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.

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.

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.

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.

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.

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

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

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.

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.

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

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.

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

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

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.

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

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

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.

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.

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

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

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.

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

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.

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.

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...

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.

Diagnosing the Dynamics of Observed and Simulated Ecosystem Gross Primary Productivity with Time Causal Information Theory Quantifiers.

Directory of Open Access Journals (Sweden)

Sebastian Sippel

Full Text Available Data analysis and model-data comparisons in the environmental sciences require diagnostic measures that quantify time series dynamics and structure, and are robust to noise in observational data. This paper investigates the temporal dynamics of environmental time series using measures quantifying their information content and complexity. The measures are used to classify natural processes on one hand, and to compare models with observations on the other. The present analysis focuses on the global carbon cycle as an area of research in which model-data integration and comparisons are key to improving our understanding of natural phenomena. We investigate the dynamics of observed and simulated time series of Gross Primary Productivity (GPP, a key variable in terrestrial ecosystems that quantifies ecosystem carbon uptake. However, the dynamics, patterns and magnitudes of GPP time series, both observed and simulated, vary substantially on different temporal and spatial scales. We demonstrate here that information content and complexity, or Information Theory Quantifiers (ITQ for short, serve as robust and efficient data-analytical and model benchmarking tools for evaluating the temporal structure and dynamical properties of simulated or observed time series at various spatial scales. At continental scale, we compare GPP time series simulated with two models and an observations-based product. This analysis reveals qualitative differences between model evaluation based on ITQ compared to traditional model performance metrics, indicating that good model performance in terms of absolute or relative error does not imply that the dynamics of the observations is captured well. Furthermore, we show, using an ensemble of site-scale measurements obtained from the FLUXNET archive in the Mediterranean, that model-data or model-model mismatches as indicated by ITQ can be attributed to and interpreted as differences in the temporal structure of the respective

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...

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....

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.

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...

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.

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)

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

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.

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.

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

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.

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

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

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.

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.

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.

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

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)

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.

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.

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

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...

A Nonlinear Dynamic Subscale Model for Partially Resolved Numerical Simulation (PRNS)/Very Large Eddy Simulation (VLES) of Internal Non-Reacting Flows

Science.gov (United States)

Shih, Tsan-Hsing; Liu, nan-Suey

2010-01-01

A brief introduction of the temporal filter based partially resolved numerical simulation/very large eddy simulation approach (PRNS/VLES) and its distinct features are presented. A nonlinear dynamic subscale model and its advantages over the linear subscale eddy viscosity model are described. In addition, a guideline for conducting a PRNS/VLES simulation is provided. Results are presented for three turbulent internal flows. The first one is the turbulent pipe flow at low and high Reynolds numbers to illustrate the basic features of PRNS/VLES; the second one is the swirling turbulent flow in a LM6000 single injector to further demonstrate the differences in the calculated flow fields resulting from the nonlinear model versus the pure eddy viscosity model; the third one is a more complex turbulent flow generated in a single-element lean direct injection (LDI) combustor, the calculated result has demonstrated that the current PRNS/VLES approach is capable of capturing the dynamically important, unsteady turbulent structures while using a relatively coarse grid.

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

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)

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

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...

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

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.

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

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.

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

A temporal modelling environment for internally grounded beliefs, desires and intentions

NARCIS (Netherlands)

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

In this paper the internal dynamics of mental states, in particular states based on beliefs, desires and intentions, is formalised using a temporal language. A software environment is presented that can be used to specify, simulate and analyse temporal dependencies between mental states in

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.

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.

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.

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

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.

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

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.…

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.

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.

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

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.

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...

Long-time atomistic simulations with the Parallel Replica Dynamics method

Science.gov (United States)

Perez, Danny

Molecular Dynamics (MD) -- the numerical integration of atomistic equations of motion -- is a workhorse of computational materials science. Indeed, MD can in principle be used to obtain any thermodynamic or kinetic quantity, without introducing any approximation or assumptions beyond the adequacy of the interaction potential. It is therefore an extremely powerful and flexible tool to study materials with atomistic spatio-temporal resolution. These enviable qualities however come at a steep computational price, hence limiting the system sizes and simulation times that can be achieved in practice. While the size limitation can be efficiently addressed with massively parallel implementations of MD based on spatial decomposition strategies, allowing for the simulation of trillions of atoms, the same approach usually cannot extend the timescales much beyond microseconds. In this article, we discuss an alternative parallel-in-time approach, the Parallel Replica Dynamics (ParRep) method, that aims at addressing the timescale limitation of MD for systems that evolve through rare state-to-state transitions. We review the formal underpinnings of the method and demonstrate that it can provide arbitrarily accurate results for any definition of the states. When an adequate definition of the states is available, ParRep can simulate trajectories with a parallel speedup approaching the number of replicas used. We demonstrate the usefulness of ParRep by presenting different examples of materials simulations where access to long timescales was essential to access the physical regime of interest and discuss practical considerations that must be addressed to carry out these simulations. Work supported by the United States Department of Energy (U.S. DOE), Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division.

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.

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)

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.

Simulation-based decision support framework for dynamic ambulance redeployment in Singapore.

Science.gov (United States)

Lam, Sean Shao Wei; Ng, Clarence Boon Liang; Nguyen, Francis Ngoc Hoang Long; Ng, Yih Yng; Ong, Marcus Eng Hock

2017-10-01

Dynamic ambulance redeployment policies tend to introduce much more flexibilities in improving ambulance resource allocation by capitalizing on the definite geospatial-temporal variations in ambulance demand patterns over the time-of-the-day and day-of-the-week effects. A novel modelling framework based on the Approximate Dynamic Programming (ADP) approach leveraging on a Discrete Events Simulation (DES) model for dynamic ambulance redeployment in Singapore is proposed in this paper. The study was based on the Singapore's national Emergency Medical Services (EMS) system. Based on a dataset comprising 216,973 valid incidents over a continuous two-years study period from 1 January 2011-31 December 2012, a DES model for the EMS system was developed. An ADP model based on linear value function approximations was then evaluated using the DES model via the temporal difference (TD) learning family of algorithms. The objective of the ADP model is to derive approximate optimal dynamic redeployment policies based on the primary outcome of ambulance coverage. Considering an 8min response time threshold, an estimated 5% reduction in the proportion of calls that cannot be reached within the threshold (equivalent to approximately 8000 dispatches) was observed from the computational experiments. The study also revealed that the redeployment policies which are restricted within the same operational division could potentially result in a more promising response time performance. Furthermore, the best policy involved the combination of redeploying ambulances whenever they are released from service and that of relocating ambulances that are idle in bases. This study demonstrated the successful application of an approximate modelling framework based on ADP that leverages upon a detailed DES model of the Singapore's EMS system to generate approximate optimal dynamic redeployment plans. Various policies and scenarios relevant to the Singapore EMS system were evaluated. Copyright © 2017

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

Science.gov (United States)

2018-01-01

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA–ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field. PMID:29297679

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.

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.

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.

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 ...

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.

Visualization of spatial-temporal data based on 3D virtual scene

Science.gov (United States)

Wang, Xianghong; Liu, Jiping; Wang, Yong; Bi, Junfang

2009-10-01

The main purpose of this paper is to realize the expression of the three-dimensional dynamic visualization of spatialtemporal data based on three-dimensional virtual scene, using three-dimensional visualization technology, and combining with GIS so that the people's abilities of cognizing time and space are enhanced and improved by designing dynamic symbol and interactive expression. Using particle systems, three-dimensional simulation, virtual reality and other visual means, we can simulate the situations produced by changing the spatial location and property information of geographical entities over time, then explore and analyze its movement and transformation rules by changing the interactive manner, and also replay history and forecast of future. In this paper, the main research object is the vehicle track and the typhoon path and spatial-temporal data, through three-dimensional dynamic simulation of its track, and realize its timely monitoring its trends and historical track replaying; according to visualization techniques of spatialtemporal data in Three-dimensional virtual scene, providing us with excellent spatial-temporal information cognitive instrument not only can add clarity to show spatial-temporal information of the changes and developments in the situation, but also be used for future development and changes in the prediction and deduction.

[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.

A Multi-Stage Method for Connecting Participatory Sensing and Noise Simulations

Directory of Open Access Journals (Sweden)

Mingyuan Hu

2015-01-01

Full Text Available Most simulation-based noise maps are important for official noise assessment but lack local noise characteristics. The main reasons for this lack of information are that official noise simulations only provide information about expected noise levels, which is limited by the use of large-scale monitoring of noise sources, and are updated infrequently. With the emergence of smart cities and ubiquitous sensing, the possible improvements enabled by sensing technologies provide the possibility to resolve this problem. This study proposed an integrated methodology to propel participatory sensing from its current random and distributed sampling origins to professional noise simulation. The aims of this study were to effectively organize the participatory noise data, to dynamically refine the granularity of the noise features on road segments (e.g., different portions of a road segment, and then to provide a reasonable spatio-temporal data foundation to support noise simulations, which can be of help to researchers in understanding how participatory sensing can play a role in smart cities. This study first discusses the potential limitations of the current participatory sensing and simulation-based official noise maps. Next, we explain how participatory noise data can contribute to a simulation-based noise map by providing (1 spatial matching of the participatory noise data to the virtual partitions at a more microscopic level of road networks; (2 multi-temporal scale noise estimations at the spatial level of virtual partitions; and (3 dynamic aggregation of virtual partitions by comparing the noise values at the relevant temporal scale to form a dynamic segmentation of each road segment to support multiple spatio-temporal noise simulations. In this case study, we demonstrate how this method could play a significant role in a simulation-based noise map. Together, these results demonstrate the potential benefits of participatory noise data as dynamic

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

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 ...

Temporal networks

CERN Document Server

Saramäki, Jari

2013-01-01

The concept of temporal networks is an extension of complex networks as a modeling framework to include information on when interactions between nodes happen. Many studies of the last decade examine how the static network structure affect dynamic systems on the network. In this traditional approach  the temporal aspects are pre-encoded in the dynamic system model. Temporal-network methods, on the other hand, lift the temporal information from the level of system dynamics to the mathematical representation of the contact network itself. This framework becomes particularly useful for cases where there is a lot of structure and heterogeneity both in the timings of interaction events and the network topology. The advantage compared to common static network approaches is the ability to design more accurate models in order to explain and predict large-scale dynamic phenomena (such as, e.g., epidemic outbreaks and other spreading phenomena). On the other hand, temporal network methods are mathematically and concept...

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

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.

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.

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)

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)

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.

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)

Shocked materials at the intersection of experiment and simulation

Energy Technology Data Exchange (ETDEWEB)

Lorenzana, H. E.; Belak, J. F.; Bradley, K. S.; Bringa, E. M.; Budil, K. S.; Cazamias, J. U.; El-Dasher, B.; Hawreliak, J. A.; Hessler, J.; Kadau, K.; Kalantar, D. H.; McNaney, J. M.; Milathianaki, D.; Rosolankova, K.; Swift, D. C.; Taravillo, M.; Van Buuren, T. W.; Wark, J. S.; de la Rubia, T. Diaz

2008-04-01

Understanding the dynamic lattice response of solids under the extreme conditions of pressure, temperature and strain rate is a scientific quest that spans nearly a century. Critical to developing this understanding is the ability to probe and model the spatial and temporal evolution of the material microstructure and properties at the scale of the relevant physical phenomena-nanometers to micrometers and picoseconds to nanoseconds. While experimental investigations over this range of spatial and temporal scales were unimaginable just a decade ago, new technologies and facilities currently under development and on the horizon have brought these goals within reach for the first time. The equivalent advancements in simulation capabilities now mean that we can conduct simulations and experiments at overlapping temporal and spatial scales. In this article, we describe some of our studies which exploit existing and new generation ultrabright, ultrafast x-ray sources and large scale molecular dynamics simulations to investigate the real-time physical phenomena that control the dynamic response of shocked materials.

Shocked materials at the intersection of experiment and simulation

Energy Technology Data Exchange (ETDEWEB)

Kadau, Kai [Los Alamos National Laboratory

2008-01-01

Understanding the dynamic lattice response of solids under the extreme conditions of pressure, temperature and strain rate is a scientific quest that spans nearly a century. Critical to developing this understanding is the ability to probe and model the spatial and temporal evolution of the material microstructure and properties at the scale of the relevant physical phenomena -- nanometers to micrometers and picoseconds to nanoseconds. While experimental investigations over this range of spatial and temporal scales were unimaginable just a decade ago, new technologies and facilities currently under development and on the horizon have brought these goals within reach for the first time. The equivalent advancements in simulation capabilities now mean that we can conduct simulations and experiments at overlapping temporal and spatial scales. In this article, we describe some of our studies which exploit existing and new generation ultrabright, ultrafast x-ray sources and large scale molecular dynamics simulations to investigate the real-time physical phenomena that control the dynamic response of shocked materials.

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)

Neuromorphic Implementation of Attractor Dynamics in a Two-Variable Winner-Take-All Circuit with NMDARs: A Simulation Study.

Science.gov (United States)

You, Hongzhi; Wang, Da-Hui

2017-01-01

Neural networks configured with winner-take-all (WTA) competition and N-methyl-D-aspartate receptor (NMDAR)-mediated synaptic dynamics are endowed with various dynamic characteristics of attractors underlying many cognitive functions. This paper presents a novel method for neuromorphic implementation of a two-variable WTA circuit with NMDARs aimed at implementing decision-making, working memory and hysteresis in visual perceptions. The method proposed is a dynamical system approach of circuit synthesis based on a biophysically plausible WTA model. Notably, slow and non-linear temporal dynamics of NMDAR-mediated synapses was generated. Circuit simulations in Cadence reproduced ramping neural activities observed in electrophysiological recordings in experiments of decision-making, the sustained activities observed in the prefrontal cortex during working memory, and classical hysteresis behavior during visual discrimination tasks. Furthermore, theoretical analysis of the dynamical system approach illuminated the underlying mechanisms of decision-making, memory capacity and hysteresis loops. The consistence between the circuit simulations and theoretical analysis demonstrated that the WTA circuit with NMDARs was able to capture the attractor dynamics underlying these cognitive functions. Their physical implementations as elementary modules are promising for assembly into integrated neuromorphic cognitive systems.

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.

Algorithm for simulation of quantum many-body dynamics using dynamical coarse-graining

International Nuclear Information System (INIS)

Khasin, M.; Kosloff, R.

2010-01-01

An algorithm for simulation of quantum many-body dynamics having su(2) spectrum-generating algebra is developed. The algorithm is based on the idea of dynamical coarse-graining. The original unitary dynamics of the target observables--the elements of the spectrum-generating algebra--is simulated by a surrogate open-system dynamics, which can be interpreted as weak measurement of the target observables, performed on the evolving system. The open-system state can be represented by a mixture of pure states, localized in the phase space. The localization reduces the scaling of the computational resources with the Hilbert-space dimension n by factor n 3/2 (ln n) -1 compared to conventional sparse-matrix methods. The guidelines for the choice of parameters for the simulation are presented and the scaling of the computational resources with the Hilbert-space dimension of the system is estimated. The algorithm is applied to the simulation of the dynamics of systems of 2x10 4 and 2x10 6 cold atoms in a double-well trap, described by the two-site Bose-Hubbard model.

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.

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.

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.

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.

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

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)

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.

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

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.

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...

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.

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.

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.)

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

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.

