as a series of two-dimensional images. With recent advances in visual computing and interactive technologies, there is much opportunity to provide surgeons an ability to actively manipulate and interpret digital image data in a surgically meaningful way. This article describes the design and initial evaluation of a virtual surgical environment that supports patient-specific simulation of temporal bone surgery using pre-operative medical image data. Computational methods are presented that enable six degree-of-freedom haptic feedback during manipulation, and that simulate virtual dissection according to the mechanical principles of orthogonal cutting and abrasive wear. A highly efficient direct volume renderer simultaneously provides high-fidelity visual feedback during surgical manipulation of the virtual anatomy. The resulting virtual surgical environment was assessed by evaluating its ability to replicate findings in the operating room, using pre-operative imaging of the same patient. Correspondences between surgical exposure, anatomical features, and the locations of pathology were readily observed when comparing intra-operative video with the simulation, indicating the predictive ability of the virtual surgical environment.

  12. Object Oriented Toolbox for Modelling and Simulation of Dynamical Systems

    DEFF Research Database (Denmark)

    Poulsen, Mikael Zebbelin; Wagner, Falko Jens; Thomsen, Per Grove

    1998-01-01

    This paper presents the results of an ongoing project, dealing with design and implementation of a simulation toolbox based on object oriented modelling techniques. The paper describes an experimental implementation of parts of such a toolbox in C++, and discusses the experiences drawn from that ...... that process. Essential to the work is the focus on simulation of complex dynamical systems, from modelling the single components/subsystems to building complete systemssuch a toolbox in C++, and discusses the experiences drawn from that process....

  13. A review on computational fluid dynamic simulation techniques for Darrieus vertical axis wind turbines

    International Nuclear Information System (INIS)

    Ghasemian, Masoud; Ashrafi, Z. Najafian; Sedaghat, Ahmad

    2017-01-01

    Highlights: • A review on CFD simulation technique for Darrieus wind turbines is provided. • Recommendations and guidelines toward reliable and accurate simulations are presented. • Different progresses in CFD simulation of Darrieus wind turbines are addressed. - Abstract: The global warming threats, the presence of policies on support of renewable energies, and the desire for clean smart cities are the major drives for most recent researches on developing small wind turbines in urban environments. VAWTs (vertical axis wind turbines) are most appealing for energy harvesting in the urban environment. This is attributed due to structural simplicity, wind direction independency, no yaw mechanism required, withstand high turbulence winds, cost effectiveness, easier maintenance, and lower noise emission of VAWTs. This paper reviews recent published works on CFD (computational fluid dynamic) simulations of Darrieus VAWTs. Recommendations and guidelines are presented for turbulence modeling, spatial and temporal discretization, numerical schemes and algorithms, and computational domain size. The operating and geometrical parameters such as tip speed ratio, wind speed, solidity, blade number and blade shapes are fully investigated. The purpose is to address different progresses in simulations areas such as blade profile modification and optimization, wind turbine performance augmentation using guide vanes, wind turbine wake interaction in wind farms, wind turbine aerodynamic noise reduction, dynamic stall control, self-starting characteristics, and effects of unsteady and skewed wind conditions.

  14. Dynamic Hybrid Simulation of the Lunar Wake During ARTEMIS Crossing

    Science.gov (United States)

    Wiehle, S.; Plaschke, F.; Angelopoulos, V.; Auster, H.; Glassmeier, K.; Kriegel, H.; Motschmann, U. M.; Mueller, J.

    2010-12-01

    The interaction of the highly dynamic solar wind with the Moon is simulated with the A.I.K.E.F. (Adaptive Ion Kinetic Electron Fluid) code for the ARTEMIS P1 flyby on February 13, 2010. The A.I.K.E.F. hybrid plasma simulation code is the improved version of the Braunschweig code. It is able to automatically increase simulation grid resolution in areas of interest during runtime, which greatly increases resolution as well as performance. As the Moon has no intrinsic magnetic field and no ionosphere, the solar wind particles are absorbed at its surface, resulting in the formation of the lunar wake at the nightside. The solar wind magnetic field is basically convected through the Moon and the wake is slowly filled up with solar wind particles. However, this interaction is strongly influenced by the highly dynamic solar wind during the flyby. This is considered by a dynamic variation of the upstream conditions in the simulation using OMNI solar wind measurement data. By this method, a very good agreement between simulation and observations is achieved. The simulations show that the stationary structure of the lunar wake constitutes a tableau vivant in space representing the well-known Friedrichs diagram for MHD waves.

  15. Integrating atomistic molecular dynamics simulations, experiments and network analysis to study protein dynamics: strength in unity

    Directory of Open Access Journals (Sweden)

    Elena ePapaleo

    2015-05-01

    Full Text Available In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.

  16. Selecting a Dynamic Simulation Modeling Method for Health Care Delivery Research—Part 2: Report of the ISPOR Dynamic Simulation Modeling Emerging Good Practices Task Force

    NARCIS (Netherlands)

    Marshall, Deborah A.; Burgos-Liz, Lina; IJzerman, Maarten Joost; Crown, William; Padula, William V.; Wong, Peter K.; Pasupathy, Kalyan S.; Higashi, Mitchell K.; Osgood, Nathaniel D.

    2015-01-01

    In a previous report, the ISPOR Task Force on Dynamic Simulation Modeling Applications in Health Care Delivery Research Emerging Good Practices introduced the fundamentals of dynamic simulation modeling and identified the types of health care delivery problems for which dynamic simulation modeling

  17. Spatio-temporal dynamics of the penetration resistance of recultivated soils formed after open cast mining

    Directory of Open Access Journals (Sweden)

    A. V. Zhukov

    2016-01-01

    Full Text Available On the basis of studying the spatio-temporal dynamics of soil penetration resistance we proved the existence of the technozem ecomorphs as above horizon soil formations. Research was carried out at a research center for study of recultivation processes in Ordzhonikidze city. Measurement of soils penetration was made in field conditions using an Eijkelkamp penetrometer on a regular grid at depths of up to50 cmwith intervals of5 cm. Calculation of average values and degrees of variation was performed by means of descriptive statistical tools. The extent of soil penetration spatial dependence was assessed and the existence of ecomorphs was proved by means of geostatistical analysis. The degree of associativity of spatial distribution of indicators of a soil body in different years of research was established by means of correlation analysis. The level of variation in space and in time of  technozem penetration generated on loess-like loams, grey-green, red-brown clays, and also pedozems was revealed. The degree of spatial dependence of  technozem penetration within soil layers and also the linear sizes of ecomorphs as above horizon soil structures was established. The time dynamics of  penetration of various recultozems were described. As a result of research into the spatio-temporal dynamics of penetration of technozems, data confirming the hypothesis of the existence of ecomorphs as above horizon morphological soil formations were obtained. An ecomorphic approach to the study of the morphological structure of technozems is proposed. The comparative characteristics of ecomorphs from various types of technozem are presented. The results obtained solve the problem of combining the higher and lowest levels in the hierarchical system of soil organisation as a natural body, which should raise the efficiency of the analysis of relations of morphological elements as a basis for detailed reconstruction of recultivation processes, soil formation, and

  18. Frontiers in Fluctuation Spectroscopy: Measuring protein dynamics and protein spatio-temporal connectivity

    Science.gov (United States)

    Digman, Michelle

    Fluorescence fluctuation spectroscopy has evolved from single point detection of molecular diffusion to a family of microscopy imaging correlation tools (i.e. ICS, RICS, STICS, and kICS) useful in deriving spatial-temporal dynamics of proteins in living cells The advantage of the imaging techniques is the simultaneous measurement of all points in an image with a frame rate that is increasingly becoming faster with better sensitivity cameras and new microscopy modalities such as the sheet illumination technique. A new frontier in this area is now emerging towards a high level of mapping diffusion rates and protein dynamics in the 2 and 3 dimensions. In this talk, I will discuss the evolution of fluctuation analysis from the single point source to mapping diffusion in whole cells and the technology behind this technique. In particular, new methods of analysis exploit correlation of molecular fluctuations originating from measurement of fluctuation correlations at distant points (pair correlation analysis) and methods that exploit spatial averaging of fluctuations in small regions (iMSD). For example the pair correlation fluctuation (pCF) analyses done between adjacent pixels in all possible radial directions provide a window into anisotropic molecular diffusion. Similar to the connectivity atlas of neuronal connections from the MRI diffusion tensor imaging these new tools will be used to map the connectome of protein diffusion in living cells. For biological reaction-diffusion systems, live single cell spatial-temporal analysis of protein dynamics provides a mean to observe stochastic biochemical signaling in the context of the intracellular environment which may lead to better understanding of cancer cell invasion, stem cell differentiation and other fundamental biological processes. National Institutes of Health Grant P41-RRO3155.

  19. Predicting Surgery Targets in Temporal Lobe Epilepsy through Structural Connectome Based Simulations.

    Directory of Open Access Journals (Sweden)

    Frances Hutchings

    2015-12-01

    Full Text Available Temporal lobe epilepsy (TLE is a prevalent neurological disorder resulting in disruptive seizures. In the case of drug resistant epilepsy resective surgery is often considered. This is a procedure hampered by unpredictable success rates, with many patients continuing to have seizures even after surgery. In this study we apply a computational model of epilepsy to patient specific structural connectivity derived from diffusion tensor imaging (DTI of 22 individuals with left TLE and 39 healthy controls. We validate the model by examining patient-control differences in simulated seizure onset time and network location. We then investigate the potential of the model for surgery prediction by performing in silico surgical resections, removing nodes from patient networks and comparing seizure likelihood post-surgery to pre-surgery simulations. We find that, first, patients tend to transit from non-epileptic to epileptic states more often than controls in the model. Second, regions in the left hemisphere (particularly within temporal and subcortical regions that are known to be involved in TLE are the most frequent starting points for seizures in patients in the model. In addition, our analysis also implicates regions in the contralateral and frontal locations which may play a role in seizure spreading or surgery resistance. Finally, the model predicts that patient-specific surgery (resection areas chosen on an individual, model-prompted, basis and not following a predefined procedure may lead to better outcomes than the currently used routine clinical procedure. Taken together this work provides a first step towards patient specific computational modelling of epilepsy surgery in order to inform treatment strategies in individuals.

  20. Improvement in visibility of simulated lung nodules on computed radiography (CR) chest images by use of temporal subtraction technique

    International Nuclear Information System (INIS)

    Oda, Nobuhiro; Fujimoto, Keiji; Murakami, Seiichi; Katsuragawa, Shigehiko; Doi, Kunio; Nakata, Hajime

    1999-01-01

    A temporal subtraction image obtained by subtraction of a previous image from a current one can enhance interval change on chest images. In this study, we compared the visibility of simulated lung nodules on CR images with and without temporal subtraction. Chest phantom images without and with simulated nodules were obtained as previous and current images, respectively, by a CR system. Then, subtraction images were produced with an iterative image warping technique. Twelve simulated nodules were attached on various locations of the chest phantom. The diameter of nodules having a CT number of 47 ranged from 3 mm to 10 mm. Seven radiologists subjectively evaluated the visibility of simulated nodules on CR images with and without temporal subtraction using a three-point rating scale (0: invisible, +1: questionable, +2:visible). The minimum diameter of simulated nodules visible at a frequency greater than 50% was 4 mm on the CR images with temporal subtraction and 6 mm on those without. Our results indicated that the subtraction images clearly improved the visibility of simulated nodules. (author)

  1. Validating clustering of molecular dynamics simulations using polymer models

    Directory of Open Access Journals (Sweden)

    Phillips Joshua L

    2011-11-01

    Full Text Available Abstract Background Molecular dynamics (MD simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. Results We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. Conclusions We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our

  2. Developments of multibody system dynamics: computer simulations and experiments

    International Nuclear Information System (INIS)

    Yoo, Wan-Suk; Kim, Kee-Nam; Kim, Hyun-Woo; Sohn, Jeong-Hyun

    2007-01-01

    It is an exceptional success when multibody dynamics researchers Multibody System Dynamics journal one of the most highly ranked journals in the last 10 years. In the inaugural issue, Professor Schiehlen wrote an interesting article explaining the roots and perspectives of multibody system dynamics. Professor Shabana also wrote an interesting article to review developments in flexible multibody dynamics. The application possibilities of multibody system dynamics have grown wider and deeper, with many application examples being introduced with multibody techniques in the past 10 years. In this paper, the development of multibody dynamics is briefly reviewed and several applications of multibody dynamics are described according to the author's research results. Simulation examples are compared to physical experiments, which show reasonableness and accuracy of the multibody formulation applied to real problems. Computer simulations using the absolute nodal coordinate formulation (ANCF) were also compared to physical experiments; therefore, the validity of ANCF for large-displacement and large-deformation problems was shown. Physical experiments for large deformation problems include beam, plate, chain, and strip. Other research topics currently being carried out in the author's laboratory are also briefly explained

  3. The Emergence of Visual Awareness: Temporal Dynamics in Relation to Task and Mask Type

    Science.gov (United States)

    Kiefer, Markus; Kammer, Thomas

    2017-01-01

    One aspect of consciousness phenomena, the temporal emergence of visual awareness, has been subject of a controversial debate. How can visual awareness, that is the experiential quality of visual stimuli, be characterized best? Is there a sharp discontinuous or dichotomous transition between unaware and fully aware states, or does awareness emerge gradually encompassing intermediate states? Previous studies yielded conflicting results and supported both dichotomous and gradual views. It is well conceivable that these conflicting results are more than noise, but reflect the dynamic nature of the temporal emergence of visual awareness. Using a psychophysical approach, the present research tested whether the emergence of visual awareness is context-dependent with a temporal two-alternative forced choice task. During backward masking of word targets, it was assessed whether the relative temporal sequence of stimulus thresholds is modulated by the task (stimulus presence, letter case, lexical decision, and semantic category) and by mask type. Four masks with different similarity to the target features were created. Psychophysical functions were then fitted to the accuracy data in the different task conditions as a function of the stimulus mask SOA in order to determine the inflection point (conscious threshold of each feature) and slope of the psychophysical function (transition from unaware to aware within each feature). Depending on feature-mask similarity, thresholds in the different tasks were highly dispersed suggesting a graded transition from unawareness to awareness or had less differentiated thresholds indicating that clusters of features probed by the tasks quite simultaneously contribute to the percept. The latter observation, although not compatible with the notion of a sharp all-or-none transition between unaware and aware states, suggests a less gradual or more discontinuous emergence of awareness. Analyses of slopes of the fitted psychophysical functions

  4. Molecular dynamics simulations of oscillatory flows in microfluidic channels

    DEFF Research Database (Denmark)

    Hansen, J.S.; Ottesen, Johnny T.

