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Sample records for subcellular dynamics computer

  1. Programmed subcellular release to study the dynamics of cell detachment

    Science.gov (United States)

    Wildt, Bridget

    Cell detachment is central to a broad range of physio-pathological changes however there are no quantitative methods to study this process. Here we report programmed subcellular release, a method for spatially and temporally controlled cellular detachment and present the first quantitative results of the detachment dynamics of 3T3 fibroblasts at the subcellular level. Programmed subcellular release is an in vitro technique designed to trigger the detachment of distinct parts of a single cell from a patterned substrate with both spatial and temporal control. Subcellular release is achieved by plating cells on an array of patterned gold electrodes created by standard microfabrication techniques. The electrodes are biochemically functionalized with an adhesion-promoting RGD peptide sequence that is attached to the gold electrode via a thiol linkage. Each electrode is electrically isolated so that a subcellular section of a single cell spanning multiple electrodes can be released independently. Upon application of a voltage pulse to a single electrode, RGD-thiol molecules on an individual electrode undergo rapid electrochemical desorption that leads to subsequent cell contraction. The dynamics of cell contraction are found to have characteristic induction and contraction times. This thesis presents the first molecular inhibition studies conducted using programmed subcellular release verifying that this technique can be used to study complex signaling pathways critical to cell motility. Molecular level dynamics of focal adhesion proteins and actin stress fibers provide some insight into the complexities associated with triggered cell detachment. In addition to subcellular release, the programmed release of alkanethiols provides a tool for to study the spatially and temporally controlled release of small molecules or particles from individually addressable gold electrodes. Here we report on experiments which determine the dynamics of programmed release using fluorophore

  2. Understanding the sub-cellular dynamics of silicon transportation and synthesis in diatoms using population-level data and computational optimization.

    Directory of Open Access Journals (Sweden)

    Narjes Javaheri

    2014-06-01

    Full Text Available Controlled synthesis of silicon is a major challenge in nanotechnology and material science. Diatoms, the unicellular algae, are an inspiring example of silica biosynthesis, producing complex and delicate nano-structures. This happens in several cell compartments, including cytoplasm and silica deposition vesicle (SDV. Considering the low concentration of silicic acid in oceans, cells have developed silicon transporter proteins (SIT. Moreover, cells change the level of active SITs during one cell cycle, likely as a response to the level of external nutrients and internal deposition rates. Despite this topic being of fundamental interest, the intracellular dynamics of nutrients and cell regulation strategies remain poorly understood. One reason is the difficulties in measurements and manipulation of these mechanisms at such small scales, and even when possible, data often contain large errors. Therefore, using computational techniques seems inevitable. We have constructed a mathematical model for silicon dynamics in the diatom Thalassiosira pseudonana in four compartments: external environment, cytoplasm, SDV and deposited silica. The model builds on mass conservation and Michaelis-Menten kinetics as mass transport equations. In order to find the free parameters of the model from sparse, noisy experimental data, an optimization technique (global and local search, together with enzyme related penalty terms, has been applied. We have connected population-level data to individual-cell-level quantities including the effect of early division of non-synchronized cells. Our model is robust, proven by sensitivity and perturbation analysis, and predicts dynamics of intracellular nutrients and enzymes in different compartments. The model produces different uptake regimes, previously recognized as surge, externally-controlled and internally-controlled uptakes. Finally, we imposed a flux of SITs to the model and compared it with previous classical kinetics

  3. Dynamic subcellular localization of a respiratory complex controls bacterial respiration.

    Science.gov (United States)

    Alberge, François; Espinosa, Leon; Seduk, Farida; Sylvi, Léa; Toci, René; Walburger, Anne; Magalon, Axel

    2015-06-16

    Respiration, an essential process for most organisms, has to optimally respond to changes in the metabolic demand or the environmental conditions. The branched character of their respiratory chains allows bacteria to do so by providing a great metabolic and regulatory flexibility. Here, we show that the native localization of the nitrate reductase, a major respiratory complex under anaerobiosis in Escherichia coli, is submitted to tight spatiotemporal regulation in response to metabolic conditions via a mechanism using the transmembrane proton gradient as a cue for polar localization. These dynamics are critical for controlling the activity of nitrate reductase, as the formation of polar assemblies potentiates the electron flux through the complex. Thus, dynamic subcellular localization emerges as a critical factor in the control of respiration in bacteria.

  4. Spatiotemporal visualization of subcellular dynamics of carbon nanotubes

    KAUST Repository

    Serag, Maged F.

    2012-12-12

    To date, there is no consensus on the relationship between the physicochemical characteristics of carbon nanotubes (CNTs) and their biological behavior; however, there is growing evidence that the versatile characteristics make their biological fate largely unpredictable and remain an issue of limited knowledge. Here we introduce an experimental methodology for tracking and visualization of postuptake behavior and the intracellular fate of CNTs based on the spatial distribution of diffusion values throughout the plant cell. By using raster scan image correlation spectroscopy (RICS), we were able to generate highly quantitative spatial maps of CNTs diffusion in different cell compartments. The spatial map of diffusion values revealed that the uptake of CNTs is associated with important subcellular events such as carrier-mediated vacuolar transport and autophagy. These results show that RICS is a useful methodology to elucidate the intracellular behavior mechanisms of carbon nanotubes and potentially other fluorescently labeled nanoparticles, which is of relevance for the important issues related to the environmental impact and health hazards. © 2012 American Chemical Society.

  5. A Computational Modeling and Simulation Approach to Investigate Mechanisms of Subcellular cAMP Compartmentation.

    Directory of Open Access Journals (Sweden)

    Pei-Chi Yang

    2016-07-01

    Full Text Available Subcellular compartmentation of the ubiquitous second messenger cAMP has been widely proposed as a mechanism to explain unique receptor-dependent functional responses. How exactly compartmentation is achieved, however, has remained a mystery for more than 40 years. In this study, we developed computational and mathematical models to represent a subcellular sarcomeric space in a cardiac myocyte with varying detail. We then used these models to predict the contributions of various mechanisms that establish subcellular cAMP microdomains. We used the models to test the hypothesis that phosphodiesterases act as functional barriers to diffusion, creating discrete cAMP signaling domains. We also used the models to predict the effect of a range of experimentally measured diffusion rates on cAMP compartmentation. Finally, we modeled the anatomical structures in a cardiac myocyte diad, to predict the effects of anatomical diffusion barriers on cAMP compartmentation. When we incorporated experimentally informed model parameters to reconstruct an in silico subcellular sarcomeric space with spatially distinct cAMP production sites linked to caveloar domains, the models predict that under realistic conditions phosphodiesterases alone were insufficient to generate significant cAMP gradients. This prediction persisted even when combined with slow cAMP diffusion. When we additionally considered the effects of anatomic barriers to diffusion that are expected in the cardiac myocyte dyadic space, cAMP compartmentation did occur, but only when diffusion was slow. Our model simulations suggest that additional mechanisms likely contribute to cAMP gradients occurring in submicroscopic domains. The difference between the physiological and pathological effects resulting from the production of cAMP may be a function of appropriate compartmentation of cAMP signaling. Therefore, understanding the contribution of factors that are responsible for coordinating the spatial and

  6. Perspective: On the importance of hydrodynamic interactions in the subcellular dynamics of macromolecules.

    Science.gov (United States)

    Skolnick, Jeffrey

    2016-09-14

    An outstanding challenge in computational biophysics is the simulation of a living cell at molecular detail. Over the past several years, using Stokesian dynamics, progress has been made in simulating coarse grained molecular models of the cytoplasm. Since macromolecules comprise 20%-40% of the volume of a cell, one would expect that steric interactions dominate macromolecular diffusion. However, the reduction in cellular diffusion rates relative to infinite dilution is due, roughly equally, to steric and hydrodynamic interactions, HI, with nonspecific attractive interactions likely playing rather a minor role. HI not only serve to slow down long time diffusion rates but also cause a considerable reduction in the magnitude of the short time diffusion coefficient relative to that at infinite dilution. More importantly, the long range contribution of the Rotne-Prager-Yamakawa diffusion tensor results in temporal and spatial correlations that persist up to microseconds and for intermolecular distances on the order of protein radii. While HI slow down the bimolecular association rate in the early stages of lipid bilayer formation, they accelerate the rate of large scale assembly of lipid aggregates. This is suggestive of an important role for HI in the self-assembly kinetics of large macromolecular complexes such as tubulin. Since HI are important, questions as to whether continuum models of HI are adequate as well as improved simulation methodologies that will make simulations of more complex cellular processes practical need to be addressed. Nevertheless, the stage is set for the molecular simulations of ever more complex subcellular processes.

  7. Imaging cellular and subcellular structure of human brain tissue using micro computed tomography

    Science.gov (United States)

    Khimchenko, Anna; Bikis, Christos; Schweighauser, Gabriel; Hench, Jürgen; Joita-Pacureanu, Alexandra-Teodora; Thalmann, Peter; Deyhle, Hans; Osmani, Bekim; Chicherova, Natalia; Hieber, Simone E.; Cloetens, Peter; Müller-Gerbl, Magdalena; Schulz, Georg; Müller, Bert

    2017-09-01

    Brain tissues have been an attractive subject for investigations in neuropathology, neuroscience, and neurobiol- ogy. Nevertheless, existing imaging methodologies have intrinsic limitations in three-dimensional (3D) label-free visualisation of extended tissue samples down to (sub)cellular level. For a long time, these morphological features were visualised by electron or light microscopies. In addition to being time-consuming, microscopic investigation includes specimen fixation, embedding, sectioning, staining, and imaging with the associated artefacts. More- over, optical microscopy remains hampered by a fundamental limit in the spatial resolution that is imposed by the diffraction of visible light wavefront. In contrast, various tomography approaches do not require a complex specimen preparation and can now reach a true (sub)cellular resolution. Even laboratory-based micro computed tomography in the absorption-contrast mode of formalin-fixed paraffin-embedded (FFPE) human cerebellum yields an image contrast comparable to conventional histological sections. Data of a superior image quality was obtained by means of synchrotron radiation-based single-distance X-ray phase-contrast tomography enabling the visualisation of non-stained Purkinje cells down to the subcellular level and automated cell counting. The question arises, whether the data quality of the hard X-ray tomography can be superior to optical microscopy. Herein, we discuss the label-free investigation of the human brain ultramorphology be means of synchrotron radiation-based hard X-ray magnified phase-contrast in-line tomography at the nano-imaging beamline ID16A (ESRF, Grenoble, France). As an example, we present images of FFPE human cerebellum block. Hard X-ray tomography can provide detailed information on human tissues in health and disease with a spatial resolution below the optical limit, improving understanding of the neuro-degenerative diseases.

  8. Subcellular targeting and dynamic regulation of PTEN: Implications for neuronal cells and neurological disorders

    Directory of Open Access Journals (Sweden)

    Patricia eKreis

    2014-04-01

    Full Text Available PTEN is a lipid and protein phosphatase that regulates a diverse range of cellular mechanisms. PTEN is mainly present in the cytosol and transiently associates with the plasma membrane to dephosphorylate PI(3,4,5P3, thereby antagonizing the PI3-Kinase signaling pathway. Recently, PTEN has been shown to associate also with organelles such as the endoplasmic reticulum, the mitochondria or the nucleus, and to be secreted outside of the cell. In addition, PTEN dynamically localizes to specialized sub-cellular compartments such as the neuronal growth cone or dendritic spines. The diverse localizations of PTEN imply a tight temporal and spatial regulation, orchestrated by mechanisms such as posttranslational modifications, formation of distinct protein-protein interactions or the activation/recruitment of PTEN downstream of external cues. The regulation of PTEN function is thus not only important at the enzymatic activity level, but is also associated to its spatial distribution. In this review we will summarize (i recent findings that highlight mechanisms controlling PTEN movement and sub-cellular localization, and (ii current understanding of how PTEN localization is achieved by mechanisms controlling posttranslational modification, by association with binding partners and by PTEN structural or activity requirements. Finally, we will discuss the possible roles of compartmentalized PTEN in developing and mature neurons in health and disease.

  9. Subcellular targeting and dynamic regulation of PTEN: implications for neuronal cells and neurological disorders.

    Science.gov (United States)

    Kreis, Patricia; Leondaritis, George; Lieberam, Ivo; Eickholt, Britta J

    2014-01-01

    PTEN is a lipid and protein phosphatase that regulates a diverse range of cellular mechanisms. PTEN is mainly present in the cytosol and transiently associates with the plasma membrane to dephosphorylate PI(3,4,5)P3, thereby antagonizing the PI3-Kinase signaling pathway. Recently, PTEN has been shown to associate also with organelles such as the endoplasmic reticulum (ER), the mitochondria, or the nucleus, and to be secreted outside of the cell. In addition, PTEN dynamically localizes to specialized sub-cellular compartments such as the neuronal growth cone or dendritic spines. The diverse localizations of PTEN imply a tight temporal and spatial regulation, orchestrated by mechanisms such as posttranslational modifications, formation of distinct protein-protein interactions, or the activation/recruitment of PTEN downstream of external cues. The regulation of PTEN function is thus not only important at the enzymatic activity level, but is also associated to its spatial distribution. In this review we will summarize (i) recent findings that highlight mechanisms controlling PTEN movement and sub-cellular localization, and (ii) current understanding of how PTEN localization is achieved by mechanisms controlling posttranslational modification, by association with binding partners and by PTEN structural or activity requirements. Finally, we will discuss the possible roles of compartmentalized PTEN in developing and mature neurons in health and disease.

  10. Agent-Based Modeling of Mitochondria Links Sub-Cellular Dynamics to Cellular Homeostasis and Heterogeneity.

    Directory of Open Access Journals (Sweden)

    Giovanni Dalmasso

    amplifying, cell-to-cell variability of mitochondrial morphology and energetic stress states. Overall, our modeling approach integrates biochemical and imaging knowledge, and presents a novel open-modeling approach to investigate how spatial and temporal mitochondrial dynamics contribute to functional homeostasis, and how subcellular organelle heterogeneity contributes to the emergence of cell heterogeneity.

  11. Precise Photodynamic Therapy of Cancer via Subcellular Dynamic Tracing of Dual-loaded Upconversion Nanophotosensitizers

    National Research Council Canada - National Science Library

    Yulei Chang; Xiaodan Li; Li Zhang; Lu Xia; Xiaomin Liu; Cuixia Li; Youlin Zhang; Langping Tu; Bin Xue; Huiying Zhao; Hong Zhang; Xianggui Kong

    2017-01-01

    ...) light have led to substantial progress in improving photodynamic therapy (PDT) of cancer. For a successful PDT, subcellular organelles are promising therapeutic targets for reaching a satisfactory efficacy...

  12. Fast two-photon imaging of subcellular voltage dynamics in neuronal tissue with genetically encoded indicators.

    Science.gov (United States)

    Chamberland, Simon; Yang, Helen H; Pan, Michael M; Evans, Stephen W; Guan, Sihui; Chavarha, Mariya; Yang, Ying; Salesse, Charleen; Wu, Haodi; Wu, Joseph C; Clandinin, Thomas R; Toth, Katalin; Lin, Michael Z; St-Pierre, François

    2017-07-27

    Monitoring voltage dynamics in defined neurons deep in the brain is critical for unraveling the function of neuronal circuits but is challenging due to the limited performance of existing tools. In particular, while genetically encoded voltage indicators have shown promise for optical detection of voltage transients, many indicators exhibit low sensitivity when imaged under two-photon illumination. Previous studies thus fell short of visualizing voltage dynamics in individual neurons in single trials. Here, we report ASAP2s, a novel voltage indicator with improved sensitivity. By imaging ASAP2s using random-access multi-photon microscopy, we demonstrate robust single-trial detection of action potentials in organotypic slice cultures. We also show that ASAP2s enables two-photon imaging of graded potentials in organotypic slice cultures and in Drosophila . These results demonstrate that the combination of ASAP2s and fast two-photon imaging methods enables detection of neural electrical activity with subcellular spatial resolution and millisecond-timescale precision.

  13. Computational reacting gas dynamics

    Science.gov (United States)

    Lam, S. H.

    1993-01-01

    In the study of high speed flows at high altitudes, such as that encountered by re-entry spacecrafts, the interaction of chemical reactions and other non-equilibrium processes in the flow field with the gas dynamics is crucial. Generally speaking, problems of this level of complexity must resort to numerical methods for solutions, using sophisticated computational fluid dynamics (CFD) codes. The difficulties introduced by reacting gas dynamics can be classified into three distinct headings: (1) the usually inadequate knowledge of the reaction rate coefficients in the non-equilibrium reaction system; (2) the vastly larger number of unknowns involved in the computation and the expected stiffness of the equations; and (3) the interpretation of the detailed reacting CFD numerical results. The research performed accepts the premise that reacting flows of practical interest in the future will in general be too complex or 'untractable' for traditional analytical developments. The power of modern computers must be exploited. However, instead of focusing solely on the construction of numerical solutions of full-model equations, attention is also directed to the 'derivation' of the simplified model from the given full-model. In other words, the present research aims to utilize computations to do tasks which have traditionally been done by skilled theoreticians: to reduce an originally complex full-model system into an approximate but otherwise equivalent simplified model system. The tacit assumption is that once the appropriate simplified model is derived, the interpretation of the detailed numerical reacting CFD numerical results will become much easier. The approach of the research is called computational singular perturbation (CSP).

  14. Genome-wide identification of the subcellular localization of the Escherichia coli B proteome using experimental and computational methods.

    Science.gov (United States)

    Han, Mee-Jung; Yun, Hongseok; Lee, Jeong Wook; Lee, Yu Hyun; Lee, Sang Yup; Yoo, Jong-Shin; Kim, Jin Young; Kim, Jihyun F; Hur, Cheol-Goo

    2011-04-01

    Escherichia coli K-12 and B strains have most widely been employed for scientific studies as well as industrial applications. Recently, the complete genome sequences of two representative descendants of E. coli B strains, REL606 and BL21(DE3), have been determined. Here, we report the subproteome reference maps of E. coli B REL606 by analyzing cytoplasmic, periplasmic, inner and outer membrane, and extracellular proteomes based on the genome information using experimental and computational approaches. Among the total of 3487 spots, 651 proteins including 410 non-redundant proteins were identified and characterized by 2-DE and LC-MS/MS; they include 440 cytoplasmic, 45 periplasmic, 50 inner membrane, 61 outer membrane, and 55 extracellular proteins. In addition, subcellular localizations of all 4205 ORFs of E. coli B were predicted by combined computational prediction methods. The subcellular localizations of 1812 (43.09%) proteins of currently unknown function were newly assigned. The results of computational prediction were also compared with the experimental results, showing that overall precision and recall were 92.16 and 92.16%, respectively. This work represents the most comprehensive analyses of the subproteomes of E. coli B, and will be useful as a reference for proteome profiling studies under various conditions. The complete proteome data are available online (http://ecolib.kaist.ac.kr). Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Essential Computational Fluid Dynamics

    CERN Document Server

    Zikanov, Oleg

    2011-01-01

    This book serves as a complete and self-contained introduction to the principles of Computational Fluid Dynamic (CFD) analysis. It is deliberately short (at approximately 300 pages) and can be used as a text for the first part of the course of applied CFD followed by a software tutorial. The main objectives of this non-traditional format are: 1) To introduce and explain, using simple examples where possible, the principles and methods of CFD analysis and to demystify the `black box’ of a CFD software tool, and 2) To provide a basic understanding of how CFD problems are set and

  16. Computational fluid dynamics

    CERN Document Server

    Magoules, Frederic

    2011-01-01

    Exploring new variations of classical methods as well as recent approaches appearing in the field, Computational Fluid Dynamics demonstrates the extensive use of numerical techniques and mathematical models in fluid mechanics. It presents various numerical methods, including finite volume, finite difference, finite element, spectral, smoothed particle hydrodynamics (SPH), mixed-element-volume, and free surface flow.Taking a unified point of view, the book first introduces the basis of finite volume, weighted residual, and spectral approaches. The contributors present the SPH method, a novel ap

  17. Novel Application of Fluorescence Lifetime and Fluorescence Microscopy Enables Quantitative Access to Subcellular Dynamics in Plant Cells

    Science.gov (United States)

    Elgass, Kirstin; Caesar, Katharina; Schleifenbaum, Frank; Stierhof, York-Dieter; Meixner, Alfred J.; Harter, Klaus

    2009-01-01

    Background Optical and spectroscopic technologies working at subcellular resolution with quantitative output are required for a deeper understanding of molecular processes and mechanisms in living cells. Such technologies are prerequisite for the realisation of predictive biology at cellular and subcellular level. However, although established in the physical sciences, these techniques are rarely applied to cell biology in the plant sciences. Principal Findings Here, we present a combined application of one-chromophore fluorescence lifetime microscopy and wavelength-selective fluorescence microscopy to analyse the function of a GFP fusion of the Brassinosteroid Insensitive 1 Receptor (BRI1-GFP) with high spatial and temporal resolution in living Arabidopsis cells in their tissue environment. We show a rapid, brassinolide-induced cell wall expansion and a fast BR-regulated change in the BRI1-GFP fluorescence lifetime in the plasmamembrane in vivo. Both cell wall expansion and changes in fluorescence lifetime reflect early BR-induced and BRI1-dependent physiological or signalling processes. Our experiments also show the potential of one-chromophore fluorescence lifetime microscopy for the in vivo monitoring of the biochemical and biophysical subcellular environment using GFP fusion proteins as probes. Significance One-chromophore fluorescence lifetime microscopy, combined with wavelength-specific fluorescence microscopy, opens up new frontiers for in vivo dynamic and quantitative analysis of cellular processes at high resolution which are not addressable by pure imaging technologies or transmission electron microscopy. PMID:19492078

  18. Computational fluid dynamic applications

    Energy Technology Data Exchange (ETDEWEB)

    Chang, S.-L.; Lottes, S. A.; Zhou, C. Q.

    2000-04-03

    The rapid advancement of computational capability including speed and memory size has prompted the wide use of computational fluid dynamics (CFD) codes to simulate complex flow systems. CFD simulations are used to study the operating problems encountered in system, to evaluate the impacts of operation/design parameters on the performance of a system, and to investigate novel design concepts. CFD codes are generally developed based on the conservation laws of mass, momentum, and energy that govern the characteristics of a flow. The governing equations are simplified and discretized for a selected computational grid system. Numerical methods are selected to simplify and calculate approximate flow properties. For turbulent, reacting, and multiphase flow systems the complex processes relating to these aspects of the flow, i.e., turbulent diffusion, combustion kinetics, interfacial drag and heat and mass transfer, etc., are described in mathematical models, based on a combination of fundamental physics and empirical data, that are incorporated into the code. CFD simulation has been applied to a large variety of practical and industrial scale flow systems.

  19. Dynamic full field optical coherence tomography: subcellular metabolic contrast revealed in tissues by temporal analysis of interferometric signals

    CERN Document Server

    Apelian, Clement; Thouvenin, Olivier; Boccara, A Claude

    2016-01-01

    We developed a new endogenous approach to reveal subcellular metabolic contrast in fresh ex vivo tissues taking advantage of the time dependence of the full field optical coherence tomography interferometric signals. This method reveals signals linked with local activity of the endogenous scattering elements which can reveal cells where other imaging techniques fail or need exogenous contrast agents. We benefit from the micrometric transverse resolution of full field OCT to image intracellular features. We used this time dependence to identify different dynamics at the millisecond scale on a wide range of organs in normal or pathological conditions.

  20. Assessing the precision of high-throughput computational and laboratory approaches for the genome-wide identification of protein subcellular localization in bacteria

    Directory of Open Access Journals (Sweden)

    Brinkman Fiona SL

    2005-11-01

    Full Text Available Abstract Background Identification of a bacterial protein's subcellular localization (SCL is important for genome annotation, function prediction and drug or vaccine target identification. Subcellular fractionation techniques combined with recent proteomics technology permits the identification of large numbers of proteins from distinct bacterial compartments. However, the fractionation of a complex structure like the cell into several subcellular compartments is not a trivial task. Contamination from other compartments may occur, and some proteins may reside in multiple localizations. New computational methods have been reported over the past few years that now permit much more accurate, genome-wide analysis of the SCL of protein sequences deduced from genomes. There is a need to compare such computational methods with laboratory proteomics approaches to identify the most effective current approach for genome-wide localization characterization and annotation. Results In this study, ten subcellular proteome analyses of bacterial compartments were reviewed. PSORTb version 2.0 was used to computationally predict the localization of proteins reported in these publications, and these computational predictions were then compared to the localizations determined by the proteomics study. By using a combined approach, we were able to identify a number of contaminants and proteins with dual localizations, and were able to more accurately identify membrane subproteomes. Our results allowed us to estimate the precision level of laboratory subproteome studies and we show here that, on average, recent high-precision computational methods such as PSORTb now have a lower error rate than laboratory methods. Conclusion We have performed the first focused comparison of genome-wide proteomic and computational methods for subcellular localization identification, and show that computational methods have now attained a level of precision that is exceeding that of high

  1. Computational methods in stochastic dynamics

    CERN Document Server

    Papadrakakis, Manolis; Papadopoulos, Vissarion

    2011-01-01

    Covering what is an emerging frontier in research, this book focuses on advanced computational methods and software tools. These can be of huge assistance in tackling complex problems in stochastic dynamic and seismic analysis as well as structure design.

  2. Dynamic Subcellular Localization of Iron during Embryo Development in Brassicaceae Seeds

    Directory of Open Access Journals (Sweden)

    Miguel A. Ibeas

    2017-12-01

    Full Text Available Iron is an essential micronutrient for plants. Little is know about how iron is loaded in embryo during seed development. In this article we used Perls/DAB staining in order to reveal iron localization at the cellular and subcellular levels in different Brassicaceae seed species. In dry seeds of Brassica napus, Nasturtium officinale, Lepidium sativum, Camelina sativa, and Brassica oleracea iron localizes in vacuoles of cells surrounding provasculature in cotyledons and hypocotyl. Using B. napus and N. officinale as model plants we determined where iron localizes during seed development. Our results indicate that iron is not detectable by Perls/DAB staining in heart stage embryo cells. Interestingly, at torpedo development stage iron localizes in nuclei of different cells type, including integument, free cell endosperm and almost all embryo cells. Later, iron is detected in cytoplasmic structures in different embryo cell types. Our results indicate that iron accumulates in nuclei in specific stages of embryo maturation before to be localized in vacuoles of cells surrounding provasculature in mature seeds.

  3. Dynamic Subcellular Localization of Iron during Embryo Development in Brassicaceae Seeds.

    Science.gov (United States)

    Ibeas, Miguel A; Grant-Grant, Susana; Navarro, Nathalia; Perez, M F; Roschzttardtz, Hannetz

    2017-01-01

    Iron is an essential micronutrient for plants. Little is know about how iron is loaded in embryo during seed development. In this article we used Perls/DAB staining in order to reveal iron localization at the cellular and subcellular levels in different Brassicaceae seed species. In dry seeds of Brassica napus, Nasturtium officinale, Lepidium sativum, Camelina sativa, and Brassica oleracea iron localizes in vacuoles of cells surrounding provasculature in cotyledons and hypocotyl. Using B. napus and N. officinale as model plants we determined where iron localizes during seed development. Our results indicate that iron is not detectable by Perls/DAB staining in heart stage embryo cells. Interestingly, at torpedo development stage iron localizes in nuclei of different cells type, including integument, free cell endosperm and almost all embryo cells. Later, iron is detected in cytoplasmic structures in different embryo cell types. Our results indicate that iron accumulates in nuclei in specific stages of embryo maturation before to be localized in vacuoles of cells surrounding provasculature in mature seeds.

  4. Subcellular distribution of glutathione and its dynamic changes under oxidative stress in the yeast Saccharomyces cerevisiae

    Science.gov (United States)

    Zechmann, Bernd; Liou, Liang-Chun; Koffler, Barbara E; Horvat, Lucija; Tomašić, Ana; Fulgosi, Hrvoje; Zhang, Zhaojie

    2011-01-01

    Glutathione is an important antioxidant in most prokaryotes and eukaryotes. It detoxifies reactive oxygen species and is also involved in the modulation of gene expression, in redox signaling, and in the regulation of enzymatic activities. In this study, the subcellular distribution of glutathione was studied in Saccharomyces cerevisiae by quantitative immunoelectron microscopy. Highest glutathione contents were detected in mitochondria and subsequently in the cytosol, nuclei, cell walls, and vacuoles. The induction of oxidative stress by hydrogen peroxide (H2O2) led to changes in glutathione-specific labeling. Three cell types were identified. Cell types I and II contained more glutathione than control cells. Cell type II differed from cell type I in showing a decrease in glutathione-specific labeling solely in mitochondria. Cell type III contained much less glutathione contents than the control and showed the strongest decrease in mitochondria, suggesting that high and stable levels of glutathione in mitochondria are important for the protection and survival of the cells during oxidative stress. Additionally, large amounts of glutathione were relocated and stored in vacuoles in cell type III, suggesting the importance of the sequestration of glutathione in vacuoles under oxidative stress. PMID:22093747

  5. Narciclasine, a potential allelochemical, affects subcellular trafficking of auxin transporter proteins and actin cytoskeleton dynamics in Arabidopsis roots.

    Science.gov (United States)

    Hu, Yanfeng; Na, Xiaofan; Li, Jiaolong; Yang, Lijing; You, Jia; Liang, Xiaolei; Wang, Jianfeng; Peng, Liang; Bi, Yurong

    2015-12-01

    The present study documented the action of a potential allelochemical, narciclasine, on auxin transport in Arabidopsis by mainly affecting subcellular trafficking of PIN and AUX1 proteins and through interfering actin cytoskeletal organization. Narciclasine (NCS), an Amaryllidaceae alkaloid isolated from Narcissus tazetta bulbs, has potential allelopathic activity and affects auxin transport. However, little is known about the cellular mechanism of this inhibitory effect of NCS on auxin transport. The present study characterizes the effects of NCS at the cellular level using transgenic Arabidopsis plants harboring the promoters of PIN, in combination with PIN-GFP proteins or AUX1-YFP fusions. NCS treatment caused significant reduction in the abundance of PIN and AUX1 proteins at the plasma membrane (PM). Analysis of the subcellular distribution of PIN and AUX1 proteins in roots revealed that NCS induced the intracellular accumulation of auxin transporters, including PIN2, PIN3, PIN4, PIN7 and AUX1. However, other PM proteins, such as PIP2, BRI1, and low temperature inducible protein 6b (LTI6b), were insensitive to NCS treatment. NCS-induced PIN2 compartments were further defined using endocytic tracer FM 4-64 labeled early endosomes and suggested that this compound affects the endocytosis trafficking of PIN proteins. Furthermore, pharmacological analysis indicated that the brefeldin A (BFA)-insensitive pathway is employed in the cellular effects of NCS on PIN2 trafficking. Although NCS did not alter actin dynamics in vitro, it resulted in the depolymerization of the actin cytoskeleton in vivo. This disruption of actin filaments by NCS subsequently influences the actin-based vesicle motility. Hence, the elucidation of the specific role of NCS is useful for further understanding the mechanisms of allelopathy at the phytohormone levels.

  6. Integrating Molecular Computation and Material Production in an Artificial Subcellular Matrix

    DEFF Research Database (Denmark)

    Fellermann, Harold; Hadorn, Maik; Bönzli, Eva

    compartmentalized re- action compartments that interact and get delivered through vesicle trafficking. The European Commission funded project MatchIT (Matrix for Chemical IT) aims at creating an artificial cellular matrix that seamlessly integrates infor- mation processing and material production in much the same......Living systems are unique in that they integrate molecular recognition and information processing with material production on the molecular scale. Pre- dominant locus of this integration is the cellular matrix, where a multitude of biochemical reactions proceed simultaneously in highly...... way as its biological counterpart: the project employs addressable chemical containers (chemtainers) interfaced with electronic computers via mechano-electronic microfluidics....

  7. The effect of pH dependence of antibody-antigen interactions on subcellular trafficking dynamics

    Science.gov (United States)

    Devanaboyina, Siva Charan; Lynch, Sandra M; Ober, Raimund J; Ram, Sripad; Kim, Dongyoung; Puig-Canto, Alberto; Breen, Shannon; Kasturirangan, Srinath; Fowler, Susan; Peng, Li; Zhong, Haihong; Jermutus, Lutz; Wu, Herren; Webster, Carl; Ward, E Sally; Gao, Changshou

    2013-01-01

    A drawback of targeting soluble antigens such as cytokines or toxins with long-lived antibodies is that such antibodies can prolong the half-life of the target antigen by a “buffering” effect. This has motivated the design of antibodies that bind to target with higher affinity at near neutral pH relative to acidic endosomal pH (~pH 6.0). Such antibodies are expected to release antigen within endosomes following uptake into cells, whereas antibody will be recycled and exocytosed in FcRn-expressing cells. To understand how the pH dependence of antibody-antigen interactions affects intracellular trafficking, we generated three antibodies that bind IL-6 with different pH dependencies in the range pH 6.0–7.4. The behavior of antigen in the presence of these antibodies has been characterized using a combination of fixed and live cell fluorescence microscopy. As the affinity of the antibody:IL-6 interaction at pH 6.0 decreases, an increasing amount of antigen dissociates from FcRn-bound antibody in early and late endosomes, and then enters lysosomes. Segregation of antibody and FcRn from endosomes in tubulovesicular transport carriers (TCs) into the recycling pathway can also be observed in live cells, and the extent of IL-6 association with TCs correlates with increasing affinity of the antibody:IL-6 interaction at acidic pH. These analyses result in an understanding, in spatiotemporal terms, of the effect of pH dependence of antibody-antigen interactions on subcellular trafficking and inform the design of antibodies with optimized binding properties for antigen elimination. PMID:24492341

  8. Topography on a subcellular scale modulates cellular adhesions and actin stress fiber dynamics in tumor associated fibroblasts

    Science.gov (United States)

    Azatov, Mikheil; Sun, Xiaoyu; Suberi, Alexandra; Fourkas, John T.; Upadhyaya, Arpita

    2017-12-01

    Cells can sense and adapt to mechanical properties of their environment. The local geometry of the extracellular matrix, such as its topography, has been shown to modulate cell morphology, migration, and proliferation. Here we investigate the effect of micro/nanotopography on the morphology and cytoskeletal dynamics of human pancreatic tumor-associated fibroblast cells (TAFs). We use arrays of parallel nanoridges with variable spacings on a subcellular scale to investigate the response of TAFs to the topography of their environment. We find that cell shape and stress fiber organization both align along the direction of the nanoridges. Our analysis reveals a strong bimodal relationship between the degree of alignment and the spacing of the nanoridges. Furthermore, focal adhesions align along ridges and form preferentially on top of the ridges. Tracking actin stress fiber movement reveals enhanced dynamics of stress fibers on topographically patterned surfaces. We find that components of the actin cytoskeleton move preferentially along the ridges with a significantly higher velocity along the ridges than on a flat surface. Our results suggest that a complex interplay between the actin cytoskeleton and focal adhesions coordinates the cellular response to micro/nanotopography.

  9. Subcellular metabolic organization in the context of dynamic energy budget and biochemical systems theories

    NARCIS (Netherlands)

    Vinga, S.; Neves, A.S.; Santos, H.; Brandt, B.W.; Kooijman, S.A.L.M.

    2010-01-01

    The dynamic modelling of metabolic networks aims to describe the temporal evolution of metabolite concentrations in cells. This area has attracted increasing attention in recent years owing to the availability of high-throughput data and the general development of systems biology as a promising

  10. Computational dynamics of soft machines

    Science.gov (United States)

    Hu, Haiyan; Tian, Qiang; Liu, Cheng

    2017-06-01

    Soft machine refers to a kind of mechanical system made of soft materials to complete sophisticated missions, such as handling a fragile object and crawling along a narrow tunnel corner, under low cost control and actuation. Hence, soft machines have raised great challenges to computational dynamics. In this review article, recent studies of the authors on the dynamic modeling, numerical simulation, and experimental validation of soft machines are summarized in the framework of multibody system dynamics. The dynamic modeling approaches are presented first for the geometric nonlinearities of coupled overall motions and large deformations of a soft component, the physical nonlinearities of a soft component made of hyperelastic or elastoplastic materials, and the frictional contacts/impacts of soft components, respectively. Then the computation approach is outlined for the dynamic simulation of soft machines governed by a set of differential-algebraic equations of very high dimensions, with an emphasis on the efficient computations of the nonlinear elastic force vector of finite elements. The validations of the proposed approaches are given via three case studies, including the locomotion of a soft quadrupedal robot, the spinning deployment of a solar sail of a spacecraft, and the deployment of a mesh reflector of a satellite antenna, as well as the corresponding experimental studies. Finally, some remarks are made for future studies.

  11. Validation of computational fluid dynamics

    Science.gov (United States)

    Sacher, P. W.; Bradley, R. G., Jr.; Schmidt, W.

    1989-05-01

    The Fluid Dynamics Panel AGARD Symposium entitled Validation of Computational Fluid Dynamics is reviewed and evaluated. The purpose of the Symposium was to assess the state of the art of Validation of Computer Codes and to ensure that the mathematical and numerical schemes employed in the codes correctly model the critical physics of the flow field under consideration. The evaluator addresses each of the papers presented separately and makes general comments on the seven major topic sessions. In addition, a Poster Session is reviewed in detail. It is evident that the new possibilities of CFD provide efficient tools for Analysis and Design in the Aeronautical Industry, but it is also evident that in spite of the existence of a number of excellent experimental databases, there is still a need for efforts in validating the computer programs both by experiment as well as by numerical exercises.

  12. Principles of computational fluid dynamics

    CERN Document Server

    Wesseling, Pieter

    2001-01-01

    The book is aimed at graduate students, researchers, engineers and physicists involved in flow computations. An up-to-date account is given of the present state-of-the-art of numerical methods employed in computational fluid dynamics. The underlying numerical principles are treated with a fair amount of detail, using elementary mathematical analysis. Attention is given to difficulties arising from geometric complexity of the flow domain and of nonuniform structured boundary-fitted grids. Uniform accuracy and efficiency for singular perturbation problems is studied, pointing the way to accurate computation of flows at high Reynolds number. Much attention is given to stability analysis, and useful stability conditions are provided, some of them new, for many numerical schemes used in practice. Unified methods for compressible and incompressible flows are discussed. Numerical analysis of the shallow-water equations is included. The theory of hyperbolic conservation laws is treated. Godunov's order barrier and ho...

  13. Dynamic computing random access memory

    Science.gov (United States)

    Traversa, F. L.; Bonani, F.; Pershin, Y. V.; Di Ventra, M.

    2014-07-01

    The present von Neumann computing paradigm involves a significant amount of information transfer between a central processing unit and memory, with concomitant limitations in the actual execution speed. However, it has been recently argued that a different form of computation, dubbed memcomputing (Di Ventra and Pershin 2013 Nat. Phys. 9 200-2) and inspired by the operation of our brain, can resolve the intrinsic limitations of present day architectures by allowing for computing and storing of information on the same physical platform. Here we show a simple and practical realization of memcomputing that utilizes easy-to-build memcapacitive systems. We name this architecture dynamic computing random access memory (DCRAM). We show that DCRAM provides massively-parallel and polymorphic digital logic, namely it allows for different logic operations with the same architecture, by varying only the control signals. In addition, by taking into account realistic parameters, its energy expenditures can be as low as a few fJ per operation. DCRAM is fully compatible with CMOS technology, can be realized with current fabrication facilities, and therefore can really serve as an alternative to the present computing technology.

  14. Computational Fluid Dynamics in Ventilation

    DEFF Research Database (Denmark)

    Nielsen, Peter V.; Allard, Francis; Awbi, Hazim B.

    2008-01-01

    Computational Fluid Dynamics in Ventilation Design is a new title in the is a new title in the REHVA guidebook series. The guidebook is written for people who need to use and discuss results based on CFD predictions, and it gives insight into the subject for those who are not used to work with CFD....... The guidebook is also written for people working with CFD which have to be more aware of how this numerical method is applied in the area of ventilation. The guidebook has, for example, chapters that are very important for CFD quality control in general and for the quality control of ventilation related...

  15. Computational Methods for Structural Mechanics and Dynamics

    Science.gov (United States)

    Stroud, W. Jefferson (Editor); Housner, Jerrold M. (Editor); Tanner, John A. (Editor); Hayduk, Robert J. (Editor)

    1989-01-01

    Topics addressed include: transient dynamics; transient finite element method; transient analysis in impact and crash dynamic studies; multibody computer codes; dynamic analysis of space structures; multibody mechanics and manipulators; spatial and coplanar linkage systems; flexible body simulation; multibody dynamics; dynamical systems; and nonlinear characteristics of joints.

  16. Oleuropein: Molecular Dynamics and Computation.

    Science.gov (United States)

    Gentile, Luigi; Uccella, Nicola A; Sivakumar, Ganapathy

    2017-09-11

    Olive oil and table olive biophenols have been shown to significantly enrich the hedonic-sensory and nutritional quality of the Mediterranean diet. Oleuropein is one of the predominate biophenols in green olives and leaves, which not only has noteworthy free-radical quenching activity but also putatively reduces the incidence of various cancers. Clinical trials suggest that the consumption of extra virgin olive oil reduces the risk of several degenerative diseases. The oleuropein-based bioactives in olive oil could reduce tumor necrosis factor α, interleukin-1β and nitric oxide. Therefore, olive bioactives quality should be preserved and even improved due to their disease-fighting properties. Understanding the molecular dynamics of oleuropein is crucial to increase olive oil and table olive quality. The objective of this review is to provide the molecular dynamics and computational mapping of oleuropein. It is a biophenol-secoiridoid expressing different functionalities such as two π-bonds, two esters, two acetals, one catechol, and four hexose hydroxyls within 540 mw. The molecular bond sequential breaking mechanisms were analyzed through unimolecular reactions under electron spray ionization, collision activated dissociations, and fast atom bombardment mass spectrometry. The oleuropein solvent-free reactivity is leading to glucose loss and bioactive aglycone-dialdehydes via secoiridoid ring opening. Oleuropein electron distribution revealed that the free-radical non-polar processes occur from its highest occupied molecular orbital, while the lowest unoccupied molecular orbital is clearly devoted to nucleophilic and base site reactivity. This molecular dynamics and computational mapping of oleuropein could contribute to the engineering of olive-based biomedicine and/or functional food. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  17. Computational methods for fluid dynamics

    CERN Document Server

    Ferziger, Joel H

    2002-01-01

    In its 3rd revised and extended edition the book offers an overview of the techniques used to solve problems in fluid mechanics on computers and describes in detail those most often used in practice. Included are advanced methods in computational fluid dynamics, like direct and large-eddy simulation of turbulence, multigrid methods, parallel computing, moving grids, structured, block-structured and unstructured boundary-fitted grids, free surface flows. The 3rd edition contains a new section dealing with grid quality and an extended description of discretization methods. The book shows common roots and basic principles for many different methods. The book also contains a great deal of practical advice for code developers and users, it is designed to be equally useful to beginners and experts. The issues of numerical accuracy, estimation and reduction of numerical errors are dealt with in detail, with many examples. A full-feature user-friendly demo-version of a commercial CFD software has been added, which ca...