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

Temporal networks

Science.gov (United States)

Holme, Petter; Saramäki, Jari

2012-10-01

A great variety of systems in nature, society and technology-from the web of sexual contacts to the Internet, from the nervous system to power grids-can be modeled as graphs of vertices coupled by edges. The network structure, describing how the graph is wired, helps us understand, predict and optimize the behavior of dynamical systems. In many cases, however, the edges are not continuously active. As an example, in networks of communication via e-mail, text messages, or phone calls, edges represent sequences of instantaneous or practically instantaneous contacts. In some cases, edges are active for non-negligible periods of time: e.g., the proximity patterns of inpatients at hospitals can be represented by a graph where an edge between two individuals is on throughout the time they are at the same ward. Like network topology, the temporal structure of edge activations can affect dynamics of systems interacting through the network, from disease contagion on the network of patients to information diffusion over an e-mail network. In this review, we present the emergent field of temporal networks, and discuss methods for analyzing topological and temporal structure and models for elucidating their relation to the behavior of dynamical systems. In the light of traditional network theory, one can see this framework as moving the information of when things happen from the dynamical system on the network, to the network itself. Since fundamental properties, such as the transitivity of edges, do not necessarily hold in temporal networks, many of these methods need to be quite different from those for static networks. The study of temporal networks is very interdisciplinary in nature. Reflecting this, even the object of study has many names-temporal graphs, evolving graphs, time-varying graphs, time-aggregated graphs, time-stamped graphs, dynamic networks, dynamic graphs, dynamical graphs, and so on. This review covers different fields where temporal graphs are considered

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.

Dynamic skin deformation simulation using musculoskeletal model and soft tissue dynamics

Institute of Scientific and Technical Information of China (English)

Akihiko Murai; Q. Youn Hong; Katsu Yamane; Jessica K. Hodgins

2017-01-01

Deformation of skin and muscle is essential for bringing an animated character to life. This deformation is difficult to animate in a realistic fashion using traditional techniques because of the subtlety of the skin deformations that must move appropriately for the character design. In this paper, we present an algorithm that generates natural, dynamic, and detailed skin deformation (movement and jiggle) from joint angle data sequences. The algorithm has two steps: identification of parameters for a quasi-static muscle deformation model, and simulation of skin deformation. In the identification step, we identify the model parameters using a musculoskeletal model and a short sequence of skin deformation data captured via a dense marker set. The simulation step first uses the quasi-static muscle deformation model to obtain the quasi-static muscle shape at each frame of the given motion sequence (slow jump). Dynamic skin deformation is then computed by simulating the passive muscle and soft tissue dynamics modeled as a mass–spring–damper system. Having obtained the model parameters, we can simulate dynamic skin deformations for subjects with similar body types from new motion data. We demonstrate our method by creating skin deformations for muscle co-contraction and external impacts from four different behaviors captured as skeletal motion capture data. Experimental results show that the simulated skin deformations are quantitatively and qualitatively similar to measured actual skin deformations.

Dynamic skin deformation simulation using musculoskeletal model and soft tissue dynamics

Institute of Scientific and Technical Information of China (English)

Akihiko Murai; Q.Youn Hong; Katsu Yamane; Jessica K.Hodgins

2017-01-01

Deformation of skin and muscle is essential for bringing an animated character to life. This deformation is difficult to animate in a realistic fashion using traditional techniques because of the subtlety of the skin deformations that must move appropriately for the character design. In this paper, we present an algorithm that generates natural, dynamic, and detailed skin deformation(movement and jiggle) from joint angle data sequences. The algorithm has two steps: identification of parameters for a quasi-static muscle deformation model, and simulation of skin deformation. In the identification step, we identify the model parameters using a musculoskeletal model and a short sequence of skin deformation data captured via a dense marker set. The simulation step first uses the quasi-static muscle deformation model to obtain the quasi-static muscle shape at each frame of the given motion sequence(slow jump). Dynamic skin deformation is then computed by simulating the passive muscle and soft tissue dynamics modeled as a mass–spring–damper system. Having obtained the model parameters, we can simulate dynamic skin deformations for subjects with similar body types from new motion data. We demonstrate our method by creating skin deformations for muscle co-contraction and external impacts from four different behaviors captured as skeletal motion capture data. Experimental results show that the simulated skin deformations are quantitatively and qualitatively similar to measured actual skin deformations.

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

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

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....

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.…

Modelling spatio-temporal variability of Mytilus edulis (L.) growth by forcing a dynamic energy budget model with satellite-derived environmental data

Science.gov (United States)

Thomas, Yoann; Mazurié, Joseph; Alunno-Bruscia, Marianne; Bacher, Cédric; Bouget, Jean-François; Gohin, Francis; Pouvreau, Stéphane; Struski, Caroline

2011-11-01

In order to assess the potential of various marine ecosystems for shellfish aquaculture and to evaluate their carrying capacities, there is a need to clarify the response of exploited species to environmental variations using robust ecophysiological models and available environmental data. For a large range of applications and comparison purposes, a non-specific approach based on 'generic' individual growth models offers many advantages. In this context, we simulated the response of blue mussel ( Mytilus edulis L.) to the spatio-temporal fluctuations of the environment in Mont Saint-Michel Bay (North Brittany) by forcing a generic growth model based on Dynamic Energy Budgets with satellite-derived environmental data (i.e. temperature and food). After a calibration step based on data from mussel growth surveys, the model was applied over nine years on a large area covering the entire bay. These simulations provide an evaluation of the spatio-temporal variability in mussel growth and also show the ability of the DEB model to integrate satellite-derived data and to predict spatial and temporal growth variability of mussels. Observed seasonal, inter-annual and spatial growth variations are well simulated. The large-scale application highlights the strong link between food and mussel growth. The methodology described in this study may be considered as a suitable approach to account for environmental effects (food and temperature variations) on physiological responses (growth and reproduction) of filter feeders in varying environments. Such physiological responses may then be useful for evaluating the suitability of coastal ecosystems for shellfish aquaculture.

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.

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.

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)

Exploring diversity of crop and soil management within smallholder African farms: A dynamic model for simulation of N balances and use efficiencies at field scale

NARCIS (Netherlands)

Tittonell, P.A.; Leffelaar, P.A.; Vanlauwe, B.; Wijk, van M.T.; Giller, K.E.

2006-01-01

Adding a dynamic, temporal dimension to the calculation of nitrogen balances is proposed as an alternative approach to assessing the impact of crop and soil management decisions on the establishment of farmer-induced soil fertility gradients within smallholder African farms. A simulation model that

The consequences of time averaging for measuring temporal species turnover in the fossil record

Science.gov (United States)

Tomašových, Adam; Kidwell, Susan

2010-05-01

Modeling time averaging effects with simple simulations allows us to evaluate the magnitude of change in temporal species turnover that is expected to occur in long (paleoecological) time series with fossil assemblages. Distinguishing different modes of metacommunity dynamics (such as neutral, density-dependent, or trade-off dynamics) with time-averaged fossil assemblages requires scaling-up time-averaging effects because the decrease in temporal resolution and the decrease in temporal inter-sample separation (i.e., the two main effects of time averaging) substantially increase community stability relative to assemblages without or with weak time averaging. Large changes in temporal scale that cover centuries to millennia can lead to unprecedented effects on temporal rate of change in species composition. Temporal variation in species composition monotonically decreases with increasing duration of time-averaging in simulated fossil assemblages. Time averaging is also associated with the reduction of species dominance owing to the temporal switching in the identity of dominant species. High degrees of time averaging can cause that community parameters of local fossil assemblages converge to parameters of metacommunity rather that to parameters of individual local non-averaged communities. We find that the low variation in species composition observed among mollusk and ostracod subfossil assemblages can be explained by time averaging alone, and low temporal resolution and reduced temporal separation among assemblages in time series can thus explain a substantial part of the reduced variation in species composition relative to unscaled predictions of neutral model (i.e., species do not differ in birth, death, and immigration rates on per capita basis). The structure of time-averaged assemblages can thus provide important insights into processes that act over larger temporal scales, such as evolution of niches and dispersal, range-limit dynamics, taxon cycles, and

Generating spatial precipitation ensembles: impact of temporal correlation structure

Science.gov (United States)

Rakovec, O.; Hazenberg, P.; Torfs, P. J. J. F.; Weerts, A. H.; Uijlenhoet, R.

2012-09-01

Sound spatially distributed rainfall fields including a proper spatial and temporal error structure are of key interest for hydrologists to force hydrological models and to identify uncertainties in the simulated and forecasted catchment response. The current paper presents a temporally coherent error identification method based on time-dependent multivariate spatial conditional simulations, which are conditioned on preceding simulations. A sensitivity analysis and real-world experiment are carried out within the hilly region of the Belgian Ardennes. Precipitation fields are simulated for pixels of 10 km × 10 km resolution. Uncertainty analyses in the simulated fields focus on (1) the number of previous simulation hours on which the new simulation is conditioned, (2) the advection speed of the rainfall event, (3) the size of the catchment considered, and (4) the rain gauge density within the catchment. The results for a sensitivity analysis show for typical advection speeds >20 km h-1, no uncertainty is added in terms of across ensemble spread when conditioned on more than one or two previous hourly simulations. However, for the real-world experiment, additional uncertainty can still be added when conditioning on a larger number of previous simulations. This is because for actual precipitation fields, the dynamics exhibit a larger spatial and temporal variability. Moreover, by thinning the observation network with 50%, the added uncertainty increases only slightly and the cross-validation shows that the simulations at the unobserved locations are unbiased. Finally, the first-order autocorrelation coefficients show clear temporal coherence in the time series of the areal precipitation using the time-dependent multivariate conditional simulations, which was not the case using the time-independent univariate conditional simulations. The presented work can be easily implemented within a hydrological calibration and data assimilation framework and can be used as an

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.

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

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.

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

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.

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...

Dynamic modelling and simulation for control of a cylindrical robotic manipulator

International Nuclear Information System (INIS)

Iqbal, A.; Athar, S.M.

1995-03-01

In this report a dynamic model for the three degrees-of-freedom cylindrical manipulator, INFOMATE has been developed. Although the robot dynamics are highly coupled and non-linear, the developed model is relatively straight forward and compact for control engineering and simulation applications. The model has been simulated using the graphical simulation package SIMULINK. Different aspects of INFOMATE associated with forward dynamics, inverse dynamics and control have been investigated by performing various simulation experiments. These simulation experiments confirm the accuracy and applicability of the dynamic robot model. (author) 18 figs

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.)

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.

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...

Temporal expression-based analysis of metabolism.

Directory of Open Access Journals (Sweden)

Sara B Collins

Full Text Available Metabolic flux is frequently rerouted through cellular metabolism in response to dynamic changes in the intra- and extra-cellular environment. Capturing the mechanisms underlying these metabolic transitions in quantitative and predictive models is a prominent challenge in systems biology. Progress in this regard has been made by integrating high-throughput gene expression data into genome-scale stoichiometric models of metabolism. Here, we extend previous approaches to perform a Temporal Expression-based Analysis of Metabolism (TEAM. We apply TEAM to understanding the complex metabolic dynamics of the respiratorily versatile bacterium Shewanella oneidensis grown under aerobic, lactate-limited conditions. TEAM predicts temporal metabolic flux distributions using time-series gene expression data. Increased predictive power is achieved by supplementing these data with a large reference compendium of gene expression, which allows us to take into account the unique character of the distribution of expression of each individual gene. We further propose a straightforward method for studying the sensitivity of TEAM to changes in its fundamental free threshold parameter θ, and reveal that discrete zones of distinct metabolic behavior arise as this parameter is changed. By comparing the qualitative characteristics of these zones to additional experimental data, we are able to constrain the range of θ to a small, well-defined interval. In parallel, the sensitivity analysis reveals the inherently difficult nature of dynamic metabolic flux modeling: small errors early in the simulation propagate to relatively large changes later in the simulation. We expect that handling such "history-dependent" sensitivities will be a major challenge in the future development of dynamic metabolic-modeling techniques.

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...

A Probabilistic Framework for Constructing Temporal Relations in Replica Exchange Molecular Trajectories.

Science.gov (United States)

Chattopadhyay, Aditya; Zheng, Min; Waller, Mark Paul; Priyakumar, U Deva

2018-05-23

Knowledge of the structure and dynamics of biomolecules is essential for elucidating the underlying mechanisms of biological processes. Given the stochastic nature of many biological processes, like protein unfolding, it's almost impossible that two independent simulations will generate the exact same sequence of events, which makes direct analysis of simulations difficult. Statistical models like Markov Chains, transition networks etc. help in shedding some light on the mechanistic nature of such processes by predicting long-time dynamics of these systems from short simulations. However, such methods fall short in analyzing trajectories with partial or no temporal information, for example, replica exchange molecular dynamics or Monte Carlo simulations. In this work we propose a probabilistic algorithm, borrowing concepts from graph theory and machine learning, to extract reactive pathways from molecular trajectories in the absence of temporal data. A suitable vector representation was chosen to represent each frame in the macromolecular trajectory (as a series of interaction and conformational energies) and dimensionality reduction was performed using principal component analysis (PCA). The trajectory was then clustered using a density-based clustering algorithm, where each cluster represents a metastable state on the potential energy surface (PES) of the biomolecule under study. A graph was created with these clusters as nodes with the edges learnt using an iterative expectation maximization algorithm. The most reactive path is conceived as the widest path along this graph. We have tested our method on RNA hairpin unfolding trajectory in aqueous urea solution. Our method makes the understanding of the mechanism of unfolding in RNA hairpin molecule more tractable. As this method doesn't rely on temporal data it can be used to analyze trajectories from Monte Carlo sampling techniques and replica exchange molecular dynamics (REMD).

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.

Statistical dynamic imaging of RI-labeled tracer from list-mode PET data

International Nuclear Information System (INIS)

Tanimoto, Michiaki; Kuroda, Yoshihiro; Oshiro, Osamu; Watabe, Hiroshi; Kuroda, Tomohiro

2009-01-01

Positron emission tomography (PET) can be used in physiological analysis to illustrate physiological states by visualizing the accumulation of radioisotope (RI)-labeled tracer in specific organs or tissues. PET obtains spatio-temporal statistics in the form of list-mode data. However, conventional imaging techniques, which sum up list-mode data over a given time period, cannot depict detailed temporal dynamics of the RI-labeled tracer. In this study, a spatio-temporal analysis approach was employed to visualize the temporal flow dynamics of RI-labeled tracer from the obtained list-mode data. Experiments to assess the visualization of simulated RI-labeled tracer dynamics as well as RI-labeled tracer dynamics in a vascular phantom showed that the proposed method successfully depicted detailed temporal flow dynamics that could not be visualized using conventional methods. (author)

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

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...

Dynamic simulation of 10 kW Brayton cryocooler for HTS cable

Science.gov (United States)

Chang, Ho-Myung; Park, Chan Woo; Yang, Hyung Suk; Hwang, Si Dole

2014-01-01

Dynamic simulation of a Brayton cryocooler is presented as a partial effort of a Korean governmental project to develop 1˜3 km HTS cable systems at transmission level in Jeju Island. Thermodynamic design of a 10 kW Brayton cryocooler was completed, and a prototype construction is underway with a basis of steady-state operation. This study is the next step to investigate the transient behavior of cryocooler for two purposes. The first is to simulate and design the cool-down process after scheduled or unscheduled stoppage. The second is to predict the transient behavior following the variation of external conditions such as cryogenic load or outdoor temperature. The detailed specifications of key components, including plate-fin heat exchangers and cryogenic turbo-expanders are incorporated into a commercial software (Aspen HYSYS) to estimate the temporal change of temperature and flow rate over the cryocooler. An initial cool-down scenario and some examples on daily variation of cryocooler are presented and discussed, aiming at stable control schemes of a long cable system.