    2006-01-01

    In this paper we apply the direct non-equilibrium molecular dynamics technique to oscillatory flows of fluids in microscopic channels. Initially, we show that the microscopic simulations resemble the macroscopic predictions based on the Navier–Stokes equation very well for large channel width, high...... density and low temperature. Further simulations for high temperature and low density show that the non-slip boundary condition traditionally used in the macroscopic equation is greatly compromised when the fluid–wall interactions are the same as the fluid–fluid interactions. Simulations of a system...

  5. A statistical-dynamical downscaling procedure for global climate simulations

    International Nuclear Information System (INIS)

    Frey-Buness, A.; Heimann, D.; Sausen, R.; Schumann, U.

    1994-01-01

    A statistical-dynamical downscaling procedure for global climate simulations is described. The procedure is based on the assumption that any regional climate is associated with a specific frequency distribution of classified large-scale weather situations. The frequency distributions are derived from multi-year episodes of low resolution global climate simulations. Highly resolved regional distributions of wind and temperature are calculated with a regional model for each class of large-scale weather situation. They are statistically evaluated by weighting them with the according climate-specific frequency. The procedure is exemplarily applied to the Alpine region for a global climate simulation of the present climate. (orig.)

  6. Application of dynamic susceptibility contrast-enhanced perfusion in temporal lobe epilepsy

    Energy Technology Data Exchange (ETDEWEB)

    Xing, Wu; Wang, Xiaoyi; Xie, Fangfang; Liao, Weihua [Dept. of Radiology, Xiangya Hospital of Central South Univ., Changsha (China)], e-mail: doctoring@sina.com

    2013-02-15

    Background: Accurately locatithe epileptogenic focus in temporal lobe epilepsy (TLE) is important in clinical practice. Single-photon emission computed tomography (SPECT) and positron-emission tomography (PET) have been widely used in the lateralization of TLE, but both have limitations. Magnetic resonance perfusion imaging can accurately and reliably reflect differences in cerebral blood flow and volume. Purpose: To investigate the diagnostic value of dynamic susceptibility contrast-enhanced (DSC) perfusion magnetic resonance imaging (MRI) in the lateralization of the epileptogenic focus in TLE. Material and Methods: Conventional MRI and DSC-MRI scanning was performed in 20 interictal cases of TLE and 20 healthy volunteers. The relative cerebral blood volume (rCBV) and relative cerebral blood flow (rCBF) of the bilateral mesial temporal lobes of the TLE cases and healthy control groups were calculated. The differences in the perfusion asymmetry indices (AIs), derived from the rCBV and rCBF of the bilateral mesial temporal lobes, were pared between the two groups. Results: In the control group, there were no statistically significant differences between the left and right sides in terms of rCBV (left 1.55 {+-} 0.32, right 1.57 {+-} 0.28) or rCBF (left 99.00 {+-} 24.61, right 100.38 {+-} 23.46) of the bilateral mesial temporal lobes. However, in the case group the ipsilateral rCBV and rCBF values (1.75 {+-} 0.64 and 96.35 {+-} 22.63, respectively) were markedly lower than those of the contralateral side (2.01 {+-} 0.79 and 108.56 {+-} 26.92; P < 0.05). Both the AI of the rCBV (AIrCBV; 13.03 {+-} 10.33) and the AI of the rCBF (AIrCBF; 11.24 {+-} 8.70) of the case group were significantly higher than that of the control group (AIrCBV 5.55 {+-} 3.74, AIrCBF 5.12 {+-} 3.48; P < 0.05). The epileptogenic foci of nine patients were correctly lateralized using the 95th percentile of the AIrCBV and AIrCBF of the control group as the normal upper limits. Conclusion: In

  7. Application of dynamic susceptibility contrast-enhanced perfusion in temporal lobe epilepsy

    International Nuclear Information System (INIS)

    Xing, Wu; Wang, Xiaoyi; Xie, Fangfang; Liao, Weihua

    2013-01-01

    Background: Accurately locatithe epileptogenic focus in temporal lobe epilepsy (TLE) is important in clinical practice. Single-photon emission computed tomography (SPECT) and positron-emission tomography (PET) have been widely used in the lateralization of TLE, but both have limitations. Magnetic resonance perfusion imaging can accurately and reliably reflect differences in cerebral blood flow and volume. Purpose: To investigate the diagnostic value of dynamic susceptibility contrast-enhanced (DSC) perfusion magnetic resonance imaging (MRI) in the lateralization of the epileptogenic focus in TLE. Material and Methods: Conventional MRI and DSC-MRI scanning was performed in 20 interictal cases of TLE and 20 healthy volunteers. The relative cerebral blood volume (rCBV) and relative cerebral blood flow (rCBF) of the bilateral mesial temporal lobes of the TLE cases and healthy control groups were calculated. The differences in the perfusion asymmetry indices (AIs), derived from the rCBV and rCBF of the bilateral mesial temporal lobes, were pared between the two groups. Results: In the control group, there were no statistically significant differences between the left and right sides in terms of rCBV (left 1.55 ± 0.32, right 1.57 ± 0.28) or rCBF (left 99.00 ± 24.61, right 100.38 ± 23.46) of the bilateral mesial temporal lobes. However, in the case group the ipsilateral rCBV and rCBF values (1.75 ± 0.64 and 96.35 ± 22.63, respectively) were markedly lower than those of the contralateral side (2.01 ± 0.79 and 108.56 ± 26.92; P < 0.05). Both the AI of the rCBV (AIrCBV; 13.03 ± 10.33) and the AI of the rCBF (AIrCBF; 11.24 ± 8.70) of the case group were significantly higher than that of the control group (AIrCBV 5.55 ± 3.74, AIrCBF 5.12 ± 3.48; P < 0.05). The epileptogenic foci of nine patients were correctly lateralized using the 95th percentile of the AIrCBV and AIrCBF of the control group as the normal upper limits. Conclusion: In patients with TLE interictal

  8. Dynamic simulation of a steam generator by neural networks

    International Nuclear Information System (INIS)

    Masini, R.; Padovani, E.; Ricotti, M.E.; Zio, E.

    1999-01-01

    Numerical simulation by computers of the dynamic evolution of complex systems and components is a fundamental phase of any modern engineering design activity. This is of particular importance for risk-based design projects which require that the system behavior be analyzed under several and often extreme conditions. The traditional methods of simulation typically entail long, iterative, processes which lead to large simulation times, often exceeding the transients real time. Artificial neural networks (ANNs) may be exploited in this context, their advantages residing mainly in the speed of computation, in the capability of generalizing from few examples, in the robustness to noisy and partially incomplete data and in the capability of performing empirical input-output mapping without complete knowledge of the underlying physics. In this paper we present a novel approach to dynamic simulation by ANNs based on a superposition scheme in which a set of networks are individually trained, each one to respond to a different input forcing function. The dynamic simulation of a steam generator is considered as an example to show the potentialities of this tool and to point out the difficulties and crucial issues which typically arise when attempting to establish an efficient neural network simulator. The structure of the networks system is such to feedback, at each time step, a portion of the past evolution of the transient and this allows a good reproduction of also non-linear dynamic behaviors. A nice characteristic of the approach is that the modularization of the training reduces substantially its burden and gives this neural simulation tool a nice feature of transportability. (orig.)

  9. Simulation Analysis of Helicopter Ground Resonance Nonlinear Dynamics

    Science.gov (United States)

    Zhu, Yan; Lu, Yu-hui; Ling, Ai-min

    2017-07-01

    In order to accurately predict the dynamic instability of helicopter ground resonance, a modeling and simulation method of helicopter ground resonance considering nonlinear dynamic characteristics of components (rotor lead-lag damper, landing gear wheel and absorber) is presented. The numerical integral method is used to calculate the transient responses of the body and rotor, simulating some disturbance. To obtain quantitative instabilities, Fast Fourier Transform (FFT) is conducted to estimate the modal frequencies, and the mobile rectangular window method is employed in the predictions of the modal damping in terms of the response time history. Simulation results show that ground resonance simulation test can exactly lead up the blade lead-lag regressing mode frequency, and the modal damping obtained according to attenuation curves are close to the test results. The simulation test results are in accordance with the actual accident situation, and prove the correctness of the simulation method. This analysis method used for ground resonance simulation test can give out the results according with real helicopter engineering tests.

  10. Computational Dehydration of Crystalline Hydrates Using Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Larsen, Anders Støttrup; Rantanen, Jukka; Johansson, Kristoffer E

    2017-01-01

    Molecular dynamics (MD) simulations have evolved to an increasingly reliable and accessible technique and are today implemented in many areas of biomedical sciences. We present a generally applicable method to study dehydration of hydrates based on MD simulations and apply this approach...... to the dehydration of ampicillin trihydrate. The crystallographic unit cell of the trihydrate is used to construct the simulation cell containing 216 ampicillin and 648 water molecules. This system is dehydrated by removing water molecules during a 2200 ps simulation, and depending on the computational dehydration....... The structural changes could be followed in real time, and in addition, an intermediate amorphous phase was identified. The computationally identified dehydrated structure (anhydrate) was slightly different from the experimentally known anhydrate structure suggesting that the simulated computational structure...

  11. Using simulation to assess the opportunities of dynamic waste collection

    NARCIS (Netherlands)

    Mes, Martijn R.K.; Bangsow, S.

    2012-01-01

    In this chapter, we illustrate the use of discrete event simulation to evaluate how dynamic planning methodologies can be best applied for the collection of waste from underground containers. We present a case study that took place at the waste collection company Twente Milieu, located in The

  12. Using Simulation to Assess the Opportunities of Dynamic Waste Collection

    NARCIS (Netherlands)

    Mes, Martijn R.K.

    In this paper, we illustrate the use of discrete event simulation to evaluate how dynamic planning methodologies can be best applied for the collection of waste from underground containers. We present a case study that took place at the waste collection company Twente Milieu, located in The

  13. Computational Fluid Dynamics and Building Energy Performance Simulation

    DEFF Research Database (Denmark)

    Nielsen, Peter V.; Tryggvason, Tryggvi

    An interconnection between a building energy performance simulation program and a Computational Fluid Dynamics program (CFD) for room air distribution will be introduced for improvement of the predictions of both the energy consumption and the indoor environment. The building energy performance...

  14. Accurate simulation dynamics of microscopic filaments using "caterpillar" Oseen hydrodynamics

    NARCIS (Netherlands)

    Bailey, A.G.; Lowe, C.P.; Pagonabarraga, I.; Cosentino Lagomarsino, M.

    2009-01-01

    Microscopic semiflexible filaments suspended in a viscous fluid are widely encountered in biophysical problems. The classic example is the flagella used by microorganisms to generate propulsion. Simulating the dynamics of these filaments numerically is complicated because of the coupling between the

  15. Effects of transition on wind tunnel simulation of vehicel dynamics

    Science.gov (United States)

    Ericsson, L. E.

    Among the many problems the test engineer faces when trying to simulate full-scale vehicle dynamics in a wind tunnel test is the fact that the test usually will be performed at Reynolds numbers far below those existing on the full-scale vehicle. It is found that a severe scaling problem may exist even in the case of attached flow. The strong coupling existing between boundary layer transition and vehicle motion can cause the wind tunnel results to be very misleading, in some cases dangerously so. For example, the subscale test could fail to show a dynamic stability problem existing in full-scale flight, or, conversely, show one that does not exist. When flow separation occurs together with boundary layer transition, the scaling problem becomes more complicated, and the potential for dangerously misleading subscale test results increases. The existing literature is reviewed to provide examples of the different types of dynamic simulation problems that the test engineer is likely to face. It should be emphasized that the difficulties presented by transition effects in the case of wind tunnel simulation of vehicle dynamics apply to the same extent to numeric simulation methods.

  16. Ab initio molecular dynamics simulation of laser melting of silicon

    NARCIS (Netherlands)

    Silvestrelli, P.-L.; Alavi, A.; Parrinello, M.; Frenkel, D.

    1996-01-01

    The method of ab initio molecular dynamics, based on finite temperature density functional theory, is used to simulate laser heating of crystal silicon. We have found that a high concentration of excited electrons dramatically weakens the covalent bond. As a result, the system undergoes a melting

  17. Simulating Poverty and Inequality Dynamics in Developing Countries

    Science.gov (United States)

    Ansoms, An; Geenen, Sara

    2012-01-01

    This article considers how the simulation game of DEVELOPMENT MONOPOLY provides insight into poverty and inequality dynamics in a development context. It first discusses how the game is rooted in theoretical and conceptual frameworks on poverty and inequality. Subsequently, it reflects on selected playing experiences, with special focus on the…

  18. Simulation of the substrate cavity dynamics of quercetinase

    NARCIS (Netherlands)

    van den Bosch, M; Swart, M; van Gunsteren, WF; Canters, GW

    2004-01-01

    Molecular dynamics (MD) simulations have been performed on quercetin 2,3 dioxygenase (2,3QD) to study the mobility and flexibility of the substrate cavity. 2,3QD is the only firmly established Cu-containing dioxygenase known so far. It catalyses the breakage of the O-heterocycle of flavonols. The

  19. Microsecond atomic-scale molecular dynamics simulations of polyimides

    NARCIS (Netherlands)

    Lyulin, S.V.; Gurtovenko, A.A.; Larin, S.V.; Nazarychev, V.M.; Lyulin, A.V.

    2013-01-01

    We employ microsecond atomic-scale molecular dynamics simulations to get insight into the structural and thermal properties of heat-resistant bulk polyimides. As electrostatic interactions are essential for the polyimides considered, we propose a two-step equilibration protocol that includes long

  20. Simulating an arbitrary number of flavors of dynamical overlap fermions

    International Nuclear Information System (INIS)

    DeGrand, T.; Schaefer, S.