  18. Dynamics of Information as Natural Computation

    Directory of Open Access Journals (Sweden)

    Gordana Dodig Crnkovic

    2011-08-01

    Full Text Available Processes considered rendering information dynamics have been studied, among others in: questions and answers, observations, communication, learning, belief revision, logical inference, game-theoretic interactions and computation. This article will put the computational approaches into a broader context of natural computation, where information dynamics is not only found in human communication and computational machinery but also in the entire nature. Information is understood as representing the world (reality as an informational web for a cognizing agent, while information dynamics (information processing, computation realizes physical laws through which all the changes of informational structures unfold. Computation as it appears in the natural world is more general than the human process of calculation modeled by the Turing machine. Natural computing is epitomized through the interactions of concurrent, in general asynchronous computational processes which are adequately represented by what Abramsky names “the second generation models of computation” [1] which we argue to be the most general representation of information dynamics.

  19. Model dynamics for quantum computing

    Science.gov (United States)

    Tabakin, Frank

    2017-08-01

    A model master equation suitable for quantum computing dynamics is presented. In an ideal quantum computer (QC), a system of qubits evolves in time unitarily and, by virtue of their entanglement, interfere quantum mechanically to solve otherwise intractable problems. In the real situation, a QC is subject to decoherence and attenuation effects due to interaction with an environment and with possible short-term random disturbances and gate deficiencies. The stability of a QC under such attacks is a key issue for the development of realistic devices. We assume that the influence of the environment can be incorporated by a master equation that includes unitary evolution with gates, supplemented by a Lindblad term. Lindblad operators of various types are explored; namely, steady, pulsed, gate friction, and measurement operators. In the master equation, we use the Lindblad term to describe short time intrusions by random Lindblad pulses. The phenomenological master equation is then extended to include a nonlinear Beretta term that describes the evolution of a closed system with increasing entropy. An external Bath environment is stipulated by a fixed temperature in two different ways. Here we explore the case of a simple one-qubit system in preparation for generalization to multi-qubit, qutrit and hybrid qubit-qutrit systems. This model master equation can be used to test the stability of memory and the efficacy of quantum gates. The properties of such hybrid master equations are explored, with emphasis on the role of thermal equilibrium and entropy constraints. Several significant properties of time-dependent qubit evolution are revealed by this simple study.

  20. Automated Multi-Peak Tracking Kymography (AMTraK: A Tool to Quantify Sub-Cellular Dynamics with Sub-Pixel Accuracy.

    Directory of Open Access Journals (Sweden)

    Anushree R Chaphalkar

    Full Text Available Kymographs or space-time plots are widely used in cell biology to reduce the dimensions of a time-series in microscopy for both qualitative and quantitative insight into spatio-temporal dynamics. While multiple tools for image kymography have been described before, quantification remains largely manual. Here, we describe a novel software tool for automated multi-peak tracking kymography (AMTraK, which uses peak information and distance minimization to track and automatically quantify kymographs, integrated in a GUI. The program takes fluorescence time-series data as an input and tracks contours in the kymographs based on intensity and gradient peaks. By integrating a branch-point detection method, it can be used to identify merging and splitting events of tracks, important in separation and coalescence events. In tests with synthetic images, we demonstrate sub-pixel positional accuracy of the program. We test the program by quantifying sub-cellular dynamics in rod-shaped bacteria, microtubule (MT transport and vesicle dynamics. A time-series of E. coli cell division with labeled nucleoid DNA is used to identify the time-point and rate at which the nucleoid segregates. The mean velocity of microtubule (MT gliding motility due to a recombinant kinesin motor is estimated as 0.5 μm/s, in agreement with published values, and comparable to estimates using software for nanometer precision filament-tracking. We proceed to employ AMTraK to analyze previously published time-series microscopy data where kymographs had been manually quantified: clathrin polymerization kinetics during vesicle formation and anterograde and retrograde transport in axons. AMTraK analysis not only reproduces the reported parameters, it also provides an objective and automated method for reproducible analysis of kymographs from in vitro and in vivo fluorescence microscopy time-series of sub-cellular dynamics.

  1. Automated Multi-Peak Tracking Kymography (AMTraK): A Tool to Quantify Sub-Cellular Dynamics with Sub-Pixel Accuracy.

    Science.gov (United States)

    Chaphalkar, Anushree R; Jain, Kunalika; Gangan, Manasi S; Athale, Chaitanya A

    2016-01-01

    Kymographs or space-time plots are widely used in cell biology to reduce the dimensions of a time-series in microscopy for both qualitative and quantitative insight into spatio-temporal dynamics. While multiple tools for image kymography have been described before, quantification remains largely manual. Here, we describe a novel software tool for automated multi-peak tracking kymography (AMTraK), which uses peak information and distance minimization to track and automatically quantify kymographs, integrated in a GUI. The program takes fluorescence time-series data as an input and tracks contours in the kymographs based on intensity and gradient peaks. By integrating a branch-point detection method, it can be used to identify merging and splitting events of tracks, important in separation and coalescence events. In tests with synthetic images, we demonstrate sub-pixel positional accuracy of the program. We test the program by quantifying sub-cellular dynamics in rod-shaped bacteria, microtubule (MT) transport and vesicle dynamics. A time-series of E. coli cell division with labeled nucleoid DNA is used to identify the time-point and rate at which the nucleoid segregates. The mean velocity of microtubule (MT) gliding motility due to a recombinant kinesin motor is estimated as 0.5 μm/s, in agreement with published values, and comparable to estimates using software for nanometer precision filament-tracking. We proceed to employ AMTraK to analyze previously published time-series microscopy data where kymographs had been manually quantified: clathrin polymerization kinetics during vesicle formation and anterograde and retrograde transport in axons. AMTraK analysis not only reproduces the reported parameters, it also provides an objective and automated method for reproducible analysis of kymographs from in vitro and in vivo fluorescence microscopy time-series of sub-cellular dynamics.

  2. Modeling Computer Virus and Its Dynamics

    OpenAIRE

    Peng, Mei; He, Xing; Huang, Junjian; Dong, Tao

    2013-01-01

    Based on that the computer will be infected by infected computer and exposed computer, and some of the computers which are in suscepitible status and exposed status can get immunity by antivirus ability, a novel coumputer virus model is established. The dynamic behaviors of this model are investigated. First, the basic reproduction number R0, which is a threshold of the computer virus spreading in internet, is determined. Second, this model has a virus-free equilibrium P0, which means that th...

  3. Rapid and dynamic subcellular reorganization following mechanical stimulation of Arabidopsis epidermal cells mimics responses to fungal and oomycete attack

    Directory of Open Access Journals (Sweden)

    Takemoto Daigo

    2008-06-01

    Full Text Available Abstract Background Plant cells respond to the presence of potential fungal or oomycete pathogens by mounting a basal defence response that involves aggregation of cytoplasm, reorganization of cytoskeletal, endomembrane and other cell components and development of cell wall appositions beneath the infection site. This response is induced by non-adapted, avirulent and virulent pathogens alike, and in the majority of cases achieves penetration resistance against the microorganism on the plant surface. To explore the nature of signals that trigger this subcellular response and to determine the timing of its induction, we have monitored the reorganization of GFP-tagged actin, microtubules, endoplasmic reticulum (ER and peroxisomes in Arabidopsis plants – after touching the epidermal surface with a microneedle. Results Within 3 to 5 minutes of touching the surface of Arabidopsis cotyledon epidermal cells with fine glass or tungsten needles, actin microfilaments, ER and peroxisomes began to accumulate beneath the point of contact with the needle. Formation of a dense patch of actin was followed by focusing of actin cables on the site of contact. Touching the cell surface induced localized depolymerization of microtubules to form a microtubule-depleted zone surrounding a dense patch of GFP-tubulin beneath the needle tip. The concentration of actin, GFP-tubulin, ER and peroxisomes remained focused on the contact site as the needle moved across the cell surface and quickly dispersed when the needle was removed. Conclusion Our results show that plant cells can detect the gentle pressure of a microneedle on the epidermal cell surface and respond by reorganizing subcellular components in a manner similar to that induced during attack by potential fungal or oomycete pathogens. The results of our study indicate that during plant-pathogen interactions, the basal defence response may be induced by the plant's perception of the physical force exerted by the

  4. 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 ...

  5. Fluid dynamics theory, computation, and numerical simulation

    CERN Document Server

    Pozrikidis, C

    2001-01-01

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

  6. Nonlinear dynamics as an engine of computation.

    Science.gov (United States)

    Kia, Behnam; Lindner, John F; Ditto, William L

    2017-03-06

    Control of chaos teaches that control theory can tame the complex, random-like behaviour of chaotic systems. This alliance between control methods and physics-cybernetical physics-opens the door to many applications, including dynamics-based computing. In this article, we introduce nonlinear dynamics and its rich, sometimes chaotic behaviour as an engine of computation. We review our work that has demonstrated how to compute using nonlinear dynamics. Furthermore, we investigate the interrelationship between invariant measures of a dynamical system and its computing power to strengthen the bridge between physics and computation.This article is part of the themed issue 'Horizons of cybernetical physics'. © 2017 The Author(s).

  7. Computational fluid dynamics modeling in yarn engineering

    CSIR Research Space (South Africa)

    Patanaik, A

    2011-07-01

    Full Text Available This chapter deals with the application of computational fluid dynamics (CFD) modeling in reducing yarn hairiness during the ring spinning process and thereby “engineering” yarn with desired properties. Hairiness significantly affects the appearance...

  8. Fluid dynamics theory, computation, and numerical simulation

    CERN Document Server

    Pozrikidis, C

    2017-01-01

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

  9. Hardware for dynamic quantum computing.

    Science.gov (United States)

    Ryan, Colm A; Johnson, Blake R; Ristè, Diego; Donovan, Brian; Ohki, Thomas A

    2017-10-01

    We describe the hardware, gateware, and software developed at Raytheon BBN Technologies for dynamic quantum information processing experiments on superconducting qubits. In dynamic experiments, real-time qubit state information is fed back or fed forward within a fraction of the qubits' coherence time to dynamically change the implemented sequence. The hardware presented here covers both control and readout of superconducting qubits. For readout, we created a custom signal processing gateware and software stack on commercial hardware to convert pulses in a heterodyne receiver into qubit state assignments with minimal latency, alongside data taking capability. For control, we developed custom hardware with gateware and software for pulse sequencing and steering information distribution that is capable of arbitrary control flow in a fraction of superconducting qubit coherence times. Both readout and control platforms make extensive use of field programmable gate arrays to enable tailored qubit control systems in a reconfigurable fabric suitable for iterative development.

  10. Hardware for dynamic quantum computing

    Science.gov (United States)

    Ryan, Colm A.; Johnson, Blake R.; Ristè, Diego; Donovan, Brian; Ohki, Thomas A.

    2017-10-01

    We describe the hardware, gateware, and software developed at Raytheon BBN Technologies for dynamic quantum information processing experiments on superconducting qubits. In dynamic experiments, real-time qubit state information is fed back or fed forward within a fraction of the qubits' coherence time to dynamically change the implemented sequence. The hardware presented here covers both control and readout of superconducting qubits. For readout, we created a custom signal processing gateware and software stack on commercial hardware to convert pulses in a heterodyne receiver into qubit state assignments with minimal latency, alongside data taking capability. For control, we developed custom hardware with gateware and software for pulse sequencing and steering information distribution that is capable of arbitrary control flow in a fraction of superconducting qubit coherence times. Both readout and control platforms make extensive use of field programmable gate arrays to enable tailored qubit control systems in a reconfigurable fabric suitable for iterative development.

  11. The Dynamic Geometrisation of Computer Programming

    Science.gov (United States)

    Sinclair, Nathalie; Patterson, Margaret

    2018-01-01

    The goal of this paper is to explore dynamic geometry environments (DGE) as a type of computer programming language. Using projects created by secondary students in one particular DGE, we analyse the extent to which the various aspects of computational thinking--including both ways of doing things and particular concepts--were evident in their…

  12. Computational Fluid Dynamics for Missiles

    Science.gov (United States)

    1989-11-01

    MISSILES by J. Hodges November 1989 DL~M* !7!J’nTMN A Approv"d ir public teleaol Distnution Ur- datod Procurement Executive, Ministry of Defence...large computer resources. These methods depend on experimental data- bases as input to a simple theoretical framework. The more comprehensive the...practical difficulties of providing an experimental data- base covering all possible missile configurations, all semi-empirical methods are restricted to a

  13. 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.

  14. Modeling Computer Virus and Its Dynamics

    Directory of Open Access Journals (Sweden)

    Mei Peng

    2013-01-01

    Full Text Available Based on that the computer will be infected by infected computer and exposed computer, and some of the computers which are in suscepitible status and exposed status can get immunity by antivirus ability, a novel coumputer virus model is established. The dynamic behaviors of this model are investigated. First, the basic reproduction number R0, which is a threshold of the computer virus spreading in internet, is determined. Second, this model has a virus-free equilibrium P0, which means that the infected part of the computer disappears, and the virus dies out, and P0 is a globally asymptotically stable equilibrium if R01 then this model has only one viral equilibrium P*, which means that the computer persists at a constant endemic level, and P* is also globally asymptotically stable. Finally, some numerical examples are given to demonstrate the analytical results.

  15. Three-Dimensional Computational Fluid Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Haworth, D.C.; O' Rourke, P.J.; Ranganathan, R.

    1998-09-01

    Computational fluid dynamics (CFD) is one discipline falling under the broad heading of computer-aided engineering (CAE). CAE, together with computer-aided design (CAD) and computer-aided manufacturing (CAM), comprise a mathematical-based approach to engineering product and process design, analysis and fabrication. In this overview of CFD for the design engineer, our purposes are three-fold: (1) to define the scope of CFD and motivate its utility for engineering, (2) to provide a basic technical foundation for CFD, and (3) to convey how CFD is incorporated into engineering product and process design.

  16. Computational Fluid Dynamics and Room Air Movement

    DEFF Research Database (Denmark)

    Nielsen, Peter Vilhelm

    2004-01-01

    on the mass fraction transport equation. The importance of ?false? or numerical diffusion is also addressed in connection with the simple description of a supply opening. The different aspects of boundary conditions in the indoor environment as e.g. the simulation of Air Terminal Devices and the simulation......Nielsen, P.V. Computational Fluid Dynamics and Room Air Movement. Indoor Air, International Journal of Indoor Environment and Health, Vol. 14, Supplement 7, pp. 134-143, 2004. ABSTRACT Computational Fluid Dynamics (CFD) and new developments of CFD in the indoor environment as well as quality...... considerations are important elements in the study of energy consumption, thermal comfort and indoor air quality in buildings. The paper discusses the quality level of Computational Fluid Dynamics and the involved schemes (first, second and third order schemes) by the use of the Smith and Hutton problem...

  17. An introduction to Computational Fluid Dynamics

    DEFF Research Database (Denmark)

    Sørensen, Lars Schiøtt

    1999-01-01

    CFD is the shortname for Computational Fluid Dynamics and is a numerical method by means of which we can analyze systems containing fluids. For instance systems dealing with heat flow or smoke control systems acting when a fire occur in a building.......CFD is the shortname for Computational Fluid Dynamics and is a numerical method by means of which we can analyze systems containing fluids. For instance systems dealing with heat flow or smoke control systems acting when a fire occur in a building....

  18. Fractional Dynamics of Computer Virus Propagation

    Directory of Open Access Journals (Sweden)

    Carla M. A. Pinto

    2014-01-01

    Full Text Available We propose a fractional model for computer virus propagation. The model includes the interaction between computers and removable devices. We simulate numerically the model for distinct values of the order of the fractional derivative and for two sets of initial conditions adopted in the literature. We conclude that fractional order systems reveal richer dynamics than the classical integer order counterpart. Therefore, fractional dynamics leads to time responses with super-fast transients and super-slow evolutions towards the steady-state, effects not easily captured by the integer order models.

  19. Computational fluid dynamics a practical approach

    CERN Document Server

    Tu, Jiyuan; Liu, Chaoqun

    2018-01-01

    Computational Fluid Dynamics: A Practical Approach, Third Edition, is an introduction to CFD fundamentals and commercial CFD software to solve engineering problems. The book is designed for a wide variety of engineering students new to CFD, and for practicing engineers learning CFD for the first time. Combining an appropriate level of mathematical background, worked examples, computer screen shots, and step-by-step processes, this book walks the reader through modeling and computing, as well as interpreting CFD results. This new edition has been updated throughout, with new content and improved figures, examples and problems.

  20. A Stochastic Dynamic Model of Computer Viruses

    Directory of Open Access Journals (Sweden)

    Chunming Zhang

    2012-01-01

    Full Text Available A stochastic computer virus spread model is proposed and its dynamic behavior is fully investigated. Specifically, we prove the existence and uniqueness of positive solutions, and the stability of the virus-free equilibrium and viral equilibrium by constructing Lyapunov functions and applying Ito's formula. Some numerical simulations are finally given to illustrate our main results.

  1. Engineering applications of computational fluid dynamics

    CERN Document Server

    Awang, Mokhtar

    2015-01-01

    This volume presents the results of Computational Fluid Dynamics (CFD) analysis that can be used for conceptual studies of product design, detail product development, process troubleshooting. It demonstrates the benefit of CFD modeling as a cost saving, timely, safe and easy to scale-up methodology.

  2. Computational fluid dynamics: science and tool

    NARCIS (Netherlands)

    B. Koren (Barry)

    2006-01-01

    textabstractThe year 2003 marked the 100th anniversary of both the birth of John von Neumann and the first manned flight with a power plane. In the current paper, from a Dutch perspective, attention is paid to the great importance of both events for computational fluid dynamics in general and

  3. Computational fluid dynamics in oil burner design

    Energy Technology Data Exchange (ETDEWEB)

    Butcher, T.A. [Brookhaven National Labs., Upton, NY (United States)

    1997-09-01

    In Computational Fluid Dynamics, the differential equations which describe flow, heat transfer, and mass transfer are approximately solved using a very laborious numerical procedure. Flows of practical interest to burner designs are always turbulent, adding to the complexity of requiring a turbulence model. This paper presents a model for burner design.

  4. Computational Methods in Stochastic Dynamics Volume 2

    CERN Document Server

    Stefanou, George; Papadopoulos, Vissarion

    2013-01-01

    The considerable influence of inherent uncertainties on structural behavior has led the engineering community to recognize the importance of a stochastic approach to structural problems. Issues related to uncertainty quantification and its influence on the reliability of the computational models are continuously gaining in significance. In particular, the problems of dynamic response analysis and reliability assessment of structures with uncertain system and excitation parameters have been the subject of continuous research over the last two decades as a result of the increasing availability of powerful computing resources and technology.   This book is a follow up of a previous book with the same subject (ISBN 978-90-481-9986-0) and focuses on advanced computational methods and software tools which can highly assist in tackling complex problems in stochastic dynamic/seismic analysis and design of structures. The selected chapters are authored by some of the most active scholars in their respective areas and...

  5. Distributed memory parallel computers and computational fluid dynamics

    Science.gov (United States)

    Roose, D.; Vandriessche, R.

    A tutorial on aspects of parallel computing that are important for the development of efficient parallel algorithms and software for Computational Fluid Dynamics (CFD) is presented. Some important concepts concerning distributed memory parallel computers and parallel algorithms and the parallelization of CFD algorithms on structured grids are given. Many techniques used in CFD are shown to be suited for parallelization. The minimization of work load imbalance and communication and the expectation of a general high speedup and parallel efficiency are outlined. Some methods for partitioning and mapping unstructured grids are described. These methods range from simple heuristics to global optimization methods. Methods that show a good tradeoff between execution time and quality of the result, such as inertial recursive bisection and eigenvector recursive bisection, are considered.

  6. The brain dynamics of linguistic computation.

    Science.gov (United States)

    Murphy, Elliot

    2015-01-01

    Neural oscillations at distinct frequencies are increasingly being related to a number of basic and higher cognitive faculties. Oscillations enable the construction of coherently organized neuronal assemblies through establishing transitory temporal correlations. By exploring the elementary operations of the language faculty-labeling, concatenation, cyclic transfer-alongside neural dynamics, a new model of linguistic computation is proposed. It is argued that the universality of language, and the true biological source of Universal Grammar, is not to be found purely in the genome as has long been suggested, but more specifically within the extraordinarily preserved nature of mammalian brain rhythms employed in the computation of linguistic structures. Computational-representational theories are used as a guide in investigating the neurobiological foundations of the human "cognome"-the set of computations performed by the nervous system-and new directions are suggested for how the dynamics of the brain (the "dynome") operate and execute linguistic operations. The extent to which brain rhythms are the suitable neuronal processes which can capture the computational properties of the human language faculty is considered against a backdrop of existing cartographic research into the localization of linguistic interpretation. Particular focus is placed on labeling, the operation elsewhere argued to be species-specific. A Basic Label model of the human cognome-dynome is proposed, leading to clear, causally-addressable empirical predictions, to be investigated by a suggested research program, Dynamic Cognomics. In addition, a distinction between minimal and maximal degrees of explanation is introduced to differentiate between the depth of analysis provided by cartographic, rhythmic, neurochemical, and other approaches to computation.

  7. The Brain Dynamics of Linguistic Computation

    Directory of Open Access Journals (Sweden)

    Elliot eMurphy

    2015-10-01

    Full Text Available Neural oscillations at distinct frequencies are increasingly being related to a number of basic and higher cognitive faculties. Oscillations enable the construction of coherently organised neuronal assemblies through establishing transitory temporal correlations. By exploring the elementary operations of the language faculty – labeling, concatenation, cyclic transfer – alongside neural dynamics, a new model of linguistic computation is proposed. It is argued that the universality of language, and the true biological source of Universal Grammar, is not to be found purely in the genome as has long been suggested, but more specifically within the extraordinarily preserved nature of mammalian brain rhythms employed in the computation of linguistic structures. Computational-representational theories are used as a guide in investigating the neurobiological foundations of the human ‘cognome’ – the set of computations performed by the nervous system – and new directions are suggested for how the dynamics of brain (the ‘dynome’ operates and execute linguistic operations. The extent to which brain rhythms are the suitable neuronal processes which can capture the computational properties of the human language faculty is considered against a backdrop of existing cartographic research into the localisation of linguistic interpretation. Particular focus is placed on labeling, the operation elsewhere argued to be species-specific. A Basic Label model of the human cognome-dynome is proposed, leading to clear, causally-addressable empirical predictions, to be investigated by a suggested research program, Dynamic Cognomics. In addition, a distinction between minimal and maximal degrees of explanation is introduced to differentiate between the depth of analysis provided by cartographic, rhythmic, neurochemical and other approaches to computation.

  8. Computational Fluid Dynamics and Ventilation Airflow

    DEFF Research Database (Denmark)

    Nielsen, Peter Vilhelm

    2014-01-01

    Computational fluid dynamics (CFD) was first introduced in the ventilation industry in the 1970s. CFD has been increasingly used since then, as testified by the number of peer-reviewed articles, which was less than 10 per year in the 1990s, and which is now 60 to 70 per year. This article discusses...... the principle behind CFD, the development in numerical schemes and computer size since the 1970s. Special attention is given to the selection of the correct governing equations, to the understanding of low turbulent flow, to the selection of turbulence models, and to addressing situations with more steady...

  9. [A dynamic phantom for computer tomography].

    Science.gov (United States)

    Nüsslin, F

    1981-06-01

    A phantom is described which has been developed for investigating factors depending on the scanner itself and on the scanned object which potentially influence the kind and the extent of motion artefacts on the CT-image. Additionally, the phantom may be applied to qualify assurance measurements in computer tomography. A cylindrical insert mounted on a motor driven axis is fitted centrally in a cylindrical block machined from lucite. Two interchangeable inserts are available, one containing test objects made of various materials, and another one containing small vessels which can be filled with test solutions. The insert positioned in the phantom can rotate either continuously or with the direction of motion being altered periodically. Speed, frequency and arc can be varied within wide limits. Examples demonstrating the static and the dynamic mode of the phantom are shown. By means of the dynamic phantom it is quite easy to directly determine the scan-time of a Computer tomograph.

  10. Computational fluid dynamics in ventilation design

    CERN Document Server

    Allard, Francis; Awbi, Hazim B; Davidson, Lars; Schälin, Alois

    2007-01-01

    CFD-calculations have been rapidly developed to a powerful tool for the analysis of air pollution distribution in various spaces. However, the user of CFD-calculation should be aware of the basic principles of calculations and specifically the boundary conditions. Computational Fluid Dynamics (CFD) – in Ventilation Design models is written by a working group of highly qualified international experts representing research, consulting and design.

  11. Dynamic subcellular localization of isoforms of the folate pathway enzyme serine hydroxymethyltransferase (SHMT through the erythrocytic cycle of Plasmodium falciparum

    Directory of Open Access Journals (Sweden)

    Mitchell Sarah L

    2010-12-01

    the ends of elongating apicoplasts. In very late post-mitotic schizonts, both PfSHMTc and PfSHMTm were concentrated in the central region of the parasite that becomes the residual body on erythrocyte lysis and merozoite release. Conclusions Both PfSHMTc and PfSHMTm show dynamic, stage-dependent localization among the different compartments of the parasite and sequence analysis suggests they may also reversibly associate with each other, a factor that may be critical to folate cofactor function, given the apparent lack of enzymic activity of PfSHMTm.

  12. Computation in Dynamically Bounded Asymmetric Systems

    Science.gov (United States)

    Rutishauser, Ueli; Slotine, Jean-Jacques; Douglas, Rodney

    2015-01-01

    Previous explanations of computations performed by recurrent networks have focused on symmetrically connected saturating neurons and their convergence toward attractors. Here we analyze the behavior of asymmetrical connected networks of linear threshold neurons, whose positive response is unbounded. We show that, for a wide range of parameters, this asymmetry brings interesting and computationally useful dynamical properties. When driven by input, the network explores potential solutions through highly unstable ‘expansion’ dynamics. This expansion is steered and constrained by negative divergence of the dynamics, which ensures that the dimensionality of the solution space continues to reduce until an acceptable solution manifold is reached. Then the system contracts stably on this manifold towards its final solution trajectory. The unstable positive feedback and cross inhibition that underlie expansion and divergence are common motifs in molecular and neuronal networks. Therefore we propose that very simple organizational constraints that combine these motifs can lead to spontaneous computation and so to the spontaneous modification of entropy that is characteristic of living systems. PMID:25617645

  13. Exact Mean Computation in Dynamic Time Warping Spaces

    OpenAIRE

    Brill, Markus; Fluschnik, Till; Froese, Vincent; Jain, Brijnesh; Niedermeier, Rolf; Schultz, David

    2017-01-01

    Dynamic time warping constitutes a major tool for analyzing time series. In particular, computing a mean series of a given sample of series in dynamic time warping spaces (by minimizing the Fr\\'echet function) is a challenging computational problem, so far solved by several heuristic, inexact strategies. We spot several inaccuracies in the literature on exact mean computation in dynamic time warping spaces. Our contributions comprise an exact dynamic program computing a mean (useful for bench...

  14. Computational Fluid Dynamics of rising droplets

    Energy Technology Data Exchange (ETDEWEB)

    Wagner, Matthew [Lake Superior State University; Francois, Marianne M. [Los Alamos National Laboratory

    2012-09-05

    The main goal of this study is to perform simulations of droplet dynamics using Truchas, a LANL-developed computational fluid dynamics (CFD) software, and compare them to a computational study of Hysing et al.[IJNMF, 2009, 60:1259]. Understanding droplet dynamics is of fundamental importance in liquid-liquid extraction, a process used in the nuclear fuel cycle to separate various components. Simulations of a single droplet rising by buoyancy are conducted in two-dimensions. Multiple parametric studies are carried out to ensure the problem set-up is optimized. An Interface Smoothing Length (ISL) study and mesh resolution study are performed to verify convergence of the calculations. ISL is a parameter for the interface curvature calculation. Further, wall effects are investigated and checked against existing correlations. The ISL study found that the optimal ISL value is 2.5{Delta}x, with {Delta}x being the mesh cell spacing. The mesh resolution study found that the optimal mesh resolution is d/h=40, for d=drop diameter and h={Delta}x. In order for wall effects on terminal velocity to be insignificant, a conservative wall width of 9d or a nonconservative wall width of 7d can be used. The percentage difference between Hysing et al.[IJNMF, 2009, 60:1259] and Truchas for the velocity profiles vary from 7.9% to 9.9%. The computed droplet velocity and interface profiles are found in agreement with the study. The CFD calculations are performed on multiple cores, using LANL's Institutional High Performance Computing.

  15. Dynamical Systems Theory for Transparent Symbolic Computation in Neuronal Networks

    OpenAIRE

    Carmantini, Giovanni Sirio

    2017-01-01

    In this thesis, we explore the interface between symbolic and dynamical system computation, with particular regard to dynamical system models of neuronal networks. In doing so, we adhere to a definition of computation as the physical realization of a formal system, where we say that a dynamical system performs a computation if a correspondence can be found between its dynamics on a vectorial space and the formal system’s dynamics on a symbolic space. Guided by this definition, we characterize...

  16. Fundamental algorithms in computational fluid dynamics

    CERN Document Server

    Pulliam, Thomas H

    2014-01-01

    Intended as a textbook for courses in computational fluid dynamics at the senior undergraduate or graduate level, this book is a follow-up to the book Fundamentals of Computational Fluid Dynamics by the same authors, which was published in the series Scientific Computation in 2001. Whereas the earlier book concentrated on the analysis of numerical methods applied to model equations, this new book concentrates on algorithms for the numerical solution of the Euler and Navier-Stokes equations. It focuses on some classical algorithms as well as the underlying ideas based on the latest methods. A key feature of the book is the inclusion of programming exercises at the end of each chapter based on the numerical solution of the quasi-one-dimensional Euler equations and the shock-tube problem. These exercises can be included in the context of a typical course, and sample solutions are provided in each chapter, so readers can confirm that they have coded the algorithms correctly.

  17. Dynamical Models for Computer Viruses Propagation

    Directory of Open Access Journals (Sweden)

    José R. C. Piqueira

    2008-01-01

    Full Text Available Nowadays, digital computer systems and networks are the main engineering tools, being used in planning, design, operation, and control of all sizes of building, transportation, machinery, business, and life maintaining devices. Consequently, computer viruses became one of the most important sources of uncertainty, contributing to decrease the reliability of vital activities. A lot of antivirus programs have been developed, but they are limited to detecting and removing infections, based on previous knowledge of the virus code. In spite of having good adaptation capability, these programs work just as vaccines against diseases and are not able to prevent new infections based on the network state. Here, a trial on modeling computer viruses propagation dynamics relates it to other notable events occurring in the network permitting to establish preventive policies in the network management. Data from three different viruses are collected in the Internet and two different identification techniques, autoregressive and Fourier analyses, are applied showing that it is possible to forecast the dynamics of a new virus propagation by using the data collected from other viruses that formerly infected the network.

  18. Utilizing parallel optimization in computational fluid dynamics

    Science.gov (United States)

    Kokkolaras, Michael

    1998-12-01

    General problems of interest in computational fluid dynamics are investigated by means of optimization. Specifically, in the first part of the dissertation, a method of optimal incremental function approximation is developed for the adaptive solution of differential equations. Various concepts and ideas utilized by numerical techniques employed in computational mechanics and artificial neural networks (e.g. function approximation and error minimization, variational principles and weighted residuals, and adaptive grid optimization) are combined to formulate the proposed method. The basis functions and associated coefficients of a series expansion, representing the solution, are optimally selected by a parallel direct search technique at each step of the algorithm according to appropriate criteria; the solution is built sequentially. In this manner, the proposed method is adaptive in nature, although a grid is neither built nor adapted in the traditional sense using a-posteriori error estimates. Variational principles are utilized for the definition of the objective function to be extremized in the associated optimization problems, ensuring that the problem is well-posed. Complicated data structures and expensive remeshing algorithms and systems solvers are avoided. Computational efficiency is increased by using low-order basis functions and concurrent computing. Numerical results and convergence rates are reported for a range of steady-state problems, including linear and nonlinear differential equations associated with general boundary conditions, and illustrate the potential of the proposed method. Fluid dynamics applications are emphasized. Conclusions are drawn by discussing the method's limitations, advantages, and possible extensions. The second part of the dissertation is concerned with the optimization of the viscous-inviscid-interaction (VII) mechanism in an airfoil flow analysis code. The VII mechanism is based on the concept of a transpiration velocity

  19. Subcellular Organization of GPCR Signaling.

    Science.gov (United States)

    Eichel, Kelsie; von Zastrow, Mark

    2018-02-01

    G protein-coupled receptors (GPCRs) comprise a large and diverse class of signal-transducing receptors that undergo dynamic and isoform-specific membrane trafficking. GPCRs thus have an inherent potential to initiate or regulate signaling reactions from multiple membrane locations. This review discusses emerging insights into the subcellular organization of GPCR function in mammalian cells, focusing on signaling transduced by heterotrimeric G proteins and β-arrestins. We summarize recent evidence indicating that GPCR-mediated activation of G proteins occurs not only from the plasma membrane (PM) but also from endosomes and Golgi membranes and that β-arrestin-dependent signaling can be transduced from the PM by β-arrestin trafficking to clathrin-coated pits (CCPs) after dissociation from a ligand-activated GPCR. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Artificial Intelligence In Computational Fluid Dynamics

    Science.gov (United States)

    Vogel, Alison Andrews

    1991-01-01

    Paper compares four first-generation artificial-intelligence (Al) software systems for computational fluid dynamics. Includes: Expert Cooling Fan Design System (EXFAN), PAN AIR Knowledge System (PAKS), grid-adaptation program MITOSIS, and Expert Zonal Grid Generation (EZGrid). Focuses on knowledge-based ("expert") software systems. Analyzes intended tasks, kinds of knowledge possessed, magnitude of effort required to codify knowledge, how quickly constructed, performances, and return on investment. On basis of comparison, concludes Al most successful when applied to well-formulated problems solved by classifying or selecting preenumerated solutions. In contrast, application of Al to poorly understood or poorly formulated problems generally results in long development time and large investment of effort, with no guarantee of success.

  1. Wingless signalling alters the levels, subcellular distribution and dynamics of Armadillo and E-cadherin in third instar larval wing imaginal discs.

    Directory of Open Access Journals (Sweden)

    Ildiko M L Somorjai

    2008-08-01

    Full Text Available Armadillo, the Drosophila orthologue of vertebrate ss-catenin, plays a dual role as the key effector of Wingless/Wnt1 signalling, and as a bridge between E-Cadherin and the actin cytoskeleton. In the absence of ligand, Armadillo is phosphorylated and targeted to the proteasome. Upon binding of Wg to its receptors, the "degradation complex" is inhibited; Armadillo is stabilised and enters the nucleus to transcribe targets.Although the relationship between signalling and adhesion has been extensively studied, few in vivo data exist concerning how the "transcriptional" and "adhesive" pools of Armadillo are regulated to orchestrate development. We have therefore addressed how the subcellular distribution of Armadillo and its association with E-Cadherin change in larval wing imaginal discs, under wild type conditions and upon signalling. Using confocal microscopy, we show that Armadillo and E-Cadherin are spatio-temporally regulated during development, and that a punctate species becomes concentrated in a subapical compartment in response to Wingless. In order to further dissect this phenomenon, we overexpressed Armadillo mutants exhibiting different levels of activity and stability, but retaining E-Cadherin binding. Arm(S10 displaces endogenous Armadillo from the AJ and the basolateral membrane, while leaving E-Cadherin relatively undisturbed. Surprisingly, DeltaNArm(1-155 caused displacement of both Armadillo and E-Cadherin, results supported by our novel method of quantification. However, only membrane-targeted Myr-DeltaNArm(1-155 produced comparable nuclear accumulation of Armadillo and signalling to Arm(S10. These experiments also highlighted a row of cells at the A/P boundary depleted of E-Cadherin at the AJ, but containing actin.Taken together, our results provide in vivo evidence for a complex non-linear relationship between Armadillo levels, subcellular distribution and Wingless signalling. Moreover, this study highlights the importance of

  2. Computational fluid dynamics modelling in cardiovascular medicine.

    Science.gov (United States)

    Morris, Paul D; Narracott, Andrew; von Tengg-Kobligk, Hendrik; Silva Soto, Daniel Alejandro; Hsiao, Sarah; Lungu, Angela; Evans, Paul; Bressloff, Neil W; Lawford, Patricia V; Hose, D Rodney; Gunn, Julian P

    2016-01-01

    This paper reviews the methods, benefits and challenges associated with the adoption and translation of computational fluid dynamics (CFD) modelling within cardiovascular medicine. CFD, a specialist area of mathematics and a branch of fluid mechanics, is used routinely in a diverse range of safety-critical engineering systems, which increasingly is being applied to the cardiovascular system. By facilitating rapid, economical, low-risk prototyping, CFD modelling has already revolutionised research and development of devices such as stents, valve prostheses, and ventricular assist devices. Combined with cardiovascular imaging, CFD simulation enables detailed characterisation of complex physiological pressure and flow fields and the computation of metrics which cannot be directly measured, for example, wall shear stress. CFD models are now being translated into clinical tools for physicians to use across the spectrum of coronary, valvular, congenital, myocardial and peripheral vascular diseases. CFD modelling is apposite for minimally-invasive patient assessment. Patient-specific (incorporating data unique to the individual) and multi-scale (combining models of different length- and time-scales) modelling enables individualised risk prediction and virtual treatment planning. This represents a significant departure from traditional dependence upon registry-based, population-averaged data. Model integration is progressively moving towards 'digital patient' or 'virtual physiological human' representations. When combined with population-scale numerical models, these models have the potential to reduce the cost, time and risk associated with clinical trials. The adoption of CFD modelling signals a new era in cardiovascular medicine. While potentially highly beneficial, a number of academic and commercial groups are addressing the associated methodological, regulatory, education- and service-related challenges. Published by the BMJ Publishing Group Limited. For permission

  3. Computer modeling of dynamic necking in bars

    Science.gov (United States)

    Partom, Yehuda; Lindenfeld, Avishay

    2017-06-01

    Necking of thin bodies (bars, plates, shells) is one form of strain localization in ductile materials that may lead to fracture. The phenomenon of necking has been studied extensively, initially for quasistatic loading and then also for dynamic loading. Nevertheless, many issues concerning necking are still unclear. Among these are: 1) is necking a random or deterministic process; 2) how does the specimen choose the final neck location; 3) to what extent do perturbations (material or geometrical) influence the neck forming process; and 4) how do various parameters (material, geometrical, loading) influence the neck forming process. Here we address these issues and others using computer simulations with a hydrocode. Among other things we find that: 1) neck formation is a deterministic process, and by changing one of the parameters influencing it monotonously, the final neck location moves monotonously as well; 2) the final neck location is sensitive to the radial velocity of the end boundaries, and as motion of these boundaries is not fully controlled in tests, this may be the reason why neck formation is sometimes regarded as a random process; and 3) neck formation is insensitive to small perturbations, which is probably why it is a deterministic process.

  4. Meshfree methods for computational fluid dynamics

    Directory of Open Access Journals (Sweden)

    Jícha M.

    2013-04-01

    Full Text Available The paper deals with the convergence problem of the SPH (Smoothed Particle Hydrodynamics meshfree method for the solution of fluid dynamics tasks. In the introductory part, fundamental aspects of mesh- free methods, their definition, computational approaches and classification are discussed. In the following part, the methods of local integral representation, where SPH belongs are analyzed and specifically the method RKPM (Reproducing Kernel Particle Method is described. In the contribution, also the influence of boundary conditions on the SPH approximation consistence is analyzed, which has a direct impact on the convergence of the method. A classical boundary condition in the form of virtual particles does not ensure a sufficient order of consistence near the boundary of the definition domain of the task. This problem is solved by using ghost particles as a boundary condition, which was implemented into the SPH code as part of this work. Further, several numerical aspects linked with the SPH method are described. In the concluding part, results are presented of the application of the SPH method with ghost particles to the 2D shock tube example. Also results of tests of several parameters and modifications of the SPH code are shown.

  5. Computational social dynamic modeling of group recruitment.

    Energy Technology Data Exchange (ETDEWEB)

    Berry, Nina M.; Lee, Marinna; Pickett, Marc; Turnley, Jessica Glicken (Sandia National Laboratories, Albuquerque, NM); Smrcka, Julianne D. (Sandia National Laboratories, Albuquerque, NM); Ko, Teresa H.; Moy, Timothy David (Sandia National Laboratories, Albuquerque, NM); Wu, Benjamin C.

    2004-01-01

    The Seldon software toolkit combines concepts from agent-based modeling and social science to create a computationally social dynamic model for group recruitment. The underlying recruitment model is based on a unique three-level hybrid agent-based architecture that contains simple agents (level one), abstract agents (level two), and cognitive agents (level three). This uniqueness of this architecture begins with abstract agents that permit the model to include social concepts (gang) or institutional concepts (school) into a typical software simulation environment. The future addition of cognitive agents to the recruitment model will provide a unique entity that does not exist in any agent-based modeling toolkits to date. We use social networks to provide an integrated mesh within and between the different levels. This Java based toolkit is used to analyze different social concepts based on initialization input from the user. The input alters a set of parameters used to influence the values associated with the simple agents, abstract agents, and the interactions (simple agent-simple agent or simple agent-abstract agent) between these entities. The results of phase-1 Seldon toolkit provide insight into how certain social concepts apply to different scenario development for inner city gang recruitment.

  6. Visualization of vortical flows in computational fluid dynamics

    Science.gov (United States)

    Volkov, K. N.; Emel'yanov, V. N.; Teterina, I. V.; Yakovchuk, M. S.

    2017-08-01

    The concepts and methods of the visual representation of fluid dynamics computations of vortical flows are studied. Approaches to the visualization of vortical flows based on the use of various definitions of a vortex and various tests for its identification are discussed. Examples of the visual representation of solutions to some fluid dynamics problems related to the computation of vortical flows in jets, channels, and cavities and of the computation of separated flows occurring in flows around bodies of various shapes are discussed.