Dynamic simulation of 10 kW Brayton cryocooler for HTS cable

International Nuclear Information System (INIS)

Chang, Ho-Myung; Park, Chan Woo; Yang, Hyung Suk; Hwang, Si Dole

2014-01-01

Dynamic simulation of a Brayton cryocooler is presented as a partial effort of a Korean governmental project to develop 1∼3 km HTS cable systems at transmission level in Jeju Island. Thermodynamic design of a 10 kW Brayton cryocooler was completed, and a prototype construction is underway with a basis of steady-state operation. This study is the next step to investigate the transient behavior of cryocooler for two purposes. The first is to simulate and design the cool-down process after scheduled or unscheduled stoppage. The second is to predict the transient behavior following the variation of external conditions such as cryogenic load or outdoor temperature. The detailed specifications of key components, including plate-fin heat exchangers and cryogenic turbo-expanders are incorporated into a commercial software (Aspen HYSYS) to estimate the temporal change of temperature and flow rate over the cryocooler. An initial cool-down scenario and some examples on daily variation of cryocooler are presented and discussed, aiming at stable control schemes of a long cable system

Dynamic simulation of 10 kW Brayton cryocooler for HTS cable

Energy Technology Data Exchange (ETDEWEB)

Chang, Ho-Myung; Park, Chan Woo [Hong Ik University, Department of Mechanical Engineering, Seoul, 121-791 (Korea, Republic of); Yang, Hyung Suk; Hwang, Si Dole [KEPCO Research Institute, Daejeon, 305-760 (Korea, Republic of)

2014-01-29

Dynamic simulation of a Brayton cryocooler is presented as a partial effort of a Korean governmental project to develop 1∼3 km HTS cable systems at transmission level in Jeju Island. Thermodynamic design of a 10 kW Brayton cryocooler was completed, and a prototype construction is underway with a basis of steady-state operation. This study is the next step to investigate the transient behavior of cryocooler for two purposes. The first is to simulate and design the cool-down process after scheduled or unscheduled stoppage. The second is to predict the transient behavior following the variation of external conditions such as cryogenic load or outdoor temperature. The detailed specifications of key components, including plate-fin heat exchangers and cryogenic turbo-expanders are incorporated into a commercial software (Aspen HYSYS) to estimate the temporal change of temperature and flow rate over the cryocooler. An initial cool-down scenario and some examples on daily variation of cryocooler are presented and discussed, aiming at stable control schemes of a long cable system.

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

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)

Stabilities and Dynamics of Protein Folding Nuclei by Molecular Dynamics Simulation

Science.gov (United States)

Song, Yong-Shun; Zhou, Xin; Zheng, Wei-Mou; Wang, Yan-Ting

2017-07-01

To understand how the stabilities of key nuclei fragments affect protein folding dynamics, we simulate by molecular dynamics (MD) simulation in aqueous solution four fragments cut out of a protein G, including one α-helix (seqB: KVFKQYAN), two β-turns (seqA: LNGKTLKG and seqC: YDDATKTF), and one β-strand (seqD: DGEWTYDD). The Markov State Model clustering method combined with the coarse-grained conformation letters method are employed to analyze the data sampled from 2-μs equilibrium MD simulation trajectories. We find that seqA and seqB have more stable structures than their native structures which become metastable when cut out of the protein structure. As expected, seqD alone is flexible and does not have a stable structure. Throughout our simulations, the native structure of seqC is stable but cannot be reached if starting from a structure other than the native one, implying a funnel-shape free energy landscape of seqC in aqueous solution. All the above results suggest that different nuclei have different formation dynamics during protein folding, which may have a major contribution to the hierarchy of protein folding dynamics. Supported by the National Basic Research Program of China under Grant No. 2013CB932804, the National Natural Science Foundation of China under Grant No. 11421063, and the CAS Biophysics Interdisciplinary Innovation Team Project

The effect of STDP temporal kernel structure on the learning dynamics of single excitatory and inhibitory synapses.

Directory of Open Access Journals (Sweden)

Yotam Luz

Full Text Available Spike-Timing Dependent Plasticity (STDP is characterized by a wide range of temporal kernels. However, much of the theoretical work has focused on a specific kernel - the "temporally asymmetric Hebbian" learning rules. Previous studies linked excitatory STDP to positive feedback that can account for the emergence of response selectivity. Inhibitory plasticity was associated with negative feedback that can balance the excitatory and inhibitory inputs. Here we study the possible computational role of the temporal structure of the STDP. We represent the STDP as a superposition of two processes: potentiation and depression. This allows us to model a wide range of experimentally observed STDP kernels, from Hebbian to anti-Hebbian, by varying a single parameter. We investigate STDP dynamics of a single excitatory or inhibitory synapse in purely feed-forward architecture. We derive a mean-field-Fokker-Planck dynamics for the synaptic weight and analyze the effect of STDP structure on the fixed points of the mean field dynamics. We find a phase transition along the Hebbian to anti-Hebbian parameter from a phase that is characterized by a unimodal distribution of the synaptic weight, in which the STDP dynamics is governed by negative feedback, to a phase with positive feedback characterized by a bimodal distribution. The critical point of this transition depends on general properties of the STDP dynamics and not on the fine details. Namely, the dynamics is affected by the pre-post correlations only via a single number that quantifies its overlap with the STDP kernel. We find that by manipulating the STDP temporal kernel, negative feedback can be induced in excitatory synapses and positive feedback in inhibitory. Moreover, there is an exact symmetry between inhibitory and excitatory plasticity, i.e., for every STDP rule of inhibitory synapse there exists an STDP rule for excitatory synapse, such that their dynamics is identical.

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.

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.

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.

Equivalence of Brownian dynamics and dynamic Monte Carlo simulations in multicomponent colloidal suspensions.

Science.gov (United States)

Cuetos, Alejandro; Patti, Alessandro

2015-08-01

We propose a simple but powerful theoretical framework to quantitatively compare Brownian dynamics (BD) and dynamic Monte Carlo (DMC) simulations of multicomponent colloidal suspensions. By extending our previous study focusing on monodisperse systems of rodlike colloids, here we generalize the formalism described there to multicomponent colloidal mixtures and validate it by investigating the dynamics in isotropic and liquid crystalline phases containing spherical and rodlike particles. In order to investigate the dynamics of multicomponent colloidal systems by DMC simulations, it is key to determine the elementary time step of each species and establish a unique timescale. This is crucial to consistently study the dynamics of colloidal particles with different geometry. By analyzing the mean-square displacement, the orientation autocorrelation functions, and the self part of the van Hove correlation functions, we show that DMC simulation is a very convenient and reliable technique to describe the stochastic dynamics of any multicomponent colloidal system. Our theoretical formalism can be easily extended to any colloidal system containing size and/or shape polydisperse particles.

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

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.

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.

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...

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

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…

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.

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.

GIS and agent based spatial-temporal simulation modeling for assessing tourism social carrying capacity: a study on Mount Emei scenic area, China

Science.gov (United States)

Zhang, Renjun

2007-06-01

Each scenic area can sustain a specific level of acceptance of tourist development and use, beyond which further development can result in socio-cultural deterioration or a decline in the quality of the experience gained by visitors. This specific level is called carrying capacity. Social carrying capacity can be defined as the maximum level of use (in terms of numbers and activities) that can be absorbed by an area without an unacceptable decline in the quality of experience of visitors and without an unacceptable adverse impact on the society of the area. It is difficult to assess the carrying capacity, because the carrying capacity is determined by not only the number of visitors, but also the time, the type of the recreation, the characters of each individual and the physical environment. The objective of this study is to build a spatial-temporal simulation model to simulate the spatial-temporal distribution of tourists. This model is a tourist spatial behaviors simulator (TSBS). Based on TSBS, the changes of each visitor's travel patterns such as location, cost, and other states data are recoded in a state table. By analyzing this table, the intensity of the tourist use in any area can be calculated; the changes of the quality of tourism experience can be quantized and analyzed. So based on this micro simulation method the social carrying capacity can be assessed more accurately, can be monitored proactively and managed adaptively. In this paper, the carrying capacity of Mount Emei scenic area is analyzed as followed: The author selected the intensity of the crowd as the monitoring Indicators. it is regarded that longer waiting time means more crowded. TSBS was used to simulate the spatial-temporal distribution of tourists. the average of waiting time all the visitors is calculated. And then the author assessed the social carrying capacity of Mount Emei scenic area, found the key factors have impacted on social carrying capacity. The results show that the TSBS

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.

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...

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.

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

Structural controllability and controlling centrality of temporal networks.

Science.gov (United States)

Pan, Yujian; Li, Xiang

2014-01-01

Temporal networks are such networks where nodes and interactions may appear and disappear at various time scales. With the evidence of ubiquity of temporal networks in our economy, nature and society, it's urgent and significant to focus on its structural controllability as well as the corresponding characteristics, which nowadays is still an untouched topic. We develop graphic tools to study the structural controllability as well as its characteristics, identifying the intrinsic mechanism of the ability of individuals in controlling a dynamic and large-scale temporal network. Classifying temporal trees of a temporal network into different types, we give (both upper and lower) analytical bounds of the controlling centrality, which are verified by numerical simulations of both artificial and empirical temporal networks. We find that the positive relationship between aggregated degree and controlling centrality as well as the scale-free distribution of node's controlling centrality are virtually independent of the time scale and types of datasets, meaning the inherent robustness and heterogeneity of the controlling centrality of nodes within temporal networks.

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

Extended-Term Dynamic Simulations with High Penetrations of Photovoltaic 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); Donnelly, Matt [Montana Tech., Butte, MT (United States); Sanchez-Gasca, Juan [GE Energy, Schenectady, NY (United States)

2016-01-01

The uncontrolled intermittent availability of renewable energy sources makes integration of such devices into today's grid a challenge. Thus, it is imperative that dynamic simulation tools used to analyze power system performance are able to support systems with high amounts of photovoltaic (PV) generation. Additionally, simulation durations expanding beyond minutes into hours must be supported. This report aims to identify the path forward for dynamic simulation tools to accom- modate 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 po- tential problems. We present a study of fixed time step, explicit numerical integration schemes that may be more suitable for these goals, based on identified requirements for simulating high PV penetration systems. We also present the alternative of variable time step integration. To help determine the characteristics of systems with high PV generation, we performed small signal sta- bility studies and time domain simulations of two representative systems. Along with feedback from stakeholders and vendors, we identify the current gaps in power system modeling including fast and slow dynamics and propose a new simulation framework to improve our ability to model and simulate longer-term dynamics.

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

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...

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.

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.

A Computational Model Based on Multi-Regional Calcium Imaging Represents the Spatio-Temporal Dynamics in a Caenorhabditis elegans Sensory Neuron.

Directory of Open Access Journals (Sweden)

Masahiro Kuramochi

Full Text Available Due to the huge number of neuronal cells in the brain and their complex circuit formation, computer simulation of neuronal activity is indispensable to understanding whole brain dynamics. Recently, various computational models have been developed based on whole-brain calcium imaging data. However, these analyses monitor only the activity of neuronal cell bodies and treat the cells as point unit. This point-neuron model is inexpensive in computational costs, but the model is unrealistically simplistic at representing intact neural activities in the brain. Here, we describe a novel three-unit Ordinary Differential Equation (ODE model based on the neuronal responses derived from a Caenorhabditis elegans salt-sensing neuron. We recorded calcium responses in three regions of the ASER neuron using a simple downstep of NaCl concentration. Our simple ODE model generated from a single recording can adequately reproduce and predict the temporal responses of each part of the neuron to various types of NaCl concentration changes. Our strategy which combines a simple recording data and an ODE mathematical model may be extended to realistically understand whole brain dynamics by computational simulation.

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

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.

Generating spatial precipitation ensembles: impact of temporal correlation structure

Directory of Open Access Journals (Sweden)

O. Rakovec

2012-09-01

Full Text Available Sound spatially distributed rainfall fields including a proper spatial and temporal error structure are of key interest for hydrologists to force hydrological models and to identify uncertainties in the simulated and forecasted catchment response. The current paper presents a temporally coherent error identification method based on time-dependent multivariate spatial conditional simulations, which are conditioned on preceding simulations. A sensitivity analysis and real-world experiment are carried out within the hilly region of the Belgian Ardennes. Precipitation fields are simulated for pixels of 10 km × 10 km resolution. Uncertainty analyses in the simulated fields focus on (1 the number of previous simulation hours on which the new simulation is conditioned, (2 the advection speed of the rainfall event, (3 the size of the catchment considered, and (4 the rain gauge density within the catchment. The results for a sensitivity analysis show for typical advection speeds >20 km h⁻¹, no uncertainty is added in terms of across ensemble spread when conditioned on more than one or two previous hourly simulations. However, for the real-world experiment, additional uncertainty can still be added when conditioning on a larger number of previous simulations. This is because for actual precipitation fields, the dynamics exhibit a larger spatial and temporal variability. Moreover, by thinning the observation network with 50%, the added uncertainty increases only slightly and the cross-validation shows that the simulations at the unobserved locations are unbiased. Finally, the first-order autocorrelation coefficients show clear temporal coherence in the time series of the areal precipitation using the time-dependent multivariate conditional simulations, which was not the case using the time-independent univariate conditional simulations. The presented work can be easily implemented within a hydrological calibration and data assimilation

Simulation of sensory integration dysfunction in autism with dynamic neural fields model

NARCIS (Netherlands)

Chonnaparamutt, W.; Barakova, E.I.; Rutkowski, L.; Taseusiewicz, R.

2008-01-01

This paper applies dynamic neural fields model [1,23,7] to multimodal interaction of sensory cues obtained from a mobile robot, and shows the impact of different temporal aspects of the integration to the precision of movements. We speculate that temporally uncoordinated sensory integration might be

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.

The use of a priori information in ICA-based techniques for real-time fMRI: an evaluation of static/dynamic and spatial/temporal characteristics

Directory of Open Access Journals (Sweden)

Nicola eSoldati

2013-03-01

Full Text Available Real-time brain functional MRI (rt-fMRI allows in-vivo non-invasive monitoring of neural networks. The use of multivariate data-driven analysis methods such as independent component analysis (ICA offers an attractive trade-off between data interpretability and information extraction, and can be used during both task-based and rest experiments. The purpose of this study was to assess the effectiveness of different ICA-based procedures to monitor in real-time a target IC defined from a functional localizer which also used ICA. Four novel methods were implemented to monitor ongoing brain activity in a sliding window approach. The methods differed in the ways in which a priori information, derived from ICA algorithms, was used to monitora target independent component (IC. We implemented four different algorithms, all based on ICA. One Back-projection method used ICA to derive static spatial information from the functional localizer, off line, which was then back-projected dynamically during the real-time acquisition. The other three methods used real-time ICA algorithms that dynamically exploited temporal, spatial, or spatial-temporal priors during the real-time acquisition. The methods were evaluated by simulating a rt-fMRI experiment that used real fMRI data. The performance of each method was characterized by the spatial and/or temporal correlation with the target IC component monitored, computation time and intrinsic stochastic variability of the algorithms. In this study the Back-projection method, which could monitor more than one IC of interest, outperformed the other methods. These results are consistent with a functional task that gives stable target ICs over time. The dynamic adaptation possibilities offered by the other ICA methods proposed may offer better performance than the Back-projection in conditions where the functional activation shows higher spatial and/or temporal variability.

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.

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

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

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

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.

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.

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.

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.)

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

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

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.