    2006-05-01

    We present a set of related Hybrid Monte Carlo methods to simulate an arbitrary number of dynamical overlap fermions. Each fermion is represented by a chiral pseudo-fermion field. The new algorithm reduces critical slowing down in the chiral limit and for sectors of nontrivial topology. (Orig.)

  1. Efficient dynamic simulation of flexible link manipulators with PID control

    NARCIS (Netherlands)

    Aarts, Ronald G.K.M.; Jonker, Jan B.; Mook, D.T.; Balachandran, B.

    2001-01-01

    For accurate simulations of the dynamic behavior of flexible manipulators the combination of a perturbation method and modal analysis is proposed. First, the vibrational motion is modeled as a first-order perturbation of a nominal rigid link motion. The vibrational motion is then described by a set

  2. Molecular dynamics simulations and free energy profile of ...

    Indian Academy of Sciences (India)

    aDepartment of Chemical Engineering, bDepartment of Chemistry, Amirkabir University of Technology,. 15875-4413 ... Lipid bilayers; Paracetamol; free energy; molecular dynamics simulation; membrane. 1. ..... bilayer is less favourable due to the hydrophobic nature .... Orsi M and Essex J W 2010 Soft Matter 6 3797. 54.

  3. Molecular dynamics simulations of lipid vesicle fusion in atomic detail

    NARCIS (Netherlands)

    Knecht, Volker; Marrink, Siewert-Jan

    The fusion of a membrane-bounded vesicle with a target membrane is a key step in intracellular trafficking, exocytosis, and drug delivery. Molecular dynamics simulations have been used to study the fusion of small unilamellar vesicles composed of a dipalmitoyl-phosphatidylcholine (DPPC)/palmitic

  4. Dynamical simulation of heavy ion collisions; VUU and QMD method

    International Nuclear Information System (INIS)

    Niita, Koji

    1992-01-01

    We review two simulation methods based on the Vlasov-Uehling-Uhlenbeck (VUU) equation and Quantum Molecular Dynamics (QMD), which are the most widely accepted theoretical framework for the description of intermediate-energy heavy-ion reactions. We show some results of the calculations and compare them with the experimental data. (author)

  5. Molecular dynamics simulations on PGLa using NMR orientational constraints

    Energy Technology Data Exchange (ETDEWEB)

    Sternberg, Ulrich, E-mail: ulrich.sternberg@partner.kit.edu; Witter, Raiker [Tallinn University of Technology, Technomedicum (Estonia)

    2015-11-15

    NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide.

  6. A new simulation algorithm for lattice QCD with dynamical quarks

    CERN Document Server

    Bunk, B.; Jegerlehner, B.; Luscher, M.; Simma, H.; Sommer, R.; Bunk, B; Jansen, K; Jegerlehner, B; Luscher, M; Simma, H

    1994-01-01

    A previously introduced multi-boson technique for the simulation of QCD with dynamical quarks is described and some results of first test runs on a 6^3\\times12 lattice with Wilson quarks and gauge group SU(2) are reported.

  7. Hotspots of Community Change: Temporal Dynamics Are Spatially Variable in Understory Plant Composition of a California Oak Woodland.

    Directory of Open Access Journals (Sweden)

    Erica N Spotswood

    Full Text Available Community response to external drivers such climate and disturbance can lead to fluctuations in community composition, or to directional change. Temporal dynamics can be influenced by a combination of drivers operating at multiple spatial scales, including external landscape scale drivers, local abiotic conditions, and local species pools. We hypothesized that spatial variation in these factors can create heterogeneity in temporal dynamics within landscapes. We used understory plant species composition from an 11 year dataset from a California oak woodland to compare plots where disturbance was experimentally manipulated with the removal of livestock grazing and a prescribed burn. We quantified three properties of temporal variation: compositional change (reflecting the appearance and disappearance of species, temporal fluctuation, and directional change. Directional change was related most strongly to disturbance type, and was highest at plots where grazing was removed during the study. Temporal fluctuations, compositional change, and directional change were all related to intrinsic abiotic factors, suggesting that some locations are more responsive to external drivers than others. Temporal fluctuations and compositional change were linked to local functional composition, indicating that environmental filters can create subsets of the local species pool that do not respond in the same way to external drivers. Temporal dynamics are often assumed to be relatively static at the landscape scale, provided disturbance and climate are continuous. This study shows that local and landscape scale factors jointly influence temporal dynamics creating hotspots that are particularly responsive to climate and disturbance. Thus, adequate predictions of response to disturbance or to changing climate will only be achieved by considering how factors at multiple spatial scales influence community resilience and recovery.

  8. Hotspots of Community Change: Temporal Dynamics Are Spatially Variable in Understory Plant Composition of a California Oak Woodland.

    Science.gov (United States)

    Spotswood, Erica N; Bartolome, James W; Allen-Diaz, Barbara

    2015-01-01

    Community response to external drivers such climate and disturbance can lead to fluctuations in community composition, or to directional change. Temporal dynamics can be influenced by a combination of drivers operating at multiple spatial scales, including external landscape scale drivers, local abiotic conditions, and local species pools. We hypothesized that spatial variation in these factors can create heterogeneity in temporal dynamics within landscapes. We used understory plant species composition from an 11 year dataset from a California oak woodland to compare plots where disturbance was experimentally manipulated with the removal of livestock grazing and a prescribed burn. We quantified three properties of temporal variation: compositional change (reflecting the appearance and disappearance of species), temporal fluctuation, and directional change. Directional change was related most strongly to disturbance type, and was highest at plots where grazing was removed during the study. Temporal fluctuations, compositional change, and directional change were all related to intrinsic abiotic factors, suggesting that some locations are more responsive to external drivers than others. Temporal fluctuations and compositional change were linked to local functional composition, indicating that environmental filters can create subsets of the local species pool that do not respond in the same way to external drivers. Temporal dynamics are often assumed to be relatively static at the landscape scale, provided disturbance and climate are continuous. This study shows that local and landscape scale factors jointly influence temporal dynamics creating hotspots that are particularly responsive to climate and disturbance. Thus, adequate predictions of response to disturbance or to changing climate will only be achieved by considering how factors at multiple spatial scales influence community resilience and recovery.

  9. Dynamic simulation for effective workforce management in new product development

    Directory of Open Access Journals (Sweden)

    M. Mutingi

    2012-10-01

    Full Text Available Effective planning and management of workforce for new product development (NPD projects is a great challenge to many organisations, especially in the presence of engineering changes during the product development process. The management objective in effective workforce management is to recruit, develop and deploy the right people at the right place at the right time so as to fulfill organizational objectives. In this paper, we propose a dynamic simulation model to address the workforce management problem in a typical NPD project consisting of design, prototyping, and production phases. We assume that workforce demand is a function of project work remaining and the current available skill pool. System dynamics simulation concepts are used to capture the causality relationships and feedback loops in the workforce system from a systems thinking. The evaluation of system dynamics simulation reveals the dynamic behaviour in NPD workforce management systems and shows how adaptive dynamic recruitment and training decisions can effectively balance the workforce system during the NPD process.

  10. Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Vijaykumar, Adithya, E-mail: vijaykumar@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands); van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam (Netherlands); Bolhuis, Peter G. [van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam (Netherlands); Rein ten Wolde, Pieter, E-mail: p.t.wolde@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands)

    2015-12-07

    In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.

  11. Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations

    International Nuclear Information System (INIS)

    Vijaykumar, Adithya; Bolhuis, Peter G.; Rein ten Wolde, Pieter

    2015-01-01

    In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level

  12. Quadratic temporal finite element method for linear elastic structural dynamics based on mixed convolved action

    International Nuclear Information System (INIS)

    Kim, Jin Kyu; Kim, Dong Keon

    2016-01-01

    A common approach for dynamic analysis in current practice is based on a discrete time-integration scheme. This approach can be largely attributed to the absence of a true variational framework for initial value problems. To resolve this problem, a new stationary variational principle was recently established for single-degree-of-freedom oscillating systems using mixed variables, fractional derivatives and convolutions of convolutions. In this mixed convolved action, all the governing differential equations and initial conditions are recovered from the stationarity of a single functional action. Thus, the entire description of linear elastic dynamical systems is encapsulated. For its practical application to structural dynamics, this variational formalism is systemically extended to linear elastic multidegree- of-freedom systems in this study, and a corresponding weak form is numerically implemented via a quadratic temporal finite element method. The developed numerical method is symplectic and unconditionally stable with respect to a time step for the underlying conservative system. For the forced-damped vibration, a three-story shear building is used as an example to investigate the performance of the developed numerical method, which provides accurate results with good convergence characteristics

  13. Population responses to environmental change in a tropical ant: the interaction of spatial and temporal dynamics.

    Science.gov (United States)

    Jackson, Doug; Vandermeer, John; Perfecto, Ivette; Philpott, Stacy M

    2014-01-01

    Spatial structure can have a profound, but often underappreciated, effect on the temporal dynamics of ecosystems. Here we report on a counterintuitive increase in the population of a tree-nesting ant, Azteca sericeasur, in response to a drastic reduction in the number of potential nesting sites. This surprising result is comprehensible when viewed in the context of the self-organized spatial dynamics of the ants and their effect on the ants' dispersal-limited natural enemies. Approximately 30% of the trees in the study site, a coffee agroecosystem in southern Mexico, were pruned or felled over a two-year period, and yet the abundance of the ant nests more than doubled over the seven-year study. Throughout the transition, the spatial distribution of the ants maintained a power-law distribution - a signal of spatial self organization - but the local clustering of the nests was reduced post-pruning. A cellular automata model incorporating the changed spatial structure of the ants and the resulting partial escape from antagonists reproduced the observed increase in abundance, highlighting how self-organized spatial dynamics can profoundly influence the responses of ecosystems to perturbations.

  14. Population responses to environmental change in a tropical ant: the interaction of spatial and temporal dynamics.

    Directory of Open Access Journals (Sweden)

    Doug Jackson

    Full Text Available Spatial structure can have a profound, but often underappreciated, effect on the temporal dynamics of ecosystems. Here we report on a counterintuitive increase in the population of a tree-nesting ant, Azteca sericeasur, in response to a drastic reduction in the number of potential nesting sites. This surprising result is comprehensible when viewed in the context of the self-organized spatial dynamics of the ants and their effect on the ants' dispersal-limited natural enemies. Approximately 30% of the trees in the study site, a coffee agroecosystem in southern Mexico, were pruned or felled over a two-year period, and yet the abundance of the ant nests more than doubled over the seven-year study. Throughout the transition, the spatial distribution of the ants maintained a power-law distribution - a signal of spatial self organization - but the local clustering of the nests was reduced post-pruning. A cellular automata model incorporating the changed spatial structure of the ants and the resulting partial escape from antagonists reproduced the observed increase in abundance, highlighting how self-organized spatial dynamics can profoundly influence the responses of ecosystems to perturbations.

  15. Quadratic temporal finite element method for linear elastic structural dynamics based on mixed convolved action

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jin Kyu [School of Architecture and Architectural Engineering, Hanyang University, Ansan (Korea, Republic of); Kim, Dong Keon [Dept. of Architectural Engineering, Dong A University, Busan (Korea, Republic of)

    2016-09-15

    A common approach for dynamic analysis in current practice is based on a discrete time-integration scheme. This approach can be largely attributed to the absence of a true variational framework for initial value problems. To resolve this problem, a new stationary variational principle was recently established for single-degree-of-freedom oscillating systems using mixed variables, fractional derivatives and convolutions of convolutions. In this mixed convolved action, all the governing differential equations and initial conditions are recovered from the stationarity of a single functional action. Thus, the entire description of linear elastic dynamical systems is encapsulated. For its practical application to structural dynamics, this variational formalism is systemically extended to linear elastic multidegree- of-freedom systems in this study, and a corresponding weak form is numerically implemented via a quadratic temporal finite element method. The developed numerical method is symplectic and unconditionally stable with respect to a time step for the underlying conservative system. For the forced-damped vibration, a three-story shear building is used as an example to investigate the performance of the developed numerical method, which provides accurate results with good convergence characteristics.

  16. Dynamic simulation of sustainable farm development scenarios using cognitive modeling

    Directory of Open Access Journals (Sweden)

    Tuzhyk Kateryna

    2017-03-01

    Full Text Available Dynamic simulation of sustainable farm development scenarios using cognitive modeling. The paper presents a dynamic simulation system of sustainable development scenarios on farms using cognitive modeling. The system incorporates relevant variables which affect the sustainable development of farms. Its user provides answers to strategic issues connected with the level of farm sustainability over a long-term perspective of dynamic development. The work contains a description of the model structure as well as the results of simulations carried out on 16 farms in northern Ukraine. The results show that the process of sustainability is based mainly on the potential for innovation in agricultural production and biodiversity. The user is able to simulate various scenarios for the sustainable development of a farm and visualize the influence of factors on the economic and social situation, as well as on environmental aspects. Upon carrying out a series of simulations, it was determined that the development of farms characterized by sustainable development is based on additional profit, which serves as the main motivation for transforming a conventional farm into a sustainable one. Nevertheless, additional profit is not the only driving force in the system of sustainable development. The standard of living, market condition, and legal regulations as well as government support also play a significant motivational role.

  17. Liquid-vapor coexistence by molecular dynamics simulation

    International Nuclear Information System (INIS)

    Baranyai, Andras; Cummings, Peter T.

    2000-01-01

    We present a simple and consistent molecular dynamics algorithm for determining the equilibrium properties of a bulk liquid and its coexisting vapor phase. The simulation follows the dynamics of the two systems simultaneously while maintaining the volume and the number of particles of the composite system fixed. The thermostat can constrain either the total energy or the temperature at a desired value. Division of the extensive properties between the two phases is governed by the difference of the corresponding intensive state variables. Particle numbers are continuous variables and vary only in virtual sense, i.e., the real sizes of the two systems are the same and do not change during the course of the simulation. Calculation of the chemical potential is separate from the dynamics; thus, one can replace the particle exchange step with other method if it improves the efficiency of the code. (c) 2000 American Institute of Physics

  18. On the characteristics of a numerical fluid dynamics simulator

    International Nuclear Information System (INIS)

    Winkler, K.H.A.; Norman, M.L.; Norton, J.L.