  7. Dynamic leaching test of personal computer components

    Energy Technology Data Exchange (ETDEWEB)

    Li Yadong, E-mail: yadong.li@jsums.edu [Department of Civil and Environmental Engineering, Jackson State University, Jackson, MS 39217 (United States); Richardson, Jay B.; Niu Xiaojun; Jackson, Ollie J.; Laster, Jeremy D.; Walker, Aaron K. [Department of Civil and Environmental Engineering, Jackson State University, Jackson, MS 39217 (United States)

    2009-11-15

    A dynamic leaching test (DLT) was developed and used to evaluate the leaching of toxic substances for electronic waste in the environment. The major components in personal computers (PCs) including motherboards, hard disc drives, floppy disc drives, and compact disc drives were tested. The tests lasted for 2 years for motherboards and 1.5 year for the disc drives. The extraction fluids for the standard toxicity characteristic leaching procedure (TCLP) and synthetic precipitation leaching procedure (SPLP) were used as the DLT leaching solutions. A total of 18 elements including Ag, Al, As, Au, Ba, Be, Cd, Cr, Cu, Fe, Ga, Ni, Pd, Pb, Sb, Se, Sn, and Zn were analyzed in the DLT leachates. Only Al, Cu, Fe, Ni, Pb, and Zn were commonly found in the DLT leachates of the PC components. Their leaching levels were much higher in TCLP extraction fluid than in SPLP extraction fluid. The toxic heavy metal Pb was found to continuously leach out of the components over the entire test periods. The cumulative amounts of Pb leached out of the motherboards in TCLP extraction fluid reached 2.0 g per motherboard over the 2-year test period, and that in SPLP extraction fluid were 75-90% less. The leaching rates or levels of Pb were largely affected by the content of galvanized steel in the PC components. The higher was the steel content, the lower the Pb leaching rate would be. The findings suggest that the obsolete PCs disposed of in landfills or discarded in the environment continuously release Pb for years when subjected to landfill leachate or rains.

  8. AIR INGRESS ANALYSIS: COMPUTATIONAL FLUID DYNAMIC MODELS

    Energy Technology Data Exchange (ETDEWEB)

    Chang H. Oh; Eung S. Kim; Richard Schultz; Hans Gougar; David Petti; Hyung S. Kang

    2010-08-01

    The Idaho National Laboratory (INL), under the auspices of the U.S. Department of Energy, is performing research and development that focuses on key phenomena important during potential scenarios that may occur in very high temperature reactors (VHTRs). Phenomena Identification and Ranking Studies to date have ranked an air ingress event, following on the heels of a VHTR depressurization, as important with regard to core safety. Consequently, the development of advanced air ingress-related models and verification and validation data are a very high priority. Following a loss of coolant and system depressurization incident, air will enter the core of the High Temperature Gas Cooled Reactor through the break, possibly causing oxidation of the in-the core and reflector graphite structure. Simple core and plant models indicate that, under certain circumstances, the oxidation may proceed at an elevated rate with additional heat generated from the oxidation reaction itself. Under postulated conditions of fluid flow and temperature, excessive degradation of the lower plenum graphite can lead to a loss of structural support. Excessive oxidation of core graphite can also lead to the release of fission products into the confinement, which could be detrimental to a reactor safety. Computational fluid dynamic model developed in this study will improve our understanding of this phenomenon. This paper presents two-dimensional and three-dimensional CFD results for the quantitative assessment of the air ingress phenomena. A portion of results of the density-driven stratified flow in the inlet pipe will be compared with results of the experimental results.

  9. Quantum Computation and Quantum Spin Dynamics

    NARCIS (Netherlands)

    Raedt, Hans De; Michielsen, Kristel; Hams, Anthony; Miyashita, Seiji; Saito, Keiji

    2001-01-01

    We analyze the stability of quantum computations on physically realizable quantum computers by simulating quantum spin models representing quantum computer hardware. Examples of logically identical implementations of the controlled-NOT operation are used to demonstrate that the results of a quantum

  10. Propagation of Computer Virus under Human Intervention: A Dynamical Model

    OpenAIRE

    Chenquan Gan; Xiaofan Yang; Wanping Liu; Qingyi Zhu; Xulong Zhang

    2012-01-01

    This paper examines the propagation behavior of computer virus under human intervention. A dynamical model describing the spread of computer virus, under which a susceptible computer can become recovered directly and an infected computer can become susceptible directly, is proposed. Through a qualitative analysis of this model, it is found that the virus-free equilibrium is globally asymptotically stable when the basic reproduction number R0≤1, whereas the viral equilibrium is globally asympt...

  11. Computational Fluid Dynamics (CFD): Element-by-Element Analysis for Advanced Computers

    Science.gov (United States)

    1988-11-14

    WORK UNIT ELEMENT NO. NO. NO. ACCESSION NO 11. TITLE (Include Y’ecurity Classification) Computational Fluid Dynamics ( CFD ): Element-by-Element...All other editions are obsolete. V L ?, AFOSR Report Grant #AFOSR-87-0153 Computational Fluid Dynamics ( CFD ): Element-by-Element Analysis for Advanced

  12. Computable Analysis with Applications to Dynamic Systems

    NARCIS (Netherlands)

    P.J. Collins (Pieter)

    2010-01-01

    htmlabstractIn this article we develop a theory of computation for continuous mathematics. The theory is based on earlier developments of computable analysis, especially that of the school of Weihrauch, and is presented as a model of intuitionistic type theory. Every effort has been made to keep the

  13. Multitask learning for protein subcellular location prediction.

    Science.gov (United States)

    Xu, Qian; Pan, Sinno Jialin; Xue, Hannah Hong; Yang, Qiang

    2011-01-01

    Protein subcellular localization is concerned with predicting the location of a protein within a cell using computational methods. The location information can indicate key functionalities of proteins. Thus, accurate prediction of subcellular localizations of proteins can help the prediction of protein functions and genome annotations, as well as the identification of drug targets. Machine learning methods such as Support Vector Machines (SVMs) have been used in the past for the problem of protein subcellular localization, but have been shown to suffer from a lack of annotated training data in each species under study. To overcome this data sparsity problem, we observe that because some of the organisms may be related to each other, there may be some commonalities across different organisms that can be discovered and used to help boost the data in each localization task. In this paper, we formulate protein subcellular localization problem as one of multitask learning across different organisms. We adapt and compare two specializations of the multitask learning algorithms on 20 different organisms. Our experimental results show that multitask learning performs much better than the traditional single-task methods. Among the different multitask learning methods, we found that the multitask kernels and supertype kernels under multitask learning that share parameters perform slightly better than multitask learning by sharing latent features. The most significant improvement in terms of localization accuracy is about 25 percent. We find that if the organisms are very different or are remotely related from a biological point of view, then jointly training the multiple models cannot lead to significant improvement. However, if they are closely related biologically, the multitask learning can do much better than individual learning.

  14. Automated Computational Fluid Dynamics Design With Shape Optimization Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Computational fluid dynamics (CFD) is used as an analysis tool to help the designer gain greater understanding of the fluid flow phenomena involved in the components...

  15. Computational Simulation of Droplet Collision Dynamics

    National Research Council Canada - National Science Library

    Law, Chung

    2000-01-01

    ..., and the energy partition among the various modes was identified. By using the molecular dynamics method, bouncing and coalescence were successfully simulated for the first time without the artificial manipulation of the inter-droplet gaseous film...

  16. Dynamics of Propagation of Premature Impulses in Structurally Remodeled Infarcted Myocardium: A Computational Analysis

    Directory of Open Access Journals (Sweden)

    Candido eCabo

    2014-12-01

    Full Text Available Initiation of cardiac arrhythmias typically follows one or more premature impulses either occurring spontaneously or applied externally. In this study, we characterize the dynamics of propagation of single (S2 and double premature impulses (S3, and the mechanisms of block of premature impulses at structural heterogeneities caused by remodeling of gap junctional conductance (Gj in infarcted myocardium. Using a sub-cellular computer model of infarcted tissue, we found that |INa,max|, prematurity (coupling interval with the previous impulse, and conduction velocity (CV of premature impulses change dynamically as they propagate away from the site of initiation. There are fundamental differences between the dynamics of propagation of S2 and S3 premature impulses: for S2 impulses |INa,max| recovers fast, prematurity decreases and CV increases as propagation proceeds; for S3 impulses low values of |INa,max| persist, prematurity could increase, and CV could decrease as impulses propagate away from the site of initiation. As a consequence it is more likely that S3 impulses block at sites of structural heterogeneities causing source/sink mismatch than S2 impulses block. Whether premature impulses block at Gj heterogeneities or not is also determined by the values of Gj (and space constant λ in regions proximal and distal to the heterogeneity: when λ in the direction of propagation increases >40%, premature impulses could block. The maximum slope of CV restitution curves for S2 impulses is larger than for S3 impulses. In conclusion: 1 The dynamics of propagation of premature impulses make more likely that S3 impulses block at sites of structural heterogeneities than S2 impulses block; 2 Structural heterogeneities causing an increase in λ (or CV of >40% could result in block of premature impulses; 3 A decrease in the maximum slope of CV restitution curves of propagating premature impulses is indicative of an increased potential for block at structural

  17. Dynamics of Bottlebrush Networks: A Computational Study

    Science.gov (United States)

    Dobrynin, Andrey; Cao, Zhen; Sheiko, Sergei

    We study dynamics of deformation of bottlebrush networks using molecular dynamics simulations and theoretical calculations. Analysis of our simulation results show that the dynamics of bottlebrush network deformation can be described by a Rouse model for polydisperse networks with effective Rouse time of the bottlebrush network strand, τR =τ0Ns2 (Nsc + 1) where, Ns is the number-average degree of polymerization of the bottlebrush backbone strands between crosslinks, Nsc is the degree of polymerization of the side chains and τ0is a characteristic monomeric relaxation time. At time scales t smaller than the Rouse time, t crosslinks, the network response is pure elastic with shear modulus G (t) =G0 , where G0 is the equilibrium shear modulus at small deformation. The stress evolution in the bottlebrush networks can be described by a universal function of t /τR . NSF DMR-1409710.

  18. Computer Programme for the Dynamic Analysis of Tall Regular ...

    African Journals Online (AJOL)

    Models that allow joint rotations with/without the inclusion of the column axial loads give improved results but pose much more computational difficulty. In this work a computer program Natfrequency that determines the dynamic stiffness matrix of tall frames and solves the eigenvalue problem when modeled as a shear frame ...

  19. Computational fluid dynamics simulations and validations of results

    CSIR Research Space (South Africa)

    Sitek, MA

    2013-09-01

    Full Text Available -1 Fifth International Conference on Structural Engineering, Mechanics and Computation, Cape Town South Africa, 2-4 September 2013 Computational fluid dynamics simulations and validation of results M.A. Sitek, M. Cwik, M.A. Gizejowski Warsaw...

  20. Prospects for Computational Fluid Dynamics in Room Air Contaminant Control

    DEFF Research Database (Denmark)

    Nielsen, Peter V.

    The fluid dynamics research is strongly influenced by the increasing computer power which has been available for the last decades. This development is obvious from the curve in figure 1 which shows the computation cost as a function of years. It is obvious that the cost for a given job will decre...

  1. A DECENTRALIZED DYNAMIC LOAD BALANCING FOR COMPUTATIONAL GRID ENVIRONMENTS

    Directory of Open Access Journals (Sweden)

    R. Chellamani

    2013-07-01

    Full Text Available With the rapid development of high-speed wide-area networks and powerful yet low-cost computational resources, grid computing has emerged as an attractive computing paradigm. The computational grid is a new parallel and distributed computing paradigm that provides resources for large scientific computing applications. The main techniques that are most suitable to cope with the dynamic nature of the grid are the effective utilization of grid resources and the distribution of application load among multiple resources in a grid environment. This paper addresses the problem of scheduling and load balancing in a grid environment. A Decentralized Dynamic load balancing algorithm is proposed which combines the strong points of neighbor based and cluster based load balancing techniques. This algorithm estimates system parameters such as resource processing capacity, load on each resource and transfer delay for scheduling and load balancing. A set of simulation experiments show that the proposed algorithm provides significant performance over existing ones.

  2. (U) Computation acceleration using dynamic memory

    Energy Technology Data Exchange (ETDEWEB)

    Hakel, Peter [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2014-10-24

    Many computational applications require the repeated use of quantities, whose calculations can be expensive. In order to speed up the overall execution of the program, it is often advantageous to replace computation with extra memory usage. In this approach, computed values are stored and then, when they are needed again, they are quickly retrieved from memory rather than being calculated again at great cost. Sometimes, however, the precise amount of memory needed to store such a collection is not known in advance, and only emerges in the course of running the calculation. One problem accompanying such a situation is wasted memory space in overdimensioned (and possibly sparse) arrays. Another issue is the overhead of copying existing values to a new, larger memory space, if the original allocation turns out to be insufficient. In order to handle these runtime problems, the programmer therefore has the extra task of addressing them in the code.

  3. Unsteady computational fluid dynamics in aeronautics

    CERN Document Server

    Tucker, P G

    2014-01-01

    The field of Large Eddy Simulation (LES) and hybrids is a vibrant research area. This book runs through all the potential unsteady modelling fidelity ranges, from low-order to LES. The latter is probably the highest fidelity for practical aerospace systems modelling. Cutting edge new frontiers are defined.  One example of a pressing environmental concern is noise. For the accurate prediction of this, unsteady modelling is needed. Hence computational aeroacoustics is explored. It is also emerging that there is a critical need for coupled simulations. Hence, this area is also considered and the tensions of utilizing such simulations with the already expensive LES.  This work has relevance to the general field of CFD and LES and to a wide variety of non-aerospace aerodynamic systems (e.g. cars, submarines, ships, electronics, buildings). Topics treated include unsteady flow techniques; LES and hybrids; general numerical methods; computational aeroacoustics; computational aeroelasticity; coupled simulations and...

  4. On the Optimal Dynamic Control Strategy of Disruptive Computer Virus

    Directory of Open Access Journals (Sweden)

    Jichao Bi

    2017-01-01

    Full Text Available Disruptive computer viruses have inflicted huge economic losses. This paper addresses the development of a cost-effective dynamic control strategy of disruptive viruses. First, the development problem is modeled as an optimal control problem. Second, a criterion for the existence of an optimal control is given. Third, the optimality system is derived. Next, some examples of the optimal dynamic control strategy are presented. Finally, the performance of actual dynamic control strategies is evaluated.

  5. Computational fluid dynamics for sport simulation

    CERN Document Server

    2009-01-01

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

  6. Symplectic molecular dynamics simulations on specially designed parallel computers.

    Science.gov (United States)

    Borstnik, Urban; Janezic, Dusanka

    2005-01-01

    We have developed a computer program for molecular dynamics (MD) simulation that implements the Split Integration Symplectic Method (SISM) and is designed to run on specialized parallel computers. The MD integration is performed by the SISM, which analytically treats high-frequency vibrational motion and thus enables the use of longer simulation time steps. The low-frequency motion is treated numerically on specially designed parallel computers, which decreases the computational time of each simulation time step. The combination of these approaches means that less time is required and fewer steps are needed and so enables fast MD simulations. We study the computational performance of MD simulation of molecular systems on specialized computers and provide a comparison to standard personal computers. The combination of the SISM with two specialized parallel computers is an effective way to increase the speed of MD simulations up to 16-fold over a single PC processor.

  7. Computing in Large-Scale Dynamic Systems

    NARCIS (Netherlands)

    Pruteanu, A.S.

    2013-01-01

    Software applications developed for large-scale systems have always been difficult to de- velop due to problems caused by the large number of computing devices involved. Above a certain network size (roughly one hundred), necessary services such as code updating, topol- ogy discovery and data

  8. Computational dynamics of fluid controlled mechanical thrust ...

    African Journals Online (AJOL)

    ... in agreement with that obtained by analytical approach. The computational method demonstrated the significance and benefits of CFD algorithms and numerical experiment-ation to configure and enhance the nozzle profile by providing quick solutions. Journal of Applied Science and Technology Vol. 13 (1 & 2) 2008: pp.

  9. Computational Modeling of Dynamic Stability Derivatives for Generic Airfoils

    Directory of Open Access Journals (Sweden)

    Mumtaz Muhammad Saleem

    2017-01-01

    Full Text Available This paper presents a method for the computation of the static and dynamic stability derivatives of generic airfoils using high fidelity Computational Fluid Dynamics. Aerodynamic coefficients are calculated for NACA 0012 airfoil and flat plate at different angles of attack. Results of lift coefficient are validated with experimental data. Static and dynamic stability derivatives are calculated by oscillating the airfoil geometry at suitable frequency. Simulations are performed at various flight conditions in terms of angles of attack, frequencies and oscillation amplitudes. The aim of the work is to decipher the behaviour of longitudinal damping derivatives used in flight mechanics through CFD. This approach enables the efficient and accurate computation of dynamic derivatives. Calculations are done for constant air velocity altering only the angle of attack. Inviscid model is tested since its results nearly match with experimental data. The simulations show that the nonlinear characteristics of the stability derivatives are captured by varying angle of attack.

  10. Neural Computations in a Dynamical System with Multiple Time Scales

    Science.gov (United States)

    Mi, Yuanyuan; Lin, Xiaohan; Wu, Si

    2016-01-01

    Neural systems display rich short-term dynamics at various levels, e.g., spike-frequency adaptation (SFA) at the single-neuron level, and short-term facilitation (STF) and depression (STD) at the synapse level. These dynamical features typically cover a broad range of time scales and exhibit large diversity in different brain regions. It remains unclear what is the computational benefit for the brain to have such variability in short-term dynamics. In this study, we propose that the brain can exploit such dynamical features to implement multiple seemingly contradictory computations in a single neural circuit. To demonstrate this idea, we use continuous attractor neural network (CANN) as a working model and include STF, SFA and STD with increasing time constants in its dynamics. Three computational tasks are considered, which are persistent activity, adaptation, and anticipative tracking. These tasks require conflicting neural mechanisms, and hence cannot be implemented by a single dynamical feature or any combination with similar time constants. However, with properly coordinated STF, SFA and STD, we show that the network is able to implement the three computational tasks concurrently. We hope this study will shed light on the understanding of how the brain orchestrates its rich dynamics at various levels to realize diverse cognitive functions. PMID:27679569

  11. Osmosis : a molecular dynamics computer simulation study

    Science.gov (United States)

    Lion, Thomas

    Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gradients are investigated using molecular dynamics (MD) simulations. I first present a new derivation for the local pressure that can be used for determining osmotic pressure gradients. Using this result, the steady-state osmotic pressure is studied in a minimal model for an osmotic system and the steady-state density gradients are explained using a simple mechanistic hopping model for the solvent particles. The simulation setup is then modified, allowing us to explore the timescales involved in the relaxation dynamics of the system in the period preceding the steady state. Further consideration is also given to the relative roles of diffusive and non-diffusive solvent transport in this period. Finally, in a novel modification to the classic osmosis experiment, the solute particles are driven out-of-equilibrium by the input of energy. The effect of this modification on the osmotic pressure and the osmotic ow is studied and we find that active solute particles can cause reverse osmosis to occur. The possibility of defining a new "osmotic effective temperature" is also considered and compared to the results of diffusive and kinetic temperatures..

  12. Robot-Arm Dynamic Control by Computer

    Science.gov (United States)

    Bejczy, Antal K.; Tarn, Tzyh J.; Chen, Yilong J.

    1987-01-01

    Feedforward and feedback schemes linearize responses to control inputs. Method for control of robot arm based on computed nonlinear feedback and state tranformations to linearize system and decouple robot end-effector motions along each of cartesian axes augmented with optimal scheme for correction of errors in workspace. Major new feature of control method is: optimal error-correction loop directly operates on task level and not on joint-servocontrol level.

  13. Computational Fluid Dynamics: Algorithms and Supercomputers

    Science.gov (United States)

    1988-03-01

    leurs remerciements au Prufesseur Dr Gentzseh et au IDr Neves potur lcx efforts qu’ils lin vIeplovui, afin die riealiser en temps voulu cet...Primary and Secondary Memon 30 Interface (between Memon and the Vector I nits 31 Paths-to-Memory 33 Control or Instruction Processors 36 Secondary...computation (functional units), instruction processing (instruction or control units), and data movement and handling (memory and I/O). The simplest of

  14. Exponential rise of dynamical complexity in quantum computing through projections.

    Science.gov (United States)

    Burgarth, Daniel Klaus; Facchi, Paolo; Giovannetti, Vittorio; Nakazato, Hiromichi; Pascazio, Saverio; Yuasa, Kazuya

    2014-10-10

    The ability of quantum systems to host exponentially complex dynamics has the potential to revolutionize science and technology. Therefore, much effort has been devoted to developing of protocols for computation, communication and metrology, which exploit this scaling, despite formidable technical difficulties. Here we show that the mere frequent observation of a small part of a quantum system can turn its dynamics from a very simple one into an exponentially complex one, capable of universal quantum computation. After discussing examples, we go on to show that this effect is generally to be expected: almost any quantum dynamics becomes universal once 'observed' as outlined above. Conversely, we show that any complex quantum dynamics can be 'purified' into a simpler one in larger dimensions. We conclude by demonstrating that even local noise can lead to an exponentially complex dynamics.

  15. A future for computational fluid dynamics at CERN

    CERN Document Server

    Battistin, M

    2005-01-01

    Computational Fluid Dynamics (CFD) is an analysis of fluid flow, heat transfer and associated phenomena in physical systems using computers. CFD has been used at CERN since 1993 by the TS-CV group, to solve thermo-fluid related problems, particularly during the development, design and construction phases of the LHC experiments. Computer models based on CFD techniques can be employed to reduce the effort required for prototype testing, saving not only time and money but offering possibilities of additional investigations and design optimisation. The development of a more efficient support team at CERN depends on to two important factors: available computing power and experienced engineers. Available computer power IS the limiting resource of CFD. Only the recent increase of computer power had allowed important high tech and industrial applications. Computer Grid is already now (OpenLab at CERN) and will be more so in the future natural environment for CFD science. At CERN, CFD activities have been developed by...

  16. Finite Element Computational Dynamics of Rotating Systems

    Directory of Open Access Journals (Sweden)

    Jaroslav Mackerle

    1999-01-01

    Full Text Available This bibliography lists references to papers, conference proceedings and theses/dissertations dealing with finite element analysis of rotor dynamics problems that were published in 1994–1998. It contains 319 citations. Also included, as separate subsections, are finite element analyses of rotor elements – discs, shafts, spindles, and blades. Topics dealing with fracture mechanics, contact and stability problems of rotating machinery are also considered in specific sections. The last part of the bibliography presents papers dealing with specific industrial applications.

  17. Computer simulation of multiple dynamic photorefractive gratings

    DEFF Research Database (Denmark)

    Buchhave, Preben

    1998-01-01

    The benefits of a direct visualization of space-charge grating buildup are described. The visualization is carried out by a simple repetitive computer program, which simulates the basic processes in the band-transport model and displays the result graphically or in the form of numerical data....... The simulation sheds light on issues that are not amenable to analytical solutions, such as the spectral content of the wave forms, cross talk in three-beam interaction, and the range of applications of the band-transport model. (C) 1998 Optical Society of America....

  18. A computer test of holographic flavour dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Filev, Veselin G.; O’Connor, Denjoe [School of Theoretical Physics, Dublin Institute for Advanced Studies,10 Burlington Road, Dublin 4 (Ireland)

    2016-05-20

    We perform computer simulations of the Berkooz-Douglas (BD) matrix model, holographically dual to the D0/D4-brane intersection. We generate the fundamental condensate versus bare mass curve of the theory both holographically and from simulations of the BD model. Our studies show excellent agreement of the two approaches in the deconfined phase of the theory and significant deviations in the confined phase. We argue the discrepancy in the confined phase is explained by the embedding of the D4-brane which yields stronger α{sup ′} corrections to the condensate in this phase.

  19. Perspective: Computer simulations of long time dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Elber, Ron [Department of Chemistry, The Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712 (United States)

    2016-02-14

    Atomically detailed computer simulations of complex molecular events attracted the imagination of many researchers in the field as providing comprehensive information on chemical, biological, and physical processes. However, one of the greatest limitations of these simulations is of time scales. The physical time scales accessible to straightforward simulations are too short to address many interesting and important molecular events. In the last decade significant advances were made in different directions (theory, software, and hardware) that significantly expand the capabilities and accuracies of these techniques. This perspective describes and critically examines some of these advances.

  20. Numerical optimization design by computational fluid dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Lee, J.W.; Moon, Y.J. [Korea University, Seoul (Korea, Republic of)

    1996-07-01

    Purpose of the present study is to develop a computational design program for shape optimization, combining the numerical optimization technique with the flow analysis code. The present methodology is then validated in three cases of aerodynamic shape optimization. In the numerical optimization, a feasible direction optimization algorithm and shape functions are considered. In the flow analysis, the Navier-Stokes equations are discretized by a cell-centered finite volume method, and Roe`s flux difference splitting TVD scheme and ADI method are used. The developed design code is applied to a transonic channel flow over a bump, and an external flow over a NACA0012 airfoil to minimize the wave drag induced by shock waves. Also a separated subsonic flow over a NACA0024 airfoil is considered to determine a maximum allowable thickness of the airfoil without separation. (author). 7 refs., 17 figs.

  1. Dynamics and control of trajectory tubes theory and computation

    CERN Document Server

    Kurzhanski, Alexander B

    2014-01-01

    This monograph presents theoretical methods involving the Hamilton–Jacobi–Bellman formalism in conjunction with set-valued techniques of nonlinear analysis to solve significant problems in dynamics and control. The emphasis is on issues of reachability, feedback control  synthesis under complex state constraints, hard or double bounds on controls, and performance in finite time. Guaranteed state estimation, output feedback control, and hybrid dynamics are also discussed. Although the focus is on systems with linear structure, the authors indicate how to apply each approach to nonlinear and nonconvex systems. The main theoretical results lead to computational schemes based on extensions of ellipsoidal calculus that provide complete solutions to the problems. These computational schemes in turn yield software tools that can be applied effectively to high-dimensional systems. Dynamics and Control of Trajectory Tubes: Theory and Computation will interest graduate and senior undergraduate students, as well as...

  2. Fluid dynamics parallel computer development at NASA Langley Research Center

    Science.gov (United States)

    Townsend, James C.; Zang, Thomas A.; Dwoyer, Douglas L.

    1987-01-01

    To accomplish more detailed simulations of highly complex flows, such as the transition to turbulence, fluid dynamics research requires computers much more powerful than any available today. Only parallel processing on multiple-processor computers offers hope for achieving the required effective speeds. Looking ahead to the use of these machines, the fluid dynamicist faces three issues: algorithm development for near-term parallel computers, architecture development for future computer power increases, and assessment of possible advantages of special purpose designs. Two projects at NASA Langley address these issues. Software development and algorithm exploration is being done on the FLEX/32 Parallel Processing Research Computer. New architecture features are being explored in the special purpose hardware design of the Navier-Stokes Computer. These projects are complementary and are producing promising results.

  3. Delta opioid receptor on equine sperm cells: subcellular localization and involvement in sperm motility analyzed by computer assisted sperm analyzer (CASA

    Directory of Open Access Journals (Sweden)

    Lacalandra Giovanni M

    2010-06-01

    Full Text Available Abstract Background Opioid receptors and endogenous opioid peptides act not only in the control of nociceptive pathways, indeed several reports demonstrate the effects of opiates on sperm cell motility and morphology suggesting the importance of these receptors in the modulation of reproduction in mammals. In this study we investigated the expression of delta opioid receptors on equine spermatozoa by western blot/indirect immunofluorescence and its relationship with sperm cell physiology. Methods We analyzed viability, motility, capacitation, acrosome reaction and mitochondrial activity in the presence of naltrindole and DPDPE by means of a computer assisted sperm analyzer and a fluorescent confocal microscope. The evaluation of viability, capacitation and acrosome reaction was carried out by the double CTC/Hoechst staining, whereas mitochondrial activity was assessed by means of MitoTracker Orange dye. Results We showed that in equine sperm cells, delta opioid receptor is expressed as a doublet of 65 and 50 kDa molecular mass and is localized in the mid piece of tail; we also demonstrated that naltrindole, a delta opioid receptor antagonist, could be utilized in modulating several physiological parameters of the equine spermatozoon in a dose-dependent way. We also found that low concentrations of the antagonist increase sperm motility whereas high concentrations show the opposite effect. Moreover low concentrations hamper capacitation, acrosome reaction and viability even if the percentage of cells with active mitochondria seems to be increased; the opposite effect is exerted at high concentrations. We have also observed that the delta opioid receptor agonist DPDPE is scarcely involved in affecting the same parameters at the employed concentrations. Conclusions The results described in this paper add new important details in the comprehension of the mammalian sperm physiology and suggest new insights for improving reproduction and for

  4. Computational Fluid and Particle Dynamics in the Human Respiratory System

    CERN Document Server

    Tu, Jiyuan; Ahmadi, Goodarz

    2013-01-01

    Traditional research methodologies in the human respiratory system have always been challenging due to their invasive nature. Recent advances in medical imaging and computational fluid dynamics (CFD) have accelerated this research. This book compiles and details recent advances in the modelling of the respiratory system for researchers, engineers, scientists, and health practitioners. It breaks down the complexities of this field and provides both students and scientists with an introduction and starting point to the physiology of the respiratory system, fluid dynamics and advanced CFD modeling tools. In addition to a brief introduction to the physics of the respiratory system and an overview of computational methods, the book contains best-practice guidelines for establishing high-quality computational models and simulations. Inspiration for new simulations can be gained through innovative case studies as well as hands-on practice using pre-made computational code. Last but not least, students and researcher...

  5. Subcellular compartmentation of glutathione in dicotyledonous plants

    Science.gov (United States)

    Müller, Maria

    2010-01-01

    This study describes the subcellular distribution of glutathione in roots and leaves of different plant species (Arabidopsis, Cucurbita, and Nicotiana). Glutathione is an important antioxidant and redox buffer which is involved in many metabolic processes including plant defense. Thus information on the subcellular distribution in these model plants especially during stress situations provides a deeper insight into compartment specific defense reactions and reflects the occurrence of compartment specific oxidative stress. With immunogold cytochemistry and computer-supported transmission electron microscopy glutathione could be localized in highest contents in mitochondria, followed by nuclei, peroxisomes, the cytosol, and plastids. Within chloroplasts and mitochondria, glutathione was restricted to the stroma and matrix, respectively, and did not occur in the lumen of cristae and thylakoids. Glutathione was also found at the membrane and in the lumen of the endoplasmic reticulum. It was also associated with the trans and cis side of dictyosomes. None or only very little glutathione was detected in vacuoles and the apoplast of mesophyll and root cells. Additionally, glutathione was found in all cell compartments of phloem vessels, vascular parenchyma cells (including vacuoles) but was absent in xylem vessels. The specificity of this method was supported by the reduction of glutathione labeling in all cell compartments (up to 98%) of the glutathione-deficient Arabidopsis thaliana rml1 mutant. Additionally, we found a similar distribution of glutathione in samples after conventional fixation and rapid microwave-supported fixation. Thus, indicating that a redistribution of glutathione does not occur during sample preparation. Summing up, this study gives a detailed insight into the subcellular distribution of glutathione in plants and presents solid evidence for the accuracy and specificity of the applied method. PMID:20186447

  6. Qualification of a computer program for drill string dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Stone, C.M.; Carne, T.G.; Caskey, B.C.

    1985-01-01

    A four point plan for the qualification of the GEODYN drill string dynamics computer program is described. The qualification plan investigates both modal response and transient response of a short drill string subjected to simulated cutting loads applied through a polycrystalline diamond compact (PDC) bit. The experimentally based qualification shows that the analytical techniques included in Phase 1 GEODYN correctly simulate the dynamic response of the bit-drill string system. 6 refs., 8 figs.

  7. Computational fluid dynamic modelling of cavitation

    Science.gov (United States)

    Deshpande, Manish; Feng, Jinzhang; Merkle, Charles L.

    1993-01-01

    Models in sheet cavitation in cryogenic fluids are developed for use in Euler and Navier-Stokes codes. The models are based upon earlier potential-flow models but enable the cavity inception point, length, and shape to be determined as part of the computation. In the present paper, numerical solutions are compared with experimental measurements for both pressure distribution and cavity length. Comparisons between models are also presented. The CFD model provides a relatively simple modification to an existing code to enable cavitation performance predictions to be included. The analysis also has the added ability of incorporating thermodynamic effects of cryogenic fluids into the analysis. Extensions of the current two-dimensional steady state analysis to three-dimensions and/or time-dependent flows are, in principle, straightforward although geometrical issues become more complicated. Linearized models, however offer promise of providing effective cavitation modeling in three-dimensions. This analysis presents good potential for improved understanding of many phenomena associated with cavity flows.

  8. Computational Fluid Dynamics. [numerical methods and algorithm development

    Science.gov (United States)

    1992-01-01

    This collection of papers was presented at the Computational Fluid Dynamics (CFD) Conference held at Ames Research Center in California on March 12 through 14, 1991. It is an overview of CFD activities at NASA Lewis Research Center. The main thrust of computational work at Lewis is aimed at propulsion systems. Specific issues related to propulsion CFD and associated modeling will also be presented. Examples of results obtained with the most recent algorithm development will also be presented.

  9. Improved Pyrolysis Micro reactor Design via Computational Fluid Dynamics Simulations

    Science.gov (United States)

    2017-05-23

    NUMBER (Include area code) 23 May 2017 Briefing Charts 25 April 2017 - 23 May 2017 Improved Pyrolysis Micro-reactor Design via Computational Fluid...PYROLYSIS MICRO-REACTOR DESIGN VIA COMPUTATIONAL FLUID DYNAMICS SIMULATIONS Ghanshyam L. Vaghjiani* DISTRIBUTION A: Approved for public release...History of Micro-Reactor (Chen-Source) T ≤ 1800 K S.D. Chambreau et al./International Journal of Mass Spectrometry 2000, 199, 17–27 DISTRIBUTION A

  10. Computational Fluid Dynamics Analysis of Freeze Drying Process and Equipment

    OpenAIRE

    Varma, Nikhil P.

    2014-01-01

    Freeze drying is an important, but expensive, inefficient and time consuming process in the pharmaceutical, chemical and food processing industries. Computational techniques could be a very effective tool in predictive design and analysis of both freeze drying process and equipment. This work is an attempt at using Computational Fluid Dynamics(CFD) and numerical simulations as a tool for freeze drying process and equipment design. Pressure control is critical in freeze dryers, keeping in v...

  11. Subcellular localization prediction through boosting association rules.

    Science.gov (United States)

    Yoon, Yongwook; Lee, Gary Geunbae

    2012-01-01

    Computational methods for predicting protein subcellular localization have used various types of features, including N-terminal sorting signals, amino acid compositions, and text annotations from protein databases. Our approach does not use biological knowledge such as the sorting signals or homologues, but use just protein sequence information. The method divides a protein sequence into short $k$-mer sequence fragments which can be mapped to word features in document classification. A large number of class association rules are mined from the protein sequence examples that range from the N-terminus to the C-terminus. Then, a boosting algorithm is applied to those rules to build up a final classifier. Experimental results using benchmark datasets show our method is excellent in terms of both the classification performance and the test coverage. The result also implies that the $k$-mer sequence features which determine subcellular locations do not necessarily exist in specific positions of a protein sequence. Online prediction service implementing our method is available at http://isoft.postech.ac.kr/research/BCAR/subcell.

  12. Application of computational fluid dynamics modelling to an ozone ...

    African Journals Online (AJOL)

    Computational fluid dynamics (CFD) modelling has been applied to examine the operation of the pre-ozonation system at Wiggins Waterworks, operated by Umgeni Water in Durban, South Africa. A hydraulic model has been satisfactorily verified by experimental tracer tests. The turbulence effect induced by the gas ...

  13. Applied Nonlinear Dynamics Analytical, Computational, and Experimental Methods

    CERN Document Server

    Nayfeh, Ali H

    1995-01-01

    A unified and coherent treatment of analytical, computational and experimental techniques of nonlinear dynamics with numerous illustrative applications. Features a discourse on geometric concepts such as Poincaré maps. Discusses chaos, stability and bifurcation analysis for systems of differential and algebraic equations. Includes scores of examples to facilitate understanding.

  14. On Computational Fluid Dynamics Tools in Architectural Design

    DEFF Research Database (Denmark)

    Kirkegaard, Poul Henning; Hougaard, Mads; Stærdahl, Jesper Winther

    In spite of being apparently easy to use, computational fluid dynamics (CFD) based tools require specialist knowledge for modeling as well as for the interpretation of results. This point of view implies also that users of CFD based tools have to be carefully choosing and using them. Especially w...

  15. Dynamics of number systems computation with arbitrary precision

    CERN Document Server

    Kurka, Petr

    2016-01-01

    This book is a source of valuable and useful information on the topics of dynamics of number systems and scientific computation with arbitrary precision. It is addressed to scholars, scientists and engineers, and graduate students. The treatment is elementary and self-contained with relevance both for theory and applications. The basic prerequisite of the book is linear algebra and matrix calculus. .

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

    African Journals Online (AJOL)

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

  17. Modelling Emission from Building Materials with Computational Fluid Dynamics

    DEFF Research Database (Denmark)

    Topp, Claus; Nielsen, Peter V.; Heiselberg, Per

    This paper presents a numerical model that by means of computational fluid dynamics (CFD) is capable of dealing with both pollutant transport across the boundary layer and internal diffusion in the source without prior knowledge of which is the limiting process. The model provides the concentration...

  18. Microchannel Emulsification: From Computational Fluid Dynamics to Predictive Analytical Model

    NARCIS (Netherlands)

    Dijke, van K.C.; Schroën, C.G.P.H.; Boom, R.M.

    2008-01-01

    Emulsion droplet formation was investigated in terrace-based microchannel systems that generate droplets through spontaneous Laplace pressure driven snap-off. The droplet formation mechanism was investigated through high-speed imaging and computational fluid dynamics (CFD) simulation, and we found

  19. Review of computational fluid dynamics for wind turbine wake aerodynamics

    NARCIS (Netherlands)

    B. Sanderse (Benjamin); S.P. van der Pijl (Sander); B. Koren (Barry)

    2011-01-01

    textabstractThis article reviews the state-of-the-art numerical calculation of wind turbine wake aerodynamics. Different computational fluid dynamics techniques for modeling the rotor and the wake are discussed. Regarding rotor modeling, recent advances in the generalized actuator approach and the

  20. Computational fluid dynamics for multistage adsorption dryer design

    NARCIS (Netherlands)

    Djaeni, M.; Bartels, P.V.; Sanders, J.P.M.; Straten, van G.; Boxtel, van A.J.B.

    2008-01-01

    Two-dimensional computational fluid dynamics calculations for multistage zeolite drying are performed for two dryer configurations (1) a continuous moving bed zeolite dryer and (2) a discrete bed zeolite dryer. The calculations concern drying of tarragon (Artemisia dracunculus L.) as an herbal

  1. Dynamic enhanced computed tomographic findings of a perirenal capillary hemangioma

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jung Min; Kim, Sang Won; Kim, Hyun Cheol; Yang, Dal Mo; Ryu, Jung Kyu; Lim, Sung Jig [Kyung Hee University Hospital at Gangdong, Seoul (Korea, Republic of)

    2016-05-15

    Hemangiomas are benign mesenchymal neoplasms that rarely occur in the kidney and perirenal space. Perirenal hemangiomas can mimic the appearance of exophytic renal cell carcinoma or various retroperitoneal tumors. We report a case of perirenal hemangioma detected by dynamic enhanced computed tomography in a 43-year-old female.

  2. Assessment of nasal resistance using computational fluid dynamics

    Directory of Open Access Journals (Sweden)

    Osman Jan

    2016-09-01

    Full Text Available Anterior rhinomanometry is the current gold standard for the objective assessment of nasal breathing by determining the nasal resistance. However, computational fluid dynamics would allow spatially and temporally well- resolved investigation of additional flow parameters. In this study, measured values of nasal resistance are compared with measured values. An unclear discrepancy between the two methods was found, suggesting further investigation.

  3. Towards dynamic remote data auditing in computational clouds.

    Science.gov (United States)

    Sookhak, Mehdi; Akhunzada, Adnan; Gani, Abdullah; Khurram Khan, Muhammad; Anuar, Nor Badrul

    2014-01-01

    Cloud computing is a significant shift of computational paradigm where computing as a utility and storing data remotely have a great potential. Enterprise and businesses are now more interested in outsourcing their data to the cloud to lessen the burden of local data storage and maintenance. However, the outsourced data and the computation outcomes are not continuously trustworthy due to the lack of control and physical possession of the data owners. To better streamline this issue, researchers have now focused on designing remote data auditing (RDA) techniques. The majority of these techniques, however, are only applicable for static archive data and are not subject to audit the dynamically updated outsourced data. We propose an effectual RDA technique based on algebraic signature properties for cloud storage system and also present a new data structure capable of efficiently supporting dynamic data operations like append, insert, modify, and delete. Moreover, this data structure empowers our method to be applicable for large-scale data with minimum computation cost. The comparative analysis with the state-of-the-art RDA schemes shows that the proposed scheme is secure and highly efficient in terms of the computation and communication overhead on the auditor and server.

  4. Towards Dynamic Remote Data Auditing in Computational Clouds

    Directory of Open Access Journals (Sweden)

    Mehdi Sookhak

    2014-01-01

    Full Text Available Cloud computing is a significant shift of computational paradigm where computing as a utility and storing data remotely have a great potential. Enterprise and businesses are now more interested in outsourcing their data to the cloud to lessen the burden of local data storage and maintenance. However, the outsourced data and the computation outcomes are not continuously trustworthy due to the lack of control and physical possession of the data owners. To better streamline this issue, researchers have now focused on designing remote data auditing (RDA techniques. The majority of these techniques, however, are only applicable for static archive data and are not subject to audit the dynamically updated outsourced data. We propose an effectual RDA technique based on algebraic signature properties for cloud storage system and also present a new data structure capable of efficiently supporting dynamic data operations like append, insert, modify, and delete. Moreover, this data structure empowers our method to be applicable for large-scale data with minimum computation cost. The comparative analysis with the state-of-the-art RDA schemes shows that the proposed scheme is secure and highly efficient in terms of the computation and communication overhead on the auditor and server.