Science.gov (United States)

Marshall, Deborah A; Burgos-Liz, Lina; IJzerman, Maarten J; Crown, William; Padula, William V; Wong, Peter K; Pasupathy, Kalyan S; Higashi, Mitchell K; Osgood, Nathaniel D

2015-03-01

In a previous report, the ISPOR Task Force on Dynamic Simulation Modeling Applications in Health Care Delivery Research Emerging Good Practices introduced the fundamentals of dynamic simulation modeling and identified the types of health care delivery problems for which dynamic simulation modeling can be used more effectively than other modeling methods. The hierarchical relationship between the health care delivery system, providers, patients, and other stakeholders exhibits a level of complexity that ought to be captured using dynamic simulation modeling methods. As a tool to help researchers decide whether dynamic simulation modeling is an appropriate method for modeling the effects of an intervention on a health care system, we presented the System, Interactions, Multilevel, Understanding, Loops, Agents, Time, Emergence (SIMULATE) checklist consisting of eight elements. This report builds on the previous work, systematically comparing each of the three most commonly used dynamic simulation modeling methods-system dynamics, discrete-event simulation, and agent-based modeling. We review criteria for selecting the most suitable method depending on 1) the purpose-type of problem and research questions being investigated, 2) the object-scope of the model, and 3) the method to model the object to achieve the purpose. Finally, we provide guidance for emerging good practices for dynamic simulation modeling in the health sector, covering all aspects, from the engagement of decision makers in the model design through model maintenance and upkeep. We conclude by providing some recommendations about the application of these methods to add value to informed decision making, with an emphasis on stakeholder engagement, starting with the problem definition. Finally, we identify areas in which further methodological development will likely occur given the growing "volume, velocity and variety" and availability of "big data" to provide empirical evidence and techniques

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

Reliability and Minimum Detectable Change of Temporal-Spatial, Kinematic, and Dynamic Stability Measures during Perturbed Gait.

Directory of Open Access Journals (Sweden)

Christopher A Rábago

Full Text Available Temporal-spatial, kinematic variability, and dynamic stability measures collected during perturbation-based assessment paradigms are often used to identify dysfunction associated with gait instability. However, it remains unclear which measures are most reliable for detecting and tracking responses to perturbations. This study systematically determined the between-session reliability and minimum detectable change values of temporal-spatial, kinematic variability, and dynamic stability measures during three types of perturbed gait. Twenty young healthy adults completed two identical testing sessions two weeks apart, comprised of an unperturbed and three perturbed (cognitive, physical, and visual walking conditions in a virtual reality environment. Within each session, perturbation responses were compared to unperturbed walking using paired t-tests. Between-session reliability and minimum detectable change values were also calculated for each measure and condition. All temporal-spatial, kinematic variability and dynamic stability measures demonstrated fair to excellent between-session reliability. Minimal detectable change values, normalized to mean values ranged from 1-50%. Step width mean and variability measures demonstrated the greatest response to perturbations with excellent between-session reliability and low minimum detectable change values. Orbital stability measures demonstrated specificity to perturbation direction and sensitivity with excellent between-session reliability and low minimum detectable change values. We observed substantially greater between-session reliability and lower minimum detectable change values for local stability measures than previously described which may be the result of averaging across trials within a session and using velocity versus acceleration data for reconstruction of state spaces. Across all perturbation types, temporal-spatial, orbital and local measures were the most reliable measures with the

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

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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

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.

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

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

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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.

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

Characterization and Simulation of Transient Vibrations Using Band Limited Temporal Moments

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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.

Switching dynamics in InP photonic-crystal nanocavity

DEFF Research Database (Denmark)

Yu, Yi; Palushani, Evarist; Heuck, Mikkel

2016-01-01

In this paper, we presented switching dynamic investigations on an InP photonic-crystal (PhC) nanocavity structure using homodyne pump-probe measurements. The measurements were compared with simulations based on temporal nonlinear coupled mode theory and carrier rate equations for the dynamics of...

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

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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.

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)

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.

Dynamic decomposition of spatiotemporal neural signals.

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Luca Ambrogioni

2017-05-01

Full Text Available Neural signals are characterized by rich temporal and spatiotemporal dynamics that reflect the organization of cortical networks. Theoretical research has shown how neural networks can operate at different dynamic ranges that correspond to specific types of information processing. Here we present a data analysis framework that uses a linearized model of these dynamic states in order to decompose the measured neural signal into a series of components that capture both rhythmic and non-rhythmic neural activity. The method is based on stochastic differential equations and Gaussian process regression. Through computer simulations and analysis of magnetoencephalographic data, we demonstrate the efficacy of the method in identifying meaningful modulations of oscillatory signals corrupted by structured temporal and spatiotemporal noise. These results suggest that the method is particularly suitable for the analysis and interpretation of complex temporal and spatiotemporal neural signals.

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

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

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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.

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.

Parameterizing Coefficients of a POD-Based Dynamical System

Science.gov (United States)

Kalb, Virginia L.

2010-01-01

A method of parameterizing the coefficients of a dynamical system based of a proper orthogonal decomposition (POD) representing the flow dynamics of a viscous fluid has been introduced. (A brief description of POD is presented in the immediately preceding article.) The present parameterization method is intended to enable construction of the dynamical system to accurately represent the temporal evolution of the flow dynamics over a range of Reynolds numbers. The need for this or a similar method arises as follows: A procedure that includes direct numerical simulation followed by POD, followed by Galerkin projection to a dynamical system has been proven to enable representation of flow dynamics by a low-dimensional model at the Reynolds number of the simulation. However, a more difficult task is to obtain models that are valid over a range of Reynolds numbers. Extrapolation of low-dimensional models by use of straightforward Reynolds-number-based parameter continuation has proven to be inadequate for successful prediction of flows. A key part of the problem of constructing a dynamical system to accurately represent the temporal evolution of the flow dynamics over a range of Reynolds numbers is the problem of understanding and providing for the variation of the coefficients of the dynamical system with the Reynolds number. Prior methods do not enable capture of temporal dynamics over ranges of Reynolds numbers in low-dimensional models, and are not even satisfactory when large numbers of modes are used. The basic idea of the present method is to solve the problem through a suitable parameterization of the coefficients of the dynamical system. The parameterization computations involve utilization of the transfer of kinetic energy between modes as a function of Reynolds number. The thus-parameterized dynamical system accurately predicts the flow dynamics and is applicable to a range of flow problems in the dynamical regime around the Hopf bifurcation. Parameter

A complex systems approach to dynamic spatial simulation modeling: LandUse and LandCover change in the Ecuadorian Amazon

Science.gov (United States)

Messina, Joseph Paul

The Ecuadorian Amazon, lying in the headwaters of the Napo and Aguarico River valleys, is experiencing rapid change in LandUse and LandCover (LULC) conditions and regional landscape diversity uniquely tied to spontaneous agricultural colonization and oil exploration. Beginning in the early 1970s, spontaneous colonization occurred on squattered lands located adjacent to oil company roads and in government development sectors composed of multiple 50 ha land parcels organized into "piano key" shaped family farms or fincas. Since fincas are managed at the household level as spatially discrete, temporally independent units, land conversion at the finca-level is recognized as the chief proximate cause of deforestation within the region. Focusing on the spatial and temporal dynamics of deforestation, agricultural extensification, and plant succession at the finca-level, and urbanization at the community-level, cell-based morphogenetic models of LandUse and LandCover Change (LULCC) were developed as the foundation for predictive models of regional LULCC dynamics and landscape diversity. Two cellular automata models were developed and used to integrate biophysical, geographical, and social variables to characterize temporally dynamic landscapes. The human, geographical, and biophysical dimensions of land use and land cover change were examined, specifically deforestation, anthropogenic extensification, and reforestation. Remotely-sensed data ranging temporally from the 1970s through 1999, combined with thematic map coverages of biophysical gradients and geographical accessibility, were linked to household and community survey data collected in 1990 and 1999. Image processing techniques for LULC characterization and spatial analyses of landscape structure were used to assess the rate and nature of LULCC throughout the time-series. In addition, LULC and LULCC associated with secondary plant succession and agricultural extensification were assessed and simulated for specific

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.

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 ...

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.

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.

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.

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

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

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

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.

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

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

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.)

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.)

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

Science.gov (United States)

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

2017-07-01

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

Non-equilibrium dynamics in disordered materials: Ab initio molecular dynamics simulations

International Nuclear Information System (INIS)

Ohmura, Satoshi; Nagaya, Kiyonobu; Yao, Makoto; Shimojo, Fuyuki

2015-01-01

The dynamic properties of liquid B 2 O 3 under pressure and highly-charged bromophenol molecule are studied by using molecular dynamics (MD) simulations based on density functional theory (DFT). Diffusion properties of covalent liquids under high pressure are very interesting in the sense that they show unexpected pressure dependence. It is found from our simulation that the magnitude relation of diffusion coefficients for boron and oxygen in liquid B 2 O 3 shows the anomalous pressure dependence. The simulation clarified the microscopic origin of the anomalous diffusion properties. Our simulation also reveals the dissociation mechanism in the coulomb explosion of the highly-charged bromophenol molecule. When the charge state n is 6, hydrogen atom in the hydroxyl group dissociates at times shorter than 20 fs while all hydrogen atoms dissociate when n is 8. After the hydrogen dissociation, the carbon ring breaks at about 100 fs. There is also a difference on the mechanism of the ring breaking depending on charge states, in which the ring breaks with expanding (n = 6) or shrink (n = 8)

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.

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.

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.

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...

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.

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

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

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.)

An individual-based process model to simulate landscape-scale forest ecosystem dynamics

Science.gov (United States)

Rupert Seidl; Werner Rammer; Robert M. Scheller; Thomas Spies

2012-01-01

Forest ecosystem dynamics emerges from nonlinear interactions between adaptive biotic agents (i.e., individual trees) and their relationship with a spatially and temporally heterogeneous abiotic environment. Understanding and predicting the dynamics resulting from these complex interactions is crucial for the sustainable stewardship of ecosystems, particularly in the...

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.

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.

Spatial and Temporal Flood Risk Assessment for Decision Making Approach

Science.gov (United States)

Azizat, Nazirah; Omar, Wan-Mohd-Sabki Wan

2018-03-01

Heavy rainfall, adversely impacting inundation areas, depends on the magnitude of the flood. Significantly, location of settlements, infrastructure and facilities in floodplains result in many regions facing flooding risks. A problem faced by the decision maker in an assessment of flood vulnerability and evaluation of adaptation measures is recurrent flooding in the same areas. Identification of recurrent flooding areas and frequency of floods should be priorities for flood risk management. However, spatial and temporal variability become major factors of uncertainty in flood risk management. Therefore, dynamic and spatial characteristics of these changes in flood impact assessment are important in making decisions about the future of infrastructure development and community life. System dynamics (SD) simulation and hydrodynamic modelling are presented as tools for modelling the dynamic characteristics of flood risk and spatial variability. This paper discusses the integration between spatial and temporal information that is required by the decision maker for the identification of multi-criteria decision problems involving multiple stakeholders.

Groundwater-fed irrigation impacts spatially distributed temporal scaling behavior of the natural system: a spatio-temporal framework for understanding water management impacts

International Nuclear Information System (INIS)

Condon, Laura E; Maxwell, Reed M

2014-01-01

Regional scale water management analysis increasingly relies on integrated modeling tools. Much recent work has focused on groundwater–surface water interactions and feedbacks. However, to our knowledge, no study has explicitly considered impacts of management operations on the temporal dynamics of the natural system. Here, we simulate twenty years of hourly moisture dependent, groundwater-fed irrigation using a three-dimensional, fully integrated, hydrologic model (ParFlow-CLM). Results highlight interconnections between irrigation demand, groundwater oscillation frequency and latent heat flux variability not previously demonstrated. Additionally, the three-dimensional model used allows for novel consideration of spatial patterns in temporal dynamics. Latent heat flux and water table depth both display spatial organization in temporal scaling, an important finding given the spatial homogeneity and weak scaling observed in atmospheric forcings. Pumping and irrigation amplify high frequency (sub-annual) variability while attenuating low frequency (inter-annual) variability. Irrigation also intensifies scaling within irrigated areas, essentially increasing temporal memory in both the surface and the subsurface. These findings demonstrate management impacts that extend beyond traditional water balance considerations to the fundamental behavior of the system itself. This is an important step to better understanding groundwater’s role as a buffer for natural variability and the impact that water management has on this capacity. (paper)

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.

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.

Modeling ramp compression experiments using large-scale molecular dynamics simulation.

Energy Technology Data Exchange (ETDEWEB)

Mattsson, Thomas Kjell Rene; Desjarlais, Michael Paul; Grest, Gary Stephen; Templeton, Jeremy Alan; Thompson, Aidan Patrick; Jones, Reese E.; Zimmerman, Jonathan A.; Baskes, Michael I. (University of California, San Diego); Winey, J. Michael (Washington State University); Gupta, Yogendra Mohan (Washington State University); Lane, J. Matthew D.; Ditmire, Todd (University of Texas at Austin); Quevedo, Hernan J. (University of Texas at Austin)

2011-10-01

Molecular dynamics simulation (MD) is an invaluable tool for studying problems sensitive to atomscale physics such as structural transitions, discontinuous interfaces, non-equilibrium dynamics, and elastic-plastic deformation. In order to apply this method to modeling of ramp-compression experiments, several challenges must be overcome: accuracy of interatomic potentials, length- and time-scales, and extraction of continuum quantities. We have completed a 3 year LDRD project with the goal of developing molecular dynamics simulation capabilities for modeling the response of materials to ramp compression. The techniques we have developed fall in to three categories (i) molecular dynamics methods (ii) interatomic potentials (iii) calculation of continuum variables. Highlights include the development of an accurate interatomic potential describing shock-melting of Beryllium, a scaling technique for modeling slow ramp compression experiments using fast ramp MD simulations, and a technique for extracting plastic strain from MD simulations. All of these methods have been implemented in Sandia's LAMMPS MD code, ensuring their widespread availability to dynamic materials research at Sandia and elsewhere.

A simulation to study the feasibility of improving the temporal resolution of LAGEOS geodynamic solutions by using a sequential process noise filter

Science.gov (United States)

Hartman, Brian Davis

1995-01-01

A key drawback to estimating geodetic and geodynamic parameters over time based on satellite laser ranging (SLR) observations is the inability to accurately model all the forces acting on the satellite. Errors associated with the observations and the measurement model can detract from the estimates as well. These 'model errors' corrupt the solutions obtained from the satellite orbit determination process. Dynamical models for satellite motion utilize known geophysical parameters to mathematically detail the forces acting on the satellite. However, these parameters, while estimated as constants, vary over time. These temporal variations must be accounted for in some fashion to maintain meaningful solutions. The primary goal of this study is to analyze the feasibility of using a sequential process noise filter for estimating geodynamic parameters over time from the Laser Geodynamics Satellite (LAGEOS) SLR data. This evaluation is achieved by first simulating a sequence of realistic LAGEOS laser ranging observations. These observations are generated using models with known temporal variations in several geodynamic parameters (along track drag and the J(sub 2), J(sub 3), J(sub 4), and J(sub 5) geopotential coefficients). A standard (non-stochastic) filter and a stochastic process noise filter are then utilized to estimate the model parameters from the simulated observations. The standard non-stochastic filter estimates these parameters as constants over consecutive fixed time intervals. Thus, the resulting solutions contain constant estimates of parameters that vary in time which limits the temporal resolution and accuracy of the solution. The stochastic process noise filter estimates these parameters as correlated process noise variables. As a result, the stochastic process noise filter has the potential to estimate the temporal variations more accurately since the constraint of estimating the parameters as constants is eliminated. A comparison of the temporal

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)

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.)

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

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

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.

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.