    1986-01-01

    John von Neumann envisioned scientists and mathematicians analyzing and controlling their numerical experiments on nonlinear dynamic systems interactively. The authors describe their concept of a real-time Numerical Fluid Dynamics Simulator NFDS. The authors envision the NFDS to be composed of simulation processors, data storage devices, and image processing devices of extremely high power and capacity, interconnected by very high throughput communication channels. They present individual component performance requirements for both real-time and playback operating modes of the NFDS, using problems of current interest in fluid dynamics as examples. Scaling relations are derived showing the dependence of system requirements on the dimensionality and complexity of the numerical model. The authors conclude by extending their analysis to the system requirements posed in modeling the more involved physics of radiation hydrodynamics

  19. Beam dynamics simulation of W-band photo injector

    International Nuclear Information System (INIS)

    Zhu Xiongwei

    2002-01-01

    The authors present a beam dynamics simulation study on 1.6 cell, high gradient W-Band photocathode RF gun which is capable of generating and accelerating 300 pC electron bunch. The design system is made up of 91.392 GHz photocathode RF gun and 91.392 GHz travelling wave linac cells. Based on the numerical simulation using SUPERFISH and PARMELA and the conventional RF linac scaling law, the design will produce 300 pC at 1.74 MeV with bunch length 0.72 ps and normalized transverse emittance 0.55 mm mrad. The authors study the beam dynamics in high frequency and high gradient; due to the high gradient, the ponderomotive effect plays an important role in beam dynamics; the authors found the ponderomotive effect still exist with only the fundamental space harmonics (synchrotron mode) due to the coupling of the transverse and longitudinal motion

  20. Image-Based Reconstruction and Analysis of Dynamic Scenes in a Landslide Simulation Facility

    Science.gov (United States)

    Scaioni, M.; Crippa, J.; Longoni, L.; Papini, M.; Zanzi, L.

    2017-12-01

    The application of image processing and photogrammetric techniques to dynamic reconstruction of landslide simulations in a scaled-down facility is described. Simulations are also used here for active-learning purpose: students are helped understand how physical processes happen and which kinds of observations may be obtained from a sensor network. In particular, the use of digital images to obtain multi-temporal information is presented. On one side, using a multi-view sensor set up based on four synchronized GoPro 4 Black® cameras, a 4D (3D spatial position and time) reconstruction of the dynamic scene is obtained through the composition of several 3D models obtained from dense image matching. The final textured 4D model allows one to revisit in dynamic and interactive mode a completed experiment at any time. On the other side, a digital image correlation (DIC) technique has been used to track surface point displacements from the image sequence obtained from the camera in front of the simulation facility. While the 4D model may provide a qualitative description and documentation of the experiment running, DIC analysis output quantitative information such as local point displacements and velocities, to be related to physical processes and to other observations. All the hardware and software equipment adopted for the photogrammetric reconstruction has been based on low-cost and open-source solutions.

  1. IMAGE-BASED RECONSTRUCTION AND ANALYSIS OF DYNAMIC SCENES IN A LANDSLIDE SIMULATION FACILITY

    Directory of Open Access Journals (Sweden)

    M. Scaioni

    2017-12-01

    Full Text Available The application of image processing and photogrammetric techniques to dynamic reconstruction of landslide simulations in a scaled-down facility is described. Simulations are also used here for active-learning purpose: students are helped understand how physical processes happen and which kinds of observations may be obtained from a sensor network. In particular, the use of digital images to obtain multi-temporal information is presented. On one side, using a multi-view sensor set up based on four synchronized GoPro 4 Black® cameras, a 4D (3D spatial position and time reconstruction of the dynamic scene is obtained through the composition of several 3D models obtained from dense image matching. The final textured 4D model allows one to revisit in dynamic and interactive mode a completed experiment at any time. On the other side, a digital image correlation (DIC technique has been used to track surface point displacements from the image sequence obtained from the camera in front of the simulation facility. While the 4D model may provide a qualitative description and documentation of the experiment running, DIC analysis output quantitative information such as local point displacements and velocities, to be related to physical processes and to other observations. All the hardware and software equipment adopted for the photogrammetric reconstruction has been based on low-cost and open-source solutions.

  2. Multiscale simulations of patchy particle systems combining Molecular Dynamics, Path Sampling and Green's Function Reaction Dynamics

    Science.gov (United States)

    Bolhuis, Peter

    Important reaction-diffusion processes, such as biochemical networks in living cells, or self-assembling soft matter, span many orders in length and time scales. In these systems, the reactants' spatial dynamics at mesoscopic length and time scales of microns and seconds is coupled to the reactions between the molecules at microscopic length and time scales of nanometers and milliseconds. This wide range of length and time scales makes these systems notoriously difficult to simulate. While mean-field rate equations cannot describe such processes, the mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. The recently developed multiscale Molecular Dynamics Green's Function Reaction Dynamics (MD-GFRD) approach combines GFRD for simulating the system at the mesocopic scale where particles are far apart, with microscopic Molecular (or Brownian) Dynamics, for simulating the system at the microscopic scale where reactants are in close proximity. The association and dissociation of particles are treated with rare event path sampling techniques. I will illustrate the efficiency of this method for patchy particle systems. Replacing the microscopic regime with a Markov State Model avoids the microscopic regime completely. The MSM is then pre-computed using advanced path-sampling techniques such as multistate transition interface sampling. I illustrate this approach on patchy particle systems that show multiple modes of binding. MD-GFRD is generic, and can be used to efficiently simulate reaction-diffusion systems at the particle level, including the orientational dynamics, opening up the possibility for large-scale simulations of e.g. protein signaling networks.

  3. Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin

    Energy Technology Data Exchange (ETDEWEB)

    Wei Gu; Garcia, A.E.; Schoenborn, B.P. [Los Alamos National Laboratory, NM (United States)

    1994-12-31

    Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies.

  4. Molecular Dynamics Simulations of Water Droplets On Hydrophilic Silica Surfaces

    DEFF Research Database (Denmark)

    Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard L.

    2009-01-01

    and DNA microarrays technologies.Although extensive experimental, theoretical and computational work has been devoted to study the nature of the interaction between silica and water, at the molecular level a complete understanding of silica-water systems has not been reached. Contact angle computations...... dynamics (MD) simulations of a hydrophilic air-water-silica system using the MD package FASTTUBE. We employ quantum chemistry calculation to obtain air-silica interaction parameters for the simulations. Our simulations are based in the following force fields: i) The silica-silica interaction is based...... of water droplets on silica surfaces offers a useful fundamental and quantitative measurement in order to study chemical and physical properties of water-silica systems. For hydrophobic systems the static and dynamic properties of the fluid-solid interface are influenced by the presence of air. Hence...

  5. Simulation of the Dynamic Inefficiency of the CMS Pixel Detector

    CERN Document Server

    INSPIRE-00380273

    2015-05-07

    The Pixel Detector is the innermost part of the CMS Tracker. It therefore has to prevail in the harshest environment in terms of particle fluence and radiation. There are several mechanisms that may decrease the efficiency of the detector. These are mainly caused by data acquisition (DAQ) problems and/or Single Event Upsets (SEU). Any remaining efficiency loss is referred to as the dynamic inefficiency. It is caused by various mechanisms inside the Readout Chip (ROC) and depends strongly on the data occupancy. In the 2012 data, at high values of instantaneous luminosity the inefficiency reached 2\\% (in the region closest to the interaction point) which is not negligible. In the 2015 run higher instantaneous luminosity is expected, which will result in lower efficiencies; therefore this effect needs to be understood and simulated. A data-driven method has been developed to simulate dynamic inefficiency, which has been shown to successfully simulate the effects.

  6. Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin

    International Nuclear Information System (INIS)

    Wei Gu; Garcia, A.E.; Schoenborn, B.P.

    1994-01-01

    Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies

  7. Haptization of molecular dynamics simulation with thermal display

    International Nuclear Information System (INIS)

    Tamura, Yuichi; Fujiwara, Susumu; Nakamura, Hiroaki

    2010-01-01

    Thermal display, which is a type of haptic display, is effective in providing intuitive information of temperature. However, in many studies, the user has assumed a sitting position during the use of these devices. In contrast, the user generally watches 3D objects while standing and walking around in large-scale virtual reality system, In addition, in scientific visualization, the response time is very important for observing physical phenomena, especially for dynamic numerical simulation. One solution is to provide two types of thermal information: information about the rate of thermal change and information about the actual temperature. We propose a thermal display with two Peltier elements which can show above two pairs of information and the result (for example energy and temperature, as thermal information) of numerical simulation. Finally, we represent an example of visualizing and haptizing the result of molecular dynamics simulation. (author)

  8. Parallel alternating direction preconditioner for isogeometric simulations of explicit dynamics

    KAUST Repository

    Łoś, Marcin

    2015-04-27

    In this paper we present a parallel implementation of the alternating direction preconditioner for isogeometric simulations of explicit dynamics. The Alternating Direction Implicit (ADI) algorithm, belongs to the category of matrix-splitting iterative methods, was proposed almost six decades ago for solving parabolic and elliptic partial differential equations, see [1–4]. The new version of this algorithm has been recently developed for isogeometric simulations of two dimensional explicit dynamics [5] and steady-state diffusion equations with orthotropic heterogenous coefficients [6]. In this paper we present a parallel version of the alternating direction implicit algorithm for three dimensional simulations. The algorithm has been incorporated as a part of PETIGA an isogeometric framework [7] build on top of PETSc [8]. We show the scalability of the parallel algorithm on STAMPEDE linux cluster up to 10,000 processors, as well as the convergence rate of the PCG solver with ADI algorithm as preconditioner.

  9. A Thermodynamic Library for Simulation and Optimization of Dynamic Processes

    DEFF Research Database (Denmark)

    Ritschel, Tobias Kasper Skovborg; Gaspar, Jozsef; Jørgensen, John Bagterp

    2017-01-01

    Process system tools, such as simulation and optimization of dynamic systems, are widely used in the process industries for development of operational strategies and control for process systems. These tools rely on thermodynamic models and many thermodynamic models have been developed for different...... compounds and mixtures. However, rigorous thermodynamic models are generally computationally intensive and not available as open-source libraries for process simulation and optimization. In this paper, we describe the application of a novel open-source rigorous thermodynamic library, ThermoLib, which...... is designed for dynamic simulation and optimization of vapor-liquid processes. ThermoLib is implemented in Matlab and C and uses cubic equations of state to compute vapor and liquid phase thermodynamic properties. The novelty of ThermoLib is that it provides analytical first and second order derivatives...

  10. Molecular dynamics simulations of a lithium/sodium carbonate mixture.

    Science.gov (United States)

    Ottochian, Alistar; Ricca, Chiara; Labat, Frederic; Adamo, Carlo

    2016-03-01

    The diffusion and ionic conductivity of Li x Na1-x CO3 salt mixtures were studied by means of Molecular Dynamics (MD) simulations, using the Janssen and Tissen model (Janssen and Tissen, Mol Simul 5:83-98; 1990). These salts have received particular attention due to their central role in fuel cells technology, and reliable numerical methods that could perform as important interpretative tool of experimental data are thus required but still lacking. The chosen computational model nicely reproduces the main structural behaviour of the pure Li2CO3, Na2CO3 and K2CO3 carbonates, but also of their Li/K and Li/Na mixtures. However, it fails to accurately describe dynamic properties such as activation energies of diffusion and conduction processes, outlining the need to develop more accurate models for the simulation of molten salt carbonates.

  11. Software life cycle dynamic simulation model: The organizational performance submodel

    Science.gov (United States)

    Tausworthe, Robert C.

    1985-01-01

    The submodel structure of a software life cycle dynamic simulation model is described. The software process is divided into seven phases, each with product, staff, and funding flows. The model is subdivided into an organizational response submodel, a management submodel, a management influence interface, and a model analyst interface. The concentration here is on the organizational response model, which simulates the performance characteristics of a software development subject to external and internal influences. These influences emanate from two sources: the model analyst interface, which configures the model to simulate the response of an implementing organization subject to its own internal influences, and the management submodel that exerts external dynamic control over the production process. A complete characterization is given of the organizational response submodel in the form of parameterized differential equations governing product, staffing, and funding levels. The parameter values and functions are allocated to the two interfaces.

  12. Why we simulate negated information: a dynamic pragmatic account.

    Science.gov (United States)

    Tian, Ye; Breheny, Richard; Ferguson, Heather J

    2010-12-01

    A well-established finding in the simulation literature is that participants simulate the positive argument of negation soon after reading a negative sentence, prior to simulating a scene consistent with the negated sentence (Kaup, Ludtke, & Zwaan, 2006; Kaup, Yaxley, Madden, Zwaan, & Ludtke, 2007). One interpretation of this finding is that negation requires two steps to process: first represent what is being negated then "reject" that in favour of a representation of a negation-consistent state of affairs (Kaup et al., 2007). In this paper we argue that this finding with negative sentences could be a by-product of the dynamic way that language is interpreted relative to a common ground and not the way that negation is represented. We present a study based on Kaup et al. (2007) that tests the competing accounts. Our results suggest that some negative sentences are not processed in two steps, but provide support for the alternative, dynamic account.

  13. Probing the limits of metal plasticity with molecular dynamics simulations

    Science.gov (United States)

    Zepeda-Ruiz, Luis A.; Stukowski, Alexander; Oppelstrup, Tomas; Bulatov, Vasily V.

    2017-10-01

    Ordinarily, the strength and plasticity properties of a metal are defined by dislocations--line defects in the crystal lattice whose motion results in material slippage along lattice planes. Dislocation dynamics models are usually used as mesoscale proxies for true atomistic dynamics, which are computationally expensive to perform routinely. However, atomistic simulations accurately capture every possible mechanism of material response, resolving every ``jiggle and wiggle'' of atomic motion, whereas dislocation dynamics models do not. Here we present fully dynamic atomistic simulations of bulk single-crystal plasticity in the body-centred-cubic metal tantalum. Our goal is to quantify the conditions under which the limits of dislocation-mediated plasticity are reached and to understand what happens to the metal beyond any such limit. In our simulations, the metal is compressed at ultrahigh strain rates along its [001] crystal axis under conditions of constant pressure, temperature and strain rate. To address the complexity of crystal plasticity processes on the length scales (85-340 nm) and timescales (1 ns-1μs) that we examine, we use recently developed methods of in situ computational microscopy to recast the enormous amount of transient trajectory data generated in our simulations into a form that can be analysed by a human. Our simulations predict that, on reaching certain limiting conditions of strain, dislocations alone can no longer relieve mechanical loads; instead, another mechanism, known as deformation twinning (the sudden re-orientation of the crystal lattice), takes over as the dominant mode of dynamic response. Below this limit, the metal assumes a strain-path-independent steady state of plastic flow in which the flow stress and the dislocation density remain constant as long as the conditions of straining thereafter remain unchanged. In this distinct state, tantalum flows like a viscous fluid while retaining its crystal lattice and remaining a strong

  14. Explicit dynamics for numerical simulation of crack propagation by the extended finite element method

    International Nuclear Information System (INIS)

    Menouillard, T.