  5. Towards Dynamic Remote Data Auditing in Computational Clouds

    Science.gov (United States)

    Khurram Khan, Muhammad; Anuar, Nor Badrul

    2014-01-01

    Cloud computing is a significant shift of computational paradigm where computing as a utility and storing data remotely have a great potential. Enterprise and businesses are now more interested in outsourcing their data to the cloud to lessen the burden of local data storage and maintenance. However, the outsourced data and the computation outcomes are not continuously trustworthy due to the lack of control and physical possession of the data owners. To better streamline this issue, researchers have now focused on designing remote data auditing (RDA) techniques. The majority of these techniques, however, are only applicable for static archive data and are not subject to audit the dynamically updated outsourced data. We propose an effectual RDA technique based on algebraic signature properties for cloud storage system and also present a new data structure capable of efficiently supporting dynamic data operations like append, insert, modify, and delete. Moreover, this data structure empowers our method to be applicable for large-scale data with minimum computation cost. The comparative analysis with the state-of-the-art RDA schemes shows that the proposed scheme is secure and highly efficient in terms of the computation and communication overhead on the auditor and server. PMID:25121114

  6. Computational Methods for Predicting Sites of Functionally Important Dynamics

    Science.gov (United States)

    Schuyler, Adam D.; Carlson, Heather A.; Feldman, Eva L.

    2009-01-01

    Understanding and controlling biological function of proteins at the atomic level is of great importance; allosteric mechanisms provide such an interface. Experimental and computational methods have been developed to search for residue mutations that produce changes in function by altering sites of correlated motion. These methods are often observational in that altered motions are achieved by random sampling without revealing the underlying mechanism(s). We present two deterministic methods founded on structure-function relationships that predict dynamic control sites (i.e. locations that experience correlated motions as a result of altered dynamics). The first method (“static”) is based on a single structure conformation (e.g. the wild type (WT)) and utilizes a graph description of atomic connectivity. The local atomic interactions are used to compute the propagation of contact paths. This description of structure connectivity reveals flexible locations that are susceptible to altered dynamics. The second method (“dynamic”) is a comparative analysis between the normal modes of a WT structure and a mutant structure. A mapping function is defined that quantifies the significance of the motions in one structure projected onto the motions of the other. Each mode is considered up- or down-regulated according to its change in relative significance. This description of altered dynamics is the basis for a motion correlation analysis, from which the dynamic control sites are readily identified. The methods are theoretically derived and applied using the canonical system dihydrofolate reductase (DHFR). Both methods demonstrate a very high predictive value (p dynamic control sites. The dynamic method also produces a new hypothesis regarding the mechanism by which the DHFR mutant achieves hyperactivity. These tools are suitable for allosteric investigations and may greatly enhance the speed and effectiveness of other computational and experimental methods. PMID

  7. SD-CAS: Spin Dynamics by Computer Algebra System.

    Science.gov (United States)

    Filip, Xenia; Filip, Claudiu

    2010-11-01

    A computer algebra tool for describing the Liouville-space quantum evolution of nuclear 1/2-spins is introduced and implemented within a computational framework named Spin Dynamics by Computer Algebra System (SD-CAS). A distinctive feature compared with numerical and previous computer algebra approaches to solving spin dynamics problems results from the fact that no matrix representation for spin operators is used in SD-CAS, which determines a full symbolic character to the performed computations. Spin correlations are stored in SD-CAS as four-entry nested lists of which size increases linearly with the number of spins into the system and are easily mapped into analytical expressions in terms of spin operator products. For the so defined SD-CAS spin correlations a set of specialized functions and procedures is introduced that are essential for implementing basic spin algebra operations, such as the spin operator products, commutators, and scalar products. They provide results in an abstract algebraic form: specific procedures to quantitatively evaluate such symbolic expressions with respect to the involved spin interaction parameters and experimental conditions are also discussed. Although the main focus in the present work is on laying the foundation for spin dynamics symbolic computation in NMR based on a non-matrix formalism, practical aspects are also considered throughout the theoretical development process. In particular, specific SD-CAS routines have been implemented using the YACAS computer algebra package (http://yacas.sourceforge.net), and their functionality was demonstrated on a few illustrative examples. Copyright © 2010 Elsevier Inc. All rights reserved.

  8. Computational dynamics of acoustically-driven microsphere systems

    CERN Document Server

    Glosser, Connor A; Dault, Daniel L; Piermarocchi, Carlo; Shanker, Balasubramaniam

    2015-01-01

    We propose a computational framework for the self-consistent dynamics of a microsphere system driven by a pulsed acoustic field in an ideal fluid. Our framework combines a molecular dynamics integrator describing the dynamics of the microsphere system with a time-dependent integral equation solver for the acoustic field that makes use of fields represented as surface expansions in spherical harmonic basis functions. The presented approach allows us to describe the inter-particle interaction induced by the field as well as the dynamics of trapping in counter-propagating acoustic pulses. The integral equation formulation leads to equations of motion for the microspheres describing the effect of non-dissipative drag forces. We show (1) that the field-induced interactions between the microspheres give rise to effective dipolar interactions, with effective dipoles defined by their velocities, and (2) that the dominant effect of an ultrasound pulse through a cloud of microspheres gives rise mainly to a translation ...

  9. Computer simulation and image guidance for individualised dynamic spinal stabilization.

    Science.gov (United States)

    Kantelhardt, S R; Hausen, U; Kosterhon, M; Amr, A N; Gruber, K; Giese, A

    2015-08-01

    Dynamic implants for the human spine are used to re-establish regular segmental motion. However, the results have often been unsatisfactory and complications such as screw loosening are common. Individualisation of appliances and precision implantation are needed to improve the outcome of this procedure. Computer simulation, virtual implant optimisation and image guidance were used to improve the technique. A human lumbar spine computer model was developed using multi-body simulation software. The model simulates spinal motion under load and degenerative changes. After virtual degeneration of a L4/5 segment, virtual pedicle screw-based implants were introduced. The implants' positions and properties were iteratively optimised. The resulting implant positions were used as operative plan for image guidance and finally implemented in a physical spine model. In the simulation, the introduction and optimisation of virtually designed dynamic implants could partly compensate for the effects of virtual lumbar segment degeneration. The optimised operative plan was exported to two different image-guidance systems for transfer to a physical spine model. Three-dimensional computer graphic simulation is a feasible means to develop operative plans for dynamic spinal stabilization. These operative plans can be transferred to commercially available image-guidance systems for use in implantation of physical implants in a spine model. This concept has important potential in the design of operative plans and implants for individualised dynamic spine stabilization surgery.

  10. Computer Vision Based Measurement of Wildfire Smoke Dynamics

    Directory of Open Access Journals (Sweden)

    BUGARIC, M.

    2015-02-01

    Full Text Available This article presents a novel method for measurement of wildfire smoke dynamics based on computer vision and augmented reality techniques. The aspect of smoke dynamics is an important feature in video smoke detection that could distinguish smoke from visually similar phenomena. However, most of the existing smoke detection systems are not capable of measuring the real-world size of the detected smoke regions. Using computer vision and GIS-based augmented reality, we measure the real dimensions of smoke plumes, and observe the change in size over time. The measurements are performed on offline video data with known camera parameters and location. The observed data is analyzed in order to create a classifier that could be used to eliminate certain categories of false alarms induced by phenomena with different dynamics than smoke. We carried out an offline evaluation where we measured the improvement in the detection process achieved using the proposed smoke dynamics characteristics. The results show a significant increase in algorithm performance, especially in terms of reducing false alarms rate. From this it follows that the proposed method for measurement of smoke dynamics could be used to improve existing smoke detection algorithms, or taken into account when designing new ones.

  11. Computations of Combustion-Powered Actuation for Dynamic Stall Suppression

    Science.gov (United States)

    Jee, Solkeun; Bowles, Patrick O.; Matalanis, Claude G.; Min, Byung-Young; Wake, Brian E.; Crittenden, Tom; Glezer, Ari

    2016-01-01

    A computational framework for the simulation of dynamic stall suppression with combustion-powered actuation (COMPACT) is validated against wind tunnel experimental results on a VR-12 airfoil. COMPACT slots are located at 10% chord from the leading edge of the airfoil and directed tangentially along the suction-side surface. Helicopter rotor-relevant flow conditions are used in the study. A computationally efficient two-dimensional approach, based on unsteady Reynolds-averaged Navier-Stokes (RANS), is compared in detail against the baseline and the modified airfoil with COMPACT, using aerodynamic forces, pressure profiles, and flow-field data. The two-dimensional RANS approach predicts baseline static and dynamic stall very well. Most of the differences between the computational and experimental results are within two standard deviations of the experimental data. The current framework demonstrates an ability to predict COMPACT efficacy across the experimental dataset. Enhanced aerodynamic lift on the downstroke of the pitching cycle due to COMPACT is well predicted, and the cycleaveraged lift enhancement computed is within 3% of the test data. Differences with experimental data are discussed with a focus on three-dimensional features not included in the simulations and the limited computational model for COMPACT.

  12. Dynamic integration of remote cloud resources into local computing clusters

    Energy Technology Data Exchange (ETDEWEB)

    Fleig, Georg; Erli, Guenther; Giffels, Manuel; Hauth, Thomas; Quast, Guenter; Schnepf, Matthias [Institut fuer Experimentelle Kernphysik, Karlsruher Institut fuer Technologie (Germany)

    2016-07-01

    In modern high-energy physics (HEP) experiments enormous amounts of data are analyzed and simulated. Traditionally dedicated HEP computing centers are built or extended to meet this steadily increasing demand for computing resources. Nowadays it is more reasonable and more flexible to utilize computing power at remote data centers providing regular cloud services to users as they can be operated in a more efficient manner. This approach uses virtualization and allows the HEP community to run virtual machines containing a dedicated operating system and transparent access to the required software stack on almost any cloud site. The dynamic management of virtual machines depending on the demand for computing power is essential for cost efficient operation and sharing of resources with other communities. For this purpose the EKP developed the on-demand cloud manager ROCED for dynamic instantiation and integration of virtualized worker nodes into the institute's computing cluster. This contribution will report on the concept of our cloud manager and the implementation utilizing a remote OpenStack cloud site and a shared HPC center (bwForCluster located in Freiburg).

  13. Dynamics of the subcellular localization of RalBP1/RLIP through the cell cycle: the role of targeting signals and of protein-protein interactions.

    Science.gov (United States)

    Fillatre, Jonathan; Delacour, Delphine; Van Hove, Lucie; Bagarre, Thomas; Houssin, Nathalie; Soulika, Marina; Veitia, Reiner A; Moreau, Jacques

    2012-05-01

    The small G protein Ras regulates many cell processes, such as gene expression, proliferation, apoptosis, and cell differentiation. Its mutations are associated with one-third of all cancers. Ras functions are mediated, at least in part, by Ral proteins and their downstream effector the Ral-binding protein 1 (RalBP1). RalBP1 is involved in endocytosis and in regulating the dynamics of the actin cytoskeleton. It also regulates early development since it is required for the completion of gastrulation in Xenopus laevis. RalBP1 has also been reported to be the main transporter of glutathione electrophiles, and it is involved in multidrug resistance. Such a variety of functions could be explained by a differential regulation of RalBP1 localization. In this study, we have detected endogenous RalBP1 in the nucleus of interphasic cells. This nuclear targeting is mediated by nuclear localization sequences that map to the N-terminal third of the protein. Moreover, in X. laevis embryos, a C-terminal coiled-coil sequence mediates RalBP1 retention in the nucleus. We have also observed RalBP1 at the level of the actin cytoskeleton, a localization that depends on interaction of the protein with active Ral. During mitosis RalBP1 also associates with the mitotic spindle and the centrosome, a localization that could be negatively regulated by active Ral. Finally, we demonstrate the presence of post-transcriptional and post-translational isoforms of RalBP1 lacking the Ral-binding domain, which opens new possibilities for the existence of Ral-independent functions.

  14. Dynamic changes in subcellular localization of cattle XLF during cell cycle, and focus formation of cattle XLF at DNA damage sites immediately after irradiation.

    Science.gov (United States)

    Koike, Manabu; Yutoku, Yasutomo; Koike, Aki

    2015-09-01

    Clinically, many chemotherapeutics and ionizing radiation (IR) have been applied for the treatment of various types of human and animal malignancies. These treatments kill tumor cells by causing DNA double-strand breaks (DSBs). Core factors of classical nonhomologous DNA-end joining (C-NHEJ) play a vital role in DSB repair. Thus, it is indispensable to clarify the mechanisms of C-NHEJ in order to develop next-generation chemotherapeutics for cancer. The XRCC4-like factor (XLF; also called Cernunnos or NHEJ1) is the lastly identified core NHEJ factor. The localization of core NHEJ factors might play a critical role in regulating NHEJ activity. The localization and function of XLF have not been elucidated in animal species other than mice and humans. Domestic cattle (Bos taurus) are the most common and vital domestic animals in many countries. Here, we show that the localization of cattle XLF changes dynamically during the cell cycle. Furthermore, EYFP-cattle XLF accumulates quickly at microirradiated sites and colocalizes with the DSB marker γH2AX. Moreover, nuclear localization and accumulation of cattle XLF at DSB sites are dependent on 12 amino acids (288-299) of the C-terminal region of XLF (XLF CTR). Furthermore, basic amino acids on the XLF CTR are highly conserved among domestic animals including cattle, goat and horses, suggesting that the CTR is essential for the function of XLF in domestic animals. These findings might be useful to develop the molecular-targeting therapeutic drug taking XLF as a target molecule for human and domestic animals.

  15. Techniques for animation of CFD results. [computational fluid dynamics

    Science.gov (United States)

    Horowitz, Jay; Hanson, Jeffery C.

    1992-01-01

    Video animation is becoming increasingly vital to the computational fluid dynamics researcher, not just for presentation, but for recording and comparing dynamic visualizations that are beyond the current capabilities of even the most powerful graphic workstation. To meet these needs, Lewis Research Center has recently established a facility to provide users with easy access to advanced video animation capabilities. However, producing animation that is both visually effective and scientifically accurate involves various technological and aesthetic considerations that must be understood both by the researcher and those supporting the visualization process. These considerations include: scan conversion, color conversion, and spatial ambiguities.

  16. Parallel Computational Fluid Dynamics 2007 : Implementations and Experiences on Large Scale and Grid Computing

    CERN Document Server

    2009-01-01

    At the 19th Annual Conference on Parallel Computational Fluid Dynamics held in Antalya, Turkey, in May 2007, the most recent developments and implementations of large-scale and grid computing were presented. This book, comprised of the invited and selected papers of this conference, details those advances, which are of particular interest to CFD and CFD-related communities. It also offers the results related to applications of various scientific and engineering problems involving flows and flow-related topics. Intended for CFD researchers and graduate students, this book is a state-of-the-art presentation of the relevant methodology and implementation techniques of large-scale computing.

  17. An evolutionary computational approach for the dynamic Stackelberg competition problems

    Directory of Open Access Journals (Sweden)

    Lorena Arboleda-Castro

    2016-06-01

    Full Text Available Stackelberg competition models are an important family of economical decision problems from game theory, in which the main goal is to find optimal strategies between two competitors taking into account their hierarchy relationship. Although these models have been widely studied in the past, it is important to note that very few works deal with uncertainty scenarios, especially those that vary over time. In this regard, the present research studies this topic and proposes a computational method for solving efficiently dynamic Stackelberg competition models. The computational experiments suggest that the proposed approach is effective for problems of this nature.

  18. Computer codes for beam dynamics analysis of cyclotronlike accelerators

    Science.gov (United States)

    Smirnov, V.

    2017-12-01

    Computer codes suitable for the study of beam dynamics in cyclotronlike (classical and isochronous cyclotrons, synchrocyclotrons, and fixed field alternating gradient) accelerators are reviewed. Computer modeling of cyclotron segments, such as the central zone, acceleration region, and extraction system is considered. The author does not claim to give a full and detailed description of the methods and algorithms used in the codes. Special attention is paid to the codes already proven and confirmed at the existing accelerating facilities. The description of the programs prepared in the worldwide known accelerator centers is provided. The basic features of the programs available to users and limitations of their applicability are described.

  19. Operational computer graphics in the flight dynamics environment

    Science.gov (United States)

    Jeletic, James F.

    1989-01-01

    Over the past five years, the Flight Dynamics Division of the National Aeronautics and Space Administration's (NASA's) Goddard Space Flight Center has incorporated computer graphics technology into its operational environment. In an attempt to increase the effectiveness and productivity of the Division, computer graphics software systems have been developed that display spacecraft tracking and telemetry data in 2-d and 3-d graphic formats that are more comprehensible than the alphanumeric tables of the past. These systems vary in functionality from real-time mission monitoring system, to mission planning utilities, to system development tools. Here, the capabilities and architecture of these systems are discussed.

  20. Multitasking the code ARC3D. [for computational fluid dynamics

    Science.gov (United States)

    Barton, John T.; Hsiung, Christopher C.

    1986-01-01

    The CRAY multitasking system was developed in order to utilize all four processors and sharply reduce the wall clock run time. This paper describes the techniques used to modify the computational fluid dynamics code ARC3D for this run and analyzes the achieved speedup. The ARC3D code solves either the Euler or thin-layer N-S equations using an implicit approximate factorization scheme. Results indicate that multitask processing can be used to achieve wall clock speedup factors of over three times, depending on the nature of the program code being used. Multitasking appears to be particularly advantageous for large-memory problems running on multiple CPU computers.

  1. The Efficient Use of Vector Computers with Emphasis on Computational Fluid Dynamics : a GAMM-Workshop

    CERN Document Server

    Gentzsch, Wolfgang

    1986-01-01

    The GAMM Committee for Numerical Methods in Fluid Mechanics organizes workshops which should bring together experts of a narrow field of computational fluid dynamics (CFD) to exchange ideas and experiences in order to speed-up the development in this field. In this sense it was suggested that a workshop should treat the solution of CFD problems on vector computers. Thus we organized a workshop with the title "The efficient use of vector computers with emphasis on computational fluid dynamics". The workshop took place at the Computing Centre of the University of Karlsruhe, March 13-15,1985. The participation had been restricted to 22 people of 7 countries. 18 papers have been presented. In the announcement of the workshop we wrote: "Fluid mechanics has actively stimulated the development of superfast vector computers like the CRAY's or CYBER 205. Now these computers on their turn stimulate the development of new algorithms which result in a high degree of vectorization (sca1ar/vectorized execution-time). But w...

  2. Symbolic dynamics and computation in model gene networks.

    Science.gov (United States)

    Edwards, R.; Siegelmann, H. T.; Aziza, K.; Glass, L.

    2001-03-01

    We analyze a class of ordinary differential equations representing a simplified model of a genetic network. In this network, the model genes control the production rates of other genes by a logical function. The dynamics in these equations are represented by a directed graph on an n-dimensional hypercube (n-cube) in which each edge is directed in a unique orientation. The vertices of the n-cube correspond to orthants of state space, and the edges correspond to boundaries between adjacent orthants. The dynamics in these equations can be represented symbolically. Starting from a point on the boundary between neighboring orthants, the equation is integrated until the boundary is crossed for a second time. Each different cycle, corresponding to a different sequence of orthants that are traversed during the integration of the equation always starting on a boundary and ending the first time that same boundary is reached, generates a different letter of the alphabet. A word consists of a sequence of letters corresponding to a possible sequence of orthants that arise from integration of the equation starting and ending on the same boundary. The union of the words defines the language. Letters and words correspond to analytically computable Poincare maps of the equation. This formalism allows us to define bifurcations of chaotic dynamics of the differential equation that correspond to changes in the associated language. Qualitative knowledge about the dynamics found by integrating the equation can be used to help solve the inverse problem of determining the underlying network generating the dynamics. This work places the study of dynamics in genetic networks in a context comprising both nonlinear dynamics and the theory of computation. (c) 2001 American Institute of Physics.

  3. Quality control of computational fluid dynamics in indoor environments

    DEFF Research Database (Denmark)

    Sørensen, Dan Nørtoft; Nielsen, P. V.

    2003-01-01

    Computational fluid dynamics (CFD) is used routinely to predict air movement and distributions of temperature and concentrations in indoor environments. Modelling and numerical errors are inherent in such studies and must be considered when the results are presented. Here, we discuss modelling as...... the quality of CFD calculations, as well as guidelines for the minimum information that should accompany all CFD-related publications to enable a scientific judgment of the quality of the study....

  4. Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps

    OpenAIRE

    Ruggerone, Paolo; Vargiu, Attilio V.; Collu, Francesca; Fischer, Nadine; Kandt, Christian

    2013-01-01

    Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND) protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformation...

  5. Computational Fluid Dynamic Approach for Biological System Modeling

    OpenAIRE

    Huang, Weidong; Wu, Chundu; Xiao, Bingjia; Xia, Weidong

    2005-01-01

    Various biological system models have been proposed in systems biology, which are based on the complex biological reactions kinetic of various components. These models are not practical because we lack of kinetic information. In this paper, it is found that the enzymatic reaction and multi-order reaction rate is often controlled by the transport of the reactants in biological systems. A Computational Fluid Dynamic (CFD) approach, which is based on transport of the components and kinetics of b...

  6. Computer simulation of methanol exchange dynamics around cations and anions

    Energy Technology Data Exchange (ETDEWEB)

    Roy, Santanu; Dang, Liem X.

    2016-03-03

    In this paper, we present the first computer simulation of methanol exchange dynamics between the first and second solvation shells around different cations and anions. After water, methanol is the most frequently used solvent for ions. Methanol has different structural and dynamical properties than water, so its ion solvation process is different. To this end, we performed molecular dynamics simulations using polarizable potential models to describe methanol-methanol and ion-methanol interactions. In particular, we computed methanol exchange rates by employing the transition state theory, the Impey-Madden-McDonald method, the reactive flux approach, and the Grote-Hynes theory. We observed that methanol exchange occurs at a nanosecond time scale for Na+ and at a picosecond time scale for other ions. We also observed a trend in which, for like charges, the exchange rate is slower for smaller ions because they are more strongly bound to methanol. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. The calculations were carried out using computer resources provided by the Office of Basic Energy Sciences.

  7. Agent-based computer simulations of language choice dynamics.

    Science.gov (United States)

    Hadzibeganovic, Tarik; Stauffer, Dietrich; Schulze, Christian

    2009-06-01

    We use agent-based Monte Carlo simulations to address the problem of language choice dynamics in a tripartite community that is linguistically homogeneous but politically divided. We observe the process of nonlocal pattern formation that causes populations to self-organize into stable antagonistic groups as a result of the local dynamics of attraction and influence between individual computational agents. Our findings uncover some of the unique properties of opinion formation in social groups when the process is affected by asymmetric noise distribution, unstable intergroup boundaries, and different migratory behaviors. Although we focus on one particular study, the proposed stochastic dynamic models can be easily generalized and applied to investigate the evolution of other complex and nonlinear features of human collective behavior.

  8. Insights from molecular dynamics simulations for computational protein design.

    Science.gov (United States)

    Childers, Matthew Carter; Daggett, Valerie

    2017-02-01

    A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures.

  9. Insights from molecular dynamics simulations for computational protein design

    Science.gov (United States)

    Childers, Matthew Carter; Daggett, Valerie

    2017-01-01

    A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures. PMID:28239489

  10. Computational Fluid Dynamics (CFD) Technology Programme 1995- 1999

    Energy Technology Data Exchange (ETDEWEB)

    Haekkinen, R.J.; Hirsch, C.; Krause, E.; Kytoemaa, H.K. [eds.

    1997-12-31

    The report is a mid-term evaluation of the Computational Fluid Dynamics (CFD) Technology Programme started by Technology Development Centre Finland (TEKES) in 1995 as a five-year initiative to be concluded in 1999. The main goal of the programme is to increase the know-how and application of CFD in Finnish industry, to coordinate and thus provide a better basis for co-operation between national CFD activities and encouraging research laboratories and industry to establish co-operation with the international CFD community. The projects of the programme focus on the following areas: (1) studies of modeling the physics and dynamics of the behaviour of fluid material, (2) expressing the physical models in a numerical mode and developing a computer codes, (3) evaluating and testing current physical models and developing new ones, (4) developing new numerical algorithms, solvers, and pre- and post-processing software, and (5) applying the new computational tools to problems relevant to their ultimate industrial use. The report consists of two sections. The first considers issues concerning the whole programme and the second reviews each project

  11. Dynamic computer-generated nonlinear-optical holograms

    Science.gov (United States)

    Liu, Haigang; Li, Jun; Fang, Xiangling; Zhao, Xiaohui; Zheng, Yuanlin; Chen, Xianfeng

    2017-08-01

    We propose and experimentally demonstrate dynamic nonlinear optical holograms by introducing the concept of computer-generated holograms for second-harmonic generation of a structured fundamental wave with a specially designed wave front. The generation of Laguerre-Gaussian second-harmonic beams is investigated in our experiment. Such a method, which only dynamically controls the wave front of the fundamental wave by a spatial light modulator, does not need domain inversion in nonlinear crystals and hence is a more flexible way to achieve the off-axis nonlinear second-harmonic beams. It can also be adopted in other schemes and has potential applications in nonlinear frequency conversion, optical signal processing, and real-time hologram, etc.

  12. Dynamics of microtubules: highlights of recent computational and experimental investigations

    Science.gov (United States)

    Barsegov, Valeri; Ross, Jennifer L.; Dima, Ruxandra I.

    2017-11-01

    Microtubules are found in most eukaryotic cells, with homologs in eubacteria and archea, and they have functional roles in mitosis, cell motility, intracellular transport, and the maintenance of cell shape. Numerous efforts have been expended over the last two decades to characterize the interactions between microtubules and the wide variety of microtubule associated proteins that control their dynamic behavior in cells resulting in microtubules being assembled and disassembled where and when they are required by the cell. We present the main findings regarding microtubule polymerization and depolymerization and review recent work about the molecular motors that modulate microtubule dynamics by inducing either microtubule depolymerization or severing. We also discuss the main experimental and computational approaches used to quantify the thermodynamics and mechanics of microtubule filaments.

  13. Computational methods of the Advanced Fluid Dynamics Model

    Energy Technology Data Exchange (ETDEWEB)

    Bohl, W.R.; Wilhelm, D.; Parker, F.R.; Berthier, J.; Maudlin, P.J.; Schmuck, P.; Goutagny, L.; Ichikawa, S.; Ninokata, H.; Luck, L.B.

    1987-01-01

    To more accurately treat severe accidents in fast reactors, a program has been set up to investigate new computational models and approaches. The product of this effort is a computer code, the Advanced Fluid Dynamics Model (AFDM). This paper describes some of the basic features of the numerical algorithm used in AFDM. Aspects receiving particular emphasis are the fractional-step method of time integration, the semi-implicit pressure iteration, the virtual mass inertial terms, the use of three velocity fields, higher order differencing, convection of interfacial area with source and sink terms, multicomponent diffusion processes in heat and mass transfer, the SESAME equation of state, and vectorized programming. A calculated comparison with an isothermal tetralin/ammonia experiment is performed. We conclude that significant improvements are possible in reliably calculating the progression of severe accidents with further development.

  14. Computational strategies in the dynamic simulation of constrained flexible MBS

    Science.gov (United States)

    Amirouche, F. M. L.; Xie, M.

    1993-01-01

    This research focuses on the computational dynamics of flexible constrained multibody systems. At first a recursive mapping formulation of the kinematical expressions in a minimum dimension as well as the matrix representation of the equations of motion are presented. The method employs Kane's equation, FEM, and concepts of continuum mechanics. The generalized active forces are extended to include the effects of high temperature conditions, such as creep, thermal stress, and elastic-plastic deformation. The time variant constraint relations for rolling/contact conditions between two flexible bodies are also studied. The constraints for validation of MBS simulation of gear meshing contact using a modified Timoshenko beam theory are also presented. The last part deals with minimization of vibration/deformation of the elastic beam in multibody systems making use of time variant boundary conditions. The above methodologies and computational procedures developed are being implemented in a program called DYAMUS.

  15. Adaptive Dynamic Process Scheduling on Distributed Memory Parallel Computers

    Directory of Open Access Journals (Sweden)

    Wei Shu

    1994-01-01

    Full Text Available One of the challenges in programming distributed memory parallel machines is deciding how to allocate work to processors. This problem is particularly important for computations with unpredictable dynamic behaviors or irregular structures. We present a scheme for dynamic scheduling of medium-grained processes that is useful in this context. The adaptive contracting within neighborhood (ACWN is a dynamic, distributed, load-dependent, and scalable scheme. It deals with dynamic and unpredictable creation of processes and adapts to different systems. The scheme is described and contrasted with two other schemes that have been proposed in this context, namely the randomized allocation and the gradient model. The performance of the three schemes on an Intel iPSC/2 hypercube is presented and analyzed. The experimental results show that even though the ACWN algorithm incurs somewhat larger overhead than the randomized allocation, it achieves better performance in most cases due to its adaptiveness. Its feature of quickly spreading the work helps it outperform the gradient model in performance and scalability.

  16. A Symbolic and Graphical Computer Representation of Dynamical Systems

    Science.gov (United States)

    Gould, Laurence I.

    2005-04-01

    AUTONO is a Macsyma/Maxima program, designed at the University of Hartford, for solving autonomous systems of differential equations as well as for relating Lagrangians and Hamiltonians to their associated dynamical equations. AUTONO can be used in a number of fields to decipher a variety of complex dynamical systems with ease, producing their Lagrangian and Hamiltonian equations in seconds. These equations can then be incorporated into VisSim, a modeling and simulation program, which yields graphical representations of motion in a given system through easily chosen input parameters. The program, along with the VisSim differential-equations graphical package, allows for resolution and easy understanding of complex problems in a relatively short time; thus enabling quicker and more advanced computing of dynamical systems on any number of platforms---from a network of sensors on a space probe, to the behavior of neural networks, to the effects of an electromagnetic field on components in a dynamical system. A flowchart of AUTONO, along with some simple applications and VisSim output, will be shown.

  17. Robust dynamical decoupling for quantum computing and quantum memory.

    Science.gov (United States)

    Souza, Alexandre M; Alvarez, Gonzalo A; Suter, Dieter

    2011-06-17

    Dynamical decoupling (DD) is a popular technique for protecting qubits from the environment. However, unless special care is taken, experimental errors in the control pulses used in this technique can destroy the quantum information instead of preserving it. Here, we investigate techniques for making DD sequences robust against different types of experimental errors while retaining good decoupling efficiency in a fluctuating environment. We present experimental data from solid-state nuclear spin qubits and introduce a new DD sequence that is suitable for quantum computing and quantum memory.

  18. Computational evaluation of convection schemes in fluid dynamics problems

    Directory of Open Access Journals (Sweden)

    Paulo Laerte Natti

    2012-11-01

    Full Text Available This article provides a computational evaluation of the popular high resolution upwind WACEB, CUBISTA and ADBQUICKEST schemes for solving non-linear fluid dynamics problems. By using the finite difference methodology, the schemes are analyzed and implemented in the context of normalized variables of Leonard. In order to access the performance of the schemes, Riemann problems for 1D Burgers, Euler and shallow water equations are considered. From the numerical results, the schemes are ranked according to their performance in solving these non-linear equations. The best scheme is then applied in the numerical simulation of tridimensional incompressible moving free surface flows.

  19. Computer Modeling of Real-Time Dynamic Lighting

    Science.gov (United States)

    Maida, James C.; Pace, J.; Novak, J.; Russo, Dane M. (Technical Monitor)

    2000-01-01

    Space Station tasks involve procedures that are very complex and highly dependent on the availability of visual information. In many situations, cameras are used as tools to help overcome the visual and physical restrictions associated with space flight. However, these cameras are effected by the dynamic lighting conditions of space. Training for these is conditions is necessary. The current project builds on the findings of an earlier NRA funded project, which revealed improved performance by humans when trained with computer graphics and lighting effects such as shadows and glare.

  20. Computational fluid dynamics using in vivo ultrasound blood flow measurements

    DEFF Research Database (Denmark)

    Traberg, Marie Sand; Pedersen, Mads Møller; Hemmsen, Martin Christian

    2012-01-01

    This paper presents a model environment for construction of patient-specific computational fluid dynamic (CFD) models for the abdominal aorta (AA). Realistic pulsatile velocity waveforms are employed by using in vivo ultrasound blood flow measurements. Ultrasound is suitable for acquisition....... The estimated and smoothed velocity profiles were quantitatively compared. The energy contained in the velocity profile after smoothing is 65% larger relative to the noise contaminated estimated profiles. In conclusion, a model environment that produces realistic patient-specific CFD simulation models without...

  1. Computational fluid dynamics in fire engineering theory, modelling and practice

    CERN Document Server

    Yuen, Kwok Kit

    2009-01-01

    Fire and combustion presents a significant engineering challenge to mechanical, civil and dedicated fire engineers, as well as specialists in the process and chemical, safety, buildings and structural fields. We are reminded of the tragic outcomes of 'untenable' fire disasters such as at King's Cross underground station or Switzerland's St Gotthard tunnel. In these and many other cases, computational fluid dynamics (CFD) is at the forefront of active research into unravelling the probable causes of fires and helping to design structures and systems to ensure that they are less likely in the f

  2. Model of Dynamic Management of Telecommunication and Computer Resources

    Directory of Open Access Journals (Sweden)

    Alla E. Goryushkina

    2016-01-01

    Full Text Available The document identified the problem and developed a model of the dynamic management of telecommunication and computer resources. The present level of development of information and telecommunication technologies, the improvement of communication and their integration into the high-performance human-machine systems administration cause the creation of a single information and telecommunication space of mobile units. The work is devoted to consideration of bases of research of a set of tasks of tactical management of information security. Presents direct and inverse problems and solution methods.

  3. Computer studies of multiple-quantum spin dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Murdoch, J.B.

    1982-11-01

    The excitation and detection of multiple-quantum (MQ) transitions in Fourier transform NMR spectroscopy is an interesting problem in the quantum mechanical dynamics of spin systems as well as an important new technique for investigation of molecular structure. In particular, multiple-quantum spectroscopy can be used to simplify overly complex spectra or to separate the various interactions between a nucleus and its environment. The emphasis of this work is on computer simulation of spin-system evolution to better relate theory and experiment.

  4. Computational Fluid Dynamics of Choanoflagellate Filter-Feeding

    DEFF Research Database (Denmark)

    Asadzadeh, Seyed Saeed; Walther, Jens Honore; Nielsen, Lasse Tor

    Choanoflagellates are unicellular aquatic organisms with a single flagellum that drives a feeding current through a funnel-shaped collar filter on which bacteria-sized prey are caught. Using computational fluid dynamics (CFD) we model the beating flagellum and the complex filter flow of the choanoflagell...... to suggest a radically different filtration mechanism that requires a flagellar vane (sheet), and addition of a wide vane in our CFD model allows us to correctly predict the observed clearance rate....

  5. Computational fluid dynamics modeling of rice husk combustion

    Science.gov (United States)

    Le, Kien Anh

    2017-09-01

    The combustion of rice husk fuel in a fixed bed reactor can be assumed very complicated. Researchers have studied this problem for many years. Such studies have been performed by both empirical and computational methods. However, due to the sharp increase in the development of computer science based packages, the Computational Fluid Dynamics (CFD) technique can be applied to simulate and analyse the performance of the combustion reaction. Consequently, this has saved on empirical expenditures and has additionally provided more understanding about the research objective. This paper models the computation of bed fuel combustion in a fixed bed reactor using Fluent version 12.0.16. The User Defined Functions (UDFs) were created to define the system as well as boundary conditions, and initial conditions. Furthermore, the source terms, heat exchanges and homogeneous reactions were also defined in UDFs. The species transport and volume reaction were used to model the gas phase, where the Eulerian model was employed to solve the problem using two phase modelling. The k-ɛsub-model was employed for turbulence, together with an unsteady model, as the problem was regarded as being unstable. The results obtained from the modelling work would give more understanding about the bed fuel combustion in fixed bed reactor.

  6. Workflow Management Systems for Molecular Dynamics on Leadership Computers

    Science.gov (United States)

    Wells, Jack; Panitkin, Sergey; Oleynik, Danila; Jha, Shantenu

    Molecular Dynamics (MD) simulations play an important role in a range of disciplines from Material Science to Biophysical systems and account for a large fraction of cycles consumed on computing resources. Increasingly science problems require the successful execution of ''many'' MD simulations as opposed to a single MD simulation. There is a need to provide scalable and flexible approaches to the execution of the workload. We present preliminary results on the Titan computer at the Oak Ridge Leadership Computing Facility that demonstrate a general capability to manage workload execution agnostic of a specific MD simulation kernel or execution pattern, and in a manner that integrates disparate grid-based and supercomputing resources. Our results build upon our extensive experience of distributed workload management in the high-energy physics ATLAS project using PanDA (Production and Distributed Analysis System), coupled with recent conceptual advances in our understanding of workload management on heterogeneous resources. We will discuss how we will generalize these initial capabilities towards a more production level service on DOE leadership resources. This research is sponsored by US DOE/ASCR and used resources of the OLCF computing facility.

  7. The role of computational fluid dynamics (CFD) in hair science.

    Science.gov (United States)

    Spicka, Peter; Grald, Eric

    2004-01-01

    The use of computational fluid dynamics (CFD) as a virtual prototyping tool is widespread in the consumer packaged goods industry. CFD refers to the calculation on a computer of the velocity, pressure, and temperature and chemical species concentrations within a flowing liquid or gas. Because the performance of manufacturing equipment and product designs can be simulated on the computer, the benefit of using CFD is significant time and cost savings when compared to traditional physical testing methods. CFD has been used to design, scale-up and troubleshoot mixing tanks, spray dryers, heat exchangers and other process equipment. Recently, computer models of the capillary wicking process inside fibrous structures have been added to CFD software. These models have been used to gain a better understanding of the absorbent performance of diapers and feminine protection products. The same models can also be used to represent the movement of shampoo, conditioner, colorants and other products through the hair and scalp. In this paper, we provide an introduction to CFD and show some examples of its application to the manufacture of consumer products. We also provide sonic examples to show the potential of CFD for understanding the performance of products applied to the hair and scalp.

  8. Ab Initio Computation of Dynamical Properties: Pressure Broadening

    Science.gov (United States)

    Wiesenfeld, Laurent; Drouin, Brian

    2014-06-01

    Rotational spectroscopy of polar molecules is the main observational tool in many areas of astrophysics, for gases of low densities (n ˜ 102 - 108 cm-3). Spectral line shapes in astrophysical media are largely dominated by turbulence-induced Doppler effects and natural line broadening are negligible. However line broadening remains an important tool for denser gases, like planetary high atmospheres. Understanding the excitation schemes of polar molecules requires the knowledge of excitation transfer rate due to collisional excitation, between the polar molecule and the ambient gas, usually H2. Transport properties in ionized media also require a precise knowledge of momentum transfer rates by elastic collisions. In order to assess the theoretically computed cross section and energy/momentum transfer rates, direct absolute experiments are scarce. The best way is to measure not individual scattering events but rather the global effect of the buffer gas, thanks to the pressure broadening cross sections, whose magnitude can be measured without any scaling parameters. At low temperatures, both elastic and inelastic scattering amplitudes are tested. At higher temperature, depending on the interaction strength, only inelastic scattering cross section are shown to play a significant role 1 ,2. Thanks to the advances of computer capabilities, it has become practical to compute spectral line parameters fromab initio quantum chemistry. In particular, the theory of rotational line broadening is readily incorporated into scattering quantum dynamical theory, like close-coupling schemes. The only approximations used in the computation are the isolated collision/isolated line approximations. We compute the non-binding interaction potential with high precision quantum chemistry and fit the resulting ab initio points onto a suitable functional. We have recently computed several such systems, for molecules in H2 buffer gas: H2O,3 H2CO,4 HCO+ .5 Detailed computations taking into

  9. Nano-Modeling and Computation in Bio and Brain Dynamics

    Directory of Open Access Journals (Sweden)

    Paolo Di Sia

    2016-04-01

    Full Text Available The study of brain dynamics currently utilizes the new features of nanobiotechnology and bioengineering. New geometric and analytical approaches appear very promising in all scientific areas, particularly in the study of brain processes. Efforts to engage in deep comprehension lead to a change in the inner brain parameters, in order to mimic the external transformation by the proper use of sensors and effectors. This paper highlights some crossing research areas of natural computing, nanotechnology, and brain modeling and considers two interesting theoretical approaches related to brain dynamics: (a the memory in neural network, not as a passive element for storing information, but integrated in the neural parameters as synaptic conductances; and (b a new transport model based on analytical expressions of the most important transport parameters, which works from sub-pico-level to macro-level, able both to understand existing data and to give new predictions. Complex biological systems are highly dependent on the context, which suggests a “more nature-oriented” computational philosophy.

  10. Issues in computational fluid dynamics code verification and validation

    Energy Technology Data Exchange (ETDEWEB)

    Oberkampf, W.L.; Blottner, F.G.

    1997-09-01

    A broad range of mathematical modeling errors of fluid flow physics and numerical approximation errors are addressed in computational fluid dynamics (CFD). It is strongly believed that if CFD is to have a major impact on the design of engineering hardware and flight systems, the level of confidence in complex simulations must substantially improve. To better understand the present limitations of CFD simulations, a wide variety of physical modeling, discretization, and solution errors are identified and discussed. Here, discretization and solution errors refer to all errors caused by conversion of the original partial differential, or integral, conservation equations representing the physical process, to algebraic equations and their solution on a computer. The impact of boundary conditions on the solution of the partial differential equations and their discrete representation will also be discussed. Throughout the article, clear distinctions are made between the analytical mathematical models of fluid dynamics and the numerical models. Lax`s Equivalence Theorem and its frailties in practical CFD solutions are pointed out. Distinctions are also made between the existence and uniqueness of solutions to the partial differential equations as opposed to the discrete equations. Two techniques are briefly discussed for the detection and quantification of certain types of discretization and grid resolution errors.

  11. Computational Fluid Dynamics Analysis of High Injection Pressure Blended Biodiesel

    Science.gov (United States)

    Khalid, Amir; Jaat, Norrizam; Faisal Hushim, Mohd; Manshoor, Bukhari; Zaman, Izzuddin; Sapit, Azwan; Razali, Azahari

    2017-08-01

    Biodiesel have great potential for substitution with petrol fuel for the purpose of achieving clean energy production and emission reduction. Among the methods that can control the combustion properties, controlling of the fuel injection conditions is one of the successful methods. The purpose of this study is to investigate the effect of high injection pressure of biodiesel blends on spray characteristics using Computational Fluid Dynamics (CFD). Injection pressure was observed at 220 MPa, 250 MPa and 280 MPa. The ambient temperature was kept held at 1050 K and ambient pressure 8 MPa in order to simulate the effect of boost pressure or turbo charger during combustion process. Computational Fluid Dynamics were used to investigate the spray characteristics of biodiesel blends such as spray penetration length, spray angle and mixture formation of fuel-air mixing. The results shows that increases of injection pressure, wider spray angle is produced by biodiesel blends and diesel fuel. The injection pressure strongly affects the mixture formation, characteristics of fuel spray, longer spray penetration length thus promotes the fuel and air mixing.