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

A Hybrid Approach Combining the Multi-Temporal Scale Spatio-Temporal Network with the Continuous Triangular Model for Exploring Dynamic Interactions in Movement Data: A Case Study of Football

Directory of Open Access Journals (Sweden)

Pengdong Zhang

2018-01-01

Full Text Available Benefiting from recent advantages in location-aware technologies, movement data are becoming ubiquitous. Hence, numerous research topics with respect to movement data have been undertaken. Yet, the research of dynamic interactions in movement data is still in its infancy. In this paper, we propose a hybrid approach combining the multi-temporal scale spatio-temporal network (MTSSTN and the continuous triangular model (CTM for exploring dynamic interactions in movement data. The approach mainly includes four steps: first, the relative trajectory calculus (RTC is used to derive three types of interaction patterns; second, for each interaction pattern, a corresponding MTSSTN is generated; third, for each MTSSTN, the interaction intensity measures and three centrality measures (i.e., degree, betweenness and closeness are calculated; finally, the results are visualized at multiple temporal scales using the CTM and analyzed based on the generated CTM diagrams. Based on the proposed approach, three distinctive aims can be achieved for each interaction pattern at multiple temporal scales: (1 exploring the interaction intensities between any two individuals; (2 exploring the interaction intensities among multiple individuals, and (3 exploring the importance of each individual and identifying the most important individuals. The movement data obtained from a real football match are used as a case study to validate the effectiveness of the proposed approach. The results demonstrate that the proposed approach is useful in exploring dynamic interactions in football movement data and discovering insightful information.

IMPROVING MEDICAL EDUCATION: SIMULATING CHANGES IN PATIENT ANATOMY USING DYNAMIC HAPTIC FEEDBACK

OpenAIRE

Yovanoff, Mary; Pepley, David; Mirkin, Katelin; Moore, Jason; Han, David; Miller, Scarlett

2016-01-01

Virtual simulation is an emerging field in medical education. Research suggests that simulation reduces complication rates and improves learning gains for medical residents. One benefit of simulators is their allowance for more realistic and dynamic patient anatomies. While potentially useful throughout medical education, few studies have explored the impact of dynamic haptic simulators on medical training. In light of this research void, this study was developed to examine how a Dynamic-Hapt...

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.

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)

Spatial-temporal consistency between gross primary productivity and solar-induced chlorophyll fluorescence of vegetation in China during 2007-2014.

Science.gov (United States)

Ma, Jun; Xiao, Xiangming; Zhang, Yao; Doughty, Russell; Chen, Bangqian; Zhao, Bin

2018-10-15

Accurately estimating spatial-temporal patterns of gross primary production (GPP) is important for the global carbon cycle. Satellite-based light use efficiency (LUE) models are regarded as an efficient tool in simulating spatial-temporal dynamics of GPP. However, the accuracy assessment of GPP simulations from LUE models at both spatial and temporal scales remains a challenge. In this study, we simulated GPP of vegetation in China during 2007-2014 using a LUE model (Vegetation Photosynthesis Model, VPM) based on MODIS (moderate-resolution imaging spectroradiometer) images with 8-day temporal and 500-m spatial resolutions and NCEP (National Center for Environmental Prediction) climate data. Global Ozone Monitoring Instrument 2 (GOME-2) solar-induced chlorophyll fluorescence (SIF) data were used to compare with VPM simulated GPP (GPP VPM ) temporally and spatially using linear correlation analysis. Significant positive linear correlations exist between monthly GPP VPM and SIF data over a single year (2010) and multiple years (2007-2014) in most areas of China. GPP VPM is also significantly positive correlated with GOME-2 SIF (R 2  > 0.43) spatially for seasonal scales. However, poor consistency was detected between GPP VPM and SIF data at yearly scale. GPP dynamic trends have high spatial-temporal variation in China during 2007-2014. Temperature, leaf area index (LAI), and precipitation are the most important factors influence GPP VPM in the regions of East Qinghai-Tibet Plateau, Loss Plateau, and Southwestern China, respectively. The results of this study indicate that GPP VPM is temporally and spatially in line with GOME-2 SIF data, and space-borne SIF data have great potential for evaluating LUE-based GPP models. Copyright © 2018 Elsevier B.V. All rights reserved.

Fast Dynamic Simulation-Based Small Signal Stability Assessment and Control

Energy Technology Data Exchange (ETDEWEB)

Acharya, Naresh [General Electric Company, Fairfield, CT (United States); Baone, Chaitanya [General Electric Company, Fairfield, CT (United States); Veda, Santosh [General Electric Company, Fairfield, CT (United States); Dai, Jing [General Electric Company, Fairfield, CT (United States); Chaudhuri, Nilanjan [General Electric Company, Fairfield, CT (United States); Leonardi, Bruno [General Electric Company, Fairfield, CT (United States); Sanches-Gasca, Juan [General Electric Company, Fairfield, CT (United States); Diao, Ruisheng [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Wu, Di [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Huang, Zhenyu [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Zhang, Yu [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Jin, Shuangshuang [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Zheng, Bin [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Chen, Yousu [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

2014-12-31

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

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

Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins

DEFF Research Database (Denmark)

Maragakis, Paul; Lindorff-Larsen, Kresten; Eastwood, Michael P

2008-01-01

. Molecular dynamics (MD) simulation provides a complementary approach to the study of protein dynamics on similar time scales. Comparisons between NMR spectroscopy and MD simulations can be used to interpret experimental results and to improve the quality of simulation-related force fields and integration......A molecular-level understanding of the function of a protein requires knowledge of both its structural and dynamic properties. NMR spectroscopy allows the measurement of generalized order parameters that provide an atomistic description of picosecond and nanosecond fluctuations in protein structure...... methods. However, apparent systematic discrepancies between order parameters extracted from simulations and experiments are common, particularly for elements of noncanonical secondary structure. In this paper, results from a 1.2 micros explicit solvent MD simulation of the protein ubiquitin are compared...

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.

Sampling of temporal networks: Methods and biases

Science.gov (United States)

Rocha, Luis E. C.; Masuda, Naoki; Holme, Petter

2017-11-01

Temporal networks have been increasingly used to model a diversity of systems that evolve in time; for example, human contact structures over which dynamic processes such as epidemics take place. A fundamental aspect of real-life networks is that they are sampled within temporal and spatial frames. Furthermore, one might wish to subsample networks to reduce their size for better visualization or to perform computationally intensive simulations. The sampling method may affect the network structure and thus caution is necessary to generalize results based on samples. In this paper, we study four sampling strategies applied to a variety of real-life temporal networks. We quantify the biases generated by each sampling strategy on a number of relevant statistics such as link activity, temporal paths and epidemic spread. We find that some biases are common in a variety of networks and statistics, but one strategy, uniform sampling of nodes, shows improved performance in most scenarios. Given the particularities of temporal network data and the variety of network structures, we recommend that the choice of sampling methods be problem oriented to minimize the potential biases for the specific research questions on hand. Our results help researchers to better design network data collection protocols and to understand the limitations of sampled temporal network data.

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.

Dynamic profiling of different ready-to-drink fermented dairy products: A comparative study using Temporal Check-All-That-Apply (TCATA), Temporal Dominance of Sensations (TDS) and Progressive Profile (PP).

Science.gov (United States)

Esmerino, Erick A; Castura, John C; Ferraz, Juliana P; Tavares Filho, Elson R; Silva, Ramon; Cruz, Adriano G; Freitas, Mônica Q; Bolini, Helena M A

2017-11-01

Despite the several differences in ingredients, processes and nutritional values, dairy foods as yogurts, fermented milks and milk beverages are widely accepted worldwide, and although they have their sensory profiling normally covered by descriptive analyses, the temporal perception involved during the consumption are rarely considered. In this sense, the present work aimed to assess the dynamic sensory profile of three categories of fermented dairy products using different temporal methodologies: Temporal Dominance of Sensations (TDS), Progressive Profiling (PP), Temporal CATA (TCATA), and compare the results obtained. The findings showed that the different sensory characteristics among the products are basically related to their commercial identity. Regarding the methods, all of them collected the variations between samples with great correlation between data. In addition, to detect differences in intensities, TCATA showed to be the most sensitive method in detecting textural changes. When using PP, a balanced experimental design considering the number of attributes, time intervals, and food matrix must be weighed. The findings are of interest to guide sensory and consumer practitioners involved in the dairy production to formulate/reformulate their products and help them choosing the most suitable dynamic method to temporally evaluate them. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Grid-Based Cyber Infrastructure for High Performance Chemical Dynamics Simulations

Directory of Open Access Journals (Sweden)

Khadka Prashant

2008-10-01

Full Text Available Chemical dynamics simulation is an effective means to study atomic level motions of molecules, collections of molecules, liquids, surfaces, interfaces of materials, and chemical reactions. To make chemical dynamics simulations globally accessible to a broad range of users, recently a cyber infrastructure was developed that provides an online portal to VENUS, a popular chemical dynamics simulation program package, to allow people to submit simulation jobs that will be executed on the web server machine. In this paper, we report new developments of the cyber infrastructure for the improvement of its quality of service by dispatching the submitted simulations jobs from the web server machine onto a cluster of workstations for execution, and by adding an animation tool, which is optimized for animating the simulation results. The separation of the server machine from the simulation-running machine improves the service quality by increasing the capacity to serve more requests simultaneously with even reduced web response time, and allows the execution of large scale, time-consuming simulation jobs on the powerful workstation cluster. With the addition of an animation tool, the cyber infrastructure automatically converts, upon the selection of the user, some simulation results into an animation file that can be viewed on usual web browsers without requiring installation of any special software on the user computer. Since animation is essential for understanding the results of chemical dynamics simulations, this animation capacity provides a better way for understanding simulation details of the chemical dynamics. By combining computing resources at locations under different administrative controls, this cyber infrastructure constitutes a grid environment providing physically and administratively distributed functionalities through a single easy-to-use online portal

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

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

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.

Review of multi-physics temporal coupling methods for analysis of nuclear reactors

International Nuclear Information System (INIS)

Zerkak, Omar; Kozlowski, Tomasz; Gajev, Ivan

2015-01-01

Highlights: • Review of the numerical methods used for the multi-physics temporal coupling. • Review of high-order improvements to the Operator Splitting coupling method. • Analysis of truncation error due to the temporal coupling. • Recommendations on best-practice approaches for multi-physics temporal coupling. - Abstract: The advanced numerical simulation of a realistic physical system typically involves multi-physics problem. For example, analysis of a LWR core involves the intricate simulation of neutron production and transport, heat transfer throughout the structures of the system and the flowing, possibly two-phase, coolant. Such analysis involves the dynamic coupling of multiple simulation codes, each one devoted to the solving of one of the coupled physics. Multiple temporal coupling methods exist, yet the accuracy of such coupling is generally driven by the least accurate numerical scheme. The goal of this paper is to review in detail the approaches and numerical methods that can be used for the multi-physics temporal coupling, including a comprehensive discussion of the issues associated with the temporal coupling, and define approaches that can be used to perform multi-physics analysis. The paper is not limited to any particular multi-physics process or situation, but is intended to provide a generic description of multi-physics temporal coupling schemes for any development stage of the individual (single-physics) tools and methods. This includes a wide spectrum of situation, where the individual (single-physics) solvers are based on pre-existing computation codes embedded as individual components, or a new development where the temporal coupling can be developed and implemented as a part of code development. The discussed coupling methods are demonstrated in the framework of LWR core analysis

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

Investigation of the Dynamic Contact Angle Using a Direct Numerical Simulation Method.

Science.gov (United States)

Zhu, Guangpu; Yao, Jun; Zhang, Lei; Sun, Hai; Li, Aifen; Shams, Bilal

2016-11-15

A large amount of residual oil, which exists as isolated oil slugs, remains trapped in reservoirs after water flooding. Numerous numerical studies are performed to investigate the fundamental flow mechanism of oil slugs to improve flooding efficiency. Dynamic contact angle models are usually introduced to simulate an accurate contact angle and meniscus displacement of oil slugs under a high capillary number. Nevertheless, in the oil slug flow simulation process, it is unnecessary to introduce the dynamic contact angle model because of a negligible change in the meniscus displacement after using the dynamic contact angle model when the capillary number is small. Therefore, a critical capillary number should be introduced to judge whether the dynamic contact model should be incorporated into simulations. In this study, a direct numerical simulation method is employed to simulate the oil slug flow in a capillary tube at the pore scale. The position of the interface between water and the oil slug is determined using the phase-field method. The capacity and accuracy of the model are validated using a classical benchmark: a dynamic capillary filling process. Then, different dynamic contact angle models and the factors that affect the dynamic contact angle are analyzed. The meniscus displacements of oil slugs with a dynamic contact angle and a static contact angle (SCA) are obtained during simulations, and the relative error between them is calculated automatically. The relative error limit has been defined to be 5%, beyond which the dynamic contact angle model needs to be incorporated into the simulation to approach the realistic displacement. Thus, the desired critical capillary number can be determined. A three-dimensional universal chart of critical capillary number, which functions as static contact angle and viscosity ratio, is given to provide a guideline for oil slug simulation. Also, a fitting formula is presented for ease of use.

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.

Temporal bird community dynamics are strongly affected by landscape fragmentation in a Central American tropical forest region

Science.gov (United States)

Blandón, A.C.; Perelman, S.B.; Ramírez, M.; López, A.; Javier, O.; Robbins, Chandler S.

2016-01-01

Habitat loss and fragmentation are considered the main causes of species extinctions, particularly in tropical ecosystems. The objective of this work was to evaluate the temporal dynamics of tropical bird communities in landscapes with different levels of fragmentation in eastern Guatemala. We evaluated five bird community dynamic parameters for forest specialists and generalists: (1) species extinction, (2) species turnover, (3) number of colonizing species, (4) relative species richness, and (5) a homogeneity index. For each of 24 landscapes, community dynamic parameters were estimated from bird point count data, for the 1998–1999 and 2008–2009 periods, accounting for species’ detection probability. Forest specialists had higher extinction rates and a smaller number of colonizing species in landscapes with higher fragmentation, thus having lower species richness in both time periods. Alternatively, forest generalists elicited a completely different pattern, showing a curvilinear association to forest fragmentation for most parameters. Thus, greater community dynamism for forest generalists was shown in landscapes with intermediate levels of fragmentation. Our study supports general theory regarding the expected negative effects of habitat loss and fragmentation on the temporal dynamics of biotic communities, particularly for forest specialists, providing strong evidence from understudied tropical bird communities.

Darlington tritium removal facility and station upgrading plant dynamic process simulation

International Nuclear Information System (INIS)

Busigin, A.; Williams, G. I. D.; Wong, T. C. W.; Kulczynski, D.; Reid, A.

2008-01-01

Ontario Power Generation Nuclear (OPGN) has a 4 x 880 MWe CANDU nuclear station at its Darlington Nuclear Div. located in Bowmanville. The station has been operating a Tritium Removal Facility (TRF) and a D 2 O station Upgrading Plant (SUP) since 1989. Both facilities were designed with a Distributed Control System (DCS) and programmable logic controllers (PLC) for process control. This control system was replaced with a DCS only, in 1998. A dynamic plant simulator was developed for the Darlington TRF (DTRF) and the SUP, as part of the computer control system replacement. The simulator was used to test the new software, required to eliminate the PLCs. The simulator is now used for operator training and testing of process control software changes prior to field installation. Dynamic simulation will be essential for the ITER isotope separation system, where the process is more dynamic than the relatively steady-state DTRF process. This paper describes the development and application of the DTRF and SUP dynamic simulator, its benefits, architecture, and the operational experience with the simulator. (authors)

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

Implementation of Parallel Dynamic Simulation on Shared-Memory vs. Distributed-Memory Environments

Energy Technology Data Exchange (ETDEWEB)

Jin, Shuangshuang; Chen, Yousu; Wu, Di; Diao, Ruisheng; Huang, Zhenyu

2015-12-09

Power system dynamic simulation computes the system response to a sequence of large disturbance, such as sudden changes in generation or load, or a network short circuit followed by protective branch switching operation. It consists of a large set of differential and algebraic equations, which is computational intensive and challenging to solve using single-processor based dynamic simulation solution. High-performance computing (HPC) based parallel computing is a very promising technology to speed up the computation and facilitate the simulation process. This paper presents two different parallel implementations of power grid dynamic simulation using Open Multi-processing (OpenMP) on shared-memory platform, and Message Passing Interface (MPI) on distributed-memory clusters, respectively. The difference of the parallel simulation algorithms and architectures of the two HPC technologies are illustrated, and their performances for running parallel dynamic simulation are compared and demonstrated.