    2007-09-01

    Computerized simulation is nowadays an integrating part of design and validation processes of mechanical structures. Simulation tools are more and more performing allowing a very acute description of the phenomena. Moreover, these tools are not limited to linear mechanics but are developed to describe more difficult behaviours as for instance structures damage which interests the safety domain. A dynamic or static load can thus lead to a damage, a crack and then a rupture of the structure. The fast dynamics allows to simulate 'fast' phenomena such as explosions, shocks and impacts on structure. The application domain is various. It concerns for instance the study of the lifetime and the accidents scenario of the nuclear reactor vessel. It is then very interesting, for fast dynamics codes, to be able to anticipate in a robust and stable way such phenomena: the assessment of damage in the structure and the simulation of crack propagation form an essential stake. The extended finite element method has the advantage to break away from mesh generation and from fields projection during the crack propagation. Effectively, crack is described kinematically by an appropriate strategy of enrichment of supplementary freedom degrees. Difficulties connecting the spatial discretization of this method with the temporal discretization of an explicit calculation scheme has then been revealed; these difficulties are the diagonal writing of the mass matrix and the associated stability time step. Here are presented two methods of mass matrix diagonalization based on the kinetic energy conservation, and studies of critical time steps for various enriched finite elements. The interest revealed here is that the time step is not more penalizing than those of the standard finite elements problem. Comparisons with numerical simulations on another code allow to validate the theoretical works. A crack propagation test in mixed mode has been exploited in order to verify the simulation

  15. Direct Numerical Simulation of a Compressible Reacting Boundary Layer using a Temporal Slow Growth Homogenization

    Science.gov (United States)

    Topalian, Victor; Oliver, Todd; Ulerich, Rhys; Moser, Robert

    2013-11-01

    A DNS of a compressible, reacting boundary layer flow at Reθ ~ 430 was performed using a temporal slow-growth homogenization, for a multispecies flow model of air at supersonic regime. The overall scenario parameters are related to those of the flow over an ablating surface of a space capsule upon Earth's atmospheric re-entry. The simulation algorithm features Fourier spatial discretization in the streamwise and spanwise directions, B-splines in the wall normal direction, and is marched semi-implicitly in time using the SMR91 scheme. Flow statistics will be presented for relevant flow quantities, in particular those related with RANS modeling. Since analogous slow growth computations can be performed using RANS to predict the flow mean profiles, the use of data gathered from this type of simulation as a vehicle for the calibration and uncertainty quantification of RANS models will be discussed. This work is supported by the Department of Energy [National Nuclear Security Administration] under Award Number [DE-FC52-08NA28615].

  16. Spatial-temporal-covariance-based modeling, analysis, and simulation of aero-optics wavefront aberrations.

    Science.gov (United States)

    Vogel, Curtis R; Tyler, Glenn A; Wittich, Donald J

    2014-07-01

    We introduce a framework for modeling, analysis, and simulation of aero-optics wavefront aberrations that is based on spatial-temporal covariance matrices extracted from wavefront sensor measurements. Within this framework, we present a quasi-homogeneous structure function to analyze nonhomogeneous, mildly anisotropic spatial random processes, and we use this structure function to show that phase aberrations arising in aero-optics are, for an important range of operating parameters, locally Kolmogorov. This strongly suggests that the d5/3 power law for adaptive optics (AO) deformable mirror fitting error, where d denotes actuator separation, holds for certain important aero-optics scenarios. This framework also allows us to compute bounds on AO servo lag error and predictive control error. In addition, it provides us with the means to accurately simulate AO systems for the mitigation of aero-effects, and it may provide insight into underlying physical processes associated with turbulent flow. The techniques introduced here are demonstrated using data obtained from the Airborne Aero-Optics Laboratory.

  17. Simulation language of DSNP: dynamic simulator for nuclear power-plants

    International Nuclear Information System (INIS)

    Saphier, D.

    1978-09-01

    The Dynamic Simulator for Nuclear Power-plants (DSNP) is a system of programs and data sets by which a nuclear power plant or part thereof can be simulated at different levels of sophistication. The acronym DSNP is used interchangeably for the DSNP language, for the DSNP precompiler, for the DSNP libraries, and for the DSNP document generator. The DSNP language is a set of simple block oriented statements, which together with the appropriate data, comprise a simulation of a nuclear power plant. The majority of the DSNP statements will result in the inclusion of a simulated physical module into the program. FORTRAN statements can be inserted with no restrictions among DSNP statements

  18. Rarefield gas dynamics fundamentals, simulations and micro flows

    CERN Document Server

    Shen, Ching

    2006-01-01

    This book elucidates the methods of molecular gas dynamics or rarefied gas dynamics which treat the problems of gas flows when the discrete molecular effects of the gas prevail under the circumstances of low density, the emphasis being on the basis of the methods, the direct simulation Monte Carlo method applied to the simulation of non-equilibrium effects and the frontier subjects related to low speed microscale rarefied gas flows. It provides a solid basis for the study of molecular gas dynamics for senior students and graduates in the aerospace and mechanical engineering departments of universities and colleges. It gives a general acquaintance of modern developments of rarefied gas dynamics in various regimes and leads to the frontier topics of non-equilibrium rarefied gas dynamics and low speed microscale gas dynamics. It will be also of benefit to the scientific and technical researchers engaged in aerospace high altitude aerodynamic force and heating design and in the research on gas flow in MEMS.

  19. Temporal dynamics influenced by global change: bee community phenology in urban, agricultural, and natural landscapes.

    Science.gov (United States)

    Leong, Misha; Ponisio, Lauren C; Kremen, Claire; Thorp, Robbin W; Roderick, George K

    2016-03-01

    Urbanization and agricultural intensification of landscapes are important drivers of global change, which in turn have direct impacts on local ecological communities leading to shifts in species distributions and interactions. Here, we illustrate how human-altered landscapes, with novel ornamental and crop plant communities, result not only in changes to local community diversity of floral-dependent species, but also in shifts in seasonal abundance of bee pollinators. Three years of data on the spatio-temporal distributions of 91 bee species show that seasonal patterns of abundance and species richness in human-altered landscapes varied significantly less compared to natural habitats in which floral resources are relatively scarce in the dry summer months. These findings demonstrate that anthropogenic environmental changes in urban and agricultural systems, here mediated through changes in plant resources and water inputs, can alter the temporal dynamics of pollinators that depend on them. Changes in phenology of interactions can be an important, though frequently overlooked, mechanism of global change. © 2015 John Wiley & Sons Ltd.

  20. Subliminal semantic priming changes the dynamic causal influence between the left frontal and temporal cortex.

    Science.gov (United States)

    Matsumoto, Atsushi; Kakigi, Ryusuke

    2014-01-01

    Recent neuroimaging experiments have revealed that subliminal priming of a target stimulus leads to the reduction of neural activity in specific regions concerned with processing the target. Such findings lead to questions about the degree to which the subliminal priming effect is based only on decreased activity in specific local brain regions, as opposed to the influence of neural mechanisms that regulate communication between brain regions. To address this question, this study recorded EEG during performance of a subliminal semantic priming task. We adopted an information-based approach that used independent component analysis and multivariate autoregressive modeling. Results indicated that subliminal semantic priming caused significant modulation of alpha band activity in the left inferior frontal cortex and modulation of gamma band activity in the left inferior temporal regions. The multivariate autoregressive approach confirmed significant increases in information flow from the inferior frontal cortex to inferior temporal regions in the early time window that was induced by subliminal priming. In the later time window, significant enhancement of bidirectional causal flow between these two regions underlying subliminal priming was observed. Results suggest that unconscious processing of words influences not only local activity of individual brain regions but also the dynamics of neural communication between those regions.

  1. Spatio-temporal dynamics of action-effect associations in oculomotor control.

    Science.gov (United States)

    Riechelmann, Eva; Pieczykolan, Aleksandra; Horstmann, Gernot; Herwig, Arvid; Huestegge, Lynn

    2017-10-01

    While there is ample evidence that actions are guided by anticipating their effects (ideomotor control) in the manual domain, much less is known about the underlying characteristics and dynamics of effect-based oculomotor control. Here, we address three open issues. 1) Is action-effect anticipation in oculomotor control reflected in corresponding spatial saccade characteristics in inanimate environments? 2) Does the previously reported dependency of action latency on the temporal effect delay (action-effect interval) also occur in the oculomotor domain? 3) Which temporal effect delay is optimally suited to develop strong action-effect associations over time in the oculomotor domain? Participants executed left or right free-choice saccades to peripheral traffic lights, causing an (immediate or delayed) action-contingent light switch in the upper vs. lower part of the traffic light. Results indicated that saccades were spatially shifted toward the location of the upcoming change, indicating anticipation of the effect (location). Saccade latency was affected by effect delay, suggesting that corresponding time information is integrated into event representations. Finally, delayed (vs. immediate) effects were more effective in strengthening action-effect associations over the course of the experiment, likely due to greater saliency of perceptual changes occurring during target fixation as opposed to changes during saccades (saccadic suppression). Overall, basic principles underlying ideomotor control appear to generalize to the oculomotor domain. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Dynamics of Disagreement: Large-Scale Temporal Network Analysis Reveals Negative Interactions in Online Collaboration

    Science.gov (United States)

    Tsvetkova, Milena; García-Gavilanes, Ruth; Yasseri, Taha

    2016-11-01

    Disagreement and conflict are a fact of social life. However, negative interactions are rarely explicitly declared and recorded and this makes them hard for scientists to study. In an attempt to understand the structural and temporal features of negative interactions in the community, we use complex network methods to analyze patterns in the timing and configuration of reverts of article edits to Wikipedia. We investigate how often and how fast pairs of reverts occur compared to a null model in order to control for patterns that are natural to the content production or are due to the internal rules of Wikipedia. Our results suggest that Wikipedia editors systematically revert the same person, revert back their reverter, and come to defend a reverted editor. We further relate these interactions to the status of the involved editors. Even though the individual reverts might not necessarily be negative social interactions, our analysis points to the existence of certain patterns of negative social dynamics within the community of editors. Some of these patterns have not been previously explored and carry implications for the knowledge collection practice conducted on Wikipedia. Our method can be applied to other large-scale temporal collaboration networks to identify the existence of negative social interactions and other social processes.

  3. Temporal dynamics of genetic variability in a mountain goat (Oreamnos americanus) population.

    Science.gov (United States)

    Ortego, Joaquín; Yannic, Glenn; Shafer, Aaron B A; Mainguy, Julien; Festa-Bianchet, Marco; Coltman, David W; Côté, Steeve D

    2011-04-01

    The association between population dynamics and genetic variability is of fundamental importance for both evolutionary and conservation biology. We combined long-term population monitoring and molecular genetic data from 123 offspring and their parents at 28 microsatellite loci to investigate changes in genetic diversity over 14 cohorts in a small and relatively isolated population of mountain goats (Oreamnos americanus) during a period of demographic increase. Offspring heterozygosity decreased while parental genetic similarity and inbreeding coefficients (F(IS) ) increased over the study period (1995-2008). Immigrants introduced three novel alleles into the population and matings between residents and immigrants produced more heterozygous offspring than local crosses, suggesting that immigration can increase population genetic variability. The population experienced genetic drift over the study period, reflected by a reduced allelic richness over time and an 'isolation-by-time' pattern of genetic structure. The temporal decline of individual genetic diversity despite increasing population size probably resulted from a combination of genetic drift due to small effective population size, inbreeding and insufficient counterbalancing by immigration. This study highlights the importance of long-term genetic monitoring to understand how demographic processes influence temporal changes of genetic diversity in long-lived organisms. © 2011 Blackwell Publishing Ltd.

  4. Right mesial temporal lobe epilepsy impairs empathy-related brain responses to dynamic fearful faces.

    Science.gov (United States)

    Toller, Gianina; Adhimoolam, Babu; Grunwald, Thomas; Huppertz, Hans-Jürgen; Kurthen, Martin; Rankin, Katherine P; Jokeit, Hennric

    2015-03-01

    Unilateral mesial temporal lobe epilepsy (MTLE) has been associated with reduced amygdala responsiveness to fearful faces. However, the effect of unilateral MTLE on empathy-related brain responses in extra-amygdalar regions has not been investigated. Using functional magnetic resonance imaging, we measured empathy-related brain responses to dynamic fearful faces in 34 patients with unilateral MTLE (18 right sided), in an epilepsy (extra-MTLE; n = 16) and in a healthy control group (n = 30). The primary finding was that right MTLE (RMTLE) was associated with decreased activity predominantly in the right amygdala and also in bilateral periaqueductal gray (PAG) but normal activity in the right anterior insula. The results of the extra-MTLE group demonstrate that these reduced amygdala and PAG responses go beyond the attenuation caused by antiepileptic and antidepressant medication. These findings clearly indicate that RMTLE affects the function of mesial temporal and midbrain structures that mediate basic interoceptive input necessary for the emotional awareness of empathic experiences of fear. Together with the decreased empathic concern found in the RMTLE group, this study provides neurobehavioral evidence that patients with RMTLE are at increased risk for reduced empathy towards others' internal states and sheds new light on the nature of social-cognitive impairments frequently accompanying MTLE.