  12. A paradigm for modeling and computation of gas dynamics

    Science.gov (United States)

    Xu, Kun; Liu, Chang

    2017-02-01

    In the continuum flow regime, the Navier-Stokes (NS) equations are usually used for the description of gas dynamics. On the other hand, the Boltzmann equation is applied for the rarefied flow. These two equations are based on distinguishable modeling scales for flow physics. Fortunately, due to the scale separation, i.e., the hydrodynamic and kinetic ones, both the Navier-Stokes equations and the Boltzmann equation are applicable in their respective domains. However, in real science and engineering applications, they may not have such a distinctive scale separation. For example, around a hypersonic flying vehicle, the flow physics at different regions may correspond to different regimes, where the local Knudsen number can be changed significantly in several orders of magnitude. With a variation of flow physics, theoretically a continuous governing equation from the kinetic Boltzmann modeling to the hydrodynamic Navier-Stokes dynamics should be used for its efficient description. However, due to the difficulties of a direct modeling of flow physics in the scale between the kinetic and hydrodynamic ones, there is basically no reliable theory or valid governing equations to cover the whole transition regime, except resolving flow physics always down to the mean free path scale, such as the direct Boltzmann solver and the Direct Simulation Monte Carlo (DSMC) method. In fact, it is an unresolved problem about the exact scale for the validity of the NS equations, especially in the small Reynolds number cases. The computational fluid dynamics (CFD) is usually based on the numerical solution of partial differential equations (PDEs), and it targets on the recovering of the exact solution of the PDEs as mesh size and time step converging to zero. This methodology can be hardly applied to solve the multiple scale problem efficiently because there is no such a complete PDE for flow physics through a continuous variation of scales. For the non-equilibrium flow study, the direct

  13. Supercoiled DNA energetics and dynamics by computer simulation.

    Science.gov (United States)

    Schlick, T; Olson, W K

    1992-02-20

    A new formulation is presented for investigating supercoiled DNA configurations by deterministic techniques. Thus far, the computational difficulties involved in applying deterministic methods to supercoiled DNA studies have generally limited computer simulations to stochastic approaches. While stochastic methods, such as simulated annealing and Metropolis-Monte Carlo sampling, are successful at generating a large number of configurations and estimating thermodynamic properties of topoisomer ensembles, deterministic methods offer an accurate characterization of the minima and a systematic following of their dynamics. To make this feasible, we model circular duplex DNA compactly by a B-spline ribbon-like model in terms of a small number of control vertices. We associate an elastic deformation energy composed of bending and twisting integrals and represent intrachain contact by a 6-12 Lennard Jones potential. The latter is parameterized to yield an energy minimum at the observed DNA-helix diameter inclusive of a hydration shell. A penalty term to ensure fixed contour length is also included. First and second partial derivatives of the energy function have been derived by using various mathematical simplifications. First derivatives are essential for Newton-type minimization as well as molecular dynamics, and partial second-derivative information can significantly accelerate minimization convergence through preconditioning. Here we apply a new large-scale truncated-Newton algorithm for minimization and a Langevin/implicit-Euler scheme for molecular dynamics. Our truncated-Newton method exploits the separability of potential energy functions into terms of differing complexity. It relies on a preconditioned conjugate gradient method that is efficient for large-scale problems to solve approximately for the search direction at every step. Our dynamics algorithm is numerically stable over large time steps. It also introduces a frequency-discriminating mechanism so that

  14. Energy Conservation Using Dynamic Voltage Frequency Scaling for Computational Cloud

    Directory of Open Access Journals (Sweden)

    A. Paulin Florence

    2016-01-01

    Full Text Available Cloud computing is a new technology which supports resource sharing on a “Pay as you go” basis around the world. It provides various services such as SaaS, IaaS, and PaaS. Computation is a part of IaaS and the entire computational requests are to be served efficiently with optimal power utilization in the cloud. Recently, various algorithms are developed to reduce power consumption and even Dynamic Voltage and Frequency Scaling (DVFS scheme is also used in this perspective. In this paper we have devised methodology which analyzes the behavior of the given cloud request and identifies the associated type of algorithm. Once the type of algorithm is identified, using their asymptotic notations, its time complexity is calculated. Using best fit strategy the appropriate host is identified and the incoming job is allocated to the victimized host. Using the measured time complexity the required clock frequency of the host is measured. According to that CPU frequency is scaled up or down using DVFS scheme, enabling energy to be saved up to 55% of total Watts consumption.

  15. Energy Conservation Using Dynamic Voltage Frequency Scaling for Computational Cloud.

    Science.gov (United States)

    Florence, A Paulin; Shanthi, V; Simon, C B Sunil

    2016-01-01

    Cloud computing is a new technology which supports resource sharing on a "Pay as you go" basis around the world. It provides various services such as SaaS, IaaS, and PaaS. Computation is a part of IaaS and the entire computational requests are to be served efficiently with optimal power utilization in the cloud. Recently, various algorithms are developed to reduce power consumption and even Dynamic Voltage and Frequency Scaling (DVFS) scheme is also used in this perspective. In this paper we have devised methodology which analyzes the behavior of the given cloud request and identifies the associated type of algorithm. Once the type of algorithm is identified, using their asymptotic notations, its time complexity is calculated. Using best fit strategy the appropriate host is identified and the incoming job is allocated to the victimized host. Using the measured time complexity the required clock frequency of the host is measured. According to that CPU frequency is scaled up or down using DVFS scheme, enabling energy to be saved up to 55% of total Watts consumption.

  16. High-Precision Computation: Mathematical Physics and Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Bailey, D. H.; Barrio, R.; Borwein, J. M.

    2010-04-01

    At the present time, IEEE 64-bit oating-point arithmetic is suficiently accurate for most scientic applications. However, for a rapidly growing body of important scientic computing applications, a higher level of numeric precision is required. Such calculations are facilitated by high-precision software packages that include high-level language translation modules to minimize the conversion e ort. This pa- per presents a survey of recent applications of these techniques and provides someanalysis of their numerical requirements. These applications include supernova simulations, climate modeling, planetary orbit calculations, Coulomb n-body atomic systems, studies of the one structure constant, scattering amplitudes of quarks, glu- ons and bosons, nonlinear oscillator theory, experimental mathematics, evaluation of orthogonal polynomials, numerical integration of ODEs, computation of periodic orbits, studies of the splitting of separatrices, detection of strange nonchaotic at- tractors, Ising theory, quantum held theory, and discrete dynamical systems. We conclude that high-precision arithmetic facilities are now an indispensable compo- nent of a modern large-scale scientic computing environment.

  17. High-Performance Java Codes for Computational Fluid Dynamics

    Science.gov (United States)

    Riley, Christopher; Chatterjee, Siddhartha; Biswas, Rupak; Biegel, Bryan (Technical Monitor)

    2001-01-01

    The computational science community is reluctant to write large-scale computationally -intensive applications in Java due to concerns over Java's poor performance, despite the claimed software engineering advantages of its object-oriented features. Naive Java implementations of numerical algorithms can perform poorly compared to corresponding Fortran or C implementations. To achieve high performance, Java applications must be designed with good performance as a primary goal. This paper presents the object-oriented design and implementation of two real-world applications from the field of Computational Fluid Dynamics (CFD): a finite-volume fluid flow solver (LAURA, from NASA Langley Research Center), and an unstructured mesh adaptation algorithm (2D_TAG, from NASA Ames Research Center). This work builds on our previous experience with the design of high-performance numerical libraries in Java. We examine the performance of the applications using the currently available Java infrastructure and show that the Java version of the flow solver LAURA performs almost within a factor of 2 of the original procedural version. Our Java version of the mesh adaptation algorithm 2D_TAG performs within a factor of 1.5 of its original procedural version on certain platforms. Our results demonstrate that object-oriented software design principles are not necessarily inimical to high performance.

  18. Fluid Dynamics of Competitive Swimming: A Computational Study

    Science.gov (United States)

    Mittal, Rajat; Loebbeck, Alfred; Singh, Hersh; Mark, Russell; Wei, Timothy

    2004-11-01

    The dolphin kick is an important component in competitive swimming and is used extensively by swimmers immediately following the starting dive as well as after turns. In this stroke, the swimmer swims about three feet under the water surface and the stroke is executed by performing an undulating wave-like motion of the body that is quite similar to the anguilliform propulsion mode in fish. Despite the relatively simple kinematics of this stoke, considerable variability in style and performance is observed even among Olympic level swimmers. Motivated by this, a joint experimental-numerical study has been initiated to examine the fluid-dynamics of this stroke. The current presentation will describe the computational portion of this study. The computations employ a sharp interface immersed boundary method (IBM) which allows us to simulate flows with complex moving boudnaries on stationary Cartesian grids. 3D body scans of male and female Olympic swimmers have been obtained and these are used in conjuction with high speed videos to recreate a realistic dolphin kick for the IBM solver. Preliminary results from these computations will be presented.

  19. A method to compare computational fluid dynamics (CFD) and multizonal dynamics simulations in buildings physics

    OpenAIRE

    Deltour, Jade; Van Moeseke, Geoffrey; Barbason, Mathieu; Reiter, Sigrid

    2011-01-01

    This paper focuses on the development of a new evaluation method that combines data obtained by two different approaches: “multizonal dynamics” and “computational fluid dynamics (CFD)”. This research is a part of a project whose the main objective is to define guidelines for architects and buildings engineers. This guidelines aims at determining the adequate approach needed to evaluate the occupant thermal comfort and the building energy consumption for cooling and heating. Peer review...

  20. Secure Dynamic access control scheme of PHR in cloud computing.

    Science.gov (United States)

    Chen, Tzer-Shyong; Liu, Chia-Hui; Chen, Tzer-Long; Chen, Chin-Sheng; Bau, Jian-Guo; Lin, Tzu-Ching

    2012-12-01

    With the development of information technology and medical technology, medical information has been developed from traditional paper records into electronic medical records, which have now been widely applied. The new-style medical information exchange system "personal health records (PHR)" is gradually developed. PHR is a kind of health records maintained and recorded by individuals. An ideal personal health record could integrate personal medical information from different sources and provide complete and correct personal health and medical summary through the Internet or portable media under the requirements of security and privacy. A lot of personal health records are being utilized. The patient-centered PHR information exchange system allows the public autonomously maintain and manage personal health records. Such management is convenient for storing, accessing, and sharing personal medical records. With the emergence of Cloud computing, PHR service has been transferred to storing data into Cloud servers that the resources could be flexibly utilized and the operation cost can be reduced. Nevertheless, patients would face privacy problem when storing PHR data into Cloud. Besides, it requires a secure protection scheme to encrypt the medical records of each patient for storing PHR into Cloud server. In the encryption process, it would be a challenge to achieve accurately accessing to medical records and corresponding to flexibility and efficiency. A new PHR access control scheme under Cloud computing environments is proposed in this study. With Lagrange interpolation polynomial to establish a secure and effective PHR information access scheme, it allows to accurately access to PHR with security and is suitable for enormous multi-users. Moreover, this scheme also dynamically supports multi-users in Cloud computing environments with personal privacy and offers legal authorities to access to PHR. From security and effectiveness analyses, the proposed PHR access

  1. A membrane computing simulator of trans-hierarchical antibiotic resistance evolution dynamics in nested ecological compartments (ARES).

    Science.gov (United States)

    Campos, Marcelino; Llorens, Carlos; Sempere, José M; Futami, Ricardo; Rodriguez, Irene; Carrasco, Purificación; Capilla, Rafael; Latorre, Amparo; Coque, Teresa M; Moya, Andres; Baquero, Fernando

    2015-08-05

    Antibiotic resistance is a major biomedical problem upon which public health systems demand solutions to construe the dynamics and epidemiological risk of resistant bacteria in anthropogenically-altered environments. The implementation of computable models with reciprocity within and between levels of biological organization (i.e. essential nesting) is central for studying antibiotic resistances. Antibiotic resistance is not just the result of antibiotic-driven selection but more properly the consequence of a complex hierarchy of processes shaping the ecology and evolution of the distinct subcellular, cellular and supra-cellular vehicles involved in the dissemination of resistance genes. Such a complex background motivated us to explore the P-system standards of membrane computing an innovative natural computing formalism that abstracts the notion of movement across membranes to simulate antibiotic resistance evolution processes across nested levels of micro- and macro-environmental organization in a given ecosystem. In this article, we introduce ARES (Antibiotic Resistance Evolution Simulator) a software device that simulates P-system model scenarios with five types of nested computing membranes oriented to emulate a hierarchy of eco-biological compartments, i.e. a) peripheral ecosystem; b) local environment; c) reservoir of supplies; d) animal host; and e) host's associated bacterial organisms (microbiome). Computational objects emulating molecular entities such as plasmids, antibiotic resistance genes, antimicrobials, and/or other substances can be introduced into this framework and may interact and evolve together with the membranes, according to a set of pre-established rules and specifications. ARES has been implemented as an online server and offers additional tools for storage and model editing and downstream analysis. The stochastic nature of the P-system model implemented in ARES explicitly links within and between host dynamics into a simulation, with

  2. Quinoa - Adaptive Computational Fluid Dynamics, 0.2

    Energy Technology Data Exchange (ETDEWEB)

    2017-09-22

    Quinoa is a set of computational tools that enables research and numerical analysis in fluid dynamics. At this time it remains a test-bed to experiment with various algorithms using fully asynchronous runtime systems. Currently, Quinoa consists of the following tools: (1) Walker, a numerical integrator for systems of stochastic differential equations in time. It is a mathematical tool to analyze and design the behavior of stochastic differential equations. It allows the estimation of arbitrary coupled statistics and probability density functions and is currently used for the design of statistical moment approximations for multiple mixing materials in variable-density turbulence. (2) Inciter, an overdecomposition-aware finite element field solver for partial differential equations using 3D unstructured grids. Inciter is used to research asynchronous mesh-based algorithms and to experiment with coupling asynchronous to bulk-synchronous parallel code. Two planned new features of Inciter, compared to the previous release (LA-CC-16-015), to be implemented in 2017, are (a) a simple Navier-Stokes solver for ideal single-material compressible gases, and (b) solution-adaptive mesh refinement (AMR), which enables dynamically concentrating compute resources to regions with interesting physics. Using the NS-AMR problem we plan to explore how to scale such high-load-imbalance simulations, representative of large production multiphysics codes, to very large problems on very large computers using an asynchronous runtime system. (3) RNGTest, a test harness to subject random number generators to stringent statistical tests enabling quantitative ranking with respect to their quality and computational cost. (4) UnitTest, a unit test harness, running hundreds of tests per second, capable of testing serial, synchronous, and asynchronous functions. (5) MeshConv, a mesh file converter that can be used to convert 3D tetrahedron meshes from and to either of the following formats: Gmsh

  3. Protein subcellular localization prediction using artificial intelligence technology.

    Science.gov (United States)

    Nair, Rajesh; Rost, Burkhard

    2008-01-01

    Proteins perform many important tasks in living organisms, such as catalysis of biochemical reactions, transport of nutrients, and recognition and transmission of signals. The plethora of aspects of the role of any particular protein is referred to as its "function." One aspect of protein function that has been the target of intensive research by computational biologists is its subcellular localization. Proteins must be localized in the same subcellular compartment to cooperate toward a common physiological function. Aberrant subcellular localization of proteins can result in several diseases, including kidney stones, cancer, and Alzheimer's disease. To date, sequence homology remains the most widely used method for inferring the function of a protein. However, the application of advanced artificial intelligence (AI)-based techniques in recent years has resulted in significant improvements in our ability to predict the subcellular localization of a protein. The prediction accuracy has risen steadily over the years, in large part due to the application of AI-based methods such as hidden Markov models (HMMs), neural networks (NNs), and support vector machines (SVMs), although the availability of larger experimental datasets has also played a role. Automatic methods that mine textual information from the biological literature and molecular biology databases have considerably sped up the process of annotation for proteins for which some information regarding function is available in the literature. State-of-the-art methods based on NNs and HMMs can predict the presence of N-terminal sorting signals extremely accurately. Ab initio methods that predict subcellular localization for any protein sequence using only the native amino acid sequence and features predicted from the native sequence have shown the most remarkable improvements. The prediction accuracy of these methods has increased by over 30% in the past decade. The accuracy of these methods is now on par with

  4. A formal ontology of subcellular neuroanatomy

    Directory of Open Access Journals (Sweden)

    Stephen D Larson

    2007-11-01

    Full Text Available The complexity of the nervous system requires high-resolution microscopy to resolve the detailed 3D structure of nerve cells and supracellular domains. The analysis of such imaging data to extract cellular surfaces and cell components often requires the combination of expert human knowledge with carefully engineered software tools. In an effort to make better tools to assist humans in this endeavor, create a more accessible and permanent record of their data, and to aid the process of constructing complex and detailed computational models, we have created a core of formalized knowledge about the structure of the nervous system and have integrated that core into several software applications. In this paper, we describe the structure and content of a formal ontology whose scope is the subcellular anatomy of the nervous system (SAO, covering nerve cells, their parts, and interactions between these parts. Many applications of this ontology to image annotation, content-based retrieval of structural data, and integration of shared data across scales and researchers are also described.

  5. Computational Fluid Dynamics Analysis of an Evaporative Cooling System

    Directory of Open Access Journals (Sweden)

    Kapilan N.

    2016-11-01

    Full Text Available The use of chlorofluorocarbon based refrigerants in the air-conditioning system increases the global warming and causes the climate change. The climate change is expected to present a number of challenges for the built environment and an evaporative cooling system is one of the simplest and environmentally friendly cooling system. The evaporative cooling system is most widely used in summer and in rural and urban areas of India for human comfort. In evaporative cooling system, the addition of water into air reduces the temperature of the air as the energy needed to evaporate the water is taken from the air. Computational fluid dynamics is a numerical analysis and was used to analyse the evaporative cooling system. The CFD results are matches with the experimental results.

  6. Mapping flow distortion on oceanographic platforms using computational fluid dynamics

    Directory of Open Access Journals (Sweden)

    N. O'Sullivan

    2013-10-01

    Full Text Available Wind speed measurements over the ocean on ships or buoys are affected by flow distortion from the platform and by the anemometer itself. This can lead to errors in direct measurements and the derived parametrisations. Here we computational fluid dynamics (CFD to simulate the errors in wind speed measurements caused by flow distortion on the RV Celtic Explorer. Numerical measurements were obtained from the finite-volume CFD code OpenFOAM, which was used to simulate the velocity fields. This was done over a range of orientations in the test domain from −60 to +60° in increments of 10°. The simulation was also set up for a range of velocities, ranging from 5 to 25 m s−1 in increments of 0.5 m s−1. The numerical analysis showed close agreement to experimental measurements.

  7. The Piecewise Cubic Method (PCM) for computational fluid dynamics

    Science.gov (United States)

    Lee, Dongwook; Faller, Hugues; Reyes, Adam

    2017-07-01

    We present a new high-order finite volume reconstruction method for hyperbolic conservation laws. The method is based on a piecewise cubic polynomial which provides its solutions a fifth-order accuracy in space. The spatially reconstructed solutions are evolved in time with a fourth-order accuracy by tracing the characteristics of the cubic polynomials. As a result, our temporal update scheme provides a significantly simpler and computationally more efficient approach in achieving fourth order accuracy in time, relative to the comparable fourth-order Runge-Kutta method. We demonstrate that the solutions of PCM converges at fifth-order in solving 1D smooth flows described by hyperbolic conservation laws. We test the new scheme on a range of numerical experiments, including both gas dynamics and magnetohydrodynamics applications in multiple spatial dimensions.

  8. Simulation of Tailrace Hydrodynamics Using Computational Fluid Dynamics Models

    Energy Technology Data Exchange (ETDEWEB)

    Cook, Christopher B.; Richmond, Marshall C.

    2001-05-01

    This report investigates the feasibility of using computational fluid dynamics (CFD) tools to investigate hydrodynamic flow fields surrounding the tailrace zone below large hydraulic structures. Previous and ongoing studies using CFD tools to simulate gradually varied flow with multiple constituents and forebay/intake hydrodynamics have shown that CFD tools can provide valuable information for hydraulic and biological evaluation of fish passage near hydraulic structures. These studies however are incapable of simulating the rapidly varying flow fields that involving breakup of the free-surface, such as those through and below high flow outfalls and spillways. Although the use of CFD tools for these types of flow are still an active area of research, initial applications discussed in this report show that these tools are capable of simulating the primary features of these highly transient flow fields.

  9. Using computational fluid dynamics to characterize and improve bioreactor performance.

    Science.gov (United States)

    Kelly, William J

    2008-04-01

    CFD (computational fluid dynamics) has been used to model upstream bioprocessing steps such as fermentation and homogenization. The focus of these studies has oftentimes been to characterize single-phase (liquid) flow and hydrodynamic shear. In the actual bioprocessing operations, however, there are at least two phases (cells and liquid) present. In the bioreactor, the gas bubbles constitute a third phase. More recent CFD models have considered the momentum and mass transfer that occurs between the phases. This review summarizes studies from the biochemical and biomedical literature relating to the use of CFD to model the performance of a variety of bioreactor types. Particular emphasis will be placed on describing current methods for handling multi-phase flow involving animal cells and/or gas bubbles.

  10. A Dynamic Bayesian Approach to Computational Laban Shape Quality Analysis

    Directory of Open Access Journals (Sweden)

    Dilip Swaminathan

    2009-01-01

    kinesiology. LMA (especially Effort/Shape emphasizes how internal feelings and intentions govern the patterning of movement throughout the whole body. As we argue, a complex understanding of intention via LMA is necessary for human-computer interaction to become embodied in ways that resemble interaction in the physical world. We thus introduce a novel, flexible Bayesian fusion approach for identifying LMA Shape qualities from raw motion capture data in real time. The method uses a dynamic Bayesian network (DBN to fuse movement features across the body and across time and as we discuss can be readily adapted for low-cost video. It has delivered excellent performance in preliminary studies comprising improvisatory movements. Our approach has been incorporated in Response, a mixed-reality environment where users interact via natural, full-body human movement and enhance their bodily-kinesthetic awareness through immersive sound and light feedback, with applications to kinesiology training, Parkinson's patient rehabilitation, interactive dance, and many other areas.

  11. Uncertainty quantification in computational fluid dynamics and aircraft engines

    CERN Document Server

    Montomoli, Francesco; D'Ammaro, Antonio; Massini, Michela; Salvadori, Simone

    2015-01-01

    This book introduces novel design techniques developed to increase the safety of aircraft engines. The authors demonstrate how the application of uncertainty methods can overcome problems in the accurate prediction of engine lift, caused by manufacturing error. This in turn ameliorates the difficulty of achieving required safety margins imposed by limits in current design and manufacturing methods. This text shows that even state-of-the-art computational fluid dynamics (CFD) are not able to predict the same performance measured in experiments; CFD methods assume idealised geometries but ideal geometries do not exist, cannot be manufactured and their performance differs from real-world ones. By applying geometrical variations of a few microns, the agreement with experiments improves dramatically, but unfortunately the manufacturing errors in engines or in experiments are unknown. In order to overcome this limitation, uncertainty quantification considers the probability density functions of manufacturing errors...

  12. Simulating Smoke Filling in Big Halls by Computational Fluid Dynamics

    Directory of Open Access Journals (Sweden)

    W. K. Chow

    2011-01-01

    Full Text Available Many tall halls of big space volume were built and, to be built in many construction projects in the Far East, particularly Mainland China, Hong Kong, and Taiwan. Smoke is identified to be the key hazard to handle. Consequently, smoke exhaust systems are specified in the fire code in those areas. An update on applying Computational Fluid Dynamics (CFD in smoke exhaust design will be presented in this paper. Key points to note in CFD simulations on smoke filling due to a fire in a big hall will be discussed. Mathematical aspects concerning of discretization of partial differential equations and algorithms for solving the velocity-pressure linked equations are briefly outlined. Results predicted by CFD with different free boundary conditions are compared with those on room fire tests. Standards on grid size, relaxation factors, convergence criteria, and false diffusion should be set up for numerical experiments with CFD.

  13. Use of Computational Fluid Dynamics for Absorption Packed Column Design

    Directory of Open Access Journals (Sweden)

    Haroun Yacine

    2016-05-01

    Full Text Available Computational Fluid Dynamics (CFD is today commonly used in a wide variety of process industries and disciplines for the development of innovative technologies. The present article aims to show how CFD can be used as an effective analysis and design tool for the development and design of packed gas/liquid absorption columns. It is first shown how CFD can be used for the characterisation of packings. The different hydrodynamic and mass transfer design parameters are investigated and adapted CFD methods are suggested. Secondly, column distribution internal development is discussed to show how CFD simulations should be performed to improve the design of gas and liquid distributors. An example of the development of new distribution technologies for floating installation of a reactive absorption column is also presented.

  14. Computational Fluid Dynamics and Building Energy Performance Simulation

    DEFF Research Database (Denmark)

    Nielsen, Peter Vilhelm; Tryggvason, T.

    1998-01-01

    An interconnection between a building energy performance simulation program and a Computational Fluid Dynamics program (CFD) for room air distribution will be introduced for improvement of the predictions of both the energy consumption and the indoor environment. The building energy performance...... simulation program requires a detailed description of the energy flow in the air movement which can be obtained by a CFD program. The paper describes an energy consumption calculation in a large building, where the building energy simulation program is modified by CFD predictions of the flow between three...... zones connected by open areas with pressure and buoyancy driven air flow. The two programs are interconnected in an iterative procedure. The paper shows also an evaluation of the air quality in the main area of the buildings based on CFD predictions. It is shown that an interconnection between a CFD...

  15. Computational Fluid Dynamics and Building Energy Performance Simulation

    DEFF Research Database (Denmark)

    Nielsen, Peter V.; Tryggvason, Tryggvi

    An interconnection between a building energy performance simulation program and a Computational Fluid Dynamics program (CFD) for room air distribution will be introduced for improvement of the predictions of both the energy consumption and the indoor environment. The building energy performance...... simulation program requires a detailed description of the energy flow in the air movement which can be obtained by a CFD program. The paper describes an energy consumption calculation in a large building, where the building energy simulation program is modified by CFD predictions of the flow between three...... program and a building energy performance simulation program will improve both the energy consumption data and the prediction of thermal comfort and air quality in a selected area of the building....

  16. Numerical computations of the dynamics of fluidic membranes and vesicles

    CERN Document Server

    Barrett, John W; Nürnberg, Robert

    2015-01-01

    Vesicles and many biological membranes are made of two monolayers of lipid molecules and form closed lipid bilayers. The dynamical behaviour of vesicles is very complex and a variety of forms and shapes appear. Lipid bilayers can be considered as a surface fluid and hence the governing equations for the evolution include the surface (Navier--)Stokes equations, which in particular take the membrane viscosity into account. The evolution is driven by forces stemming from the curvature elasticity of the membrane. In addition, the surface fluid equations are coupled to bulk (Navier--)Stokes equations. We introduce a parametric finite element method to solve this complex free boundary problem, and present the first three dimensional numerical computations based on the full (Navier--)Stokes system for several different scenarios. For example, the effects of the membrane viscosity, spontaneous curvature and area difference elasticity (ADE) are studied. In particular, it turns out, that even in the case of no viscosit...

  17. Computational and theoretical aspects of biomolecular structure and dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Garcia, A.E.; Berendzen, J.; Catasti, P., Chen, X. [and others

    1996-09-01

    This is the final report for a project that sought to evaluate and develop theoretical, and computational bases for designing, performing, and analyzing experimental studies in structural biology. Simulations of large biomolecular systems in solution, hydrophobic interactions, and quantum chemical calculations for large systems have been performed. We have developed a code that implements the Fast Multipole Algorithm (FMA) that scales linearly in the number of particles simulated in a large system. New methods have been developed for the analysis of multidimensional NMR data in order to obtain high resolution atomic structures. These methods have been applied to the study of DNA sequences in the human centromere, sequences linked to genetic diseases, and the dynamics and structure of myoglobin.

  18. Monoterpene biosynthesis potential of plant subcellular compartments

    NARCIS (Netherlands)

    Dong, L.; Jongedijk, E.J.; Bouwmeester, H.J.; Krol, van der A.R.

    2016-01-01

    Subcellular monoterpene biosynthesis capacity based on local geranyl diphosphate (GDP) availability or locally boosted GDP production was determined for plastids, cytosol and mitochondria. A geraniol synthase (GES) was targeted to plastids, cytosol, or mitochondria. Transient expression in Nicotiana

  19. Expression and subcellular localization of antiporter regulating ...

    African Journals Online (AJOL)

    Expression and subcellular localization of antiporter regulating protein OsARP in rice induced by submergence, salt and drought stresses. Md Imtiaz Uddin, Maki Kihara, Lina Yin, Mst Farida Perveen, Kiyoshi Tanaka ...

  20. Optogenetic Tools for Subcellular Applications in Neuroscience.

    Science.gov (United States)

    Rost, Benjamin R; Schneider-Warme, Franziska; Schmitz, Dietmar; Hegemann, Peter

    2017-11-01

    The ability to study cellular physiology using photosensitive, genetically encoded molecules has profoundly transformed neuroscience. The modern optogenetic toolbox includes fluorescent sensors to visualize signaling events in living cells and optogenetic actuators enabling manipulation of numerous cellular activities. Most optogenetic tools are not targeted to specific subcellular compartments but are localized with limited discrimination throughout the cell. Therefore, optogenetic activation often does not reflect context-dependent effects of highly localized intracellular signaling events. Subcellular targeting is required to achieve more specific optogenetic readouts and photomanipulation. Here we first provide a detailed overview of the available optogenetic tools with a focus on optogenetic actuators. Second, we review established strategies for targeting these tools to specific subcellular compartments. Finally, we discuss useful tools and targeting strategies that are currently missing from the optogenetics repertoire and provide suggestions for novel subcellular optogenetic applications. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Unsteady computational fluid dynamics in front crawl swimming.

    Science.gov (United States)

    Samson, Mathias; Bernard, Anthony; Monnet, Tony; Lacouture, Patrick; David, Laurent

    2017-05-01

    The development of codes and power calculations currently allows the simulation of increasingly complex flows, especially in the turbulent regime. Swimming research should benefit from these technological advances to try to better understand the dynamic mechanisms involved in swimming. An unsteady Computational Fluid Dynamics (CFD) study is conducted in crawl, in order to analyse the propulsive forces generated by the hand and forearm. The k-ω SST turbulence model and an overset grid method have been used. The main objectives are to analyse the evolution of the hand-forearm propulsive forces and to explain this relative to the arm kinematics parameters. In order to validate our simulation model, the calculated forces and pressures were compared with several other experimental and numerical studies. A good agreement is found between our results and those of other studies. The hand is the segment that generates the most propulsive forces during the aquatic stroke. As the pressure component is the main source of force, the orientation of the hand-forearm in the absolute coordinate system is an important kinematic parameter in the swimming performance. The propulsive forces are biggest when the angles of attack are high. CFD appears as a very valuable tool to better analyze the mechanisms of swimming performance and offers some promising developments, especially for optimizing the performance from a parametric study.

  2. Application of computational fluid dynamics in tissue engineering.

    Science.gov (United States)

    Patrachari, Anirudh R; Podichetty, Jagdeep T; Madihally, Sundararajan V

    2012-08-01

    The process of tissue regeneration consists of a set of complex phenomena such as hydrodynamics, nutrient transfer, cell growth, and matrix deposition. Traditional cell culture and bioreactor design procedure follow trial-and-error analyses to understand the effects of varying physical, chemical, and mechanical parameters that govern the process of tissue regeneration. This trend has been changing as computational fluid dynamics (CFD) analysis can now be used to understand the effects of flow, cell proliferation, and consumption kinetics on the dynamics involved with in vitro tissue regeneration. Furthermore, CFD analyses enable understanding the influence of nutrient transport on cell growth and the effect of cell proliferation as the tissue regenerates. This is especially advantageous in improving and optimizing the design of bioreactors and tissue culture. Influence of parameters such as velocity, oxygen tension, stress, and strain on tissue growth can be effectively studied throughout the bioreactor using CFD as it becomes impractical and cumbersome to install probes at several locations in the bioreactor. Hence, CFD offers several advantages for the advancement of tissue engineering. Copyright © 2012 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  3. Molecular Dynamics with the massively parallel APE computers

    Science.gov (United States)

    La Penna, G.; Minicozzi, V.; Morante, S.; Rossi, G. C.; Salina, G.

    1997-10-01

    In this paper we discuss the general question of the portability of Molecular Dynamics codes for diffusive systems (liquids) on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does not seem to affect the numerical accuracy of the simulations, while the absence of integer addressing from the CPU to individual nodes puts strong constraints on the possible programming strategies. As a test case, we report the results of the simulation of the dynamics of 512 molecules of liquid butane (C 4H 10) ta room temperature. After 30 to 50 ps of equilibrium, the system was followed along four long trajectories, each one more than 1.3 ns. The effective CPU time corresponding to the simulation of a trajectory of 1 ns on the Torre (512 nodes ≈ 25 Gigaflops) was ≈ 50 hours. The CPU time can be substantially reduced (by almost a factor 3), if the APE- assembler micro-code of the most time-consuming part of the program is carefully optimized.

  4. Computational fluid dynamics: A two-edged sword

    Energy Technology Data Exchange (ETDEWEB)

    Baker, A.J.; Kelso, R.M. [Univ. of Tennessee, Knoxville, TN (United States); Gordon, E.B. [AGA Labs., Cleveland, OH (United States); Roy, S.; Schaub, E.G. [Computational Mechanics Corp., Knoxville, TN (United States)

    1997-08-01

    This article examines computational fluid dynamics (CFD) limitations as a design tool. Two decades have passed since the first paper was published in the ASHRAE Transactions suggesting the use of CFD for quantitative prediction of room air motion. CFD is an emerging methodology, with roots in the defense/aerospace industry, wherein a mathematical model of fluid flow is converted into a digital computational procedure, yielding numbers that approximate the solution of this modeled system, hence the genuine flow state. CFD methodology has indeed brought bright glimmers of an ability to establish firm quantitative data regarding how room air moves. In fact, CFD can predict fluid levels and pressure differences to very low levels, that are essentially impossible to experimentally measure. However, a CFD model constitutes the culmination of a large number of assumptions and approximations, such that the answers produced are essentially never correct. Further, it is the very approximation process in CFD theory that leads to intrinsic error mechanisms that can range from benign to pathological. The ASHRAE professional who seeks to use CFD to assist in system design needs to be fully aware of these two edges of the CFD sword.

  5. DYNAMICS OF DETECTED FIRE FACTORS IN CLOSED COMPARTMENT: COMPUTER SIMULATION

    Directory of Open Access Journals (Sweden)

    V. V. Nevdakh

    2015-01-01

    Full Text Available Computer simulation of the initial fire stages in closed compartment with the volume of ≈ 60 m3 and with a burner on a floor and 2 m above floor have been carried using FDS software. Fires with different t 2 –power low heat release rates have been modeled. Fires which growth times to reach 1055 kW were 100 s and 500 s have been considered as fast and slow fires respectively. Dynamics of heat release rates and detected fire factors such as spatial distributions of air temperature, smoke obscuration and variations of indoor pressure have been studied. It has been obtained that dynamics of heat release rates of the initial fire stages in closed compartment consists of two stages. During the first stage the heat release rate is proportional to mass burning rate and flaming occurs only above a burner. At the second stage dynamics of heat release rates has a form of irregular in amplitude and duration pulsations, which are caused by self-ignition in the smoke layer. The compartment air volume may be layered with respect to the height and every layer has its oven temperature, smoke obscuration, self-ignition areas have been shown. The layer thickness, gradients of temperature and obscuration depend on a fire growth rate and on a burner height above floor have been concluded. The spatial distributions of air temperature and pressure variation have the opposite gradients on a height have been obtained. Maximal pressure variation and its gradient occurs under the fast fire with a burner on a floor have been obtained too. 

  6. Turbomachinery computational fluid dynamics: asymptotes and paradigm shifts.

    Science.gov (United States)

    Dawes, W N

    2007-10-15

    This paper reviews the development of computational fluid dynamics (CFD) specifically for turbomachinery simulations and with a particular focus on application to problems with complex geometry. The review is structured by considering this development as a series of paradigm shifts, followed by asymptotes. The original S1-S2 blade-blade-throughflow model is briefly described, followed by the development of two-dimensional then three-dimensional blade-blade analysis. This in turn evolved from inviscid to viscous analysis and then from steady to unsteady flow simulations. This development trajectory led over a surprisingly small number of years to an accepted approach-a 'CFD orthodoxy'. A very important current area of intense interest and activity in turbomachinery simulation is in accounting for real geometry effects, not just in the secondary air and turbine cooling systems but also associated with the primary path. The requirements here are threefold: capturing and representing these geometries in a computer model; making rapid design changes to these complex geometries; and managing the very large associated computational models on PC clusters. Accordingly, the challenges in the application of the current CFD orthodoxy to complex geometries are described in some detail. The main aim of this paper is to argue that the current CFD orthodoxy is on a new asymptote and is not in fact suited for application to complex geometries and that a paradigm shift must be sought. In particular, the new paradigm must be geometry centric and inherently parallel without serial bottlenecks. The main contribution of this paper is to describe such a potential paradigm shift, inspired by the animation industry, based on a fundamental shift in perspective from explicit to implicit geometry and then illustrate this with a number of applications to turbomachinery.

  7. Evaluation and comparison of mammalian subcellular localization prediction methods

    Directory of Open Access Journals (Sweden)

    Fink J Lynn

    2006-12-01

    Full Text Available Abstract Background Determination of the subcellular location of a protein is essential to understanding its biochemical function. This information can provide insight into the function of hypothetical or novel proteins. These data are difficult to obtain experimentally but have become especially important since many whole genome sequencing projects have been finished and many resulting protein sequences are still lacking detailed functional information. In order to address this paucity of data, many computational prediction methods have been developed. However, these methods have varying levels of accuracy and perform differently based on the sequences that are presented to the underlying algorithm. It is therefore useful to compare these methods and monitor their performance. Results In order to perform a comprehensive survey of prediction methods, we selected only methods that accepted large batches of protein sequences, were publicly available, and were able to predict localization to at least nine of the major subcellular locations (nucleus, cytosol, mitochondrion, extracellular region, plasma membrane, Golgi apparatus, endoplasmic reticulum (ER, peroxisome, and lysosome. The selected methods were CELLO, MultiLoc, Proteome Analyst, pTarget and WoLF PSORT. These methods were evaluated using 3763 mouse proteins from SwissProt that represent the source of the training sets used in development of the individual methods. In addition, an independent evaluation set of 2145 mouse proteins from LOCATE with a bias towards the subcellular localization underrepresented in SwissProt was used. The sensitivity and specificity were calculated for each method and compared to a theoretical value based on what might be observed by random chance. Conclusion No individual method had a sufficient level of sensitivity across both evaluation sets that would enable reliable application to hypothetical proteins. All methods showed lower performance on the LOCATE

  8. Frequency Domain Computer Programs for Prediction and Analysis of Rail Vehicle Dynamics : Volume 1. Technical Report

    Science.gov (United States)

    1975-12-01

    Frequency domain computer programs developed or acquired by TSC for the analysis of rail vehicle dynamics are described in two volumes. Volume I defines the general analytical capabilities required for computer programs applicable to single rail vehi...

  9. An Automated High Aspect Ratio Mesher for Computational Fluid Dynamics Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Computational fluid dynamics (CFD) simulations are routinely used while designing, analyzing, and optimizing air- and spacecraft. An important component of CFD...

  10. Prediction of Projectile Performance, Stability, and Free-Flight Motion Using Computational Fluid Dynamics

    National Research Council Canada - National Science Library

    Weinacht, Paul

    2003-01-01

    ... that are derived solely from computational fluid dynamics (CFD). As a demonstration of the capability, this report presents results for a family of axisymmetric projectiles in supersonic flight...

  11. Distributed computations in a dynamic, heterogeneous Grid environment

    Science.gov (United States)

    Dramlitsch, Thomas

    2003-06-01

    other reasons for low performance - develop new and advanced algorithms for parallelisation that are aware of a Grid environment in order to generelize the traditional parallelization schemes - implement and test these new methods, replace and compare with the classical ones - introduce dynamic strategies that automatically adapt the running code to the nature of the underlying Grid environment. The higher the performance one can achieve for a single application by manual tuning for a Grid environment, the lower the chance that those changes are widely applicable to other programs. In our analysis as well as in our implementation we tried to keep the balance between high performance and generality. None of our changes directly affect code on the application level which makes our algorithms applicable to a whole class of real world applications. The implementation of our work is done within the Cactus framework using the Globus toolkit, since we think that these are the most reliable and advanced programming frameworks for supporting computations in Grid environments. On the other hand, however, we tried to be as general as possible, i.e. all methods and algorithms discussed in this thesis are independent of Cactus or Globus. Die immer dichtere und schnellere Vernetzung von Rechnern und Rechenzentren über Hochgeschwindigkeitsnetzwerke ermöglicht eine neue Art des wissenschaftlich verteilten Rechnens, bei der geographisch weit auseinanderliegende Rechenkapazitäten zu einer Gesamtheit zusammengefasst werden können. Dieser so entstehende virtuelle Superrechner, der selbst aus mehreren Grossrechnern besteht, kann dazu genutzt werden Probleme zu berechnen, für die die einzelnen Grossrechner zu klein sind. Die Probleme, die numerisch mit heutigen Rechenkapazitäten nicht lösbar sind, erstrecken sich durch sämtliche Gebiete der heutigen Wissenschaft, angefangen von Astrophysik, Molekülphysik, Bioinformatik, Meteorologie, bis hin zur Zahlentheorie und Fluiddynamik um nur

  12. Computational fluid dynamic modeling of fluidized-bed polymerization reactors

    Energy Technology Data Exchange (ETDEWEB)

    Rokkam, Ram [Iowa State Univ., Ames, IA (United States)

    2012-01-01

    Polyethylene is one of the most widely used plastics, and over 60 million tons are produced worldwide every year. Polyethylene is obtained by the catalytic polymerization of ethylene in gas and liquid phase reactors. The gas phase processes are more advantageous, and use fluidized-bed reactors for production of polyethylene. Since they operate so close to the melting point of the polymer, agglomeration is an operational concern in all slurry and gas polymerization processes. Electrostatics and hot spot formation are the main factors that contribute to agglomeration in gas-phase processes. Electrostatic charges in gas phase polymerization fluidized bed reactors are known to influence the bed hydrodynamics, particle elutriation, bubble size, bubble shape etc. Accumulation of electrostatic charges in the fluidized-bed can lead to operational issues. In this work a first-principles electrostatic model is developed and coupled with a multi-fluid computational fluid dynamic (CFD) model to understand the effect of electrostatics on the dynamics of a fluidized-bed. The multi-fluid CFD model for gas-particle flow is based on the kinetic theory of granular flows closures. The electrostatic model is developed based on a fixed, size-dependent charge for each type of particle (catalyst, polymer, polymer fines) phase. The combined CFD model is first verified using simple test cases, validated with experiments and applied to a pilot-scale polymerization fluidized-bed reactor. The CFD model reproduced qualitative trends in particle segregation and entrainment due to electrostatic charges observed in experiments. For the scale up of fluidized bed reactor, filtered models are developed and implemented on pilot scale reactor.