Development of a quantum chemical molecular dynamics tribochemical simulator and its application to tribochemical reaction dynamics of lubricant additives

International Nuclear Information System (INIS)

Onodera, T; Tsuboi, H; Hatakeyama, N; Endou, A; Miyamoto, A; Miura, R; Takaba, H; Suzuki, A; Kubo, M

2010-01-01

Tribology at the atomistic and molecular levels has been theoretically studied by a classical molecular dynamics (MD) method. However, this method inherently cannot simulate the tribochemical reaction dynamics because it does not consider the electrons in nature. Although the first-principles based MD method has recently been used for understanding the chemical reaction dynamics of several molecules in the tribology field, the method cannot simulate the tribochemical reaction dynamics of a large complex system including solid surfaces and interfaces due to its huge computation costs. On the other hand, we have developed a quantum chemical MD tribochemical simulator on the basis of a hybrid tight-binding quantum chemical/classical MD method. In the simulator, the central part of the chemical reaction dynamics is calculated by the tight-binding quantum chemical MD method, and the remaining part is calculated by the classical MD method. Therefore, the developed tribochemical simulator realizes the study on tribochemical reaction dynamics of a large complex system, which cannot be treated by using the conventional classical MD or the first-principles MD methods. In this paper, we review our developed quantum chemical MD tribochemical simulator and its application to the tribochemical reaction dynamics of a few lubricant additives

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

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.

Dynamic solar-powered multi-stage direct contact membrane distillation system: Concept design, modeling and simulation

KAUST Repository

Lee, Jung Gil

2017-04-26

This paper presents a theoretical analysis of the monthly average daily and hourly performances of a solar-powered multi-stage direct contact membrane distillation (SMDCMD) system with an energy recovery scheme and dynamic operating system. Mid-latitude meteorological data from Busan, Korea is employed, featuring large climate variation over the course of one year. The number of module stages used by the dynamic operating scheme changes dynamically based on the inlet feed temperature of the successive modules, which results in an improvement of the water production and thermal efficiency. The simulations of the SMDCMD system are carried out to investigate the spatial and temporal variations in the feed and permeate temperatures and permeate flux. The monthly average daily water production increases from 0.37m3/day to 0.4m3/day and thermal efficiency increases from 31% to 45% when comparing systems both without and with dynamic operation in December. The water production with respect to collector area ranged from 350m2 to 550m2 and the seawater storage tank volume ranged from 16m3 to 28.8m3, and the solar fraction at various desired feed temperatures from 50°C to 80°C have been investigated in October and December.

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

Monte Carlo-molecular dynamics simulations for two-dimensional magnets

International Nuclear Information System (INIS)

Kawabata, C.; takeuchi, M.; Bishop, A.R.

1985-01-01

A combined Monte Carlo-molecular dynamics simulation technique is used to study the dynamic structure factor on a square lattice for isotropic Heisenberg and planar classical ferromagnetic spin Hamiltonians

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.

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.

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.

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.

Extending Virtual Reality simulation of ITER maintenance operations with dynamic effects

International Nuclear Information System (INIS)

Heemskerk, C.J.M.; Baar, M.R. de; Boessenkool, H.; Graafland, B.; Haye, M.J.; Koning, J.F.; Vahedi, M.; Visser, M.

2011-01-01

Virtual Reality (VR) simulation can be used to study, improve and verify ITER maintenance operations during preparation. VR can also improve the situational awareness of human operators during actual Remote Handling (RH) operations. Until now, VR systems use geometric models of the environment and the objects being handled and kinematic models of the manipulation systems. The addition of dynamic effects into the VR simulation was investigated. Important dynamic effects are forces due to contact transitions and the bending of beams under heavy loads. A novel dynamics simulation module was developed and introduced as an add-on to the VR4Robots VR software. Tests were performed under simplified test conditions and in the context of realistic ITER maintenance tasks on a benchmark product and on the ECRH Upper Port Launcher Plug (UPL). The introduction of dynamic effects into VR simulations was found to add realism and provide new insights in procedure development. The quality of the haptic feedback depends strongly on the haptic device used to 'display' haptic feedback to the operator. Dynamic effect simulation can also form the basis for real-time guidance support to operators during the execution of maintenance tasks (augmented reality).

3-D dynamic rupture simulations of the 2016 Kumamoto, Japan, earthquake

Science.gov (United States)

Urata, Yumi; Yoshida, Keisuke; Fukuyama, Eiichi; Kubo, Hisahiko

2017-11-01

Using 3-D dynamic rupture simulations, we investigated the 2016 Mw7.1 Kumamoto, Japan, earthquake to elucidate why and how the rupture of the main shock propagated successfully, assuming a complicated fault geometry estimated on the basis of the distributions of the aftershocks. The Mw7.1 main shock occurred along the Futagawa and Hinagu faults. Within 28 h before the main shock, three M6-class foreshocks occurred. Their hypocenters were located along the Hinagu and Futagawa faults, and their focal mechanisms were similar to that of the main shock. Therefore, an extensive stress shadow should have been generated on the fault plane of the main shock. First, we estimated the geometry of the fault planes of the three foreshocks as well as that of the main shock based on the temporal evolution of the relocated aftershock hypocenters. We then evaluated the static stress changes on the main shock fault plane that were due to the occurrence of the three foreshocks, assuming elliptical cracks with constant stress drops on the estimated fault planes. The obtained static stress change distribution indicated that Coulomb failure stress change (ΔCFS) was positive just below the hypocenter of the main shock, while the ΔCFS in the shallow region above the hypocenter was negative. Therefore, these foreshocks could encourage the initiation of the main shock rupture and could hinder the propagation of the rupture toward the shallow region. Finally, we conducted 3-D dynamic rupture simulations of the main shock using the initial stress distribution, which was the sum of the static stress changes caused by these foreshocks and the regional stress field. Assuming a slip-weakening law with uniform friction parameters, we computed 3-D dynamic rupture by varying the friction parameters and the values of the principal stresses. We obtained feasible parameter ranges that could reproduce the characteristic features of the main shock rupture revealed by seismic waveform analyses. We also

Improvement of Lambert-Beer law dynamic range by the use of temporal gates on transmitted light pulse through a scattering medium

International Nuclear Information System (INIS)

Yoshino, Hironori; Wada, Kenji; Horinaka, Hiromichi; Cho, Yoshio; Umeda, Tokuo; Osawa, Masahiko.

1995-01-01

The Lambert-Beer law holding for pulsed lights transmitted through a scattering medium was examined using a streak camera. The Lambert-Beer law dynamic range is found to be limited by floor levels that are caused by scattered photons and are controllable by the use of a temporal gate on the transmitted pulse. The dynamic range improvement obtained for a scattering medium of 2.8 cm -1 scattering coefficient of a thickness of 80 mm by a temporal gate of 60 ps was as much as 50 dB and the Lambert-Beer law dynamic rang reached to 140 dB. (author)

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.

Development of research reactor simulator and its application to dynamic test-bed

International Nuclear Information System (INIS)

Kwon, Kee-Choon; Baang, Dane; Park, Jae-Chang; Lee, Seung-Wook; Bae, Sung Won

2014-01-01

We developed a real-time simulator for 'High-flux Advanced Neutron Application ReactOr (HANARO), and the Jordan Research and Training Reactor (JRTR). The main purpose of this simulator is operator training, but we modified this simulator into a dynamic test-bed (DTB) to test the functions and dynamic control performance of reactor regulating system (RRS) in HANARO or JRTR before installation. The simulator hardware consists of a host computer, 6 operator stations, a network switch, and a large display panel. The software includes a mathematical model that implements plant dynamics in real-time, an instructor station module that manages user instructions, and a human machine interface module. The developed research reactor simulators are installed in the Korea Atomic Energy Research Institute nuclear training center for reactor operator training. To use the simulator as a dynamic test-bed, the reactor regulating system modeling software of the simulator was replaced by actual RRS cabinet, and was interfaced using a hard-wired and network-based interface. RRS cabinet generates control signals for reactor power control based on the various feedback signals from DTB, and the DTB runs plant dynamics based on the RRS control signals. Thus the Hardware-In-the-Loop Simulation between RRS and the emulated plant (DTB) has been implemented and tested in this configuration. The test result shows that the developed DTB and actual RRS cabinet works together simultaneously resulting in quite good dynamic control performances. (author)

Evolution of predator dispersal in relation to spatio-temporal prey dynamics: how not to get stuck in the wrong place!

Directory of Open Access Journals (Sweden)

Justin M J Travis

Full Text Available The eco-evolutionary dynamics of dispersal are recognised as key in determining the responses of populations to environmental changes. Here, by developing a novel modelling approach, we show that predators are likely to have evolved to emigrate more often and become more selective over their destination patch when their prey species exhibit spatio-temporally complex dynamics. We additionally demonstrate that the cost of dispersal can vary substantially across space and time. Perhaps as a consequence of current environmental change, many key prey species are currently exhibiting major shifts in their spatio-temporal dynamics. By exploring similar shifts in silico, we predict that predator populations will be most vulnerable when prey dynamics shift from stable to complex. The more sophisticated dispersal rules, and greater variance therein, that evolve under complex dynamics will enable persistence across a broader range of prey dynamics than the rules which evolve under relatively stable prey conditions.

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.

A Dynamic Defense Modeling and Simulation Methodology using Semantic Web Services

Directory of Open Access Journals (Sweden)

Kangsun Lee

2010-04-01

Full Text Available Defense Modeling and Simulations require interoperable and autonomous federates in order to fully simulate complex behavior of war-fighters and to dynamically adapt themselves to various war-game events, commands and controls. In this paper, we propose a semantic web service based methodology to develop war-game simulations. Our methodology encapsulates war-game logic into a set of web services with additional semantic information in WSDL (Web Service Description Language and OWL (Web Ontology Language. By utilizing dynamic discovery and binding power of semantic web services, we are able to dynamically reconfigure federates according to various simulation events. An ASuW (Anti-Surface Warfare simulator is constructed to demonstrate the methodology and successfully shows that the level of interoperability and autonomy can be greatly improved.

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.

Dynamics of Surfactant Clustering at Interfaces and Its Influence on the Interfacial Tension: Atomistic Simulation of a Sodium Hexadecane-Benzene Sulfonate-Tetradecane-Water System.

Science.gov (United States)

Paredes, Ricardo; Fariñas-Sánchez, Ana Isabel; Medina-Rodrı Guez, Bryan; Samaniego, Samantha; Aray, Yosslen; Álvarez, Luis Javier

2018-03-06

The process of equilibration of the tetradecane-water interface in the presence of sodium hexadecane-benzene sulfonate is studied using intensive atomistic molecular dynamics simulations. Starting as an initial point with all of the surfactants at the interface, it is obtained that the equilibration time of the interface (several microseconds) is orders of magnitude higher than previously reported simulated times. There is strong evidence that this slow equilibration process is due to the aggregation of surfactants molecules on the interface. To determine this fact, temporal evolution of interfacial tension and interfacial formation energy are studied and their temporal variations are correlated with cluster formation. To study cluster evolution, the mean cluster size and the probability that a molecule of surfactant chosen at random is free are obtained as a function of time. Cluster size distribution is estimated, and it is observed that some of the molecules remain free, whereas the rest agglomerate. Additionally, the temporal evolution of the interfacial thickness and the structure of the surfactant molecules on the interface are studied. It is observed how this structure depends on whether the molecules agglomerate or not.

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

Quantum algorithm for simulating the dynamics of an open quantum system

International Nuclear Information System (INIS)

Wang Hefeng; Ashhab, S.; Nori, Franco

2011-01-01

In the study of open quantum systems, one typically obtains the decoherence dynamics by solving a master equation. The master equation is derived using knowledge of some basic properties of the system, the environment, and their interaction: One basically needs to know the operators through which the system couples to the environment and the spectral density of the environment. For a large system, it could become prohibitively difficult to even write down the appropriate master equation, let alone solve it on a classical computer. In this paper, we present a quantum algorithm for simulating the dynamics of an open quantum system. On a quantum computer, the environment can be simulated using ancilla qubits with properly chosen single-qubit frequencies and with properly designed coupling to the system qubits. The parameters used in the simulation are easily derived from the parameters of the system + environment Hamiltonian. The algorithm is designed to simulate Markovian dynamics, but it can also be used to simulate non-Markovian dynamics provided that this dynamics can be obtained by embedding the system of interest into a larger system that obeys Markovian dynamics. We estimate the resource requirements for the algorithm. In particular, we show that for sufficiently slow decoherence a single ancilla qubit could be sufficient to represent the entire environment, in principle.

IMPROVING MEDICAL EDUCATION: SIMULATING CHANGES IN PATIENT ANATOMY USING DYNAMIC HAPTIC FEEDBACK.

Science.gov (United States)

Yovanoff, Mary; Pepley, David; Mirkin, Katelin; Moore, Jason; Han, David; Miller, Scarlett

2016-09-01

Virtual simulation is an emerging field in medical education. Research suggests that simulation reduces complication rates and improves learning gains for medical residents. One benefit of simulators is their allowance for more realistic and dynamic patient anatomies. While potentially useful throughout medical education, few studies have explored the impact of dynamic haptic simulators on medical training. In light of this research void, this study was developed to examine how a Dynamic-Haptic Robotic Trainer (DHRT) impacts medical student self-efficacy and skill gains compared to traditional simulators developed to train students in Internal Jugular Central Venous Catheter (IJ CVC) placement. The study was conducted with 18 third year medical students with no prior CVC insertion experience who underwent a pre-test, simulator training (manikin, robotic, or mixed) and post-test. The results revealed the DHRT as a useful method for training CVC skills and supports further research on dynamic haptic trainers in medical education.

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

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

Temporal rainfall estimation using input data reduction and model inversion

Science.gov (United States)

Wright, A. J.; Vrugt, J. A.; Walker, J. P.; Pauwels, V. R. N.

2016-12-01

Floods are devastating natural hazards. To provide accurate, precise and timely flood forecasts there is a need to understand the uncertainties associated with temporal rainfall and model parameters. The estimation of temporal rainfall and model parameter distributions from streamflow observations in complex dynamic catchments adds skill to current areal rainfall estimation methods, allows for the uncertainty of rainfall input to be considered when estimating model parameters and provides the ability to estimate rainfall from poorly gauged catchments. Current methods to estimate temporal rainfall distributions from streamflow are unable to adequately explain and invert complex non-linear hydrologic systems. This study uses the Discrete Wavelet Transform (DWT) to reduce rainfall dimensionality for the catchment of Warwick, Queensland, Australia. The reduction of rainfall to DWT coefficients allows the input rainfall time series to be simultaneously estimated along with model parameters. The estimation process is conducted using multi-chain Markov chain Monte Carlo simulation with the DREAMZS algorithm. The use of a likelihood function that considers both rainfall and streamflow error allows for model parameter and temporal rainfall distributions to be estimated. Estimation of the wavelet approximation coefficients of lower order decomposition structures was able to estimate the most realistic temporal rainfall distributions. These rainfall estimates were all able to simulate streamflow that was superior to the results of a traditional calibration approach. It is shown that the choice of wavelet has a considerable impact on the robustness of the inversion. The results demonstrate that streamflow data contains sufficient information to estimate temporal rainfall and model parameter distributions. The extent and variance of rainfall time series that are able to simulate streamflow that is superior to that simulated by a traditional calibration approach is a

Matching-pursuit/split-operator Fourier-transform simulations of nonadiabatic quantum dynamics

Science.gov (United States)

Wu, Yinghua; Herman, Michael F.; Batista, Victor S.