  5. Temporal and Spatial Dynamics of Sediment Anaerobic Ammonium Oxidation (Anammox) Bacteria in Freshwater Lakes.

    Science.gov (United States)

    Yang, Yuyin; Dai, Yu; Li, Ningning; Li, Bingxin; Xie, Shuguang; Liu, Yong

    2017-02-01

    Anaerobic ammonium-oxidizing (anammox) process can play an important role in freshwater nitrogen cycle. However, the distribution of anammox bacteria in freshwater lake and the associated environmental factors remain essentially unclear. The present study investigated the temporal and spatial dynamics of sediment anammox bacterial populations in eutrotrophic Dianchi Lake and mesotrophic Erhai Lake on the Yunnan Plateau (southwestern China). The remarkable spatial change of anammox bacterial abundance was found in Dianchi Lake, while the relatively slight spatial shift occurred in Erhai Lake. Dianchi Lake had greater anammox bacterial abundance than Erhai Lake. In both Dianchi Lake and Erhai Lake, anammox bacteria were much more abundant in summer than in spring. Anammox bacterial community richness, diversity, and structure in these two freshwater lakes were subjected to temporal and spatial variations. Sediment anammox bacterial communities in Dianchi Lake and Erhai Lake were dominated by Candidatus Brocadia and a novel phylotype followed by Candidatus Kuenenia; however, these two lakes had distinct anammox bacterial community structure. In addition, trophic status determined sediment anammox bacterial community structure.

  6. Temporal variability in phosphorus transfers: classifying concentration-discharge event dynamics

    Science.gov (United States)

    Haygarth, P.; Turner, B. L.; Fraser, A.; Jarvis, S.; Harrod, T.; Nash, D.; Halliwell, D.; Page, T.; Beven, K.

    The importance of temporal variability in relationships between phosphorus (P) concentration (Cp) and discharge (Q) is linked to a simple means of classifying the circumstances of Cp-Q relationships in terms of functional types of response. New experimental data at the upstream interface of grassland soil and catchment systems at a range of scales (lysimeters to headwaters) in England and Australia are used to demonstrate the potential of such an approach. Three types of event are defined as Types 1-3, depending on whether the relative change in Q exceeds the relative change in Cp (Type 1), whether Cp and Q are positively inter-related (Type 2) and whether Cp varies yet Q is unchanged (Type 3). The classification helps to characterise circumstances that can be explained mechanistically in relation to (i) the scale of the study (with a tendency towards Type 1 in small scale lysimeters), (ii) the form of P with a tendency for Type 1 for soluble (i.e., <0.45 μm P forms) and (iii) the sources of P with Type 3 dominant where P availability overrides transport controls. This simple framework provides a basis for development of a more complex and quantitative classification of Cp-Q relationships that can be developed further to contribute to future models of P transfer and delivery from slope to stream. Studies that evaluate the temporal dynamics of the transfer of P are currently grossly under-represented in comparison with models based on static/spatial factors.

  7. Satellite image simulations for model-supervised, dynamic retrieval of crop type and land use intensity

    Science.gov (United States)

    Bach, H.; Klug, P.; Ruf, T.; Migdall, S.; Schlenz, F.; Hank, T.; Mauser, W.

    2015-04-01

    To support food security, information products about the actual cropping area per crop type, the current status of agricultural production and estimated yields, as well as the sustainability of the agricultural management are necessary. Based on this information, well-targeted land management decisions can be made. Remote sensing is in a unique position to contribute to this task as it is globally available and provides a plethora of information about current crop status. M4Land is a comprehensive system in which a crop growth model (PROMET) and a reflectance model (SLC) are coupled in order to provide these information products by analyzing multi-temporal satellite images. SLC uses modelled surface state parameters from PROMET, such as leaf area index or phenology of different crops to simulate spatially distributed surface reflectance spectra. This is the basis for generating artificial satellite images considering sensor specific configurations (spectral bands, solar and observation geometries). Ensembles of model runs are used to represent different crop types, fertilization status, soil colour and soil moisture. By multi-temporal comparisons of simulated and real satellite images, the land cover/crop type can be classified in a dynamically, model-supervised way and without in-situ training data. The method is demonstrated in an agricultural test-site in Bavaria. Its transferability is studied by analysing PROMET model results for the rest of Germany. Especially the simulated phenological development can be verified on this scale in order to understand whether PROMET is able to adequately simulate spatial, as well as temporal (intra- and inter-season) crop growth conditions, a prerequisite for the model-supervised approach. This sophisticated new technology allows monitoring of management decisions on the field-level using high resolution optical data (presently RapidEye and Landsat). The M4Land analysis system is designed to integrate multi-mission data and is

  8. Transfer of spatio-temporal multifractal properties of rainfall to simulated surface runoff

    Science.gov (United States)

    Gires, Auguste; Giangola-Murzyn, Agathe; Richard, Julien; Abbes, Jean-Baptiste; Tchiguirinskaia, Ioulia; Schertzer, Daniel; Willinger, Bernard; Cardinal, Hervé; Thouvenot, Thomas

    2014-05-01

    In this paper we suggest to use scaling laws and more specifically Universal Multifractals (UM) to analyse in a spatio-temporal framework both the radar rainfall and the simulated surface runoff. Such tools have been extensively used to analyse and simulate geophysical fields extremely variable over wide range of spatio-temporal scales such as rainfall, but have not often if ever been applied to surface runoff. Such novel combined analysis helps to improve the understanding of the rainfall-runoff relationship. Two catchments of the chair "Hydrology for resilient cities" sponsored by Véolia, and of the European Interreg IV RainGain project are used. They are both located in the Paris area: a 144 ha flat urban area in the Seine-Saint-Denis County, and a 250 ha urban area with a significant portion of forest located on a steep hillside of the Bièvre River. A fully distributed urban hydrological model currently under development called Multi-Hydro is implemented to represent the catchments response. It consists in an interacting core between open source software packages, each of them representing a portion of the water cycle in urban environment. The fully distributed model is tested with pixels of size 5, 10 and 20 m. In a first step the model is validated for three rainfall events that occurred in 2010 and 2011, for which the Météo-France radar mosaic with a resolution of 1 km in space and 5 min in time is available. These events generated significant surface runoff and some local flooding. The sensitivity of the model to the rainfall resolution is briefly checked by stochastically generating an ensemble of realistic downscaled rainfall fields (obtained by continuing the underlying cascade process which is observed on the available range of scales) and inputting them into the model. The impact is significant on both the simulated sewer flow and surface runoff. Then rainfall fields are generated with the help of discrete multifractal cascades and inputted in the

  9. A customized light sheet microscope to measure spatio-temporal protein dynamics in small model organisms.

    Directory of Open Access Journals (Sweden)

    Matthias Rieckher

    Full Text Available We describe a customizable and cost-effective light sheet microscopy (LSM platform for rapid three-dimensional imaging of protein dynamics in small model organisms. The system is designed for high acquisition speeds and enables extended time-lapse in vivo experiments when using fluorescently labeled specimens. We demonstrate the capability of the setup to monitor gene expression and protein localization during ageing and upon starvation stress in longitudinal studies in individual or small groups of adult Caenorhabditis elegans nematodes. The system is equipped to readily perform fluorescence recovery after photobleaching (FRAP, which allows monitoring protein recovery and distribution under low photobleaching conditions. Our imaging platform is designed to easily switch between light sheet microscopy and optical projection tomography (OPT modalities. The setup permits monitoring of spatio-temporal expression and localization of ageing biomarkers of subcellular size and can be conveniently adapted to image a wide range of small model organisms and tissue samples.

  10. Spatial and temporal dynamics of dengue fever in Peru: 1994-2006.

    Science.gov (United States)

    Chowell, G; Torre, C A; Munayco-Escate, C; Suárez-Ognio, L; López-Cruz, R; Hyman, J M; Castillo-Chavez, C

    2008-12-01

    SUMMARYThe weekly number of dengue cases in Peru, South America, stratified by province for the period 1994-2006 were analysed in conjunction with associated demographic, geographic and climatological data. Estimates of the reproduction number, moderately correlated with population size (Spearman rho=0.28, P=0.03), had a median of 1.76 (IQR 0.83-4.46). The distributions of dengue attack rates and epidemic durations follow power-law (Pareto) distributions (coefficient of determination >85%, Pjungle areas. Our findings suggest a hierarchy of transmission events during the large 2000-2001 epidemic from large to small population areas when serotypes DEN-3 and DEN-4 were first identified (Spearman rho=-0.43, P=0.03). The need for spatial and temporal dengue epidemic data with a high degree of resolution not only increases our understanding of the dynamics of dengue but will also generate new hypotheses and provide a platform for testing innovative control policies.

  11. The surface chemistry determines the spatio-temporal interaction dynamics of quantum dots in atherosclerotic lesions.

    Science.gov (United States)

    Uhl, Bernd; Hirn, Stephanie; Mildner, Karina; Coletti, Raffaele; Massberg, Steffen; Reichel, Christoph A; Rehberg, Markus; Zeuschner, Dagmar; Krombach, Fritz

    2018-03-01

    To optimize the design of nanoparticles for diagnosis or therapy of vascular diseases, it is mandatory to characterize the determinants of nano-bio interactions in vascular lesions. Using ex vivo and in vivo microscopy, we analyzed the interactive behavior of quantum dots with different surface functionalizations in atherosclerotic lesions of ApoE-deficient mice. We demonstrate that quantum dots with different surface functionalizations exhibit specific interactive behaviors with distinct molecular and cellular components of the injured vessel wall. Moreover, we show a role for fibrinogen in the regulation of the spatio-temporal interaction dynamics in atherosclerotic lesions. Our findings emphasize the relevance of surface chemistry-driven nano-bio interactions on the differential in vivo behavior of nanoparticles in diseased tissue.

  12. Quantitative tradeoffs between spatial, temporal, and thermometric resolution of nonresonant Raman thermometry for dynamic experiments.

    Science.gov (United States)

    McGrane, Shawn D; Moore, David S; Goodwin, Peter M; Dattelbaum, Dana M

    2014-01-01

    The ratio of Stokes to anti-Stokes nonresonant spontaneous Raman can provide an in situ thermometer that is noncontact, independent of any material specific parameters or calibrations, can be multiplexed spatially with line imaging, and can be time resolved for dynamic measurements. However, spontaneous Raman cross sections are very small, and thermometric measurements are often limited by the amount of laser energy that can be applied without damaging the sample or changing its temperature appreciably. In this paper, we quantitatively detail the tradeoff space between spatial, temporal, and thermometric accuracy measurable with spontaneous Raman. Theoretical estimates are pinned to experimental measurements to form realistic expectations of the resolution tradeoffs appropriate to various experiments. We consider the effects of signal to noise, collection efficiency, laser heating, pulsed laser ablation, and blackbody emission as limiting factors, provide formulae to help choose optimal conditions and provide estimates relevant to planning experiments along with concrete examples for single-shot measurements.

  13. Temporal dynamics of the response to Al stress in Eucalyptus grandis × Eucalyptus camaldulensis

    Directory of Open Access Journals (Sweden)

    Berenice K. de Alcântara

    2015-06-01

    Full Text Available Lipid peroxidation and root elongation of Eucalyptus grandis × Eucalyptus camaldulensis were studied under stress conditions in response to aluminum (Al, a metal known to limit agricultural productivity in acidic soils primarily due to reduced root elongation. In Brazil, the Grancam 1277 hybrid (E. grandis × E. camaldulensis has been planted in the "Cerrado", a region of the country with a wide occurrence of acidic soils. The present study demonstrated that the hybrid exhibited root growth reduction and increased levels of lipid peroxidation after 24h of treatment with 100 µM of Al, which was followed by a reduction in lipid peroxidation levels and the recovery of root elongation after 48h of Al exposure, suggesting a rapid response to the early stressful conditions induced by Al. The understanding of the temporal dynamics of Al tolerance may be useful for selecting more tolerant genotypes and for identifying genes of interest for applications in bioengineering.

  14. Spatio-temporal dynamics of the white-eye square superlattice pattern in dielectric barrier discharge

    International Nuclear Information System (INIS)

    Wei, Lingyan; Dong, Lifang; Feng, Jianyu; Liu, Weibo; Fan, Weili; Pan, Yuyang

    2016-01-01

    We report on the first investigation of the white-eye square superlattice pattern (WESSP) in a dielectric barrier discharge system. The evolution of patterns with increasing voltage is given. A phase diagram of WESSP as functions of gas pressure p and argon concentration φ is presented. The spatio-temporal dynamics of the WESSP is studied by using an intensified charge-coupled device camera and photomultipliers. Results show that the WESSP consists of four different transient sublattices, whose discharge sequence is small spots—spots on the line—halos—central spots in each half voltage cycle. The discharge moment and position of each sublattice are dependent upon the field of the wall charges produced by all sublattices discharged previously. (paper)

  15. Comparing the temporal dynamics of thematic and taxonomic processing using event-related potentials.

    Directory of Open Access Journals (Sweden)

    Olivera Savic

    Full Text Available We report the results of a study comparing the temporal dynamics of thematic and taxonomic knowledge activation in a picture-word priming paradigm using event-related potentials. Although we found no behavioral differences between thematic and taxonomic processing, ERP data revealed distinct patterns of N400 and P600 amplitude modulation for thematic and taxonomic priming. Thematically related target stimuli elicited less negativity than taxonomic targets between 280-460 ms after stimulus onset, suggesting easier semantic processing of thematic than taxonomic relationships. Moreover, P600 mean amplitude was significantly increased for taxonomic targets between 520-600 ms, consistent with a greater need for stimulus reevaluation in that condition. These results offer novel evidence in favor of a dissociation between thematic and taxonomic thinking in the early phases of conceptual evaluation.

  16. Comparing the temporal dynamics of thematic and taxonomic processing using event-related potentials.

    Science.gov (United States)

    Savic, Olivera; Savic, Andrej M; Kovic, Vanja

    2017-01-01

    We report the results of a study comparing the temporal dynamics of thematic and taxonomic knowledge activation in a picture-word priming paradigm using event-related potentials. Although we found no behavioral differences between thematic and taxonomic processing, ERP data revealed distinct patterns of N400 and P600 amplitude modulation for thematic and taxonomic priming. Thematically related target stimuli elicited less negativity than taxonomic targets between 280-460 ms after stimulus onset, suggesting easier semantic processing of thematic than taxonomic relationships. Moreover, P600 mean amplitude was significantly increased for taxonomic targets between 520-600 ms, consistent with a greater need for stimulus reevaluation in that condition. These results offer novel evidence in favor of a dissociation between thematic and taxonomic thinking in the early phases of conceptual evaluation.