  13. Computational fluid dynamics of fish gill rakers during crossflow filtration.

    Science.gov (United States)

    Cheer, Angela; Cheung, Samson; Hung, Tien-Chieh; Piedrahita, Raul H; Sanderson, S Laurie

    2012-04-01

    We study crossflow filtration mechanisms in suspension-feeding fishes using computational fluid dynamics to model fluid flow and food particle movement in the vicinity of the gill rakers. During industrial and biological crossflow filtration, particles are retained when they remain suspended in the mainstream flow traveling across the filter surface rather than traveling perpendicularly to the filter. Here we identify physical parameters and hydrodynamic processes that determine food particle movement and retention inside the fish oral cavity. We demonstrate how five variables affect flow patterns and particle trajectories: (1) flow speed inside the fish oral cavity, (2) incident angle of the flow approaching the filter, (3) dimensions of filter structures, (4) particle size, and (5) particle density. Our study indicates that empirical experiments are needed to quantify flow parameters inside the oral cavity, and morphological research is needed to quantify dimensions of the filter apparatus such as gill rakers, the gaps between rakers, and downstream barriers. Ecological studies on suspension-feeding fishes are also needed to quantify food particle size and density, as these variables can affect particle retention due to hydrodynamic processes during crossflow filtration.

  14. Use of computational fluid dynamics in domestic oven design

    Directory of Open Access Journals (Sweden)

    Mark Fahey

    2008-03-01

    Full Text Available There is an increasing demand, both from customers and regulatory sources, for safer and more energy efficient products. Manufacturers are having to look to their design and development processes to service these demands. Traditional approaches have been to use prototype testing and only delve more deeply into specific aspects of the performance when issues arise. In this work the complex flow within the cooling circuit of the door of a pyrolytic oven is studied. A combination of Computational Fluid Dynamics (CFD and experimental techniques is used. It will be shown that CFD can help with the achievement of an optimal solution, with the understanding of the flow behaviour and that there is a synergy between the numerical and experimental techniques. Using only one of these techniques would limit the understanding of the flow behaviour and could lead to a less than optimal solution to the design problem. This work aims to explore this particular complex industrial fluid flow situation to: understand the flow around the oven door’s cooling circuit  demonstrate the synergy of CFD and experimental work within development of a complex product explore the role of CFD within the product development process.

  15. A parallel computational fluid dynamics unstructured grid generator

    Science.gov (United States)

    Davis, Deborah E.

    1993-12-01

    This research addressed the development of a parallel computational fluid dynamics unstructured grid generator using Delaunay triangulation. The generator is applied to simple elliptical and cylindrical two-dimensional bodies. The methodologies used included Watson's point insertion algorithm, Holmes and Snyder's point creation algorithm, a discretized surface definition, Anderson's clustering function, and a Laplacian smoother. The first version of the software involved a processor boundary exchange at the end of each iteration with no inter-processor communications during the iterations. The second version used inter-processor communication during each iteration instead of the boundary exchange. Version 1 demonstrated a speedup of 1.8 for some portions of the code, but proved to be unscalable for more than two nodes due to the interdependency of the triangular elements. The results of Version 2 were similar. Two distribution methodologies, a simple 360-degree distribution and recursive spectral bisection (RSB), were examined. For the initial grid distribution, the distribution generated by the RSB code would be similar to the distribution generated by the 360-degree methodology and would require significantly more time to execute.

  16. Computational Fluid Dynamics Analysis of Flexible Duct Junction Box Design

    Energy Technology Data Exchange (ETDEWEB)

    Beach, Robert [IBACOS Inc., Pittsburgh, PA (United States); Prahl, Duncan [IBACOS Inc., Pittsburgh, PA (United States); Lange, Rich [IBACOS Inc., Pittsburgh, PA (United States)

    2013-12-01

    IBACOS explored the relationships between pressure and physical configurations of flexible duct junction boxes by using computational fluid dynamics (CFD) simulations to predict individual box parameters and total system pressure, thereby ensuring improved HVAC performance. Current Air Conditioning Contractors of America (ACCA) guidance (Group 11, Appendix 3, ACCA Manual D, Rutkowski 2009) allows for unconstrained variation in the number of takeoffs, box sizes, and takeoff locations. The only variables currently used in selecting an equivalent length (EL) are velocity of air in the duct and friction rate, given the first takeoff is located at least twice its diameter away from the inlet. This condition does not account for other factors impacting pressure loss across these types of fittings. For each simulation, the IBACOS team converted pressure loss within a box to an EL to compare variation in ACCA Manual D guidance to the simulated variation. IBACOS chose cases to represent flows reasonably correlating to flows typically encountered in the field and analyzed differences in total pressure due to increases in number and location of takeoffs, box dimensions, and velocity of air, and whether an entrance fitting is included. The team also calculated additional balancing losses for all cases due to discrepancies between intended outlet flows and natural flow splits created by the fitting. In certain asymmetrical cases, the balancing losses were significantly higher than symmetrical cases where the natural splits were close to the targets. Thus, IBACOS has shown additional design constraints that can ensure better system performance.

  17. Molecular imaging with dynamic contrast-enhanced computed tomography

    Energy Technology Data Exchange (ETDEWEB)

    Miles, K.A., E-mail: k.a.miles@bsms.ac.u [Clinical Imaging Sciences Centre, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton (United Kingdom)

    2010-07-15

    Dynamic contrast-enhanced computed tomography (DCE-CT) is a quantitative technique that employs rapid sequences of CT images after bolus administration of intravenous contrast material to measure a range of physiological processes related to the microvasculature of tissues. By combining knowledge of the molecular processes underlying changes in vascular physiology with an understanding of the relationship between vascular physiology and CT contrast enhancement, DCE-CT can be redefined as a molecular imaging technique. Some DCE-CT derived parameters reflect tissue hypoxia and can, therefore, provide information about the cellular microenvironment. DCE-CT can also depict physiological processes, such as vasodilatation, that represent the physiological consequences of molecular responses to tissue hypoxia. To date the main applications have been in stroke and oncology. Unlike some other molecular imaging approaches, DCE-CT benefits from wide availability and ease of application along with the use of contrast materials and software packages that have achieved full regulatory approval. Hence, DCE-CT represents a molecular imaging technique that is applicable in clinical practice today.

  18. Structural improvements on hydrodynamic separators: a computational fluid dynamics approach.

    Science.gov (United States)

    Mendoza, Joseph Albert; Lee, Dong Hoon; Lee, Sang-Il; Kang, Joo-Hyon

    2016-12-01

    Hydrodynamic separators (HDSs) have been used extensively to reduce stormwater pollutants from urbanized areas before entering the receiving water bodies. They primarily remove particulates and associated pollutants using gravity settling. Two types of HDSs with different structural configurations of the inner vortex-inducing components were presented in this study. One configuration consisted of a dip cylindrical plate with a center shaft while the other one has a hollow screen inside. With the help of computational fluid dynamics, the performance of these different types of HDSs have been evaluated and comparatively analyzed. The results showed that the particle removal efficiency was better with the cylindrical plate type HDSs than the screen type HDSs because of the larger swirling flow regime formed inside the device. Plate type HDSs were found more effective in removing fine particles (∼50 μm) than the screen type HDSs that were only efficient in removing large particles (≥250 μm). Structural improvements in a HDS such as increase in diameter and angle of the inlet pipe can enhance the removal efficiencies by up to 20% for plate type HDS while increase in the screen diameter can increase removal efficiencies of the screen type HDS.

  19. Computational fluid dynamic analysis for independent floating water treatment device

    Science.gov (United States)

    Zawawi, M. H.; Swee, M. G.; Zainal, N. S.; Zahari, N. M.; Kamarudin, M. A.; Ramli, M. Z.

    2017-09-01

    This project is to design and develop 3D Independent Floating Water Treatment Device using 3D CAD software. The device is designed to treat water for better water qualities and water flows of the lakes. A prototype was manufactured to study the water treatment efficiency of the device. Computational Fluid Dynamic (CFD) analysis was used to capture the efficiency of the Independent Floating Water Treatment Device by simulates and model the water flows, pressure and velocity. According to the results, the maximum velocity magnitude was around 1m3/s. The velocity contour showed the device has high velocity at the pipe outlet. The velocity became lower and lower as the distance is further from the pipe outlet. The result from the velocity measurement was 1.05m/s. The pressure magnitude was in between 1426 Pa to 1429 Pa. The laboratory results based on water parameters proved that the water movement and direction of water flow of the Independent Floating Water Treatment Device enable the efficient pollutant removal. The vector plot, velocity contour, water flow path lines, water flow streamline and pressure contour was successful modeled.

  20. Computational fluid dynamics (CFD) studies of a miniaturized dissolution system.

    Science.gov (United States)

    Frenning, G; Ahnfelt, E; Sjögren, E; Lennernäs, H

    2017-04-15

    Dissolution testing is an important tool that has applications ranging from fundamental studies of drug-release mechanisms to quality control of the final product. The rate of release of the drug from the delivery system is known to be affected by hydrodynamics. In this study we used computational fluid dynamics to simulate and investigate the hydrodynamics in a novel miniaturized dissolution method for parenteral formulations. The dissolution method is based on a rotating disc system and uses a rotating sample reservoir which is separated from the remaining dissolution medium by a nylon screen. Sample reservoirs of two sizes were investigated (SR6 and SR8) and the hydrodynamic studies were performed at rotation rates of 100, 200 and 400rpm. The overall fluid flow was similar for all investigated cases, with a lateral upward spiraling motion and central downward motion in the form of a vortex to and through the screen. The simulations indicated that the exchange of dissolution medium between the sample reservoir and the remaining release medium was rapid for typical screens, for which almost complete mixing would be expected to occur within less than one minute at 400rpm. The local hydrodynamic conditions in the sample reservoirs depended on their size; SR8 appeared to be relatively more affected than SR6 by the resistance to liquid flow resulting from the screen. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Review of computational fluid dynamics applications in biotechnology processes.

    Science.gov (United States)

    Sharma, C; Malhotra, D; Rathore, A S

    2011-01-01

    Computational fluid dynamics (CFD) is well established as a tool of choice for solving problems that involve one or more of the following phenomena: flow of fluids, heat transfer,mass transfer, and chemical reaction. Unit operations that are commonly utilized in biotechnology processes are often complex and as such would greatly benefit from application of CFD. The thirst for deeper process and product understanding that has arisen out of initiatives such as quality by design provides further impetus toward usefulness of CFD for problems that may otherwise require extensive experimentation. Not surprisingly, there has been increasing interest in applying CFD toward a variety of applications in biotechnology processing in the last decade. In this article, we will review applications in the major unit operations involved with processing of biotechnology products. These include fermentation,centrifugation, chromatography, ultrafiltration, microfiltration, and freeze drying. We feel that the future applications of CFD in biotechnology processing will focus on establishing CFD as a tool of choice for providing process understanding that can be then used to guide more efficient and effective experimentation. This article puts special emphasis on the work done in the last 10 years. © 2011 American Institute of Chemical Engineers

  2. Computational fluid dynamics challenges for hybrid air vehicle applications

    Science.gov (United States)

    Carrin, M.; Biava, M.; Steijl, R.; Barakos, G. N.; Stewart, D.

    2017-06-01

    This paper begins by comparing turbulence models for the prediction of hybrid air vehicle (HAV) flows. A 6 : 1 prolate spheroid is employed for validation of the computational fluid dynamics (CFD) method. An analysis of turbulent quantities is presented and the Shear Stress Transport (SST) k-ω model is compared against a k-ω Explicit Algebraic Stress model (EASM) within the unsteady Reynolds-Averaged Navier-Stokes (RANS) framework. Further comparisons involve Scale Adaptative Simulation models and a local transition transport model. The results show that the flow around the vehicle at low pitch angles is sensitive to transition effects. At high pitch angles, the vortices generated on the suction side provide substantial lift augmentation and are better resolved by EASMs. The validated CFD method is employed for the flow around a shape similar to the Airlander aircraft of Hybrid Air Vehicles Ltd. The sensitivity of the transition location to the Reynolds number is demonstrated and the role of each vehicle£s component is analyzed. It was found that the ¦ns contributed the most to increase the lift and drag.

  3. Design of airborne wind turbine and computational fluid dynamics analysis

    Science.gov (United States)

    Anbreen, Faiqa

    Wind energy is a promising alternative to the depleting non-renewable sources. The height of the wind turbines becomes a constraint to their efficiency. Airborne wind turbine can reach much higher altitudes and produce higher power due to high wind velocity and energy density. The focus of this thesis is to design a shrouded airborne wind turbine, capable to generate 70 kW to propel a leisure boat with a capacity of 8-10 passengers. The idea of designing an airborne turbine is to take the advantage of higher velocities in the atmosphere. The Solidworks model has been analyzed numerically using Computational Fluid Dynamics (CFD) software StarCCM+. The Unsteady Reynolds Averaged Navier Stokes Simulation (URANS) with K-epsilon turbulence model has been selected, to study the physical properties of the flow, with emphasis on the performance of the turbine and the increase in air velocity at the throat. The analysis has been done using two ambient velocities of 12 m/s and 6 m/s. At 12 m/s inlet velocity, the velocity of air at the turbine has been recorded as 16 m/s. The power generated by the turbine is 61 kW. At inlet velocity of 6 m/s, the velocity of air at turbine increased to 10 m/s. The power generated by turbine is 25 kW.

  4. Simulation of climate inside tunnel greenhouses using computational fluid dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Zeroual, S.; Bougoul, S.; Labaal, C.; Aouachria, Z. [Batna Univ., Batna (Algeria). Dept. of Physics

    2009-07-01

    This paper investigated heat transfer and air flow in an open-tunnel greenhouse both with and without plants. The aim of the study was to determine the effect of wind speed on natural ventilation using computational fluid dynamics (CFD) and finite volume methods. A porous medium approach was used to to describe air flow. Turbulence in the 3-D model was described using a standard k-{epsilon} model. Air temperature variations indicated the presence of a gradient from the side walls towards the centre of the greenhouse. The gradient was caused by the movement of hot air rising towards the roof vents. A vertical gradient was attributed to the movement of the air above the surface of the heated floor. Maximum air velocity was reached at the openings of the greenhouse. The lowest heat values were measured in the middle of the greenhouse and at the crop level. Results obtained in the study were compared with results obtained in the literature. Data obtained in the study will be used to improve the design and control of both greenhouse ventilation and heating systems. 15 refs., 18 figs.

  5. Improving flow distribution in influent channels using computational fluid dynamics.

    Science.gov (United States)

    Park, No-Suk; Yoon, Sukmin; Jeong, Woochang; Lee, Seungjae

    2016-10-01

    Although the flow distribution in an influent channel where the inflow is split into each treatment process in a wastewater treatment plant greatly affects the efficiency of the process, and a weir is the typical structure for the flow distribution, to the authors' knowledge, there is a paucity of research on the flow distribution in an open channel with a weir. In this study, the influent channel of a real-scale wastewater treatment plant was used, installing a suppressed rectangular weir that has a horizontal crest to cross the full channel width. The flow distribution in the influent channel was analyzed using a validated computational fluid dynamics model to investigate (1) the comparison of single-phase and two-phase simulation, (2) the improved procedure of the prototype channel, and (3) the effect of the inflow rate on flow distribution. The results show that two-phase simulation is more reliable due to the description of the free-surface fluctuations. It should first be considered for improving flow distribution to prevent a short-circuit flow, and the difference in the kinetic energy with the inflow rate makes flow distribution trends different. The authors believe that this case study is helpful for improving flow distribution in an influent channel.

  6. Use of correspondence discriminant analysis to predict the subcellular location of bacterial proteins.

    Science.gov (United States)

    Perrière, Guy; Thioulouse, Jean

    2003-02-01

    Correspondence discriminant analysis (CDA) is a multivariate statistical method derived from discriminant analysis which can be used on contingency tables. We have used CDA to separate Gram negative bacteria proteins according to their subcellular location. The high resolution of the discrimination obtained makes this method a good tool to predict subcellular location when this information is not known. The main advantage of this technique is its simplicity. Indeed, by computing two linear formulae on amino acid composition, it is possible to classify a protein into one of the three classes of subcellular location we have defined. The CDA itself can be computed with the ADE-4 software package that can be downloaded, as well as the data set used in this study, from the Pôle Bio-Informatique Lyonnais (PBIL) server at http://pbil.univ-lyon1.fr.

  7. Integration of computer tools in lessons about motion and dynamics

    OpenAIRE

    Klinec, Dimitrij

    2016-01-01

    The diploma work is about computer tools used in physics classes and their role in teaching natural science. Due to the possibilities enabled by the multi-presentation, computer programmes with interactive simulations and programmes with mechanical equipment for computer-based experiments as well as video analyses have been put forward in natural science classes thus becoming an indispensable part of the natural science classrooms. In diploma work, computer simulations and computer-based e...

  8. Dynamic stall analysis of horizontal-axis-wind-turbine blades using computational fluid dynamics

    Science.gov (United States)

    Sayed, Mohamed A.; Kandil, Hamdy A.; Morgan, El-Sayed I.

    2012-06-01

    Dynamic stall has been widely known to significantly affect the performance of the wind turbines. In this paper, aerodynamic simulation of the unsteady low-speed flow past two-dimensional wind turbine blade profiles, developed by the National Renewable Energy Laboratory (NREL), will be performed. The aerodynamic simulation will be performed using Computational Fluid Dynamics (CFD). The governing equations used in the simulations are the Unsteady-Reynolds-Averaged-Navier-Stokes (URANS) equations. The unsteady separated turbulent flow around an oscillating airfoil pitching in a sinusoidal pattern in the regime of low Reynolds number is investigated numerically. The investigation employs the URANS approach with the most suitable turbulence model. The development of the light dynamic stall of the blades under consideration is studied. The S809 blade profile is simulated at different mean wind speeds. Moreover, the S826 blade profile is also considered for analysis of wind turbine blade which is the most suitable blade profile for the wind conditions in Egypt over the site of Gulf of El-Zayt. In order to find the best oscillating frequency, different oscillating frequencies are studied. The best frequency can then be used for the blade pitch controller. The comparisons with the experimental results showed that the used CFD code can accurately predict the blade profile unsteady aerodynamic loads.

  9. Computational Fluid Dynamics Simulation of Fluidized Bed Polymerization Reactors

    Energy Technology Data Exchange (ETDEWEB)

    Fan, Rong [Iowa State Univ., Ames, IA (United States)

    2006-01-01

    Fluidized beds (FB) reactors are widely used in the polymerization industry due to their superior heat- and mass-transfer characteristics. Nevertheless, problems associated with local overheating of polymer particles and excessive agglomeration leading to FB reactors defluidization still persist and limit the range of operating temperatures that can be safely achieved in plant-scale reactors. Many people have been worked on the modeling of FB polymerization reactors, and quite a few models are available in the open literature, such as the well-mixed model developed by McAuley, Talbot, and Harris (1994), the constant bubble size model (Choi and Ray, 1985) and the heterogeneous three phase model (Fernandes and Lona, 2002). Most these research works focus on the kinetic aspects, but from industrial viewpoint, the behavior of FB reactors should be modeled by considering the particle and fluid dynamics in the reactor. Computational fluid dynamics (CFD) is a powerful tool for understanding the effect of fluid dynamics on chemical reactor performance. For single-phase flows, CFD models for turbulent reacting flows are now well understood and routinely applied to investigate complex flows with detailed chemistry. For multiphase flows, the state-of-the-art in CFD models is changing rapidly and it is now possible to predict reasonably well the flow characteristics of gas-solid FB reactors with mono-dispersed, non-cohesive solids. This thesis is organized into seven chapters. In Chapter 2, an overview of fluidized bed polymerization reactors is given, and a simplified two-site kinetic mechanism are discussed. Some basic theories used in our work are given in detail in Chapter 3. First, the governing equations and other constitutive equations for the multi-fluid model are summarized, and the kinetic theory for describing the solid stress tensor is discussed. The detailed derivation of DQMOM for the population balance equation is given as the second section. In this section

  10. Validating subcellular localization prediction tools with mycobacterial proteins

    Directory of Open Access Journals (Sweden)

    Niño Luis F

    2009-05-01

    Full Text Available Abstract Background The computational prediction of mycobacterial proteins' subcellular localization is of key importance for proteome annotation and for the identification of new drug targets and vaccine candidates. Several subcellular localization classifiers have been developed over the past few years, which have comprised both general localization and feature-based classifiers. Here, we have validated the ability of different bioinformatics approaches, through the use of SignalP 2.0, TatP 1.0, LipoP 1.0, Phobius, PA-SUB 2.5, PSORTb v.2.0.4 and Gpos-PLoc, to predict secreted bacterial proteins. These computational tools were compared in terms of sensitivity, specificity and Matthew's correlation coefficient (MCC using a set of mycobacterial proteins having less than 40% identity, none of which are included in the training data sets of the validated tools and whose subcellular localization have been experimentally confirmed. These proteins belong to the TBpred training data set, a computational tool specifically designed to predict mycobacterial proteins. Results A final validation set of 272 mycobacterial proteins was obtained from the initial set of 852 mycobacterial proteins. According to the results of the validation metrics, all tools presented specificity above 0.90, while dispersion sensitivity and MCC values were above 0.22. PA-SUB 2.5 presented the highest values; however, these results might be biased due to the methodology used by this tool. PSORTb v.2.0.4 left 56 proteins out of the classification, while Gpos-PLoc left just one protein out. Conclusion Both subcellular localization approaches had high predictive specificity and high recognition of true negatives for the tested data set. Among those tools whose predictions are not based on homology searches against SWISS-PROT, Gpos-PLoc was the general localization tool with the best predictive performance, while SignalP 2.0 was the best tool among the ones using a feature

  11. Validating subcellular localization prediction tools with mycobacterial proteins

    Science.gov (United States)

    Restrepo-Montoya, Daniel; Vizcaíno, Carolina; Niño, Luis F; Ocampo, Marisol; Patarroyo, Manuel E; Patarroyo, Manuel A

    2009-01-01

    Background The computational prediction of mycobacterial proteins' subcellular localization is of key importance for proteome annotation and for the identification of new drug targets and vaccine candidates. Several subcellular localization classifiers have been developed over the past few years, which have comprised both general localization and feature-based classifiers. Here, we have validated the ability of different bioinformatics approaches, through the use of SignalP 2.0, TatP 1.0, LipoP 1.0, Phobius, PA-SUB 2.5, PSORTb v.2.0.4 and Gpos-PLoc, to predict secreted bacterial proteins. These computational tools were compared in terms of sensitivity, specificity and Matthew's correlation coefficient (MCC) using a set of mycobacterial proteins having less than 40% identity, none of which are included in the training data sets of the validated tools and whose subcellular localization have been experimentally confirmed. These proteins belong to the TBpred training data set, a computational tool specifically designed to predict mycobacterial proteins. Results A final validation set of 272 mycobacterial proteins was obtained from the initial set of 852 mycobacterial proteins. According to the results of the validation metrics, all tools presented specificity above 0.90, while dispersion sensitivity and MCC values were above 0.22. PA-SUB 2.5 presented the highest values; however, these results might be biased due to the methodology used by this tool. PSORTb v.2.0.4 left 56 proteins out of the classification, while Gpos-PLoc left just one protein out. Conclusion Both subcellular localization approaches had high predictive specificity and high recognition of true negatives for the tested data set. Among those tools whose predictions are not based on homology searches against SWISS-PROT, Gpos-PLoc was the general localization tool with the best predictive performance, while SignalP 2.0 was the best tool among the ones using a feature-based approach. Even though PA-SUB 2

  12. Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects.

    Science.gov (United States)

    Sumner, Isaiah; Iyengar, Srinivasan S

    2007-10-18

    We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.

  13. A full computation-relevant topological dynamics classification of elementary cellular automata.

    Science.gov (United States)

    Schüle, Martin; Stoop, Ruedi

    2012-12-01

    Cellular automata are both computational and dynamical systems. We give a complete classification of the dynamic behaviour of elementary cellular automata (ECA) in terms of fundamental dynamic system notions such as sensitivity and chaoticity. The "complex" ECA emerge to be sensitive, but not chaotic and not eventually weakly periodic. Based on this classification, we conjecture that elementary cellular automata capable of carrying out complex computations, such as needed for Turing-universality, are at the "edge of chaos."

  14. Code Verification of the HIGRAD Computational Fluid Dynamics Solver

    Energy Technology Data Exchange (ETDEWEB)

    Van Buren, Kendra L. [Los Alamos National Laboratory; Canfield, Jesse M. [Los Alamos National Laboratory; Hemez, Francois M. [Los Alamos National Laboratory; Sauer, Jeremy A. [Los Alamos National Laboratory

    2012-05-04

    The purpose of this report is to outline code and solution verification activities applied to HIGRAD, a Computational Fluid Dynamics (CFD) solver of the compressible Navier-Stokes equations developed at the Los Alamos National Laboratory, and used to simulate various phenomena such as the propagation of wildfires and atmospheric hydrodynamics. Code verification efforts, as described in this report, are an important first step to establish the credibility of numerical simulations. They provide evidence that the mathematical formulation is properly implemented without significant mistakes that would adversely impact the application of interest. Highly accurate analytical solutions are derived for four code verification test problems that exercise different aspects of the code. These test problems are referred to as: (i) the quiet start, (ii) the passive advection, (iii) the passive diffusion, and (iv) the piston-like problem. These problems are simulated using HIGRAD with different levels of mesh discretization and the numerical solutions are compared to their analytical counterparts. In addition, the rates of convergence are estimated to verify the numerical performance of the solver. The first three test problems produce numerical approximations as expected. The fourth test problem (piston-like) indicates the extent to which the code is able to simulate a 'mild' discontinuity, which is a condition that would typically be better handled by a Lagrangian formulation. The current investigation concludes that the numerical implementation of the solver performs as expected. The quality of solutions is sufficient to provide credible simulations of fluid flows around wind turbines. The main caveat associated to these findings is the low coverage provided by these four problems, and somewhat limited verification activities. A more comprehensive evaluation of HIGRAD may be beneficial for future studies.

  15. Decomposition and Cross-Product-Based Method for Computing the Dynamic Equation of Robots

    Directory of Open Access Journals (Sweden)

    Ching-Long Shih

    2012-08-01

    Full Text Available This paper aims to demonstrate a clear relationship between Lagrange equations and Newton-Euler equations regarding computational methods for robot dynamics, from which we derive a systematic method for using either symbolic or on-line numerical computations. Based on the decomposition approach and cross-product operation, a computing method for robot dynamics can be easily developed. The advantages of this computing framework are that: it can be used for both symbolic and on-line numeric computation purposes, and it can also be applied to biped systems, as well as some simple closed-chain robot systems.

  16. In situ spatiotemporal mapping of flow fields around seeded stem cells at the subcellular length scale.

    Directory of Open Access Journals (Sweden)

    Min Jae Song

    2010-09-01

    Full Text Available A major hurdle to understanding and exploiting interactions between the stem cell and its environment is the lack of a tool for precise delivery of mechanical cues concomitant to observing sub-cellular adaptation of structure. These studies demonstrate the use of microscale particle image velocimetry (μ-PIV for in situ spatiotemporal mapping of flow fields around mesenchymal stem cells, i.e. murine embryonic multipotent cell line C3H10T1/2, at the subcellular length scale, providing a tool for real time observation and analysis of stem cell adaptation to the prevailing mechanical milieu. In the absence of cells, computational fluid dynamics (CFD predicts flow regimes within 12% of μ-PIV measures, achieving the technical specifications of the chamber and the flow rates necessary to deliver target shear stresses at a particular height from the base of the flow chamber. However, our μ-PIV studies show that the presence of cells per se as well as the density at which cells are seeded significantly influences local flow fields. Furthermore, for any given cell or cell seeding density, flow regimes vary significantly along the vertical profile of the cell. Hence, the mechanical milieu of the stem cell exposed to shape changing shear stresses, induced by fluid drag, varies with respect to proximity of surrounding cells as well as with respect to apical height. The current study addresses a previously unmet need to predict and observe both flow regimes as well as mechanoadaptation of cells in flow chambers designed to deliver precisely controlled mechanical signals to live cells. An understanding of interactions and adaptation in response to forces at the interface between the surface of the cell and its immediate local environment may be key for de novo engineering of functional tissues from stem cell templates as well as for unraveling the mechanisms underlying multiscale development, growth and adaptation of organisms.

  17. In Situ Spatiotemporal Mapping of Flow Fields around Seeded Stem Cells at the Subcellular Length Scale

    Science.gov (United States)

    Song, Min Jae; Dean, David; Knothe Tate, Melissa L.

    2010-01-01

    A major hurdle to understanding and exploiting interactions between the stem cell and its environment is the lack of a tool for precise delivery of mechanical cues concomitant to observing sub-cellular adaptation of structure. These studies demonstrate the use of microscale particle image velocimetry (μ-PIV) for in situ spatiotemporal mapping of flow fields around mesenchymal stem cells, i.e. murine embryonic multipotent cell line C3H10T1/2, at the subcellular length scale, providing a tool for real time observation and analysis of stem cell adaptation to the prevailing mechanical milieu. In the absence of cells, computational fluid dynamics (CFD) predicts flow regimes within 12% of μ-PIV measures, achieving the technical specifications of the chamber and the flow rates necessary to deliver target shear stresses at a particular height from the base of the flow chamber. However, our μ-PIV studies show that the presence of cells per se as well as the density at which cells are seeded significantly influences local flow fields. Furthermore, for any given cell or cell seeding density, flow regimes vary significantly along the vertical profile of the cell. Hence, the mechanical milieu of the stem cell exposed to shape changing shear stresses, induced by fluid drag, varies with respect to proximity of surrounding cells as well as with respect to apical height. The current study addresses a previously unmet need to predict and observe both flow regimes as well as mechanoadaptation of cells in flow chambers designed to deliver precisely controlled mechanical signals to live cells. An understanding of interactions and adaptation in response to forces at the interface between the surface of the cell and its immediate local environment may be key for de novo engineering of functional tissues from stem cell templates as well as for unraveling the mechanisms underlying multiscale development, growth and adaptation of organisms. PMID:20862249

  18. 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

    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...... mathematical models such as computational fluid dynamics are preferred and over the last 5 years, computational fluid dynamics has become more frequently used in the wave energy field. However, rigorous estimation of numerical errors, convergence rates and uncertainties associated with computational fluid...... 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...

  19. Use of computational fluid dynamics in the design of dynamic contrast enhanced imaging phantoms.

    Science.gov (United States)

    Hariharan, Prasanna; Freed, Melanie; Myers, Matthew R

    2013-09-21

    Phantoms for dynamic contrast enhanced (DCE) imaging modalities such as DCE computed tomography (DCE-CT) and DCE magnetic resonance imaging (DCE-MRI) are valuable tools for evaluating and comparing imaging systems. It is important for the contrast-agent distribution within the phantom to possess a time dependence that replicates a curve observed clinically, known as the 'tumor-enhancement curve'. It is also important for the concentration field within the lesion to be as uniform as possible. This study demonstrates how computational fluid dynamics (CFD) can be applied to achieve these goals within design constraints. The distribution of the contrast agent within the simulated phantoms was investigated in relation to the influence of three factors of the phantom design. First, the interaction between the inlets and the uniformity of the contrast agent within the phantom was modeled. Second, pumps were programmed using a variety of schemes and the resultant dynamic uptake curves were compared to tumor-enhancement curves obtained from clinical data. Third, the effectiveness of pulsing the inlet flow rate to produce faster equilibration of the contrast-agent distribution was quantified. The models employed a spherical lesion and design constraints (lesion diameter, inlet-tube size and orientation, contrast-agent flow rates and fluid properties) taken from a recently published DCE-MRI phantom study. For DCE-MRI in breast cancer detection, where the target tumor-enhancement curve varies on the scale of hundreds of seconds, optimizing the number of inlet tubes and their orientation was found to be adequate for attaining concentration uniformity and reproducing the target tumor-enhancement curve. For DCE-CT in liver tumor detection, where the tumor-enhancement curve varies on a scale of tens of seconds, the use of an iterated inlet condition (programmed into the pump) enabled the phantom to reproduce the target tumor-enhancement curve within a few per cent beyond about 6

  20. Expression and subcellular localization of antiporter regulating ...

    African Journals Online (AJOL)

    Md. Imtiaz Uddin

    2012-02-14

    Feb 14, 2012 ... We examined the expression and subcellular localization of antiporter regulating protein OsARP in a submergence tolerant rice (Oryza sativa L.) cultivar FR13A. In the public databases, this protein was designated as putative Os02g0465900 protein. The cDNA containing the full-length sequence of OsARP.

  1. Domains involved in TAF15 subcellular localisation

    DEFF Research Database (Denmark)

    Marko, Marija; Vlassis, Arsenios; Guialis, Apostolia

    2012-01-01

    to play important roles in the onset of specific tumours, certain forms of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). In this study we identified the domains of TAF15 responsible for its subcellular localisation in human (HeLa) cells and experimentally confirmed...

  2. Lipidomics in tissues, cells and subcellular compartments

    National Research Council Canada - National Science Library

    Horn, Patrick J; Chapman, Kent D

    2012-01-01

    ...‐infusion MS, localization of lipids in tissues and cells by laser desorption/ionization MS, and even profiling of lipids in individual subcellular compartments by direct‐organelle MS. Applications of these approaches to achieve improved understanding of plant lipid metabolism, compartmentation and function are discussed.

  3. Functional Programming for Dynamic and Large Data with Self-Adjusting Computation

    OpenAIRE

    Chen, Yan; Acar, Umut A.; Tangwongsan, Kanat

    2014-01-01

    International audience; Combining type theory, language design, and empirical work, we present techniques for computing with large and dynamically changing datasets. Based on lambda calculus, our techniques are suitable for expressing a diverse set of algorithms on large datasets and, via self-adjusting computation, enable computations to respond automatically to changes in their data. To improve the scalability of self-adjusting computation, we present a type system for precise dependency tr...

  4. Computational fluid dynamics analysis of aerosol deposition in pebble beds

    Science.gov (United States)

    Mkhosi, Margaret Msongi

    2007-12-01

    The Pebble Bed Modular Reactor is a high temperature gas cooled reactor which uses helium gas as a coolant. The reactor uses spherical graphite pebbles as fuel. The fuel design is inherently resistant to the release of the radioactive material up to high temperatures; therefore, the plant can withstand a broad spectrum of accidents with limited release of radionuclides to the environment. Despite safety features of the concepts, these reactors still contain large inventories of radioactive materials. The transport of most of the radioactive materials in an accident occurs in the form of aerosol particles. In this dissertation, the limits of applicability of existing computational fluid dynamics code FLUENT to the prediction of aerosol transport have been explored. The code was run using the Reynolds Averaged Navier-Stokes turbulence models to determine the effects of different turbulence models on the prediction of aerosol particle deposition. Analyses were performed for up to three unit cells in the orthorhombic configuration. For low flow conditions representing natural circulation driven flow, the laminar flow model was used and the results were compared with existing experimental data for packed beds. The results compares well with experimental data in the low flow regime. For conditions corresponding to normal operating of the reactor, analyses were performed using the standard k-ɛ turbulence model. From the inertial deposition results, a correlation that can be used to estimate the deposition of aerosol particles within pebble beds given inlet flow conditions has been developed. These results were converted into a dimensionless form as a function of a modified Stokes number. Based on results obtained in the laminar regime and for individual pebbles, the correlation developed for the inertial impaction component of deposition is believed to be credible. The form of the correlation developed also allows these results to be applied to pebble beds of different

  5. A digital computer program for the dynamic interaction simulation of controls and structure (DISCOS), volume 1

    Science.gov (United States)

    Bodley, C. S.; Devers, A. D.; Park, A. C.; Frisch, H. P.

    1978-01-01

    A theoretical development and associated digital computer program system for the dynamic simulation and stability analysis of passive and actively controlled spacecraft are presented. The dynamic system (spacecraft) is modeled as an assembly of rigid and/or flexible bodies not necessarily in a topological tree configuration. The computer program system is used to investigate total system dynamic characteristics, including interaction effects between rigid and/or flexible bodies, control systems, and a wide range of environmental loadings. In addition, the program system is used for designing attitude control systems and for evaluating total dynamic system performance, including time domain response and frequency domain stability analyses.

  6. An Approach to Dynamic Provisioning of Social and Computational Services

    NARCIS (Netherlands)

    Bonino da Silva Santos, L.O.; Sorathia, V.S.; Ferreira Pires, Luis; van Sinderen, Marten J.

    Service-Oriented Computing (SOC) builds upon the intuitive notion of service already known and used in our society for a long time. SOC-related approaches are based on computer-executable functional units that often represent automation of services that exist at the social level, i.e., services at

  7. Handling membership dynamicity in service composition for ubiquitous computing

    DEFF Research Database (Denmark)

    Brønsted, Jeppe Rørbæk; Hansen, Klaus Marius

    2008-01-01

    In ubiquitous computing, as more and more devices are introduced into the environment, new applications are made possible that exploit device capabilities in new ways. Currently, however, there is a mismatch between the effort involved in implementing these applications and the benefit they provide...... for ubiquitous computing applications....

  8. Performance of a Sequential and Parallel Computational Fluid Dynamic (CFD) Solver on a Missile Body Configuration

    National Research Council Canada - National Science Library

    Hisley, Dixie

    1999-01-01

    .... The goals of this report are: (1) to investigate the performance of message passing and loop level parallelization techniques, as they were implemented in the computational fluid dynamics (CFD...

  9. Computational Fluid Dynamic (CFD) Analysis of a Generic Missile With Grid Fins

    National Research Council Canada - National Science Library

    DeSpirito, James

    2000-01-01

    This report presents the results of a study demonstrating an approach for using viscous computational fluid dynamic simulations to calculate the flow field and aerodynamic coefficients for a missile with grid fin...

  10. Frequency Domain Computer Programs for Prediction and Analysis of Rail Vehicle Dynamics : Volume 2. Appendixes

    Science.gov (United States)

    1975-12-01

    Frequency domain computer programs developed or acquired by TSC for the analysis of rail vehicle dynamics are described in two volumes. Volume 2 contains program listings including subroutines for the four TSC frequency domain programs described in V...

  11. Implementation of Keystroke Dynamics for Authentication in Computer Systems

    Directory of Open Access Journals (Sweden)

    S. V. Skuratov

    2010-06-01

    Full Text Available Implementation of keystroke dynamics in multifactor authentication systems is described in the article. Original access control system based on totality of matchers is presented. Testing results and useful recommendations are also adduced.

  12. Computer-Automated Static, Dynamic and Cellular Bone Histomorphometry

    OpenAIRE

    Hong, Seung-Hyun; Jiang, Xi; Chen,Li; Josh, Pujan; Shin, Dong-Guk; Rowe, David

    2012-01-01

    Dynamic and cellular histomorphometry of trabeculae is the most biologically relevant way of assessing steady state bone health. Traditional measurement involves manual visual feature identification by a trained and qualified professional. Inherent with this methodology is the time and cost expenditure, as well as the subjectivity that naturally arises under human visual inspection. In this work, we propose a rapidly deployable, automated, and objective method for dynamic histomorphometry. We...

  13. Computational Fluid Dynamics of Whole-Body Aircraft

    Science.gov (United States)

    Agarwal, Ramesh

    1999-01-01

    The current state of the art in computational aerodynamics for whole-body aircraft flowfield simulations is described. Recent advances in geometry modeling, surface and volume grid generation, and flow simulation algorithms have led to accurate flowfield predictions for increasingly complex and realistic configurations. As a result, computational aerodynamics has emerged as a crucial enabling technology for the design and development of flight vehicles. Examples illustrating the current capability for the prediction of transport and fighter aircraft flowfields are presented. Unfortunately, accurate modeling of turbulence remains a major difficulty in the analysis of viscosity-dominated flows. In the future, inverse design methods, multidisciplinary design optimization methods, artificial intelligence technology, and massively parallel computer technology will be incorporated into computational aerodynamics, opening up greater opportunities for improved product design at substantially reduced costs.

  14. Computing with dynamical systems based on insulator-metal-transition oscillators

    Science.gov (United States)

    Parihar, Abhinav; Shukla, Nikhil; Jerry, Matthew; Datta, Suman; Raychowdhury, Arijit

    2017-04-01

    In this paper, we review recent work on novel computing paradigms using coupled oscillatory dynamical systems. We explore systems of relaxation oscillators based on linear state transitioning devices, which switch between two discrete states with hysteresis. By harnessing the dynamics of complex, connected systems, we embrace the philosophy of "let physics do the computing" and demonstrate how complex phase and frequency dynamics of such systems can be controlled, programmed, and observed to solve computationally hard problems. Although our discussion in this paper is limited to insulator-to-metallic state transition devices, the general philosophy of such computing paradigms can be translated to other mediums including optical systems. We present the necessary mathematical treatments necessary to understand the time evolution of these systems and demonstrate through recent experimental results the potential of such computational primitives.

  15. Computational Fluid Dynamic (CFD) Study of an Articulating Turbine Blade Cascade

    Science.gov (United States)

    2016-11-01

    the fluid -structure interaction in the engine and the mechanical behavior of the shape memory alloy actuator. A simple computational fluid dynamic (CFD...optimal fluid -flow behavior is maintained.2 Fig. 1 Cutaway image of typical rotorcraft engine2 There are several candidate mechanisms and materials...ARL-TR-7871 ● NOV 2016 US Army Research Laboratory Computational Fluid Dynamic (CFD) Study of an Articulating Turbine Blade

  16. The effect of dynamic workstations on the performance of various computer and office-based tasks

    NARCIS (Netherlands)

    Burford, E.M.; Botter, J.; Commissaris, D.; Könemann, R.; Hiemstra-Van Mastrigt, S.; Ellegast, R.P.