2005-03-01

A rigorous and practical approach for simulations of nonadiabatic quantum dynamics is introduced. The algorithm involves a natural extension of the matching-pursuit/split-operator Fourier-transform (MP/SOFT) method [Y. Wu and V. S. Batista, J. Chem. Phys. 121, 1676 (2004)] recently developed for simulations of adiabatic quantum dynamics in multidimensional systems. The MP/SOFT propagation scheme, extended to nonadiabatic dynamics, recursively applies the time-evolution operator as defined by the standard perturbation expansion to first-, or second-order, accuracy. The expansion is implemented in dynamically adaptive coherent-state representations, generated by an approach that combines the matching-pursuit algorithm with a gradient-based optimization method. The accuracy and efficiency of the resulting propagation method are demonstrated as applied to the canonical model systems introduced by Tully for testing simulations of dual curve-crossing nonadiabatic dynamics.

Erythrocyte orientation and lung conductivity analysis with a high temporal resolution FEM model for bioimpedance measurements

NARCIS (Netherlands)

Ulbrich, M.; Paluchowski, P.; Muehlsteff, J.; Leonhardt, S.

2012-01-01

Impedance cardiography (ICG) is a simple and cheap method to acquirehemodynamic parameters. In this work, the influence of three dynamic physiological sources has been analyzed using a model of the humanthorax with a high temporal resolution. Therefore, simulations havebeen conducted using the

Dynamic X-ray computed tomography

International Nuclear Information System (INIS)

Grangeat, P.

2003-01-01

Paper Dynamic computed tomography (CT) imaging aims at reconstructing image sequences where the dynamic nature of the living human body is of primary interest. Main concerned applications are image-guided interventional procedures, functional studies and cardiac imaging. The introduction of ultra-fast rotating gantries along with multi-row detectors and in near future area detectors allows a huge progress toward the imaging of moving organs with low-contrast resolution. This paper gives an overview of the different concepts used in dynamic CT. A new reconstruction algorithm based on a voxel-specific dynamic evolution compensation is also presented. It provides four-dimensional image sequences with accurate spatio-temporal information, where each frame is reconstructed using a long-scan acquisition mode on several half-turns. In the same time, this technique permits to reduce the dose delivered per rotation while keeping the same signal to noise ratio for every frame using an adaptive motion-compensated temporal averaging. Results are illustrated on simulated data. (authors)

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.

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.

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

Improvement of temporal and dynamic subtraction images on abdominal CT using 3D global image matching and nonlinear image warping techniques

International Nuclear Information System (INIS)

Okumura, E; Sanada, S; Suzuki, M; Takemura, A; Matsui, O

2007-01-01

Accurate registration of the corresponding non-enhanced and arterial-phase CT images is necessary to create temporal and dynamic subtraction images for the enhancement of subtle abnormalities. However, respiratory movement causes misregistration at the periphery of the liver. To reduce these misregistration errors, we developed a temporal and dynamic subtraction technique to enhance small HCC by 3D global matching and nonlinear image warping techniques. The study population consisted of 21 patients with HCC. Using the 3D global matching and nonlinear image warping technique, we registered current and previous arterial-phase CT images or current non-enhanced and arterial-phase CT images obtained in the same position. The temporal subtraction image was obtained by subtracting the previous arterial-phase CT image from the warped current arterial-phase CT image. The dynamic subtraction image was obtained by the subtraction of the current non-enhanced CT image from the warped current arterial-phase CT image. The percentage of fair or superior temporal subtraction images increased from 52.4% to 95.2% using the new technique, while on the dynamic subtraction images, the percentage increased from 66.6% to 95.2%. The new subtraction technique may facilitate the diagnosis of subtle HCC based on the superior ability of these subtraction images to show nodular and/or ring enhancement

Explicit dynamics for numerical simulation of crack propagation by the extended finite element method; Dynamique explicite pour la simulation numerique de propagation de fissure par la methode des elements finis etendus

Energy Technology Data Exchange (ETDEWEB)

Menouillard, T

2007-09-15

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

Non-periodic molecular dynamics simulations of coarse grained lipid bilayer in water

DEFF Research Database (Denmark)

Kotsalis, E. M.; Hanasaki, I.; Walther, Jens Honore

2010-01-01

We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations o...... in simulating more complex systems by performing a non-periodic Molecular Dynamics simulation of a DPPC lipid in liquid coarse grained water.......We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations...... of the material properties of the system represented by CGMD. In this paper we extend a control algorithm originally developed for atomistic simulations [3], to conduct simulations involving coarse grained water molecules without periodic boundary conditions. We demonstrate the applicability of our method...

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).

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

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.

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.

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.

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.

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

Science.gov (United States)

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

2016-01-01

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

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...

Modeling structural change in spatial system dynamics: A Daisyworld example.

Science.gov (United States)

Neuwirth, C; Peck, A; Simonović, S P

2015-03-01

System dynamics (SD) is an effective approach for helping reveal the temporal behavior of complex systems. Although there have been recent developments in expanding SD to include systems' spatial dependencies, most applications have been restricted to the simulation of diffusion processes; this is especially true for models on structural change (e.g. LULC modeling). To address this shortcoming, a Python program is proposed to tightly couple SD software to a Geographic Information System (GIS). The approach provides the required capacities for handling bidirectional and synchronized interactions of operations between SD and GIS. In order to illustrate the concept and the techniques proposed for simulating structural changes, a fictitious environment called Daisyworld has been recreated in a spatial system dynamics (SSD) environment. The comparison of spatial and non-spatial simulations emphasizes the importance of considering spatio-temporal feedbacks. Finally, practical applications of structural change models in agriculture and disaster management are proposed.

Dynamic simulation of urban hybrid electric vehicles; Dynamische Simulation von Stadthybridfahrzeugen

Energy Technology Data Exchange (ETDEWEB)

Winke, Florian; Bargende, Michael [Stuttgart Univ. (Germany). Inst. fuer Verbrennungsmotoren und Kraftfahrwesen (IVK)

2013-09-15

As a result of the rising requirements on the development process of modern vehicles, simulation models for the prediction of fuel efficiency have become an irreplaceable tool in the automotive industry. Especially for the design of hybrid electric drivetrains, the increasingly short development cycles can only be met by the use of efficient simulation models. At the IVK of the University of Stuttgart, different approaches to simulating the longitudinal dynamics of hybrid electric vehicles were analysed and compared within the presented project. The focus of the investigations was on urban operation. The objective was to develop a hybrid vehicle concept that allows an equitable comparison with pure battery electric vehicles. (orig.)

A Numerical Approach for Hybrid Simulation of Power System Dynamics Considering Extreme Icing Events

DEFF Research Database (Denmark)

Chen, Lizheng; Zhang, Hengxu; Wu, Qiuwei

2017-01-01

numerical simulation scheme integrating icing weather events with power system dynamics is proposed to extend power system numerical simulation. A technique is developed to efficiently simulate the interaction of slow dynamics of weather events and fast dynamics of power systems. An extended package for PSS...

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.

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.

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

Time-resolved PIV technique for high temporal resolution measurement of mechanical prosthetic aortic valve fluid dynamics.

Science.gov (United States)

Kaminsky, R; Morbiducci, U; Rossi, M; Scalise, L; Verdonck, P; Grigioni, M

2007-02-01

Prosthetic heart valves (PHVs) have been used to replace diseased native valves for more than five decades. Among these, mechanical PHVs are the most frequently implanted. Unfortunately, these devices still do not achieve ideal behavior and lead to many complications, many of which are related to fluid mechanics. The fluid dynamics of mechanical PHVs are particularly complex and the fine-scale characteristics of such flows call for very accurate experimental techniques. Adequate temporal resolution can be reached by applying time-resolved PIV, a high-resolution dynamic technique which is able to capture detailed chronological changes in the velocity field. The aim of this experimental study is to investigate the evolution of the flow field in a detailed time domain of a commercial bileaflet PHV in a mock-loop mimicking unsteady conditions, by means of time-resolved 2D Particle Image Velocimetry (PIV). The investigated flow field corresponded to the region immediately downstream of the valve plane. Spatial resolution as in "standard" PIV analysis of prosthetic valve fluid dynamics was used. The combination of a Nd:YLF high-repetition-rate double-cavity laser with a high frame rate CMOS camera allowed a detailed, highly temporally resolved acquisition (up to 10000 fps depending on the resolution) of the flow downstream of the PHV. Features that were observed include the non-homogeneity and unsteadiness of the phenomenon and the presence of large-scale vortices within the field, especially in the wake of the valve leaflets. Furthermore, we observed that highly temporally cycle-resolved analysis allowed the different behaviors exhibited by the bileaflet valve at closure to be captured in different acquired cardiac cycles. By accurately capturing hemodynamically relevant time scales of motion, time-resolved PIV characterization can realistically be expected to help designers in improving PHV performance and in furnishing comprehensive validation with experimental data

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...

Molecular dynamics simulations of phase separation in the presence of surfactants

DEFF Research Database (Denmark)

Laradji, Mohamed; Mouritsen, Ole G.; Toxvaerd, Søren

1994-01-01

The dynamics of phase separation in two-dimensional binary mixtures diluted by surfactants is studied by means of molecular dynamics simulations. In contrast to pure binary systems, characterized by an algebraic time dependence of the average domain size, we find that systems containing surfactants...... not fully phase separate, we observe a dynamical scaling which is independent of the surfactant concentration. The results of these simulations are in general in agreement with previous Langevin simulations [Laradji, Guo, Grant, and Zuckermann, J. Phys. A 44, L629 (1991)] and a theory of Ostwald ripening...... exhibit nonalgebraic, slow dynamics. The average domain size eventually saturates at a value inversely proportional to the surfactant concentration. We also find that phase separation in systems with different surfactant concentrations follow a crossover scaling form. Finally, although these systems do...

Kalman filter techniques for accelerated Cartesian dynamic cardiac imaging.

Science.gov (United States)

Feng, Xue; Salerno, Michael; Kramer, Christopher M; Meyer, Craig H

2013-05-01

In dynamic MRI, spatial and temporal parallel imaging can be exploited to reduce scan time. Real-time reconstruction enables immediate visualization during the scan. Commonly used view-sharing techniques suffer from limited temporal resolution, and many of the more advanced reconstruction methods are either retrospective, time-consuming, or both. A Kalman filter model capable of real-time reconstruction can be used to increase the spatial and temporal resolution in dynamic MRI reconstruction. The original study describing the use of the Kalman filter in dynamic MRI was limited to non-Cartesian trajectories because of a limitation intrinsic to the dynamic model used in that study. Here the limitation is overcome, and the model is applied to the more commonly used Cartesian trajectory with fast reconstruction. Furthermore, a combination of the Kalman filter model with Cartesian parallel imaging is presented to further increase the spatial and temporal resolution and signal-to-noise ratio. Simulations and experiments were conducted to demonstrate that the Kalman filter model can increase the temporal resolution of the image series compared with view-sharing techniques and decrease the spatial aliasing compared with TGRAPPA. The method requires relatively little computation, and thus is suitable for real-time reconstruction. Copyright © 2012 Wiley Periodicals, Inc.

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.

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

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.

Mapping and spatial-temporal modeling of Bromus tectorum invasion in central Utah

Science.gov (United States)

Jin, Zhenyu

Cheatgrass, or Downy Brome, is an exotic winter annual weed native to the Mediterranean region. Since its introduction to the U.S., it has become a significant weed and aggressive invader of sagebrush, pinion-juniper, and other shrub communities, where it can completely out-compete native grasses and shrubs. In this research, remotely sensed data combined with field collected data are used to investigate the distribution of the cheatgrass in Central Utah, to characterize the trend of the NDVI time-series of cheatgrass, and to construct a spatially explicit population-based model to simulate the spatial-temporal dynamics of the cheatgrass. This research proposes a method for mapping the canopy closure of invasive species using remotely sensed data acquired at different dates. Different invasive species have their own distinguished phenologies and the satellite images in different dates could be used to capture the phenology. The results of cheatgrass abundance prediction have a good fit with the field data for both linear regression and regression tree models, although the regression tree model has better performance than the linear regression model. To characterize the trend of NDVI time-series of cheatgrass, a novel smoothing algorithm named RMMEH is presented in this research to overcome some drawbacks of many other algorithms. By comparing the performance of RMMEH in smoothing a 16-day composite of the MODIS NDVI time-series with that of two other methods, which are the 4253EH, twice and the MVI, we have found that RMMEH not only keeps the original valid NDVI points, but also effectively removes the spurious spikes. The reconstructed NDVI time-series of different land covers are of higher quality and have smoother temporal trend. To simulate the spatial-temporal dynamics of cheatgrass, a spatially explicit population-based model is built applying remotely sensed data. The comparison between the model output and the ground truth of cheatgrass closure demonstrates

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...

Temporal anomaly detection: an artificial immune approach based on T cell activation, clonal size regulation and homeostasis.

Science.gov (United States)

Antunes, Mário J; Correia, Manuel E

2010-01-01

This paper presents an artificial immune system (AIS) based on Grossman's tunable activation threshold (TAT) for temporal anomaly detection. We describe the generic AIS framework and the TAT model adopted for simulating T Cells behaviour, emphasizing two novel important features: the temporal dynamic adjustment of T Cells clonal size and its associated homeostasis mechanism. We also present some promising results obtained with artificially generated data sets, aiming to test the appropriateness of using TAT in dynamic changing environments, to distinguish new unseen patterns as part of what should be detected as normal or as anomalous. We conclude by discussing results obtained thus far with artificially generated data sets.

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�

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

Directory of Open Access Journals (Sweden)

Mingyuan Xu

2018-05-01

Full Text Available A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA9-NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

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.

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.

Flight Dynamic Simulation of Fighter In the Asymmetric External Store Release Process

Science.gov (United States)

Safi’i, Imam; Arifianto, Ony; Nurohman, Chandra

2018-04-01

In the fighter design, it is important to evaluate and analyze the flight dynamic of the aircraft earlier in the development process. One of the case is the dynamics of external store release process. A simulation tool can be used to analyze the fighter/external store system’s dynamics in the preliminary design stage. This paper reports the flight dynamics of Jet Fighter Experiment (JF-1 E) in asymmetric Advance Medium Range Air to Air Missile (AMRAAM) release process through simulations. The JF-1 E and AIM 120 AMRAAAM models are built by using Advanced Aircraft Analysis (AAA) and Missile Datcom software. By using these softwares, the aerodynamic stability and control derivatives can be obtained and used to model the dynamic characteristic of the fighter and the external store. The dynamic system is modeled by using MATLAB/Simulink software. By using this software, both the fighter/external store integration and the external store release process is simulated, and the dynamic of the system can be analyzed.