  17. Self-Organization of Spatio-Temporal Hierarchy via Learning of Dynamic Visual Image Patterns on Action Sequences.

    Science.gov (United States)

    Jung, Minju; Hwang, Jungsik; Tani, Jun

    2015-01-01

    It is well known that the visual cortex efficiently processes high-dimensional spatial information by using a hierarchical structure. Recently, computational models that were inspired by the spatial hierarchy of the visual cortex have shown remarkable performance in image recognition. Up to now, however, most biological and computational modeling studies have mainly focused on the spatial domain and do not discuss temporal domain processing of the visual cortex. Several studies on the visual cortex and other brain areas associated with motor control support that the brain also uses its hierarchical structure as a processing mechanism for temporal information. Based on the success of previous computational models using spatial hierarchy and temporal hierarchy observed in the brain, the current report introduces a novel neural network model for the recognition of dynamic visual image patterns based solely on the learning of exemplars. This model is characterized by the application of both spatial and temporal constraints on local neural activities, resulting in the self-organization of a spatio-temporal hierarchy necessary for the recognition of complex dynamic visual image patterns. The evaluation with the Weizmann dataset in recognition of a set of prototypical human movement patterns showed that the proposed model is significantly robust in recognizing dynamically occluded visual patterns compared to other baseline models. Furthermore, an evaluation test for the recognition of concatenated sequences of those prototypical movement patterns indicated that the model is endowed with a remarkable capability for the contextual recognition of long-range dynamic visual image patterns.

  18. Improving temporal bone dissection using self-directed virtual reality simulation: results of a randomized blinded control trial.

    Science.gov (United States)

    Zhao, Yi Chen; Kennedy, Gregor; Yukawa, Kumiko; Pyman, Brian; O'Leary, Stephen

    2011-03-01

    A significant benefit of virtual reality (VR) simulation is the ability to provide self-direct learning for trainees. This study aims to determine whether there are any differences in performance of cadaver temporal bone dissections between novices who received traditional teaching methods and those who received unsupervised self-directed learning in a VR temporal bone simulator. Randomized blinded control trial. Royal Victorian Eye and Ear Hospital. Twenty novice trainees. After receiving an hour lecture, participants were randomized into 2 groups to receive an additional 2 hours of training via traditional teaching methods or self-directed learning using a VR simulator with automated guidance. The simulation environment presented participants with structured training tasks, which were accompanied by real-time computer-generated feedback as well as real operative videos and photos. After the training, trainees were asked to perform a cortical mastoidectomy on a cadaveric temporal bone. The dissection was videotaped and assessed by 3 otologists blinded to participants' teaching group. The overall performance scores of the simulator-based training group were significantly higher than those of the traditional training group (67% vs 29%; P < .001), with an intraclass correlation coefficient of 0.93, indicating excellent interrater reliability. Using other assessments of performance, such as injury size, the VR simulator-based training group also performed better than the traditional group. This study indicates that self-directed learning on VR simulators can be used to improve performance on cadaver dissection in novice trainees compared with traditional teaching methods alone.

  19. Simulations of fluid flow through porous media based on cellular automata and non-linear dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Paulson, K V

    1992-05-15

    A study is being carried out to apply cellular automata and non-linear dynamics in the construction of efficient and accurate computer simulations of multiphase fluid flow through porous media, with the objective of application to reservoir modelling for hydrocarbon recovery. An algorithm based on Boolean operations has been developed which transforms a PC clone into a highly efficient vector processor capable of cellular automata simulation of single fluid flow through two-dimensional rock matrix models of varying porosities. Macroscopic flow patterns have been established through spatial and temporal averaging with no floating point operations. Permeabilities of the different models have been calculated. Hardware allows the algorithm to function on dual processors on a PC platform using a video recording and editing facility. Very encouraging results have been obtained. 4 figs.

  20. Temporal dynamics of abundance and composition of nitrogen-fixing communities across agricultural soils.

    Directory of Open Access Journals (Sweden)

    Michele C Pereira E Silva

    Full Text Available BACKGROUND: Despite the fact that the fixation of nitrogen is one of the most significant nutrient processes in the terrestrial ecosystem, a thorough study of the spatial and temporal patterns in the abundance and distribution of N-fixing communities has been missing so far. METHODOLOGY/PRINCIPAL FINDINGS: In order to understand the dynamics of diazotrophic communities and their resilience to external changes, we quantified the abundance and characterized the bacterial community structures based on the nifH gene, using real-time PCR, PCR-DGGE and 454-pyrosequencing, across four representative Dutch soils during one growing season. In general, higher nifH gene copy numbers were observed in soils with higher pH than in those with lower pH, but lower numbers were related to increased nitrate and ammonium levels. Results from nifH gene pyrosequencing confirmed the observed PCR-DGGE patterns, which indicated that the N fixers are highly dynamic across time, shifting around 60%. Forward selection on CCA analysis identified N availability as the main driver of these variations, as well as of the evenness of the communities, leading to very unequal communities. Moreover, deep sequencing of the nifH gene revealed that sandy soils (B and D had the lowest percentage of shared OTUs across time, compared with clayey soils (G and K, indicating the presence of a community under constant change. Cosmopolitan nifH species (present throughout the season were affiliated with Bradyrhizobium, Azospirillum and Methylocistis, whereas other species increased their abundances progressively over time, when appropriate conditions were met, as was notably the case for Paenibacilus and Burkholderia. CONCLUSIONS: Our study provides the first in-depth pyrosequencing analysis of the N-fixing community at both spatial and temporal scales, providing insights into the cosmopolitan and specific portions of the nitrogen fixing bacterial communities in soil.

  1. Retinal Vascular and Oxygen Temporal Dynamic Responses to Light Flicker in Humans.

    Science.gov (United States)

    Felder, Anthony E; Wanek, Justin; Blair, Norman P; Shahidi, Mahnaz

    2017-11-01

    To mathematically model the temporal dynamic responses of retinal vessel diameter (D), oxygen saturation (SO2), and inner retinal oxygen extraction fraction (OEF) to light flicker and to describe their responses to its cessation in humans. In 16 healthy subjects (age: 60 ± 12 years), retinal oximetry was performed before, during, and after light flicker stimulation. At each time point, five metrics were measured: retinal arterial and venous D (DA, DV) and SO2 (SO2A, SO2V), and OEF. Intra- and intersubject variability of metrics was assessed by coefficient of variation of measurements before flicker within and among subjects, respectively. Metrics during flicker were modeled by exponential functions to determine the flicker-induced steady state metric values and the time constants of changes. Metrics after the cessation of flicker were compared to those before flicker. Intra- and intersubject variability for all metrics were less than 6% and 16%, respectively. At the flicker-induced steady state, DA and DV increased by 5%, SO2V increased by 7%, and OEF decreased by 13%. The time constants of DA and DV (14, 15 seconds) were twofold smaller than those of SO2V and OEF (39, 34 seconds). Within 26 seconds after the cessation of flicker, all metrics were not significantly different from before flicker values (P ≥ 0.07). Mathematical modeling revealed considerable differences in the time courses of changes among metrics during flicker, indicating flicker duration should be considered separately for each metric. Future application of this method may be useful to elucidate alterations in temporal dynamic responses to light flicker due to retinal diseases.

  2. Research on hyperspectral dynamic scene and image sequence simulation

    Science.gov (United States)

    Sun, Dandan; Liu, Fang; Gao, Jiaobo; Sun, Kefeng; Hu, Yu; Li, Yu; Xie, Junhu; Zhang, Lei

    2016-10-01

    This paper presents a simulation method of hyperspectral dynamic scene and image sequence for hyperspectral equipment evaluation and target detection algorithm. Because of high spectral resolution, strong band continuity, anti-interference and other advantages, in recent years, hyperspectral imaging technology has been rapidly developed and is widely used in many areas such as optoelectronic target detection, military defense and remote sensing systems. Digital imaging simulation, as a crucial part of hardware in loop simulation, can be applied to testing and evaluation hyperspectral imaging equipment with lower development cost and shorter development period. Meanwhile, visual simulation can produce a lot of original image data under various conditions for hyperspectral image feature extraction and classification algorithm. Based on radiation physic model and material characteristic parameters this paper proposes a generation method of digital scene. By building multiple sensor models under different bands and different bandwidths, hyperspectral scenes in visible, MWIR, LWIR band, with spectral resolution 0.01μm, 0.05μm and 0.1μm have been simulated in this paper. The final dynamic scenes have high real-time and realistic, with frequency up to 100 HZ. By means of saving all the scene gray data in the same viewpoint image sequence is obtained. The analysis results show whether in the infrared band or the visible band, the grayscale variations of simulated hyperspectral images are consistent with the theoretical analysis results.

  3. The Fermi-Pasta-Ulam problem: Simulation and modern dynamics

    International Nuclear Information System (INIS)

    Weissert, T.P.

    1992-01-01

    In 1952, Enrico Fermi, John Pasta and Stanislaw Ulam (FPU) simulated the loaded string model, perturbed with small, nonlinear interaction terms. Because Poincare's theorem guarantees the non-existence of a complete set of integrals for three-body problem, they expected to see the diffusion of energy from its single-mode initial condition to all other modes of the string. But for every combination of initial conditions, the energy remained bounded within the lowest few modes. No theoretical explanation existed for this failure of the underlying hypothesis that erogidicity follows from the lack of a complete set of integrals of the motion in a Hamiltonian model. The author traces the history of this problem from the FPU simulation to the point that a consensus was reached concerning its solution twenty years later. During this period, the simulation of nonlinearly-perturbed integral models became the methodology for a new era in dynamics. Through the use of simulation, dynamicists discovered deterministic chaos, in which the exponential separation of pair orbits generate randomness in deterministic macroscopic systems, and a new kind of structure-related to the KAM theorem-that provides limited order in the absence of analytic integrals of the motions. The author maps the set of conceptually-related journal articles into a chronological inference topology that tracks the understanding of this problem of dynamics. Simulating non-integrable models on a digital computer requires the discretization of time and space. These approximations affect what the simulation can reveal about the model, and the model about reality. Simulations play the role of experiments on mathematical models. A discussion is presented of the issues that emerge with the use of simulation as a heuristic device and the groundwork is laid for an epistemology of simulation

  4. The future of the London Buy-To-Let property market: Simulation with temporal Bayesian Networks.

    Science.gov (United States)

    Constantinou, Anthony C; Fenton, Norman

    2017-01-01

    In 2015 the British government announced a number of major tax reforms for individual landlords. To give landlords time to adjust, some of these tax measures are being introduced gradually from April 2017, with full effect in tax year 2020/21. The changes in taxation have received much media attention since there has been widespread belief that the new measures were sufficiently skewed against landlords that they could signal the end of the Buy-To-Let (BTL) investment era in the UK. This paper assesses the prospective performance of BTL investments in London from the investor's perspective, and examines the impact of incoming tax reforms using a novel Temporal Bayesian Network model. The model captures uncertainties of interest by simulating the impact of changing circumstances and the interventions available to an investor at various time-steps of a BTL investment portfolio. The simulation results suggest that the new tax reforms are likely to have a detrimental effect on net profits from rental income, and this hits risk-seeking investors who favour leverage much harder than risk-averse investors who do not seek to expand their property portfolio. The impact on net profits also poses substantial risks for lossmaking returns excluding capital gains, especially in the case of rising interest rates. While this makes it less desirable or even non-viable for some to continue being a landlord, based on the current status of all factors taken into consideration for simulation, investment prospects are still likely to remain good within a reasonable range of interest rate and capital growth rate variations. The results also suggest that the recent trend of property prices in London increasing faster than rents will not continue for much longer; either capital growth rates will have to decrease, rental growth rates will have to increase, or we shall observe a combination of the two events.

  5. The future of the London Buy-To-Let property market: Simulation with temporal Bayesian Networks.

    Directory of Open Access Journals (Sweden)

    Anthony C Constantinou

    Full Text Available In 2015 the British government announced a number of major tax reforms for individual landlords. To give landlords time to adjust, some of these tax measures are being introduced gradually from April 2017, with full effect in tax year 2020/21. The changes in taxation have received much media attention since there has been widespread belief that the new measures were sufficiently skewed against landlords that they could signal the end of the Buy-To-Let (BTL investment era in the UK. This paper assesses the prospective performance of BTL investments in London from the investor's perspective, and examines the impact of incoming tax reforms using a novel Temporal Bayesian Network model. The model captures uncertainties of interest by simulating the impact of changing circumstances and the interventions available to an investor at various time-steps of a BTL investment portfolio. The simulation results suggest that the new tax reforms are likely to have a detrimental effect on net profits from rental income, and this hits risk-seeking investors who favour leverage much harder than risk-averse investors who do not seek to expand their property portfolio. The impact on net profits also poses substantial risks for lossmaking returns excluding capital gains, especially in the case of rising interest rates. While this makes it less desirable or even non-viable for some to continue being a landlord, based on the current status of all factors taken into consideration for simulation, investment prospects are still likely to remain good within a reasonable range of interest rate and capital growth rate variations. The results also suggest that the recent trend of property prices in London increasing faster than rents will not continue for much longer; either capital growth rates will have to decrease, rental growth rates will have to increase, or we shall observe a combination of the two events.