    2013-01-01

    The effect of different workstations, conventional and dynamic, on different types of performance measures for several different office and computer based task was investigated in this research paper. The two dynamic workstations assessed were the Lifespan Treadmill Desk and the RightAngle

  17. Effects of a standing and three dynamic workstations on computer task performance and cognitive function tests

    NARCIS (Netherlands)

    Commissaris, D.A.C.M.; Könemann, R.; Hiemstra-van Mastrigt, S.; Burford, E.M.; Botter, J.; Douwes, M.; Ellegast, R.P.

    2014-01-01

    Sedentary work entails health risks. Dynamic (or active) workstations, at which computer tasks can be combined with physical activity, may reduce the risks of sedentary behaviour. The aim of this study was to evaluate short term task performance while working on three dynamic workstations: a

  18. Dynamics of Charged Particulate Systems Modeling, Theory and Computation

    CERN Document Server

    Zohdi, Tarek I

    2012-01-01

    The objective of this monograph is to provide a concise introduction to the dynamics of systems comprised of charged small-scale particles. Flowing, small-scale, particles ("particulates'') are ubiquitous in industrial processes and in the natural sciences. Applications include electrostatic copiers, inkjet printers, powder coating machines, etc., and a variety of manufacturing processes. Due to their small-scale size, external electromagnetic fields can be utilized to manipulate and control charged particulates in industrial processes in order to achieve results that are not possible by purely mechanical means alone. A unique feature of small-scale particulate flows is that they exhibit a strong sensitivity to interparticle near-field forces, leading to nonstandard particulate dynamics, agglomeration and cluster formation, which can strongly affect manufactured product quality. This monograph also provides an introduction to the mathematically-related topic of the dynamics of swarms of interacting objects, ...

  19. Memristors with diffusive dynamics as synaptic emulators for neuromorphic computing

    Science.gov (United States)

    Wang, Zhongrui; Joshi, Saumil; Savel'Ev, Sergey E.; Jiang, Hao; Midya, Rivu; Lin, Peng; Hu, Miao; Ge, Ning; Strachan, John Paul; Li, Zhiyong; Wu, Qing; Barnell, Mark; Li, Geng-Lin; Xin, Huolin L.; Williams, R. Stanley; Xia, Qiangfei; Yang, J. Joshua

    2017-01-01

    The accumulation and extrusion of Ca2+ in the pre- and postsynaptic compartments play a critical role in initiating plastic changes in biological synapses. To emulate this fundamental process in electronic devices, we developed diffusive Ag-in-oxide memristors with a temporal response during and after stimulation similar to that of the synaptic Ca2+ dynamics. In situ high-resolution transmission electron microscopy and nanoparticle dynamics simulations both demonstrate that Ag atoms disperse under electrical bias and regroup spontaneously under zero bias because of interfacial energy minimization, closely resembling synaptic influx and extrusion of Ca2+, respectively. The diffusive memristor and its dynamics enable a direct emulation of both short- and long-term plasticity of biological synapses, representing an advance in hardware implementation of neuromorphic functionalities.

  20. Computational models of protein kinematics and dynamics: beyond simulation.

    Science.gov (United States)

    Gipson, Bryant; Hsu, David; Kavraki, Lydia E; Latombe, Jean-Claude

    2012-01-01

    Physics-based simulation represents a powerful method for investigating the time-varying behavior of dynamic protein systems at high spatial and temporal resolution. Such simulations, however, can be prohibitively difficult or lengthy for large proteins or when probing the lower-resolution, long-timescale behaviors of proteins generally. Importantly, not all questions about a protein system require full space and time resolution to produce an informative answer. For instance, by avoiding the simulation of uncorrelated, high-frequency atomic movements, a larger, domain-level picture of protein dynamics can be revealed. The purpose of this review is to highlight the growing body of complementary work that goes beyond simulation. In particular, this review focuses on methods that address kinematics and dynamics, as well as those that address larger organizational questions and can quickly yield useful information about the long-timescale behavior of a protein.

  1. Computational Investigation of Dynamic Glottal Aperture Effects on Respiratory Airflow

    Science.gov (United States)

    Xi, Jinxiang; Yan, Hong; Dong, Haibo

    2008-11-01

    The periodic movement of the glottal aperture (vocal folds) during tidal breathing has been long recognized as a factor in altering the airflow dynamics in the tracheobrnchial region. The potential influence from these altered flow structures on the transport and deposition of inhaled particles is not known. However, studies devoted to this dynamic physiological feature are scarce due to the complex anatomy in of the larynx and numerical challenges in simulating dynamic geometries. In this study, a high-fidelity immersed boundary solver is used to investigate this problem. A 3D human oral-larynx-lung model is firstly reconstructed from MRI data. The role of the vocal fold movement and associated airflow characteristics such as vortex shedding, Coanda effect etc. during inhalation and exhalation are then numerically studied.

  2. Computational Fluid Dynamics of the Boundary Layer Characteristics of a Pacific Bluefin Tuna

    Science.gov (United States)

    2015-09-18

    Harvested from the Tuna Research Conservation Center... Underwater Vehicle CAD Computer-Aided Design CFD Computational Fluid Dynamics FEA Finite Element Analysis IGES Initial Graphics Exchange...Averaged Navier-Stokes ReL Arc-Length Reynolds Number TKE Turbulent Kinetic Energy 1 1. INTRODUCTION In 2013, a research effort was

  3. Development of a generic engineering model for packed bed reactors using computational fluid dynamics

    NARCIS (Netherlands)

    Tuinstra, B.F.

    2008-01-01

    Packed bed reactors are used in many chemical processes. With the advent of modern computers, flow simulation (Computational Fluid Dynamics, CFD) can be an aid in the design of process equipment. For particulate systems like packed bed reactors, simulation of the flow around the particles is very

  4. Dynamic Scaffolding of Socially Regulated Learning in a Computer-Based Learning Environment

    NARCIS (Netherlands)

    Molenaar, I.; Roda, Claudia; van Boxtel, Carla A.M.; Sleegers, P.J.C.

    2012-01-01

    The aim of this study is to test the effects of dynamically scaffolding social regulation of middle school students working in a computer-based learning environment. Dyads in the scaffolding condition (N = 56) are supported with computer-generated scaffolds and students in the control condition (N =

  5. A Series of Molecular Dynamics and Homology Modeling Computer Labs for an Undergraduate Molecular Modeling Course

    Science.gov (United States)

    Elmore, Donald E.; Guayasamin, Ryann C.; Kieffer, Madeleine E.

    2010-01-01

    As computational modeling plays an increasingly central role in biochemical research, it is important to provide students with exposure to common modeling methods in their undergraduate curriculum. This article describes a series of computer labs designed to introduce undergraduate students to energy minimization, molecular dynamics simulations,…

  6. Quantifying thumb opposition kinematics using dynamic computed tomography.

    Science.gov (United States)

    Kerkhof, F D; Brugman, E; D'Agostino, P; Dourthe, B; van Lenthe, G H; Stockmans, F; Jonkers, I; Vereecke, E E

    2016-06-14

    Current motion capture techniques all have shortcomings when applied to the 3D quantitative evaluation of thumb base motion. Dynamic CT might overcome these shortcomings but, so far, robustness of this technique in more than one specimen has not yet been demonstrated. The aim of the current study is to further evaluate the use of dynamic CT for quantification of thumb motion in a larger cadaveric study using a protocol which is feasible in a clinical context. A dynamic CT scan was acquired from six cadaveric human forearms, while a motion simulator imposed thumb opposition. After image acquisition and segmentation, carpal bone motion was quantified using helical axes. To enable comparisons between specimens, intersection points of the instantaneous helical axis with an anatomically defined plane were determined. Precision of the dynamic CT method, measured as variation in distances between silicon nitride beads between frames of a dynamic scan, was 0.43mm (+/-0.09mm) when fixed to the skin and 0.13mm (+/-0.04mm) when embedded into the bone. Absolute deviation between known and measured distances were not larger than 0.34mm. We could demonstrate and quantify that thumb opposition is associated with motion at the trapeziometacarpal and scaphotrapezotrapezoidal joints. High consistency in motion patterns between specimen were found, while the radiation dose was limited. We conclude that dynamic CT can be used to visualize and quantify 3D thumb kinematics, making it a promising method to explore kinematics in vivo. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. Gene ontology based transfer learning for protein subcellular localization

    Directory of Open Access Journals (Sweden)

    Zhou Shuigeng

    2011-02-01

    Full Text Available Abstract Background Prediction of protein subcellular localization generally involves many complex factors, and using only one or two aspects of data information may not tell the true story. For this reason, some recent predictive models are deliberately designed to integrate multiple heterogeneous data sources for exploiting multi-aspect protein feature information. Gene ontology, hereinafter referred to as GO, uses a controlled vocabulary to depict biological molecules or gene products in terms of biological process, molecular function and cellular component. With the rapid expansion of annotated protein sequences, gene ontology has become a general protein feature that can be used to construct predictive models in computational biology. Existing models generally either concatenated the GO terms into a flat binary vector or applied majority-vote based ensemble learning for protein subcellular localization, both of which can not estimate the individual discriminative abilities of the three aspects of gene ontology. Results In this paper, we propose a Gene Ontology Based Transfer Learning Model (GO-TLM for large-scale protein subcellular localization. The model transfers the signature-based homologous GO terms to the target proteins, and further constructs a reliable learning system to reduce the adverse affect of the potential false GO terms that are resulted from evolutionary divergence. We derive three GO kernels from the three aspects of gene ontology to measure the GO similarity of two proteins, and derive two other spectrum kernels to measure the similarity of two protein sequences. We use simple non-parametric cross validation to explicitly weigh the discriminative abilities of the five kernels, such that the time & space computational complexities are greatly reduced when compared to the complicated semi-definite programming and semi-indefinite linear programming. The five kernels are then linearly merged into one single kernel for

  8. Protected quantum computing: interleaving gate operations with dynamical decoupling sequences.

    Science.gov (United States)

    Zhang, Jingfu; Souza, Alexandre M; Brandao, Frederico Dias; Suter, Dieter

    2014-02-07

    Implementing precise operations on quantum systems is one of the biggest challenges for building quantum devices in a noisy environment. Dynamical decoupling attenuates the destructive effect of the environmental noise, but so far, it has been used primarily in the context of quantum memories. Here, we experimentally demonstrate a general scheme for combining dynamical decoupling with quantum logical gate operations using the example of an electron-spin qubit of a single nitrogen-vacancy center in diamond. We achieve process fidelities >98% for gate times that are 2 orders of magnitude longer than the unprotected dephasing time T2.

  9. Computational Dehydration of Crystalline Hydrates Using Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Larsen, Anders Støttrup; Rantanen, Jukka; Johansson, Kristoffer E

    2017-01-01

    Molecular dynamics (MD) simulations have evolved to an increasingly reliable and accessible technique and are today implemented in many areas of biomedical sciences. We present a generally applicable method to study dehydration of hydrates based on MD simulations and apply this approach to the de......Molecular dynamics (MD) simulations have evolved to an increasingly reliable and accessible technique and are today implemented in many areas of biomedical sciences. We present a generally applicable method to study dehydration of hydrates based on MD simulations and apply this approach...

  10. Computing the Ediz eccentric connectivity index of discrete dynamic structures

    Directory of Open Access Journals (Sweden)

    Wu Hualong

    2017-06-01

    Full Text Available From the earlier studies in physical and chemical sciences, it is found that the physico-chemical characteristics of chemical compounds are internally connected with their molecular structures. As a theoretical basis, it provides a new way of thinking by analyzing the molecular structure of the compounds to understand their physical and chemical properties. In our article, we study the physico-chemical properties of certain molecular structures via computing the Ediz eccentric connectivity index from mathematical standpoint. The results we yielded mainly apply to the techniques of distance and degree computation of mathematical derivation, and the conclusions have guiding significance in physical engineering.

  11. Computer Algebra and Dynamic Geometry Systems in Mathematics Education

    OpenAIRE

    Kllogjeri, Pellumb

    2014-01-01

    The rapid changes in computer and information technology, the increase of computer power available and the complexity of mathematical software (Maple, Mathematica, MatLab, MuPad and Derive) now accessible to the students cannot be ignored; at the very least it demands a radical re-think on the way in which topics in the curriculum could be presented and does have an impact on the teaching of Mathematics in most ofEuropean universities. Students require a personal knowledge of mathematics t...

  12. Computing the Ediz eccentric connectivity index of discrete dynamic structures

    Science.gov (United States)

    Wu, Hualong; Kamran Siddiqui, Muhammad; Zhao, Bo; Gan, Jianhou; Gao, Wei

    2017-06-01

    From the earlier studies in physical and chemical sciences, it is found that the physico-chemical characteristics of chemical compounds are internally connected with their molecular structures. As a theoretical basis, it provides a new way of thinking by analyzing the molecular structure of the compounds to understand their physical and chemical properties. In our article, we study the physico-chemical properties of certain molecular structures via computing the Ediz eccentric connectivity index from mathematical standpoint. The results we yielded mainly apply to the techniques of distance and degree computation of mathematical derivation, and the conclusions have guiding significance in physical engineering.

  13. Dynamics of a Delay-Varying Computer Virus Propagation Model

    Directory of Open Access Journals (Sweden)

    Jianguo Ren

    2012-01-01

    Full Text Available By considering the varying latency period of computer virus, we propose a novel model for computer virus propagation in network. Under this model, we give the threshold value determining whether or not the virus finally dies out, and study the local stability of the virus-free and virus equilibrium. It is found that the model may undergo a Hopf bifurcation. Next, we use different methods to prove the global asymptotic stability of the equilibria: the virus-free equilibrium by using the direct Lyapunov method and virus equilibrium by using a geometric approach. Finally, some numerical examples are given to support our conclusions.

  14. Dissertation Defense Computational Fluid Dynamics Uncertainty Analysis for Payload Fairing Spacecraft Environmental Control Systems

    Science.gov (United States)

    Groves, Curtis Edward

    2014-01-01

    Spacecraft thermal protection systems are at risk of being damaged due to airflow produced from Environmental Control Systems. There are inherent uncertainties and errors associated with using Computational Fluid Dynamics to predict the airflow field around a spacecraft from the Environmental Control System. This paper describes an approach to quantify the uncertainty in using Computational Fluid Dynamics to predict airflow speeds around an encapsulated spacecraft without the use of test data. Quantifying the uncertainty in analytical predictions is imperative to the success of any simulation-based product. The method could provide an alternative to traditional "validation by test only" mentality. This method could be extended to other disciplines and has potential to provide uncertainty for any numerical simulation, thus lowering the cost of performing these verifications while increasing the confidence in those predictions. Spacecraft requirements can include a maximum airflow speed to protect delicate instruments during ground processing. Computational Fluid Dynamics can be used to verify these requirements; however, the model must be validated by test data. This research includes the following three objectives and methods. Objective one is develop, model, and perform a Computational Fluid Dynamics analysis of three (3) generic, non-proprietary, environmental control systems and spacecraft configurations. Several commercially available and open source solvers have the capability to model the turbulent, highly three-dimensional, incompressible flow regime. The proposed method uses FLUENT, STARCCM+, and OPENFOAM. Objective two is to perform an uncertainty analysis of the Computational Fluid Dynamics model using the methodology found in "Comprehensive Approach to Verification and Validation of Computational Fluid Dynamics Simulations". This method requires three separate grids and solutions, which quantify the error bars around Computational Fluid Dynamics

  15. Dynamic routing problems with fruitful regions: models and evolutionary computation

    NARCIS (Netherlands)

    J.I. van Hemert; J.A. La Poutré (Han)

    2004-01-01

    textabstractWe introduce the concept of fruitful regions in a dynamic routing context: regions that have a high potential of generating loads to be transported. The objective is to maximise the number of loads transported, while keeping to capacity and time constraints. Loads arrive while the

  16. Differential subcellular targeting and activity-dependent subcellular localization of diacylglycerol kinase isozymes in transfected cells.

    Science.gov (United States)

    Kobayashi, Naoki; Hozumi, Yasukazu; Ito, Tsukasa; Hosoya, Takaaki; Kondo, Hisatake; Goto, Kaoru

    2007-08-01

    Diacylglycerol kinase (DGK) plays a pivotal role in cellular signal transduction through regulating levels of the second messenger diacylglycerol (DG). Previous studies have revealed that DGK is composed of a family of isozymes that show remarkable heterogeneity in terms of molecular structure, functional domains, tissue and cellular gene expression. Recently, it has been shown that DG is produced in various subcellular compartments including the plasma membrane, internal membranes, cytoskeleton, and nucleus. However, it remains unclear how DG is regulated at distinct subcellular sites. To address this point, we have used an epitope-tag expression system in cultured cells and investigated the subcellular localization of DGK isozymes under the same experimental conditions. We show here that DGK isozymes are targeted differentially to unique subcellular sites in transfected COS7 cells, including the cytoplasm, actin stress fibers, Golgi complex, endoplasmic reticulum, and nucleus. It is also shown that among the isozymes overexpression of DGKbeta causes fragmentation of actin stress fibers while a kinase-dead mutant of DGKbeta abolishes its colocalization with actin stress fibers. These data strongly suggest that each isozyme may be responsible for the metabolism of DG that is produced upon stimulation at a different and specific subcellular site and that DGKbeta activity might have effects on the reorganization of actin stress fibers in transfected COS7 cells.

  17. On the sighting of unicorns: A variational approach to computing invariant sets in dynamical systems

    Science.gov (United States)

    Junge, Oliver; Kevrekidis, Ioannis G.

    2017-06-01

    We propose to compute approximations to invariant sets in dynamical systems by minimizing an appropriate distance between a suitably selected finite set of points and its image under the dynamics. We demonstrate, through computational experiments, that this approach can successfully converge to approximations of (maximal) invariant sets of arbitrary topology, dimension, and stability, such as, e.g., saddle type invariant sets with complicated dynamics. We further propose to extend this approach by adding a Lennard-Jones type potential term to the objective function, which yields more evenly distributed approximating finite point sets, and illustrate the procedure through corresponding numerical experiments.

  18. Computational modelling of epileptic seizure dynamics and control

    NARCIS (Netherlands)

    Koppert, M.M.J.

    2014-01-01

    Epilepsy is a neurological condition affecting about 50 million people worldwide. It is a condition of the nervous system in which neuronal populations alternate between periods of normal ongoing electrical activity and periods of paroxysmal activity. Computational models provide a powerful

  19. Constructing Scientific Arguments Using Evidence from Dynamic Computational Climate Models

    Science.gov (United States)

    Pallant, Amy; Lee, Hee-Sun

    2015-01-01

    Modeling and argumentation are two important scientific practices students need to develop throughout school years. In this paper, we investigated how middle and high school students (N = 512) construct a scientific argument based on evidence from computational models with which they simulated climate change. We designed scientific argumentation…

  20. A New Computational Methodology for Structural Dynamics Problems

    Science.gov (United States)

    2008-04-01

    with p- or h-refinements, as should be expected. Actually, an exact study on the asymptotic behaviour of mixed finite elements based on least-squares...1986. [13] Duan, H.-Y. and Liang, G.-P., Mixed and nonconforming finite element approximations of Reissner-Mindlin plates, Computer Methods in Applied

  1. A computational analysis of motor synergies by dynamic response decomposition.

    Science.gov (United States)

    Alessandro, Cristiano; Carbajal, Juan Pablo; d'Avella, Andrea

    2013-01-01

    Analyses of experimental data acquired from humans and other vertebrates have suggested that motor commands may emerge from the combination of a limited set of modules. While many studies have focused on physiological aspects of this modularity, in this paper we propose an investigation of its theoretical foundations. We consider the problem of controlling a planar kinematic chain, and we restrict the admissible actuations to linear combinations of a small set of torque profiles (i.e., motor synergies). This scheme is equivalent to the time-varying synergy model, and it is formalized by means of the dynamic response decomposition (DRD). DRD is a general method to generate open-loop controllers for a dynamical system to solve desired tasks, and it can also be used to synthesize effective motor synergies. We show that a control architecture based on synergies can greatly reduce the dimensionality of the control problem, while keeping a good performance level. Our results suggest that in order to realize an effective and low-dimensional controller, synergies should embed features of both the desired tasks and the system dynamics. These characteristics can be achieved by defining synergies as solutions to a representative set of task instances. The required number of synergies increases with the complexity of the desired tasks. However, a possible strategy to keep the number of synergies low is to construct solutions to complex tasks by concatenating synergy-based actuations associated to simple point-to-point movements, with a limited loss of performance. Ultimately, this work supports the feasibility of controlling a non-linear dynamical systems by linear combinations of basic actuations, and illustrates the fundamental relationship between synergies, desired tasks and system dynamics.

  2. A computational analysis of motor synergies by dynamic response decomposition

    Directory of Open Access Journals (Sweden)

    Cristiano eAlessandro

    2014-01-01

    Full Text Available Analyses of experimental data acquired from humans and other vertebrates have suggested that motor commands may emerge from the combination of a limited set of modules. While many studies have focused on physiological aspects of this modularity, in this paper we propose an investigation of its theoretical foundations. We consider the problem of controlling a planar kinematic chain, and we restrict the admissible actuations to linear combinations of a small set of torque profiles (i.e. motor synergies. This scheme is equivalent to the time-varying synergy model, and it is formalized by means of the dynamic response decomposition (DRD. DRD is a general method to generate open-loop controllers for a dynamical system to solve desired tasks, and it can also be used to synthesize effective motor synergies. We show that a control architecture based on synergies can greatly reduce the dimensionality of the control problem, while keeping a good performance level. Our results suggest that in order to realize an effective and low-dimensional controller, synergies should embed features of both the desired tasks and the system dynamics. These characteristics can be achieved by defining synergies as solutions to a representative set of task instances. The required number of synergies increases with the complexity of the desired tasks. However, a possible strategy to keep the number of synergies low is to construct solutions to complex tasks by concatenating synergy-based actuations associated to simple point-to-point movements, with a limited loss of performance. Ultimately, this work supports the feasibility of controlling a non-linear dynamical systems by linear combinations of basic actuations, and illustrates the fundamental relationship between synergies, desired tasks and system dynamics.

  3. Computational Fluid Dynamics Modelling and Experimental Study on a Single Silica Gel Type B

    Directory of Open Access Journals (Sweden)

    John White

    2012-01-01

    Full Text Available The application of computational fluid dynamics (CFDs in the area of porous media and adsorption cooling system is becoming more practical due to the significant improvement in computer power. The results from previous studies have shown that CFD can be useful tool for predicting the water vapour flow pattern, temperature, heat transfer and flow velocity and adsorption rate. This paper investigates the effect of silica gel granular size on the water adsorption rate using computational fluid dynamics and gravimetric experimental (TGA method.

  4. Moving finite elements: A continuously adaptive method for computational fluid dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Glasser, A.H. (Los Alamos National Lab., NM (USA)); Miller, K.; Carlson, N. (California Univ., Berkeley, CA (USA))

    1991-01-01

    Moving Finite Elements (MFE), a recently developed method for computational fluid dynamics, promises major advances in the ability of computers to model the complex behavior of liquids, gases, and plasmas. Applications of computational fluid dynamics occur in a wide range of scientifically and technologically important fields. Examples include meteorology, oceanography, global climate modeling, magnetic and inertial fusion energy research, semiconductor fabrication, biophysics, automobile and aircraft design, industrial fluid processing, chemical engineering, and combustion research. The improvements made possible by the new method could thus have substantial economic impact. This paper describes the mathematical formulation and illustrates its use.

  5. Fast subcellular localization by cascaded fusion of signal-based and homology-based methods

    Directory of Open Access Journals (Sweden)

    Wang Wei

    2011-10-01

    Full Text Available Abstract Background The functions of proteins are closely related to their subcellular locations. In the post-genomics era, the amount of gene and protein data grows exponentially, which necessitates the prediction of subcellular localization by computational means. Results This paper proposes mitigating the computation burden of alignment-based approaches to subcellular localization prediction by a cascaded fusion of cleavage site prediction and profile alignment. Specifically, the informative segments of protein sequences are identified by a cleavage site predictor using the information in their N-terminal shorting signals. Then, the sequences are truncated at the cleavage site positions, and the shortened sequences are passed to PSI-BLAST for computing their profiles. Subcellular localization are subsequently predicted by a profile-to-profile alignment support-vector-machine (SVM classifier. To further reduce the training and recognition time of the classifier, the SVM classifier is replaced by a new kernel method based on the perturbational discriminant analysis (PDA. Conclusions Experimental results on a new dataset based on Swiss-Prot Release 57.5 show that the method can make use of the best property of signal- and homology-based approaches and can attain an accuracy comparable to that achieved by using full-length sequences. Analysis of profile-alignment score matrices suggest that both profile creation time and profile alignment time can be reduced without significant reduction in subcellular localization accuracy. It was found that PDA enjoys a short training time as compared to the conventional SVM. We advocate that the method will be important for biologists to conduct large-scale protein annotation or for bioinformaticians to perform preliminary investigations on new algorithms that involve pairwise alignments.

  6. Vacuoles in mammals: a subcellular structure indispensable for early embryogenesis.

    Science.gov (United States)

    Wada, Yoh

    2013-01-01

    A vacuole is a membrane-bound subcellular structure involved in intracellular digestion. Instead of the large "vacuolar" organelles that are found in plants and fungi, animal cells possess lysosomes that are smaller in size and are enriched with hydrolytic enzymes similar to those found in the vacuoles. Large vacuolar structures are often observed in highly differentiated mammalian tissues such as embryonic visceral endoderm and absorbing epithelium. Vacuoles/lysosomes share a conserved mechanism of biogenesis, and they are at the terminal of the endocytic pathways, Recent genetic studies of the mammalian orthologs of Vam/Vps genes, which have essential functions for vacuole assembly, revealed that the dynamics of vacuoles/lysosomes are important for tissue differentiation and patterning through regulation of various molecular signaling events in mammals.

  7. Using Amazon's Elastic Compute Cloud to scale CMS' compute hardware dynamically.

    CERN Document Server

    Melo, Andrew Malone

    2011-01-01

    Large international scientific collaborations such as the Compact Muon Solenoid (CMS) experiment at the Large Hadron Collider have traditionally addressed their data reduction and analysis needs by building and maintaining dedicated computational infrastructure. Emerging cloud-computing services such as Amazon's Elastic Compute Cloud (EC2) offer short-term CPU and storage resources with costs based on usage. These services allow experiments to purchase computing resources as needed, without significant prior planning and without long term investments in facilities and their management. We have demonstrated that services such as EC2 can successfully be integrated into the production-computing model of CMS, and find that they work very well as worker nodes. The cost-structure and transient nature of EC2 services makes them inappropriate for some CMS production services and functions. We also found that the resources are not truely on-demand as limits and caps on usage are imposed. Our trial workflows allow us t...

  8. Computational Modelling of Piston Ring Dynamics in 3D

    Directory of Open Access Journals (Sweden)

    Dlugoš Jozef

    2014-12-01

    Full Text Available Advanced computational models of a piston assembly based on the level of virtual prototypes require a detailed description of piston ring behaviour. Considering these requirements, the piston rings operate in regimes that cannot, in general, be simplified into an axisymmetric model. The piston and the cylinder liner do not have a perfect round shape, mainly due to machining tolerances and external thermo-mechanical loads. If the ring cannot follow the liner deformations, a local loss of contact occurs resulting in blow-by and increased consumption of lubricant oil in the engine. Current computational models are unable to implement such effects. The paper focuses on the development of a flexible 3D piston ring model based on the Timoshenko beam theory using the multibody system (MBS. The MBS model is compared to the finite element method (FEM solution.

  9. Transition Manifolds of Complex Metastable Systems - Theory and Data-Driven Computation of Effective Dynamics

    Science.gov (United States)

    Bittracher, Andreas; Koltai, Péter; Klus, Stefan; Banisch, Ralf; Dellnitz, Michael; Schütte, Christof

    2017-10-01

    We consider complex dynamical systems showing metastable behavior, but no local separation of fast and slow time scales. The article raises the question of whether such systems exhibit a low-dimensional manifold supporting its effective dynamics. For answering this question, we aim at finding nonlinear coordinates, called reaction coordinates, such that the projection of the dynamics onto these coordinates preserves the dominant time scales of the dynamics. We show that, based on a specific reducibility property, the existence of good low-dimensional reaction coordinates preserving the dominant time scales is guaranteed. Based on this theoretical framework, we develop and test a novel numerical approach for computing good reaction coordinates. The proposed algorithmic approach is fully local and thus not prone to the curse of dimension with respect to the state space of the dynamics. Hence, it is a promising method for data-based model reduction of complex dynamical systems such as molecular dynamics.

  10. Accurate and scalable O(N) algorithm for first-principles molecular-dynamics computations on large parallel computers.

    Science.gov (United States)

    Osei-Kuffuor, Daniel; Fattebert, Jean-Luc

    2014-01-31

    We present the first truly scalable first-principles molecular dynamics algorithm with O(N) complexity and controllable accuracy, capable of simulating systems with finite band gaps of sizes that were previously impossible with this degree of accuracy. By avoiding global communications, we provide a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wave functions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 101,952 atoms on 23,328 processors, with a wall-clock time of the order of 1 min per molecular dynamics time step and numerical error on the forces of less than 7×10(-4)  Ha/Bohr.

  11. Accurate and Scalable O(N) Algorithm for First-Principles Molecular-Dynamics Computations on Large Parallel Computers

    Energy Technology Data Exchange (ETDEWEB)

    Osei-Kuffuor, Daniel [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Fattebert, Jean-Luc [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2014-01-01

    We present the first truly scalable first-principles molecular dynamics algorithm with O(N) complexity and controllable accuracy, capable of simulating systems with finite band gaps of sizes that were previously impossible with this degree of accuracy. By avoiding global communications, we provide a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wave functions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 101 952 atoms on 23 328 processors, with a wall-clock time of the order of 1 min per molecular dynamics time step and numerical error on the forces of less than 7x10-4 Ha/Bohr.

  12. Calculation of the relative metastabilities of proteins in subcellular compartments of Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Dick Jeffrey M

    2009-07-01

    Full Text Available Abstract Background Protein subcellular localization and differences in oxidation state between subcellular compartments are two well-studied features of the the cellular organization of S. cerevisiae (yeast. Theories about the origin of subcellular organization are assisted by computational models that can integrate data from observations of compositional and chemical properties of the system. Presentation and implications of the hypothesis I adopt the hypothesis that the state of yeast subcellular organization is in a local energy minimum. This hypothesis implies that equilibrium thermodynamic models can yield predictions about the interdependence between populations of proteins and their subcellular chemical environments. Testing the hypothesis Three types of tests are proposed. First, there should be correlations between modeled and observed oxidation states for different compartments. Second, there should be a correspondence between the energy requirements of protein formation and the order the appearance of organelles during cellular development. Third, there should be correlations between the predicted and observed relative abundances of interacting proteins within compartments. Results The relative metastability fields of subcellular homologs of glutaredoxin and thioredoxin indicate a trend from less to more oxidizing as mitochondrion – cytoplasm – nucleus. Representing the overall amino acid compositions of proteins in 23 different compartments each with a single reference model protein suggests that the formation reactions for proteins in the vacuole (in relatively oxidizing conditions, ER and early Golgi (in relatively reducing conditions are relatively highly favored, while that for the microtubule is the most costly. The relative abundances of model proteins for each compartment inferred from experimental data were found in some cases to correlate with the predicted abundances, and both positive and negative correlations were

  13. Dynamic Programming and Graph Algorithms in Computer Vision*

    Science.gov (United States)

    Felzenszwalb, Pedro F.; Zabih, Ramin

    2013-01-01

    Optimization is a powerful paradigm for expressing and solving problems in a wide range of areas, and has been successfully applied to many vision problems. Discrete optimization techniques are especially interesting, since by carefully exploiting problem structure they often provide non-trivial guarantees concerning solution quality. In this paper we briefly review dynamic programming and graph algorithms, and discuss representative examples of how these discrete optimization techniques have been applied to some classical vision problems. We focus on the low-level vision problem of stereo; the mid-level problem of interactive object segmentation; and the high-level problem of model-based recognition. PMID:20660950

  14. Application of computational fluid dynamics methods to improve thermal hydraulic code analysis

    Science.gov (United States)

    Sentell, Dennis Shannon, Jr.

    A computational fluid dynamics code is used to model the primary natural circulation loop of a proposed small modular reactor for comparison to experimental data and best-estimate thermal-hydraulic code results. Recent advances in computational fluid dynamics code modeling capabilities make them attractive alternatives to the current conservative approach of coupled best-estimate thermal hydraulic codes and uncertainty evaluations. The results from a computational fluid dynamics analysis are benchmarked against the experimental test results of a 1:3 length, 1:254 volume, full pressure and full temperature scale small modular reactor during steady-state power operations and during a depressurization transient. A comparative evaluation of the experimental data, the thermal hydraulic code results and the computational fluid dynamics code results provides an opportunity to validate the best-estimate thermal hydraulic code's treatment of a natural circulation loop and provide insights into expanded use of the computational fluid dynamics code in future designs and operations. Additionally, a sensitivity analysis is conducted to determine those physical phenomena most impactful on operations of the proposed reactor's natural circulation loop. The combination of the comparative evaluation and sensitivity analysis provides the resources for increased confidence in model developments for natural circulation loops and provides for reliability improvements of the thermal hydraulic code.

  15. On a computational model of building thermal dynamic response

    Science.gov (United States)

    Jarošová, Petra; Vala, Jiří

    2016-07-01

    Development and exploitation of advanced materials, structures and technologies in civil engineering, both for buildings with carefully controlled interior temperature and for common residential houses, together with new European and national directives and technical standards, stimulate the development of rather complex and robust, but sufficiently simple and inexpensive computational tools, supporting their design and optimization of energy consumption. This paper demonstrates the possibility of consideration of such seemingly contradictory requirements, using the simplified non-stationary thermal model of a building, motivated by the analogy with the analysis of electric circuits; certain semi-analytical forms of solutions come from the method of lines.

  16. Computational analysis of nonlinearities within dynamics of cable-based driving systems

    Science.gov (United States)

    Anghelache, G. D.; Nastac, S.

    2017-08-01

    This paper deals with computational nonlinear dynamics of mechanical systems containing some flexural parts within the actuating scheme, and, especially, the situations of the cable-based driving systems were treated. It was supposed both functional nonlinearities and the real characteristic of the power supply, in order to obtain a realistically computer simulation model being able to provide very feasible results regarding the system dynamics. It was taken into account the transitory and stable regimes during a regular exploitation cycle. The authors present a particular case of a lift system, supposed to be representatively for the objective of this study. The simulations were made based on the values of the essential parameters acquired from the experimental tests and/or the regular practice in the field. The results analysis and the final discussions reveal the correlated dynamic aspects within the mechanical parts, the driving system, and the power supply, whole of these supplying potential sources of particular resonances, within some transitory phases of the working cycle, and which can affect structural and functional dynamics. In addition, it was underlines the influences of computational hypotheses on the both quantitative and qualitative behaviour of the system. Obviously, the most significant consequence of this theoretical and computational research consist by developing an unitary and feasible model, useful to dignify the nonlinear dynamic effects into the systems with cable-based driving scheme, and hereby to help an optimization of the exploitation regime including a dynamics control measures.

  17. Dynamic angle selection in X-ray computed tomography

    Energy Technology Data Exchange (ETDEWEB)

    Dabravolski, Andrei, E-mail: andrei.dabravolski@uantwerpen.be [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk (Belgium); Batenburg, Kees Joost, E-mail: joost.batenburg@uantwerpen.be [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk (Belgium); Centrum Wiskunde and Informatica (CWI), Science Park 123, 1098 XG Amsterdam (Netherlands); Sijbers, Jan, E-mail: jan.sijbers@uantwerpen.be [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk (Belgium)

    2014-04-01

    Highlights: • We propose the dynamic angle selection algorithm for CT scanning. • The approach is based on the concept of information gain over a set of solutions. • Projection angles are selected based on the already available projection data. • The approach can lead to more accurate results from fewer projections. - Abstract: In X-ray tomography, a number of radiographs (projections) are recorded from which a tomogram is then reconstructed. Conventionally, these projections are acquired equiangularly, resulting in an unbiased sampling of the Radon space. However, especially in case when only a limited number of projections can be acquired, the selection of the angles has a large impact on the quality of the reconstructed image. In this paper, a dynamic algorithm is proposed, in which new projection angles are selected by maximizing the information gain about the object, given the set of possible new angles. Experiments show that this approach can select projection angles for which the accuracy of the reconstructed image is significantly higher compared to the standard angle selections schemes.

  18. Increasing the speed of computational fluid dynamics procedure for minimization the nitrogen oxide polution from the premixed atmospheric gas burner

    Directory of Open Access Journals (Sweden)

    Fotev Vasko G.

    2017-01-01

    Full Text Available This article presents innovative method for increasing the speed of procedure which includes complex computational fluid dynamic calculations for finding the distance between flame openings of atmospheric gas burner that lead to minimal NO pollution. The method is based on standard features included in commercial computational fluid dynamic software and shortens computer working time roughly seven times in this particular case.

  19. Molecular dynamics computer simulation of permeation in solids

    Energy Technology Data Exchange (ETDEWEB)

    Pohl, P.I.; Heffelfinger, G.S.; Fisler, D.K.; Ford, D.M. [Sandia National Labs., Albuquerque, NM (United States)

    1997-12-31

    In this work the authors simulate permeation of gases and cations in solid models using molecular mechanics and a dual control volume grand canonical molecular dynamics technique. The molecular sieving nature of microporous zeolites are discussed and compared with that for amorphous silica made by sol-gel methods. One mesoporous and one microporous membrane model are tested with Lennard-Jones gases corresponding to He, H{sub 2}, Ar and CH{sub 4}. The mesoporous membrane model clearly follows a Knudsen diffusion mechanism, while the microporous model having a hard-sphere cutoff pore diameter of {approximately}3.4 {angstrom} demonstrates molecular sieving of the methane ({sigma} = 3.8 {angstrom}) but anomalous behavior for Ar ({sigma} = 3.4 {angstrom}). Preliminary results of Ca{sup +} diffusion in calcite and He/H{sub 2} diffusion in polyisobutylene are also presented.

  20. Computational investigation of epithelial cell dynamic phenotype in vitro

    Directory of Open Access Journals (Sweden)

    Debnath Jayanta

    2009-05-01

    Full Text Available Abstract Background When grown in three-dimensional (3D cultures, epithelial cells typically form cystic organoids that recapitulate cardinal features of in vivo epithelial structures. Characterizing essential cell actions and their roles, which constitute the system's dynamic phenotype, is critical to gaining deeper insight into the cystogenesis phenomena. Methods Starting with an earlier in silico epithelial analogue (ISEA1 that validated for several Madin-Darby canine kidney (MDCK epithelial cell culture attributes, we built a revised analogue (ISEA2 to increase overlap between analogue and cell culture traits. Both analogues used agent-based, discrete event methods. A set of axioms determined ISEA behaviors; together, they specified the analogue's operating principles. A new experimentation framework enabled tracking relative axiom use and roles during simulated cystogenesis along with establishment of the consequences of their disruption. Results ISEA2 consistently produced convex cystic structures in a simulated embedded culture. Axiom use measures provided detailed descriptions of the analogue's dynamic phenotype. Dysregulating key cell death and division axioms led to disorganized structures. Adhering to either axiom less than 80% of the time caused ISEA1 to form easily identified morphological changes. ISEA2 was more robust to identical dysregulation. Both dysregulated analogues exhibited characteristics that resembled those associated with an in vitro model of early glandular epithelial cancer. Conclusion We documented the causal chains of events, and their relative roles, responsible for simulated cystogenesis. The results stand as an early hypothesis–a theory–of how individual MDCK cell actions give rise to consistently roundish, cystic organoids.

  1. Dynamic Security Assessment Of Computer Networks In Siem-Systems

    Directory of Open Access Journals (Sweden)

    Elena Vladimirovna Doynikova

    2015-10-01

    Full Text Available The paper suggests an approach to the security assessment of computer networks. The approach is based on attack graphs and intended for Security Information and Events Management systems (SIEM-systems. Key feature of the approach consists in the application of the multilevel security metrics taxonomy. The taxonomy allows definition of the system profile according to the input data used for the metrics calculation and techniques of security metrics calculation. This allows specification of the security assessment in near real time, identification of previous and future attacker steps, identification of attackers goals and characteristics. A security assessment system prototype is implemented for the suggested approach. Analysis of its operation is conducted for several attack scenarios.

  2. Reconfigurable Optical Interconnections Via Dynamic Computer-Generated Holograms

    Science.gov (United States)

    Liu, Hua-Kuang (Inventor); Zhou, Shao-Min (Inventor)

    1996-01-01

    A system is presented for optically providing one-to-many irregular interconnections, and strength-adjustable many-to-many irregular interconnections which may be provided with strengths (weights) w(sub ij) using multiple laser beams which address multiple holograms and means for combining the beams modified by the holograms to form multiple interconnections, such as a cross-bar switching network. The optical means for interconnection is based on entering a series of complex computer-generated holograms on an electrically addressed spatial light modulator for real-time reconfigurations, thus providing flexibility for interconnection networks for large-scale practical use. By employing multiple sources and holograms, the number of interconnection patterns achieved is increased greatly.

  3. MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction

    Directory of Open Access Journals (Sweden)

    Kohlbacher Oliver

    2009-09-01

    Full Text Available Abstract Background Knowledge of subcellular localization of proteins is crucial to proteomics, drug target discovery and systems biology since localization and biological function are highly correlated. In recent years, numerous computational prediction methods have been developed. Nevertheless, there is still a need for prediction methods that show more robustness and higher accuracy. Results We extended our previous MultiLoc predictor by incorporating phylogenetic profiles and Gene Ontology terms. Two different datasets were used for training the system, resulting in two versions of this high-accuracy prediction method. One version is specialized for globular proteins and predicts up to five localizations, whereas a second version covers all eleven main eukaryotic subcellular localizations. In a benchmark study with five localizations, MultiLoc2 performs considerably better than other methods for animal and plant proteins and comparably for fungal proteins. Furthermore, MultiLoc2 performs clearly better when using a second dataset that extends the benchmark study to all eleven main eukaryotic subcellular localizations. Conclusion MultiLoc2 is an extensive high-performance subcellular protein localization prediction system. By incorporating phylogenetic profiles and Gene Ontology terms MultiLoc2 yields higher accuracies compared to its previous version. Moreover, it outperforms other prediction systems in two benchmarks studies. MultiLoc2 is available as user-friendly and free web-service, available at: http://www-bs.informatik.uni-tuebingen.de/Services/MultiLoc2.