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

Optimal Acceleration-Velocity-Bounded Trajectory Planning in Dynamic Crowd Simulation

Directory of Open Access Journals (Sweden)

Fu Yue-wen

2014-01-01

Full Text Available Creating complex and realistic crowd behaviors, such as pedestrian navigation behavior with dynamic obstacles, is a difficult and time consuming task. In this paper, we study one special type of crowd which is composed of urgent individuals, normal individuals, and normal groups. We use three steps to construct the crowd simulation in dynamic environment. The first one is that the urgent individuals move forward along a given path around dynamic obstacles and other crowd members. An optimal acceleration-velocity-bounded trajectory planning method is utilized to model their behaviors, which ensures that the durations of the generated trajectories are minimal and the urgent individuals are collision-free with dynamic obstacles (e.g., dynamic vehicles. In the second step, a pushing model is adopted to simulate the interactions between urgent members and normal ones, which ensures that the computational cost of the optimal trajectory planning is acceptable. The third step is obligated to imitate the interactions among normal members using collision avoidance behavior and flocking behavior. Various simulation results demonstrate that these three steps give realistic crowd phenomenon just like the real world.

Development of Research Reactor Simulator and Its Application to Dynamic Test-bed

International Nuclear Information System (INIS)

Kwon, Kee Choon; Park, Jae Chang; Lee, Seung Wook; Bang, Dane; Bae, Sung Won

2014-01-01

We developed HANARO and the Jordan Research and Training Reactor (JRTR) real-time simulator for operating staff training. The main purpose of this simulator is operator training, but we modified this simulator as a dynamic test-bed to test the reactor regulating system in HANARO or JRTR before installation. The simulator configuration is divided into hardware and software. The simulator hardware consists of a host computer, 6 operator stations, a network switch, and a large display panel. The simulator software is divided into three major parts: a mathematical modeling module, which executes the plant dynamic modeling program in real-time, an instructor station module that manages user instructions, and a human machine interface (HMI) module. The developed research reactors are installed in the Korea Atomic Energy Research Institute nuclear training center for reactor operator training. To use the simulator as a dynamic test-bed, the reactor regulating system modeling software of the simulator was replaced by a hardware controller and the simulator and target controller were interfaced with a hard-wired and network-based interface

Development of Research Reactor Simulator and Its Application to Dynamic Test-bed

Energy Technology Data Exchange (ETDEWEB)

Kwon, Kee Choon; Park, Jae Chang; Lee, Seung Wook; Bang, Dane; Bae, Sung Won [KAERI, Daejeon (Korea, Republic of)

2014-08-15

We developed HANARO and the Jordan Research and Training Reactor (JRTR) real-time simulator for operating staff training. The main purpose of this simulator is operator training, but we modified this simulator as a dynamic test-bed to test the reactor regulating system in HANARO or JRTR before installation. The simulator configuration is divided into hardware and software. The simulator hardware consists of a host computer, 6 operator stations, a network switch, and a large display panel. The simulator software is divided into three major parts: a mathematical modeling module, which executes the plant dynamic modeling program in real-time, an instructor station module that manages user instructions, and a human machine interface (HMI) module. The developed research reactors are installed in the Korea Atomic Energy Research Institute nuclear training center for reactor operator training. To use the simulator as a dynamic test-bed, the reactor regulating system modeling software of the simulator was replaced by a hardware controller and the simulator and target controller were interfaced with a hard-wired and network-based interface.

Spatio-Temporal Analysis of Epidemic Phenomena Using the R Package surveillance

Directory of Open Access Journals (Sweden)

Sebastian Meyer

2017-05-01

Full Text Available The availability of geocoded health data and the inherent temporal structure of communicable diseases have led to an increased interest in statistical models and software for spatio-temporal data with epidemic features. The open source R package surveillance can handle various levels of aggregation at which infective events have been recorded: individual-level time-stamped geo-referenced data (case reports in either continuous space or discrete space, as well as counts aggregated by period and region. For each of these data types, the surveillance package implements tools for visualization, likelihoood inference and simulation from recently developed statistical regression frameworks capturing endemic and epidemic dynamics. Altogether, this paper is a guide to the spatio-temporal modeling of epidemic phenomena, exemplified by analyses of public health surveillance data on measles and invasive meningococcal disease.

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

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)

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

Temporal network epidemiology

CERN Document Server

Holme, Petter

2017-01-01

This book covers recent developments in epidemic process models and related data on temporally varying networks. It is widely recognized that contact networks are indispensable for describing, understanding, and intervening to stop the spread of infectious diseases in human and animal populations; “network epidemiology” is an umbrella term to describe this research field. More recently, contact networks have been recognized as being highly dynamic. This observation, also supported by an increasing amount of new data, has led to research on temporal networks, a rapidly growing area. Changes in network structure are often informed by epidemic (or other) dynamics, in which case they are referred to as adaptive networks. This volume gathers contributions by prominent authors working in temporal and adaptive network epidemiology, a field essential to understanding infectious diseases in real society.

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.

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.

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.

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...

Matching the reaction-diffusion simulation to dynamic [18F]FMISO PET measurements in tumors: extension to a flow-limited oxygen-dependent model.

Science.gov (United States)

Shi, Kuangyu; Bayer, Christine; Gaertner, Florian C; Astner, Sabrina T; Wilkens, Jan J; Nüsslin, Fridtjof; Vaupel, Peter; Ziegler, Sibylle I

2017-02-01

Positron-emission tomography (PET) with hypoxia specific tracers provides a noninvasive method to assess the tumor oxygenation status. Reaction-diffusion models have advantages in revealing the quantitative relation between in vivo imaging and the tumor microenvironment. However, there is no quantitative comparison of the simulation results with the real PET measurements yet. The lack of experimental support hampers further applications of computational simulation models. This study aims to compare the simulation results with a preclinical [ 18 F]FMISO PET study and to optimize the reaction-diffusion model accordingly. Nude mice with xenografted human squamous cell carcinomas (CAL33) were investigated with a 2 h dynamic [ 18 F]FMISO PET followed by immunofluorescence staining using the hypoxia marker pimonidazole and the endothelium marker CD 31. A large data pool of tumor time-activity curves (TAC) was simulated for each mouse by feeding the arterial input function (AIF) extracted from experiments into the model with different configurations of the tumor microenvironment. A measured TAC was considered to match a simulated TAC when the difference metric was below a certain, noise-dependent threshold. As an extension to the well-established Kelly model, a flow-limited oxygen-dependent (FLOD) model was developed to improve the matching between measurements and simulations. The matching rate between the simulated TACs of the Kelly model and the mouse PET data ranged from 0 to 28.1% (on average 9.8%). By modifying the Kelly model to an FLOD model, the matching rate between the simulation and the PET measurements could be improved to 41.2-84.8% (on average 64.4%). Using a simulation data pool and a matching strategy, we were able to compare the simulated temporal course of dynamic PET with in vivo measurements. By modifying the Kelly model to a FLOD model, the computational simulation was able to approach the dynamic [ 18 F]FMISO measurements in the investigated

Spatiotemporal Wave Patterns: Information Dynamics

Energy Technology Data Exchange (ETDEWEB)

Mikhail Rabinovich; Lev Tsimring

2006-01-20

Pattern formation has traditionally been studied in non-equilibrium physics from the viewpoint of describing the basic structures and their interactions. While this is still an important area of research, the emphasis in the last few years has shifted towards analysis of specific properties of patterns in various complex media. For example, diverse and unexpected phenomena occur in neuro-like media that are characterized by highly non-trivial local dynamics. We carried out an active research program on analysis of spatio-temporal patterns in various physical systems (convection, oscillating fluid layer, soap film), as well as in neuro-like media, with an emphasis on informational aspects of the dynamics. Nonlinear nonequilibrium media and their discrete analogs have a unique ability to represent, memorize, and process the information contained in spatio-temporal patterns. Recent neurophysiological experiments demonstrated a certain universality of spatio-temporal representation of information by neural ensembles. Information processing is also revealed in the spatio-temporal dynamics of cellular patterns in nonequilibrium media. It is extremely important for many applications to study the informational aspects of these dynamics, including the origins and mechanisms of information generation, propagation and storage. Some of our results are: the discovery of self-organization of periodically oscillatory patterns in chaotic heterogeneous media; the analysis of the propagation of the information along a chaotic media as function of the entropy of the signal; the analysis of wave propagation in discrete non-equilibrium media with autocatalytic properties, which simulates the calcium dynamics in cellular membranes. Based on biological experiments we suggest the mechanism by which the spatial sensory information is transferred into the spatio-temporal code in the neural media. We also found a new mechanism of self-pinning in cellular structures and the related phenomenon

A System Structure for a VHTR-SI Process Dynamic Simulation Code

International Nuclear Information System (INIS)

Chang, Jiwoon; Shin, Youngjoon; Kim, Jihwan; Lee, Kiyoung; Lee, Wonjae; Chang, Jonghwa; Youn, Cheung

2008-01-01

The VHTR-SI process dynamic simulation code embedded in a mathematical solution engine is an application software system that simulates the dynamic behavior of the VHTR-SI process. Also, the software system supports a user friendly graphical user interface (GUI) for user input/out. Structured analysis techniques were developed in the late 1970s by Yourdon, DeMarco, Gane and Sarson for applying a systematic approach to a systems analysis. It included the use of data flow diagrams and data modeling and fostered the use of an implementation-independent graphical notation for a documentation. In this paper, we present a system structure for a VHRT-SI process dynamic simulation code by using the methodologies of structured analysis

A Modified SPH Method for Dynamic Failure Simulation of Heterogeneous Material

Directory of Open Access Journals (Sweden)

G. W. Ma

2014-01-01

Full Text Available A modified smoothed particle hydrodynamics (SPH method is applied to simulate the failure process of heterogeneous materials. An elastoplastic damage model based on an extension form of the unified twin shear strength (UTSS criterion is adopted. Polycrystalline modeling is introduced to generate the artificial microstructure of specimen for the dynamic simulation of Brazilian splitting test and uniaxial compression test. The strain rate effect on the predicted dynamic tensile and compressive strength is discussed. The final failure patterns and the dynamic strength increments demonstrate good agreements with experimental results. It is illustrated that the polycrystalline modeling approach combined with the SPH method is promising to simulate more complex failure process of heterogeneous materials.

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

Science.gov (United States)

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

2017-10-01

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

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

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

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.

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...

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.

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.

HVAC-DYNAMIC; A training simulator for dynamic analysis of HVAC plants

Energy Technology Data Exchange (ETDEWEB)

Heintz, M; Novakovic, V [SINTEF Division of Applied Thermodynamic, HVAC Group, Trondheim (Norway); Oegaard, O [SINTEF Division of Automatic Control, Trondheim (Norway); Brustad, G [Computer Aided Modelling, CAMO A/S, Trondheim (Norway)

1989-01-01

HVAC-DYNAMIC is a software tool for the dynamic simulation of Heating, Ventilation and Air Conditioning (HVAC) plants. The program is designed to be used by HVAC engineers during design or troubleshooting of plants and by plant operators in their training. The program is based on a set of the most-used HVAC plant configurations and requires only a minimum of knowledge in numeric methods and programming. A brief presentation of the program structure and examples showing some of the application of the program are given. 4 figs., 4 refs.

HVAC-DYNAMIC: a training simulator for dynamic analysis of HVAC plants

Directory of Open Access Journals (Sweden)

Morten Heintz

1989-07-01

Full Text Available HVAC-DYNAMIC is a software tool for the dynamic simulation of Heating, Ventilation and Air Conditioning (HVAC plants. The program is designed to be used by HVAC engineers during design or troubleshooting of plants and by plant operators in their training. The program is based on a set of the most-used HVAC plant configurations and requires only a minimum of knowledge in numeric methods and programming. A brief presentation of the program structure and examples showing some of the application of the program are given.

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...

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

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.

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.

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...

Computational fluid dynamics simulation of transport and retention of nanoparticle in saturated sand filters

International Nuclear Information System (INIS)

Hassan, Ashraf Aly; Li, Zhen; Sahle-Demessie, Endalkachew; Sorial, George A.

2013-01-01

Highlights: ► Breakthrough curves used to study fate of NPs in slow sand filters (SSF). ► CFD simulate transport, attachment/detachment of NPs in SSFs. ► CFD predicted spatial and temporal changes for transient concentrations of NPs. ► CFD predicts low concentrations and steady NP influx would not be retained by SSFs. ► Pulse input is retained with outlet concentration of 0.2% of the inlet. -- Abstract: Experimental and computational investigation of the transport parameters of nanoparticles (NPs) flowing through porous media has been made. This work intends to develop a simulation applicable to the transport and retention of NPs in saturated porous media for investigating the effect of process conditions and operating parameters such, as ion strength, and filtration efficiency. Experimental data obtained from tracer and nano-ceria, CeO 2 , breakthrough studies were used to characterize dispersion of nanoparticle with the flow and their interaction with sand packed columns with different heights. Nanoparticle transport and concentration dynamics were solved using the Eulerian computational fluid dynamics (CFD) solver ANSYS/FLUENT ® based on a scaled down flow model. A numerical study using the Navier–Stokes equation with second order interaction terms was used to simulate the process. Parameters were estimated by fitting tracer, experimental NP transport data, and interaction of NP with the sand media. The model considers different concentrations of steady state inflow of NPs and different amounts of spike concentrations. Results suggest that steady state flow of dispersant-coated NPs would not be retained by a sand filter, while spike concentrations could be dampened effectively. Unlike analytical solutions, the CFD allows estimating flow profiles for structures with complex irregular geometry and uneven packing

Computational fluid dynamics simulation of transport and retention of nanoparticle in saturated sand filters

Energy Technology Data Exchange (ETDEWEB)

Hassan, Ashraf Aly [U.S. Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, 26 W. Martin Luther King Drive, Cincinnati, OH 45268 (United States); Li, Zhen [School of Energy, Environmental, Biological, and Medical Engineering, Environmental Engineering Program, University of Cincinnati, Cincinnati, OH (United States); Sahle-Demessie, Endalkachew, E-mail: sahle-demessie.endalkachew@epa.gov [U.S. Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, 26 W. Martin Luther King Drive, Cincinnati, OH 45268 (United States); Sorial, George A. [School of Energy, Environmental, Biological, and Medical Engineering, Environmental Engineering Program, University of Cincinnati, Cincinnati, OH (United States)

2013-01-15

Highlights: ► Breakthrough curves used to study fate of NPs in slow sand filters (SSF). ► CFD simulate transport, attachment/detachment of NPs in SSFs. ► CFD predicted spatial and temporal changes for transient concentrations of NPs. ► CFD predicts low concentrations and steady NP influx would not be retained by SSFs. ► Pulse input is retained with outlet concentration of 0.2% of the inlet. -- Abstract: Experimental and computational investigation of the transport parameters of nanoparticles (NPs) flowing through porous media has been made. This work intends to develop a simulation applicable to the transport and retention of NPs in saturated porous media for investigating the effect of process conditions and operating parameters such, as ion strength, and filtration efficiency. Experimental data obtained from tracer and nano-ceria, CeO{sub 2}, breakthrough studies were used to characterize dispersion of nanoparticle with the flow and their interaction with sand packed columns with different heights. Nanoparticle transport and concentration dynamics were solved using the Eulerian computational fluid dynamics (CFD) solver ANSYS/FLUENT{sup ®} based on a scaled down flow model. A numerical study using the Navier–Stokes equation with second order interaction terms was used to simulate the process. Parameters were estimated by fitting tracer, experimental NP transport data, and interaction of NP with the sand media. The model considers different concentrations of steady state inflow of NPs and different amounts of spike concentrations. Results suggest that steady state flow of dispersant-coated NPs would not be retained by a sand filter, while spike concentrations could be dampened effectively. Unlike analytical solutions, the CFD allows estimating flow profiles for structures with complex irregular geometry and uneven packing.

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 ...

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...

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.