  6. The future of the London Buy-To-Let property market: Simulation with temporal Bayesian Networks

    Science.gov (United States)

    Fenton, Norman

    2017-01-01

    In 2015 the British government announced a number of major tax reforms for individual landlords. To give landlords time to adjust, some of these tax measures are being introduced gradually from April 2017, with full effect in tax year 2020/21. The changes in taxation have received much media attention since there has been widespread belief that the new measures were sufficiently skewed against landlords that they could signal the end of the Buy-To-Let (BTL) investment era in the UK. This paper assesses the prospective performance of BTL investments in London from the investor’s perspective, and examines the impact of incoming tax reforms using a novel Temporal Bayesian Network model. The model captures uncertainties of interest by simulating the impact of changing circumstances and the interventions available to an investor at various time-steps of a BTL investment portfolio. The simulation results suggest that the new tax reforms are likely to have a detrimental effect on net profits from rental income, and this hits risk-seeking investors who favour leverage much harder than risk-averse investors who do not seek to expand their property portfolio. The impact on net profits also poses substantial risks for lossmaking returns excluding capital gains, especially in the case of rising interest rates. While this makes it less desirable or even non-viable for some to continue being a landlord, based on the current status of all factors taken into consideration for simulation, investment prospects are still likely to remain good within a reasonable range of interest rate and capital growth rate variations. The results also suggest that the recent trend of property prices in London increasing faster than rents will not continue for much longer; either capital growth rates will have to decrease, rental growth rates will have to increase, or we shall observe a combination of the two events. PMID:28654698

  7. Nonlinear spatio-temporal filtering of dynamic PET data using a four-dimensional Gaussian filter and expectation-maximization deconvolution

    International Nuclear Information System (INIS)

    Floberg, J M; Holden, J E

    2013-01-01

    We introduce a method for denoising dynamic PET data, spatio-temporal expectation-maximization (STEM) filtering, that combines four-dimensional Gaussian filtering with EM deconvolution. The initial Gaussian filter suppresses noise at a broad range of spatial and temporal frequencies and EM deconvolution quickly restores the frequencies most important to the signal. We aim to demonstrate that STEM filtering can improve variance in both individual time frames and in parametric images without introducing significant bias. We evaluate STEM filtering with a dynamic phantom study, and with simulated and human dynamic PET studies of a tracer with reversible binding behaviour, [C-11]raclopride, and a tracer with irreversible binding behaviour, [F-18]FDOPA. STEM filtering is compared to a number of established three and four-dimensional denoising methods. STEM filtering provides substantial improvements in variance in both individual time frames and in parametric images generated with a number of kinetic analysis techniques while introducing little bias. STEM filtering does bias early frames, but this does not affect quantitative parameter estimates. STEM filtering is shown to be superior to the other simple denoising methods studied. STEM filtering is a simple and effective denoising method that could be valuable for a wide range of dynamic PET applications. (paper)

  8. Synthesis of recurrent neural networks for dynamical system simulation.

    Science.gov (United States)

    Trischler, Adam P; D'Eleuterio, Gabriele M T

    2016-08-01

    We review several of the most widely used techniques for training recurrent neural networks to approximate dynamical systems, then describe a novel algorithm for this task. The algorithm is based on an earlier theoretical result that guarantees the quality of the network approximation. We show that a feedforward neural network can be trained on the vector-field representation of a given dynamical system using backpropagation, then recast it as a recurrent network that replicates the original system's dynamics. After detailing this algorithm and its relation to earlier approaches, we present numerical examples that demonstrate its capabilities. One of the distinguishing features of our approach is that both the original dynamical systems and the recurrent networks that simulate them operate in continuous time. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Simulation of noisy dynamical system by Deep Learning

    Science.gov (United States)

    Yeo, Kyongmin

    2017-11-01

    Deep learning has attracted huge attention due to its powerful representation capability. However, most of the studies on deep learning have been focused on visual analytics or language modeling and the capability of the deep learning in modeling dynamical systems is not well understood. In this study, we use a recurrent neural network to model noisy nonlinear dynamical systems. In particular, we use a long short-term memory (LSTM) network, which constructs internal nonlinear dynamics systems. We propose a cross-entropy loss with spatial ridge regularization to learn a non-stationary conditional probability distribution from a noisy nonlinear dynamical system. A Monte Carlo procedure to perform time-marching simulations by using the LSTM is presented. The behavior of the LSTM is studied by using noisy, forced Van der Pol oscillator and Ikeda equation.

  10. Simulation and Experimental Investigation of Structural Dynamic Frequency Characteristics Control

    Directory of Open Access Journals (Sweden)

    Bing Li

    2012-04-01

    Full Text Available In general, mechanical equipment such as cars, airplanes, and machine tools all operate with constant frequency characteristics. These constant working characteristics should be controlled if the dynamic performance of the equipment demands improvement or the dynamic characteristics is intended to change with different working conditions. Active control is a stable and beneficial method for this, but current active control methods mainly focus on vibration control for reducing the vibration amplitudes in the time domain or frequency domain. In this paper, a new method of dynamic frequency characteristics active control (DFCAC is presented for a flat plate, which can not only accomplish vibration control but also arbitrarily change the dynamic characteristics of the equipment. The proposed DFCAC algorithm is based on a neural network including two parts of the identification implement and the controller. The effectiveness of the DFCAC method is verified by several simulation and experiments, which provide desirable results.

  11. Efficient Neural Network Modeling for Flight and Space Dynamics Simulation

    Directory of Open Access Journals (Sweden)

    Ayman Hamdy Kassem

    2011-01-01

    Full Text Available This paper represents an efficient technique for neural network modeling of flight and space dynamics simulation. The technique will free the neural network designer from guessing the size and structure for the required neural network model and will help to minimize the number of neurons. For linear flight/space dynamics systems, the technique can find the network weights and biases directly by solving a system of linear equations without the need for training. Nonlinear flight dynamic systems can be easily modeled by training its linearized models keeping the same network structure. The training is fast, as it uses the linear system knowledge to speed up the training process. The technique is tested on different flight/space dynamic models and showed promising results.

  12. Spatial and temporal consumption dynamics of trout in catch-and-release areas in Arkansas tailwaters

    Science.gov (United States)

    Flinders, John M.; Magoulick, Daniel D.

    2017-01-01

    Restrictive angling regulations in tailwater trout fisheries may be unsuccessful if food availability limits energy for fish to grow. We examined spatial and temporal variation in energy intake and growth in populations of Brown Trout Salmo trutta and Rainbow Trout Oncorhynchus mykiss within three catch-and-release (C-R) areas in Arkansas tailwaters to evaluate food availability compared with consumption. Based on bioenergetic simulations, Rainbow Trout fed at submaintenance levels in both size-classes (≤400 mm TL, >400 mm TL) throughout most seasons. A particular bottleneck in food availability occurred in the winter for Rainbow Trout when the daily ration was substantially below the minimum required for maintenance, despite reduced metabolic costs associated with lower water temperatures. Rainbow Trout growth rates followed a similar pattern to consumption with negative growth rates during the winter periods. All three size-classes (400 mm TL) of Brown Trout experienced high growth rates and limited temporal bottlenecks in food availability. We observed higher mean densities for Rainbow Trout (47–342 fish/ha) than for Brown Trout (3–84 fish/ha) in all C-R areas. Lower densities of Brown Trout coupled with an ontogenetic shift towards piscivory may have allowed for higher growth rates and sufficient consumption rates to meet energetic demands. Brown Trout at current densities were more effective in maintaining adequate growth rates and larger sizes in C-R areas than were Rainbow Trout. Bioenergetic simulations suggest that reducing stocking levels of Rainbow Trout in the tailwaters may be necessary in order to achieve increased catch rates of larger trout in the C-R areas.

  13. Multiagent-Based Simulation of Temporal-Spatial Characteristics of Activity-Travel Patterns Using Interactive Reinforcement Learning

    Directory of Open Access Journals (Sweden)

    Min Yang

    2014-01-01

    Full Text Available We propose a multiagent-based reinforcement learning algorithm, in which the interactions between travelers and the environment are considered to simulate temporal-spatial characteristics of activity-travel patterns in a city. Road congestion degree is added to the reinforcement learning algorithm as a medium that passes the influence of one traveler’s decision to others. Meanwhile, the agents used in the algorithm are initialized from typical activity patterns extracted from the travel survey diary data of Shangyu city in China. In the simulation, both macroscopic activity-travel characteristics such as traffic flow spatial-temporal distribution and microscopic characteristics such as activity-travel schedules of each agent are obtained. Comparing the simulation results with the survey data, we find that deviation of the peak-hour traffic flow is less than 5%, while the correlation of the simulated versus survey location choice distribution is over 0.9.

  14. Extracting Markov Models of Peptide Conformational Dynamics from Simulation Data.

    Science.gov (United States)

    Schultheis, Verena; Hirschberger, Thomas; Carstens, Heiko; Tavan, Paul

    2005-07-01

    A high-dimensional time series obtained by simulating a complex and stochastic dynamical system (like a peptide in solution) may code an underlying multiple-state Markov process. We present a computational approach to most plausibly identify and reconstruct this process from the simulated trajectory. Using a mixture of normal distributions we first construct a maximum likelihood estimate of the point density associated with this time series and thus obtain a density-oriented partition of the data space. This discretization allows us to estimate the transfer operator as a matrix of moderate dimension at sufficient statistics. A nonlinear dynamics involving that matrix and, alternatively, a deterministic coarse-graining procedure are employed to construct respective hierarchies of Markov models, from which the model most plausibly mapping the generating stochastic process is selected by consideration of certain observables. Within both procedures the data are classified in terms of prototypical points, the conformations, marking the various Markov states. As a typical example, the approach is applied to analyze the conformational dynamics of a tripeptide in solution. The corresponding high-dimensional time series has been obtained from an extended molecular dynamics simulation.

  15. Temporal contrast enhancement and parametric imaging for the visualisation of time patterns in dynamic scintigraphic imaging

    International Nuclear Information System (INIS)

    Deconinck, F.; Bossuyt, A.; Lepoudre, R.

    1982-01-01

    Image contrast, photon noise and sampling frequency limit the visual extraction of relevant temporal information in scintigraphic image series. When the Unitation is mainly due to low temporal contrast, temporal contrast enhancement will strongly improve the perceptibility of time patterns in the series. When the limitation is due to photon noise and limited temporal sampling, parametric imaging by means of the Hadamard transform can visualise temporal patterns. (WU)

  16. Dynamics and Chemistry in Jovian Atmospheres: 2D Hydrodynamical Simulations

    Science.gov (United States)

    Bordwell, B. R.; Brown, B. P.; Oishi, J.

    2016-12-01

    A key component of our understanding of the formation and evolution of planetary systems is chemical composition. Problematically, however, in the atmospheres of cooler gas giants, dynamics on the same timescale as chemical reactions pull molecular abundances out of thermochemical equilibrium. These disequilibrium abundances are treated using what is known as the "quench" approximation, based upon the mixing length theory of convection. The validity of this approximation is questionable, though, as the atmospheres of gas giants encompass two distinct dynamic regimes: convective and radiative. To resolve this issue, we conduct 2D hydrodynamical simulations using the state-of-the-art pseudospectral simulation framework Dedalus. In these simulations, we solve the fully compressible equations of fluid motion in a local slab geometry that mimics the structure of a planetary atmosphere (convective zone underlying a radiative zone). Through the inclusion of passive tracers, we explore the transport properties of both regimes, and assess the validity of the classical eddy diffusion parameterization. With the addition of active tracers, we examine the interactions between dynamical and chemical processes, and generate prescriptions for the observational community. By providing insight into mixing and feedback mechanisms in Jovian atmospheres, this research lays a solid foundation for future global simulations and the construction of physically-sound models for current and future observations.

  17. Simulation of plume dynamics by the Lattice Boltzmann Method

    Science.gov (United States)

    Mora, Peter; Yuen, David A.

    2017-09-01

    The Lattice Boltzmann Method (LBM) is a semi-microscopic method to simulate fluid mechanics by modelling distributions of particles moving and colliding on a lattice. We present 2-D simulations using the LBM of a fluid in a rectangular box being heated from below, and cooled from above, with a Rayleigh of Ra = 108, similar to current estimates of the Earth's mantle, and a Prandtl number of 5000. At this Prandtl number, the flow is found to be in the non-inertial regime where the inertial terms denoted I ≪ 1. Hence, the simulations presented lie within the regime of relevance for geodynamical problems. We obtain narrow upwelling plumes with mushroom heads and chutes of downwelling fluid as expected of a flow in the non-inertial regime. The method developed demonstrates that the LBM has great potential for simulating thermal convection and plume dynamics relevant to geodynamics, albeit with some limitations.

  18. Molecular dynamics simulations and applications in computational toxicology and nanotoxicology.

    Science.gov (United States)

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

    2018-02-01

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

  19. Molecular dynamics simulation of amplitude modulation atomic force microscopy

    International Nuclear Information System (INIS)

    Hu, Xiaoli; Martini, Ashlie; Egberts, Philip; Dong, Yalin

    2015-01-01

    Molecular dynamics (MD) simulations were used to model amplitude modulation atomic force microscopy (AM-AFM). In this novel simulation, the model AFM tip responds to both tip–substrate interactions and to a sinusoidal excitation signal. The amplitude and phase shift of the tip oscillation observed in the simulation and their variation with tip–sample distance were found to be consistent with previously reported trends from experiments and theory. These simulation results were also fit to an expression enabling estimation of the energy dissipation, which was found to be smaller than that in a corresponding experiment. The difference was analyzed in terms of the effects of tip size and substrate thickness. Development of this model is the first step toward using MD to gain insight into the atomic-scale phenomena that occur during an AM-AFM measurement. (paper)

  20. Simulation of Forest Cover Dynamics for Eastern Eurasian Boreal Forests

    Science.gov (United States)

    Shugart, H. H.; Yan, X.; Zhang, N.; Isaev, A. S.; Shuman, J. K.

    2006-12-01

    We are developing and testing a boreal zone forest dynamics model capable of simulating the forest cover dynamics of the Eurasian boreal forest, a major biospheric ecosystem with potentially large roles in the planetary carbon cycle and in the feedback between terrestrial surface and the atmosphere. In appreciating the role of this region in the coupling between atmosphere and terrestrial surface, on must understand the interactions between CO2 source/sink relationships (associated with growing or clearing forests) and the albedo effects (from changes in terrestrial surface cover). There is some evidence that in the Eurasian Boreal zone, the Carbon budget effects from forest change may oppose the albedo changes. This creates complex feedbacks between surface and atmosphere and motivates the need for a forest dynamics model that simultaneous represents forest vegetation and carbon storage and release. A forest dynamics model applied to Eastern Eurasia, FAREAST, has been tested using three types of information: 1. Direct species composition comparisons between simulated and observed mature forests at the same locations; 2. Forest type comparisons between simulated and observed forests along altitudinal gradients of several different mountains; 3. Comparison with forest stands in different succession stages of simulated forests. Model comparisons with independent data indicate the FAREAST model is capable of representing many of the broad features of the forests of Northeastern China. After model validation in the Northeast China region, model applications were developed for the forests of the Russian Far East. Continental-scale forest cover can be simulated to a relatively realistic degree using a forest gap model with standard representations of individual-plant processes. It appears that such a model, validated relatively locally in this case, in Northeastern China, can then be applied over a much larger region and under conditions of climatic change.