  4. Trainable hardware for dynamical computing using error backpropagation through physical media.

    Science.gov (United States)

    Hermans, Michiel; Burm, Michaël; Van Vaerenbergh, Thomas; Dambre, Joni; Bienstman, Peter

    2015-03-24

    Neural networks are currently implemented on digital Von Neumann machines, which do not fully leverage their intrinsic parallelism. We demonstrate how to use a novel class of reconfigurable dynamical systems for analogue information processing, mitigating this problem. Our generic hardware platform for dynamic, analogue computing consists of a reciprocal linear dynamical system with nonlinear feedback. Thanks to reciprocity, a ubiquitous property of many physical phenomena like the propagation of light and sound, the error backpropagation-a crucial step for tuning such systems towards a specific task-can happen in hardware. This can potentially speed up the optimization process significantly, offering important benefits for the scalability of neuro-inspired hardware. In this paper, we show, using one experimentally validated and one conceptual example, that such systems may provide a straightforward mechanism for constructing highly scalable, fully dynamical analogue computers.

  5. OpenCL parallel integration of ordinary differential equations: Applications in computational dynamics

    Science.gov (United States)

    Rodríguez, Marcos; Blesa, Fernando; Barrio, Roberto

    2015-07-01

    In many physical problems the use of numerical simulations presents the only path to obtain insight into the behavior and evolution of the system of interest. GPU, CPU and MIC technologies are frequently employed for simulations on computational dynamics and we present results comparing different schemes for the numerical integration of ordinary differential systems (ODEs) in these architectures. The use of adapted methods with low memory storage (Low storage Runge-Kutta methods) gives good results for low precision studies, whereas the Taylor series method provides a powerful technique for high precision. We show how the computation of several dynamics indicators, such as a fast chaos indicator (FLI) or a phase shift indicator in small neuron networks (Central Pattern Generators), can be efficiently computed on these architectures by means of the numerical ODE methods executed through OpenCL. This high computational time reduction allows real-time simulations or generating video media.

  6. Fast Virtual Fractional Flow Reserve Based Upon Steady-State Computational Fluid Dynamics Analysis

    Directory of Open Access Journals (Sweden)

    Paul D. Morris, PhD

    2017-08-01

    Full Text Available Fractional flow reserve (FFR-guided percutaneous intervention is superior to standard assessment but remains underused. The authors have developed a novel “pseudotransient” analysis protocol for computing virtual fractional flow reserve (vFFR based upon angiographic images and steady-state computational fluid dynamics. This protocol generates vFFR results in 189 s (cf >24 h for transient analysis using a desktop PC, with <1% error relative to that of full-transient computational fluid dynamics analysis. Sensitivity analysis demonstrated that physiological lesion significance was influenced less by coronary or lesion anatomy (33% and more by microvascular physiology (59%. If coronary microvascular resistance can be estimated, vFFR can be accurately computed in less time than it takes to make invasive measurements.

  7. New Frontiers in Analyzing Dynamic Group Interactions: Bridging Social and Computer Science.

    Science.gov (United States)

    Lehmann-Willenbrock, Nale; Hung, Hayley; Keyton, Joann

    2017-10-01

    This special issue on advancing interdisciplinary collaboration between computer scientists and social scientists documents the joint results of the international Lorentz workshop, "Interdisciplinary Insights into Group and Team Dynamics," which took place in Leiden, The Netherlands, July 2016. An equal number of scholars from social and computer science participated in the workshop and contributed to the papers included in this special issue. In this introduction, we first identify interaction dynamics as the core of group and team models and review how scholars in social and computer science have typically approached behavioral interactions in groups and teams. Next, we identify key challenges for interdisciplinary collaboration between social and computer scientists, and we provide an overview of the different articles in this special issue aimed at addressing these challenges.

  8. The performance model of dynamic virtual organization (VO) formations within grid computing context

    Energy Technology Data Exchange (ETDEWEB)

    Han Liangxiu [National eScience Centre, School of Physics, University of Edinburgh, EH8 9AA (United Kingdom)], E-mail: lhan@nesc.ac.uk

    2009-05-30

    Grid computing aims to enable 'resource sharing and coordinated problem solving in dynamic, multi-institutional virtual organizations (VOs)'. Within the grid computing context, successful dynamic VO formations mean a number of individuals and institutions associated with certain resources join together and form new VOs in order to effectively execute tasks within given time steps. To date, while the concept of VOs has been accepted, few research has been done on the impact of effective dynamic virtual organization formations. In this paper, we develop a performance model of dynamic VOs formation and analyze the effect of different complex organizational structures and their various statistic parameter properties on dynamic VO formations from three aspects: (1) the probability of a successful VO formation under different organizational structures and statistic parameters change, e.g. average degree; (2) the effect of task complexity on dynamic VO formations; (3) the impact of network scales on dynamic VO formations. The experimental results show that the proposed model can be used to understand the dynamic VO formation performance of the simulated organizations. The work provides a good path to understand how to effectively schedule and utilize resources based on the complex grid network and therefore improve the overall performance within grid environment.

  9. Hepatic blood perfusion estimated by dynamic contrast-enhanced computed tomography in pigs

    DEFF Research Database (Denmark)

    Winterdahl, Michael; Sørensen, Michael; Keiding, Inger Susanne

    2012-01-01

    The aim of this study was to determine whether dynamic contrast-enhanced computed tomography (DCE-CT) and the slope method can provide absolute measures of hepatic blood perfusion from the hepatic artery (HA) and portal vein (PV) at experimentally varied blood flow rates.......The aim of this study was to determine whether dynamic contrast-enhanced computed tomography (DCE-CT) and the slope method can provide absolute measures of hepatic blood perfusion from the hepatic artery (HA) and portal vein (PV) at experimentally varied blood flow rates....

  10. Interferometry and computational studies of an oscillating airfoil compressible dynamic stall flow field

    Science.gov (United States)

    Chandrasekhara, M. S.; Carr, L. W.; Ekaterinaris, J. A.

    1992-01-01

    A unique comparison has been made between real time interferograms and full Navier-Stokes computations of the density field over an oscillating airfoil undergoing dynamic stall for compressible flow conditions. Good agreement was found until a dynamic stall vortex formed in the flow. Subsequent evolution of the flow field was found to be very different in the computations. The reasons for this difference have been explained in terms of the leading edge region flow physics and the refined flow modeling that needs to be used for the post-stall flow field.

  11. Computational Fluid Dynamics Modelling of Hydraulics and Sedimentation in Process Reactors During Aeration Tank Settling

    DEFF Research Database (Denmark)

    Dam Jensen, Mette; Ingildsen, Pernille; Rasmussen, Michael R.

    2005-01-01

    Aeration Tank Settling is a control method alowing settling in the process tank during high hydraulic load. The control method is patented. Aeration Tank Settling has been applied in several waste water treatment plant's using present design of the process tanks. Some process tank designs have...... shown to be more effective than others. To improve the design of less effective plants Computational Fluid Dynamics (CFD) modelling of hydraulics and sedimentation has been applied. The paper discusses the results at one particular plant experiencing problems with partly short-circuiting of the inlet...... been suggested and tested by means of computational fluid dynamics modelling. The most promissing design change have been found and reported....

  12. A Scheduling Algorithm for Cloud Computing System Based on the Driver of Dynamic Essential Path.

    Science.gov (United States)

    Xie, Zhiqiang; Shao, Xia; Xin, Yu

    2016-01-01

    To solve the problem of task scheduling in the cloud computing system, this paper proposes a scheduling algorithm for cloud computing based on the driver of dynamic essential path (DDEP). This algorithm applies a predecessor-task layer priority strategy to solve the problem of constraint relations among task nodes. The strategy assigns different priority values to every task node based on the scheduling order of task node as affected by the constraint relations among task nodes, and the task node list is generated by the different priority value. To address the scheduling order problem in which task nodes have the same priority value, the dynamic essential long path strategy is proposed. This strategy computes the dynamic essential path of the pre-scheduling task nodes based on the actual computation cost and communication cost of task node in the scheduling process. The task node that has the longest dynamic essential path is scheduled first as the completion time of task graph is indirectly influenced by the finishing time of task nodes in the longest dynamic essential path. Finally, we demonstrate the proposed algorithm via simulation experiments using Matlab tools. The experimental results indicate that the proposed algorithm can effectively reduce the task Makespan in most cases and meet a high quality performance objective.

  13. A Scheduling Algorithm for Cloud Computing System Based on the Driver of Dynamic Essential Path.

    Directory of Open Access Journals (Sweden)

    Zhiqiang Xie

    Full Text Available To solve the problem of task scheduling in the cloud computing system, this paper proposes a scheduling algorithm for cloud computing based on the driver of dynamic essential path (DDEP. This algorithm applies a predecessor-task layer priority strategy to solve the problem of constraint relations among task nodes. The strategy assigns different priority values to every task node based on the scheduling order of task node as affected by the constraint relations among task nodes, and the task node list is generated by the different priority value. To address the scheduling order problem in which task nodes have the same priority value, the dynamic essential long path strategy is proposed. This strategy computes the dynamic essential path of the pre-scheduling task nodes based on the actual computation cost and communication cost of task node in the scheduling process. The task node that has the longest dynamic essential path is scheduled first as the completion time of task graph is indirectly influenced by the finishing time of task nodes in the longest dynamic essential path. Finally, we demonstrate the proposed algorithm via simulation experiments using Matlab tools. The experimental results indicate that the proposed algorithm can effectively reduce the task Makespan in most cases and meet a high quality performance objective.

  14. Computational simulations of thermally activated magnetisation dynamics at high frequencies

    CERN Document Server

    Hannay, J D

    2001-01-01

    short time scale breakdown of the Arrhenius-Neel law for a single magnetic moment is demonstrated and explained in terms of the dynamics of the precessional motion. The variation in response as a function of the damping parameter is found to be an important factor determining the remanent magnetisation for a given pulse width. The effects of interactions between moments are described, including the apparent increase in effective damping. It is shown that interactions between grains can be described in terms of thermally excited spin waves. The most important device for today's large scale information storage is the magnetic hard disk drive. This is because it can store vast amounts of data and also provides the fastest way of accessing this valuable information. A current state of the art commercially available hard disk has data rates in excess of 1 GHz which means the magnetic bits are required to reverse in less than one nanosecond. The areal density is greater than 10 Gbits/in sup 2 which requires extreme...

  15. Computational Fluid Dynamic Analysis of a Vibrating Turbine Blade

    Directory of Open Access Journals (Sweden)

    Osama N. Alshroof

    2012-01-01

    Full Text Available This study presents the numerical fluid-structure interaction (FSI modelling of a vibrating turbine blade using the commercial software ANSYS-12.1. The study has two major aims: (i discussion of the current state of the art of modelling FSI in gas turbine engines and (ii development of a “tuned” one-way FSI model of a vibrating turbine blade to investigate the correlation between the pressure at the turbine casing surface and the vibrating blade motion. Firstly, the feasibility of the complete FSI coupled two-way, three-dimensional modelling of a turbine blade undergoing vibration using current commercial software is discussed. Various modelling simplifications, which reduce the full coupling between the fluid and structural domains, are then presented. The one-way FSI model of the vibrating turbine blade is introduced, which has the computational efficiency of a moving boundary CFD model. This one-way FSI model includes the corrected motion of the vibrating turbine blade under given engine flow conditions. This one-way FSI model is used to interrogate the pressure around a vibrating gas turbine blade. The results obtained show that the pressure distribution at the casing surface does not differ significantly, in its general form, from the pressure at the vibrating rotor blade tip.

  16. An Accurate and Dynamic Computer Graphics Muscle Model

    Science.gov (United States)

    Levine, David Asher

    1997-01-01

    A computer based musculo-skeletal model was developed at the University in the departments of Mechanical and Biomedical Engineering. This model accurately represents human shoulder kinematics. The result of this model is the graphical display of bones moving through an appropriate range of motion based on inputs of EMGs and external forces. The need existed to incorporate a geometric muscle model in the larger musculo-skeletal model. Previous muscle models did not accurately represent muscle geometries, nor did they account for the kinematics of tendons. This thesis covers the creation of a new muscle model for use in the above musculo-skeletal model. This muscle model was based on anatomical data from the Visible Human Project (VHP) cadaver study. Two-dimensional digital images from the VHP were analyzed and reconstructed to recreate the three-dimensional muscle geometries. The recreated geometries were smoothed, reduced, and sliced to form data files defining the surfaces of each muscle. The muscle modeling function opened these files during run-time and recreated the muscle surface. The modeling function applied constant volume limitations to the muscle and constant geometry limitations to the tendons.

  17. Computer-aided photometric analysis of dynamic digital bioluminescent images

    Science.gov (United States)

    Gorski, Zbigniew; Bembnista, T.; Floryszak-Wieczorek, J.; Domanski, Marek; Slawinski, Janusz

    2003-04-01

    The paper deals with photometric and morphologic analysis of bioluminescent images obtained by registration of light radiated directly from some plant objects. Registration of images obtained from ultra-weak light sources by the single photon counting (SPC) technique is the subject of this work. The radiation is registered by use of a 16-bit charge coupled device (CCD) camera "Night Owl" together with WinLight EG&G Berthold software. Additional application-specific software has been developed in order to deal with objects that are changing during the exposition time. Advantages of the elaborated set of easy configurable tools named FCT for a computer-aided photometric and morphologic analysis of numerous series of quantitatively imperfect chemiluminescent images are described. Instructions are given how to use these tools and exemplified with several algorithms for the transformation of images library. Using the proposed FCT set, automatic photometric and morphologic analysis of the information hidden within series of chemiluminescent images reflecting defensive processes in poinsettia (Euphorbia pulcherrima Willd) leaves affected by a pathogenic fungus Botrytis cinerea is revealed.

  18. Subcellular distribution of glutathione and cysteine in cyanobacteria

    Science.gov (United States)

    Tomašić, Ana; Horvat, Lucija; Fulgosi, Hrvoje

    2010-01-01

    Glutathione plays numerous important functions in eukaryotic and prokaryotic cells. Whereas it can be found in virtually all eukaryotic cells, its production in prokaryotes is restricted to cyanobacteria and proteobacteria and a few strains of gram-positive bacteria. In bacteria, it is involved in the protection against reactive oxygen species (ROS), osmotic shock, acidic conditions, toxic chemicals, and heavy metals. Glutathione synthesis in bacteria takes place in two steps out of cysteine, glutamate, and glycine. Cysteine is the limiting factor for glutathione biosynthesis which can be especially crucial for cyanobacteria, which rely on both the sufficient sulfur supply from the growth media and on the protection of glutathione against ROS that are produced during photosynthesis. In this study, we report a method that allows detection and visualization of the subcellular distribution of glutathione in Synechocystis sp. This method is based on immunogold cytochemistry with glutathione and cysteine antisera and computer-supported transmission electron microscopy. Labeling of glutathione and cysteine was restricted to the cytosol and interthylakoidal spaces. Glutathione and cysteine could not be detected in carboxysomes, cyanophycin granules, cell walls, intrathylakoidal spaces, periplasm, and vacuoles. The accuracy of the glutathione and cysteine labeling is supported by two observations. First, preadsorption of the antiglutathione and anticysteine antisera with glutathione and cysteine, respectively, reduced the density of the gold particles to background levels. Second, labeling of glutathione and cysteine was strongly decreased by 98.5% and 100%, respectively, in Synechocystis sp. cells grown on media without sulfur. This study indicates a strong similarity of the subcellular distribution of glutathione and cysteine in cyanobacteria and plastids of plants and provides a deeper insight into glutathione metabolism in bacteria. PMID:20349253

  19. Introducing CAFein, a New Computational Tool for Stellar Pulsations and Dynamic Tides

    OpenAIRE

    Valsecchi, Francesca; Farr, Will M.; Willems, Bart; Rasio, Frederic A.; Kalogera, Vassiliki

    2013-01-01

    Here we present CAFein, a new computational tool for investigating radiative dissipation of dynamic tides in close binaries and of non-adiabatic, non-radial stellar oscillations in isolated stars in the linear regime. For the latter, CAFein computes the non-adiabatic eigenfrequencies and eigenfunctions of detailed stellar models. The code is based on the so-called Riccati method, a numerical algorithm that has been successfully applied to a variety of stellar pulsators, and which doesn't suff...

  20. DNA Self-Assembly and Computation Studied with a Coarse-grained Dynamic Bonded Model

    DEFF Research Database (Denmark)

    Svaneborg, Carsten; Fellermann, Harold; Rasmussen, Steen

    2012-01-01

    We utilize a coarse-grained directional dynamic bonding DNA model [C. Svaneborg, Comp. Phys. Comm. (In Press DOI:10.1016/j.cpc.2012.03.005)] to study DNA self-assembly and DNA computation. In our DNA model, a single nucleotide is represented by a single interaction site, and complementary sites c...... tetrahedra at several temperatures, a DNA icosahedron, and also strand displacement operations used in DNA computation....

  1. ZEUS-MP/2: Computational Fluid Dynamics Code

    Science.gov (United States)

    Hayes, John C.; Norman, Michael L.; Fiedler, Robert A.; Bordner, James O.; Li, Pak Shing; Clark, Stephen E.; Ud-Doula, Asif; Mac Low, Mordecai-Mark

    2011-02-01

    ZEUS-MP is a multiphysics, massively parallel, message-passing implementation of the ZEUS code. ZEUS-MP offers an MHD algorithm that is better suited for multidimensional flows than the ZEUS-2D module by virtue of modifications to the method of characteristics scheme first suggested by Hawley & Stone. This MHD module is shown to compare quite favorably to the TVD scheme described by Ryu et al. ZEUS-MP is the first publicly available ZEUS code to allow the advection of multiple chemical (or nuclear) species. Radiation hydrodynamic simulations are enabled via an implicit flux-limited radiation diffusion (FLD) module. The hydrodynamic, MHD, and FLD modules can be used, singly or in concert, in one, two, or three space dimensions. In addition, so-called 1.5D and 2.5D grids, in which the "half-D'' denotes a symmetry axis along which a constant but nonzero value of velocity or magnetic field is evolved, are supported. Self-gravity can be included either through the assumption of a GM/r potential or through a solution of Poisson's equation using one of three linear solver packages (conjugate gradient, multigrid, and FFT) provided for that purpose. Point-mass potentials are also supported. Because ZEUS-MP is designed for large simulations on parallel computing platforms, considerable attention is paid to the parallel performance characteristics of each module in the code. Strong-scaling tests involving pure hydrodynamics (with and without self-gravity), MHD, and RHD are performed in which large problems (2563 zones) are distributed among as many as 1024 processors of an IBM SP3. Parallel efficiency is a strong function of the amount of communication required between processors in a given algorithm, but all modules are shown to scale well on up to 1024 processors for the chosen fixed problem size.

  2. Movies of cellular and sub-cellular motion by digital holographic microscopy

    Directory of Open Access Journals (Sweden)

    Yu Lingfeng

    2006-03-01

    Full Text Available Abstract Background Many biological specimens, such as living cells and their intracellular components, often exhibit very little amplitude contrast, making it difficult for conventional bright field microscopes to distinguish them from their surroundings. To overcome this problem phase contrast techniques such as Zernike, Normarsky and dark-field microscopies have been developed to improve specimen visibility without chemically or physically altering them by the process of staining. These techniques have proven to be invaluable tools for studying living cells and furthering scientific understanding of fundamental cellular processes such as mitosis. However a drawback of these techniques is that direct quantitative phase imaging is not possible. Quantitative phase imaging is important because it enables determination of either the refractive index or optical thickness variations from the measured optical path length with sub-wavelength accuracy. Digital holography is an emergent phase contrast technique that offers an excellent approach in obtaining both qualitative and quantitative phase information from the hologram. A CCD camera is used to record a hologram onto a computer and numerical methods are subsequently applied to reconstruct the hologram to enable direct access to both phase and amplitude information. Another attractive feature of digital holography is the ability to focus on multiple focal planes from a single hologram, emulating the focusing control of a conventional microscope. Methods A modified Mach-Zender off-axis setup in transmission is used to record and reconstruct a number of holographic amplitude and phase images of cellular and sub-cellular features. Results Both cellular and sub-cellular features are imaged with sub-micron, diffraction-limited resolution. Movies of holographic amplitude and phase images of living microbes and cells are created from a series of holograms and reconstructed with numerically adjustable

  3. Understanding Angiography-Based Aneurysm Flow Fields through Comparison with Computational Fluid Dynamics.

    Science.gov (United States)

    Cebral, J R; Mut, F; Chung, B J; Spelle, L; Moret, J; van Nijnatten, F; Ruijters, D

    2017-06-01

    Hemodynamics is thought to be an important factor for aneurysm progression and rupture. Our aim was to evaluate whether flow fields reconstructed from dynamic angiography data can be used to realistically represent the main flow structures in intracranial aneurysms. DSA-based flow reconstructions, obtained during interventional treatment, were compared qualitatively with flow fields obtained from patient-specific computational fluid dynamics models and quantitatively with projections of the computational fluid dynamics fields (by computing a directional similarity of the vector fields) in 15 cerebral aneurysms. The average similarity between the DSA and the projected computational fluid dynamics flow fields was 78% in the parent artery, while it was only 30% in the aneurysm region. Qualitatively, both the DSA and projected computational fluid dynamics flow fields captured the location of the inflow jet, the main vortex structure, the intrasaccular flow split, and the main rotation direction in approximately 60% of the cases. Several factors affect the reconstruction of 2D flow fields from dynamic angiography sequences. The most important factors are the 3-dimensionality of the intrasaccular flow patterns and inflow jets, the alignment of the main vortex structure with the line of sight, the overlapping of surrounding vessels, and possibly frame rate undersampling. Flow visualization with DSA from >1 projection is required for understanding of the 3D intrasaccular flow patterns. Although these DSA-based flow quantification techniques do not capture swirling or secondary flows in the parent artery, they still provide a good representation of the mean axial flow and the corresponding flow rate. © 2017 by American Journal of Neuroradiology.

  4. Efficient conjugate gradient algorithms for computation of the manipulator forward dynamics

    Science.gov (United States)

    Fijany, Amir; Scheid, Robert E.

    1989-01-01

    The applicability of conjugate gradient algorithms for computation of the manipulator forward dynamics is investigated. The redundancies in the previously proposed conjugate gradient algorithm are analyzed. A new version is developed which, by avoiding these redundancies, achieves a significantly greater efficiency. A preconditioned conjugate gradient algorithm is also presented. A diagonal matrix whose elements are the diagonal elements of the inertia matrix is proposed as the preconditioner. In order to increase the computational efficiency, an algorithm is developed which exploits the synergism between the computation of the diagonal elements of the inertia matrix and that required by the conjugate gradient algorithm.

  5. Computational Particle Dynamic Simulations on Multicore Processors (CPDMu) Final Report Phase I

    Energy Technology Data Exchange (ETDEWEB)

    Schmalz, Mark S

    2011-07-24

    Statement of Problem - Department of Energy has many legacy codes for simulation of computational particle dynamics and computational fluid dynamics applications that are designed to run on sequential processors and are not easily parallelized. Emerging high-performance computing architectures employ massively parallel multicore architectures (e.g., graphics processing units) to increase throughput. Parallelization of legacy simulation codes is a high priority, to achieve compatibility, efficiency, accuracy, and extensibility. General Statement of Solution - A legacy simulation application designed for implementation on mainly-sequential processors has been represented as a graph G. Mathematical transformations, applied to G, produce a graph representation {und G} for a high-performance architecture. Key computational and data movement kernels of the application were analyzed/optimized for parallel execution using the mapping G {yields} {und G}, which can be performed semi-automatically. This approach is widely applicable to many types of high-performance computing systems, such as graphics processing units or clusters comprised of nodes that contain one or more such units. Phase I Accomplishments - Phase I research decomposed/profiled computational particle dynamics simulation code for rocket fuel combustion into low and high computational cost regions (respectively, mainly sequential and mainly parallel kernels), with analysis of space and time complexity. Using the research team's expertise in algorithm-to-architecture mappings, the high-cost kernels were transformed, parallelized, and implemented on Nvidia Fermi GPUs. Measured speedups (GPU with respect to single-core CPU) were approximately 20-32X for realistic model parameters, without final optimization. Error analysis showed no loss of computational accuracy. Commercial Applications and Other Benefits - The proposed research will constitute a breakthrough in solution of problems related to efficient

  6. NMR and computational methods in the structural and dynamic characterization of ligand-receptor interactions.

    Science.gov (United States)

    Ghitti, Michela; Musco, Giovanna; Spitaleri, Andrea

    2014-01-01

    The recurrent failures in drug discovery campaigns, the asymmetry between the enormous financial investments and the relatively scarce results have fostered the development of strategies based on complementary methods. In this context in recent years the rigid lock-and-key binding concept had to be revisited in favour of a dynamic model of molecular recognition accounting for conformational changes of both the ligand and the receptor. The high level of complexity required by a dynamic description of the processes underlying molecular recognition requires a multidisciplinary investigation approach. In this perspective, the combination of nuclear magnetic resonance spectroscopy with molecular docking, conformational searches along with molecular dynamics simulations has given new insights into the dynamic mechanisms governing ligand receptor interactions, thus giving an enormous contribution to the identification and design of new and effective drugs. Herein a succinct overview on the applications of both NMR and computational methods to the structural and dynamic characterization of ligand-receptor interactions will be presented.

  7. Enhancing membrane protein subcellular localization prediction by parallel fusion of multi-view features.

    Science.gov (United States)

    Yu, Dongjun; Wu, Xiaowei; Shen, Hongbin; Yang, Jian; Tang, Zhenmin; Qi, Yong; Yang, Jingyu

    2012-12-01

    Membrane proteins are encoded by ~ 30% in the genome and function importantly in the living organisms. Previous studies have revealed that membrane proteins' structures and functions show obvious cell organelle-specific properties. Hence, it is highly desired to predict membrane protein's subcellular location from the primary sequence considering the extreme difficulties of membrane protein wet-lab studies. Although many models have been developed for predicting protein subcellular locations, only a few are specific to membrane proteins. Existing prediction approaches were constructed based on statistical machine learning algorithms with serial combination of multi-view features, i.e., different feature vectors are simply serially combined to form a super feature vector. However, such simple combination of features will simultaneously increase the information redundancy that could, in turn, deteriorate the final prediction accuracy. That's why it was often found that prediction success rates in the serial super space were even lower than those in a single-view space. The purpose of this paper is investigation of a proper method for fusing multiple multi-view protein sequential features for subcellular location predictions. Instead of serial strategy, we propose a novel parallel framework for fusing multiple membrane protein multi-view attributes that will represent protein samples in complex spaces. We also proposed generalized principle component analysis (GPCA) for feature reduction purpose in the complex geometry. All the experimental results through different machine learning algorithms on benchmark membrane protein subcellular localization datasets demonstrate that the newly proposed parallel strategy outperforms the traditional serial approach. We also demonstrate the efficacy of the parallel strategy on a soluble protein subcellular localization dataset indicating the parallel technique is flexible to suite for other computational biology problems. The

  8. A locally refined rectangular grid finite element method - Application to computational fluid dynamics and computational physics

    Science.gov (United States)

    Young, David P.; Melvin, Robin G.; Bieterman, Michael B.; Johnson, Forrester T.; Samant, Satish S.

    1991-01-01

    The present FEM technique addresses both linear and nonlinear boundary value problems encountered in computational physics by handling general three-dimensional regions, boundary conditions, and material properties. The box finite elements used are defined by a Cartesian grid independent of the boundary definition, and local refinements proceed by dividing a given box element into eight subelements. Discretization employs trilinear approximations on the box elements; special element stiffness matrices are included for boxes cut by any boundary surface. Illustrative results are presented for representative aerodynamics problems involving up to 400,000 elements.

  9. Synchronization and Registration of Cine Magnetic Resonance and Dynamic Computed Tomography Images of the Heart.

    Science.gov (United States)

    Betancur, Julian; Simon, Antoine; Langella, Bernard; Leclercq, Christophe; Hernandez, Alfredo; Garreau, Mireille

    2016-09-01

    The synchronization and registration of dynamic computed tomography (CT) and magnetic resonance images (MRI) of the heart is required to perform a combined analysis of their complementary information. We propose a novel method that synchronizes and registers intrapatient dynamic CT and cine-MRI short axis view (SAX). For the synchronization step, a normalized cross-correlation curve is computed from each image sequence to describe the global cardiac dynamics. The time axes of these curves are then warped using an adapted dynamic time warping (DTW) procedure. The adaptation constrains the time deformation to obtain a coherent warping function. The registration step then computes the rigid transformation that maximizes the multiimage normalized mutual information of DTW-synchronized images. The DTW synchronization and the multiimage registration were evaluated using dynamic CT and cine-SAX acquisitions from nine patients undergoing cardiac resynchronization therapy. The distance between the end-systolic phases after DTW was used to evaluate the synchronization. Mean errors, expressed as a percentage of the RR-intervals, were 3.9% and 3.7% after adapted DTW synchronization against 10.8% and 11.3% after linear synchronization, for dynamic CT and cine-SAX, respectively. This suggests that the adapted DTW synchronization leads to a coherent warping of cardiac dynamics. The multiimage registration was evaluated using fiducial points. Compared to a monoimage and a two-image registration, the multiimage registration of DTW-synchronized images obtained the lowest mean fiducial error showing that the use of dynamic voxel intensity information improves the registration.

  10. Critical Analysis of Underground Coal Gasification Models. Part II: Kinetic and Computational Fluid Dynamics Models

    Directory of Open Access Journals (Sweden)

    Alina Żogała

    2014-01-01

    Originality/value: This paper presents state of art in the field of coal gasification modeling using kinetic and computational fluid dynamics approach. The paper also presents own comparative analysis (concerned with mathematical formulation, input data and parameters, basic assumptions, obtained results etc. of the most important models of underground coal gasification.

  11. Level set method for computational multi-fluid dynamics: A review on ...

    Indian Academy of Sciences (India)

    Section I – Fluid Mechanics and Fluid Power (FMFP) Volume 40 Issue 3 May 2015 pp 627-652 ... In the second part of this article, LSM method based Computational Multi-Fluid Dynamics (CMFD) applications and analysis are reviewed for four different types of multi-phase flow: separated and parallel internal flow, ...

  12. Teachers' Use of Computational Tools to Construct and Explore Dynamic Mathematical Models

    Science.gov (United States)

    Santos-Trigo, Manuel; Reyes-Rodriguez, Aaron

    2011-01-01

    To what extent does the use of computational tools offer teachers the possibility of constructing dynamic models to identify and explore diverse mathematical relations? What ways of reasoning or thinking about the problems emerge during the model construction process that involves the use of the tools? These research questions guided the…

  13. Dynamics of Population and Economic Growth: A Computer-Based Instruction Program.

    Science.gov (United States)

    Roh, Chaisung; Handler, Paul

    A computer-assisted instructional (CAI) program at the University of Illinois is used to teach the dynamics of population growth. Socio-economic models are also developed to show the consequences of population growth upon variables such as income, productivity, and the demand for food. A one-sex population projection model allows students to…

  14. Dynamical Trust and Reputation Computation Model for B2C E-Commerce

    National Research Council Canada - National Science Library

    Bo Tian; Kecheng Liu; Yuanzhong Chen

    2015-01-01

    .... In this paper, a dynamical computation model of reputation for B2C e-commerce is proposed. Firstly, conceptions associated with trust and reputation are introduced, and the mathematical formula of trust for B2C e-commerce is given...

  15. Synchronous Computer-Mediated Dynamic Assessment: A Case Study of L2 Spanish Past Narration

    Science.gov (United States)

    Darhower, Mark Anthony

    2014-01-01

    In this study, dynamic assessment is employed to help understand the developmental processes of two university Spanish learners as they produce a series of past narrations in a synchronous computer mediated environment. The assessments were conducted in six weekly one-hour chat sessions about various scenes of a Spanish language film. The analysis…

  16. New Frontiers in Analyzing Dynamic Group Interactions : Bridging Social and Computer Science

    NARCIS (Netherlands)

    Lehmann-Willenbrock, Nale; Hung, H.S.; Keyton, Joann

    2017-01-01

    This special issue on advancing interdisciplinary collaboration between computer scientists and social scientists documents the joint results of the international Lorentz workshop, “Interdisciplinary Insights into Group and Team Dynamics,” which took place in Leiden, The Netherlands, July 2016.

  17. Airflow in a World Exposition Pavilion Studied by Scale-Model Experiments and Computational Flud Dynamics

    DEFF Research Database (Denmark)

    Nielsen, Peter V.

    The ventilation design concept, model experiment results, two-dimensional computational fluid dynamics simulation, and on-site measurements are presented for the Danish Pavilion project at the 1992 World Exhibition in Seville. The paper gives a short project history for the building and the venti...

  18. Preliminary analysis of the MER magnetic properties experiment using a computational fluid dynamics model

    DEFF Research Database (Denmark)

    Kinch, K.M.; Merrison, J.P.; Gunnlaugsson, H.P.

    2006-01-01

    Motivated by questions raised by the magnetic properties experiments on the NASA Mars Pathfinder and Mars Exploration Rover (MER) missions, we have studied in detail the capture of airborne magnetic dust by permanent magnets using a computational fluid dynamics (CFD) model supported by laboratory...

  19. Beyond the NAS Parallel Benchmarks: Measuring Dynamic Program Performance and Grid Computing Applications

    Science.gov (United States)

    VanderWijngaart, Rob F.; Biswas, Rupak; Frumkin, Michael; Feng, Huiyu; Biegel, Bryan (Technical Monitor)

    2001-01-01

    The contents include: 1) A brief history of NPB; 2) What is (not) being measured by NPB; 3) Irregular dynamic applications (UA Benchmark); and 4) Wide area distributed computing (NAS Grid Benchmarks-NGB). This paper is presented in viewgraph form.

  20. Computational fluid dynamics for propulsion technology: Geometric grid visualization in CFD-based propulsion technology research

    Science.gov (United States)

    Ziebarth, John P.; Meyer, Doug

    1992-01-01

    The coordination is examined of necessary resources, facilities, and special personnel to provide technical integration activities in the area of computational fluid dynamics applied to propulsion technology. Involved is the coordination of CFD activities between government, industry, and universities. Current geometry modeling, grid generation, and graphical methods are established to use in the analysis of CFD design methodologies.

  1. Analysis of the efficiency of greenhouse ventilation using computational fluid dynamics.

    NARCIS (Netherlands)

    Mistriotis, A.; Bot, G.P.A.; Picuno, P.; Scarassia-Mugnozza, G.

    1997-01-01

    A systematic analysis of the ventilation process in greenhouses was performed with the use of computational fluid dynamics (CFD). First, the validity of the model assumptions was established by comparing the numerical results with experimental data. A good agreement between the numerical data and

  2. Mesh and Time-Step Independent Computational Fluid Dynamics (CFD) Solutions

    Science.gov (United States)

    Nijdam, Justin J.

    2013-01-01

    A homework assignment is outlined in which students learn Computational Fluid Dynamics (CFD) concepts of discretization, numerical stability and accuracy, and verification in a hands-on manner by solving physically realistic problems of practical interest to engineers. The students solve a transient-diffusion problem numerically using the common…

  3. CFD application to supersonic/hypersonic inlet airframe integration. [computational fluid dynamics (CFD)

    Science.gov (United States)

    Benson, Thomas J.

    1988-01-01

    Supersonic external compression inlets are introduced, and the computational fluid dynamics (CFD) codes and tests needed to study flow associated with these inlets are outlined. Normal shock wave turbulent boundary layer interaction is discussed. Boundary layer control is considered. Glancing sidewall shock interaction is treated. The CFD validation of hypersonic inlet configurations is explained. Scramjet inlet modules are shown.

  4. Particle Image Velocimetry and Computational Fluid Dynamics Analysis of Fuel Cell Manifold

    DEFF Research Database (Denmark)

    Lebæk, Jesper; Blazniak Andreasen, Marcin; Andresen, Henrik Assenholm

    2010-01-01

    The inlet effect on the manifold flow in a fuel cell stack was investigated by means of numerical methods (computational fluid dynamics) and experimental methods (particle image velocimetry). At a simulated high current density situation the flow field was mapped on a 70 cell simulated cathode...

  5. Computation of the Exact Information Matrix of Gaussian Dynamic Regression Time Series Models

    NARCIS (Netherlands)

    Klein, A.A.B.; Melard, G.; Zahaf, T.

    1998-01-01

    In this paper, the computation of the exact Fisher information matrix of a large class of Gaussian time series models is considered. This class, which is often called the single-input-single-output (SISO) model, includes dynamic regression with autocorrelated errors and the transfer function model,

  6. Determination of greenhouse-specific aspects of ventilation using three-dimensional Computational Fluid Dynamics

    NARCIS (Netherlands)

    Campen, J.B.; Bot, G.P.A.

    2003-01-01

    The ventilation of a Spanish `parral¿ greenhouse was studied using three-dimensional computational fluid dynamics (CFD). The calculations were verified by experimental results from tracer gas measurements. Two types of roof openings have been considered; the rollup window configuration and the flap

  7. Investigations to improve and assess the accuracy of computational fluid dynamic based explosion models

    NARCIS (Netherlands)

    Popat, N.R.; Catlin, C.A.; Arntzen, B.J.; Lindstedt, R.P.; Hjertager, B.H.; Solberg, T.; Saeter, O.; Berg, A.C. van den

    1996-01-01

    A summary is given of part of the CEC co-sponsored project MERGE (Modelling and Experimental Research into Gas Explosions). The objective of this part of the project was to provide improved Computational Fluid Dynamic explosion models with the potential for use in hazard assessments. Five

  8. Case Study of an Ice Sensor using Computational Fluid Dynamics, Measurements and Pictures - Boundary displacement

    DEFF Research Database (Denmark)

    Pedersen, Marie Cecilie; Sørensen, Henrik; Martinez, Benjamin

    This paper presents an icing model developed using Computational Fluid Dynamics (CFD). One key part part of the model development is the surface boundary displacement due to the accumulated mass of ice. The paper presents the development of a boundary layer displacement method to be included...... in the CFD icing model using ANSYS-FLUENT....

  9. Nuclear Engineering Computer Modules: Reactor Dynamics, RD-1 and RD-2.

    Science.gov (United States)

    Onega, Ronald J.

    The objective of the Reactor Dynamics Module, RD-1, is to obtain the kinetics equation without feedback and solve the kinetics equations numerically for one to six delayed neutron groups for time varying reactivity insertions. The computer code FUMOKI (Fundamental Mode Kinetics) will calculate the power as a function of time for either uranium or…

  10. Computational fluid dynamics study on two-phase CO2 dispersion in a neutral atmosphere

    NARCIS (Netherlands)

    Trijssenaar, I.J.M.; Spruijt, M.P.N.; Hulsbosch, C.E.C.

    2011-01-01

    Abstract: A large release of Carbon Dioxide (CO2) is modelled with Computational Fluid Dynamics (CFD), (Fluent v12.1). Special attention is given to the modelling of a neutral atmospheric boundary layer (ABL) with gravity. Both the presence of non-vapour CO2 and the high density of CO2 require that

  11. Training Maneuver Evaluation for Reduced Order Modeling of Stability & Control Properties Using Computational Fluid Dynamics

    Science.gov (United States)

    2013-03-01

    PhD (Member) Date AFIT-ENY-13-M-28 Abstract System identification has long been used as a tool for flight test engineers to char- acterize systems ...recent effort to incorporate computational fluid dynamics (CFD) into the system identification process. An integral piece of the process is the...13 2.2 Stability and Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 2.3 System Identification

  12. Dynamical Trust and Reputation Computation Model for B2C E-Commerce

    Directory of Open Access Journals (Sweden)

    Bo Tian

    2015-10-01

    Full Text Available Trust is one of the most important factors that influence the successful application of network service environments, such as e-commerce, wireless sensor networks, and online social networks. Computation models associated with trust and reputation have been paid special attention in both computer societies and service science in recent years. In this paper, a dynamical computation model of reputation for B2C e-commerce is proposed. Firstly, conceptions associated with trust and reputation are introduced, and the mathematical formula of trust for B2C e-commerce is given. Then a dynamical computation model of reputation is further proposed based on the conception of trust and the relationship between trust and reputation. In the proposed model, classical varying processes of reputation of B2C e-commerce are discussed. Furthermore, the iterative trust and reputation computation models are formulated via a set of difference equations based on the closed-loop feedback mechanism. Finally, a group of numerical simulation experiments are performed to illustrate the proposed model of trust and reputation. Experimental results show that the proposed model is effective in simulating the dynamical processes of trust and reputation for B2C e-commerce.

  13. Computing and Network Systems Administration, Operations Research, and System Dynamics Modeling: A Proposed Research Framework

    Directory of Open Access Journals (Sweden)

    Michael W. Totaro

    2016-12-01

    Full Text Available Information and computing infrastructures (ICT involve levels of complexity that are highly dynamic in nature. This is due in no small measure to the proliferation of technologies, such as: cloud computing and distributed systems architectures, data mining and multidimensional analysis, and large scale enterprise systems, to name a few. Effective computing and network systems administration is integral to the stability and scalability of these complex software, hardware and communication systems. Systems administration involves the design, analysis, and continuous improvement of the performance or operation of information and computing systems. Additionally, social and administrative responsibilities have become nearly as integral for the systems administrator as are the technical demands that have been imposed for decades. The areas of operations research (OR and system dynamics (SD modeling offer system administrators a rich array of analytical and optimization tools that have been developed from diverse disciplines, which include: industrial, scientific, engineering, economic and financial, to name a few. This paper proposes a research framework by which OR and SD modeling techniques may prove useful to computing and network systems administration, which include: linear programming, network analysis, integer programming, nonlinear optimization, Markov processes, queueing modeling, simulation, decision analysis, heuristic techniques, and system dynamics modeling.

  14. Dynamic mechanistic explanation: computational modeling of circadian rhythms as an exemplar for cognitive science.

    Science.gov (United States)

    Bechtel, William; Abrahamsen, Adele

    2010-09-01

    We consider computational modeling in two fields: chronobiology and cognitive science. In circadian rhythm models, variables generally correspond to properties of parts and operations of the responsible mechanism. A computational model of this complex mechanism is grounded in empirical discoveries and contributes a more refined understanding of the dynamics of its behavior. In cognitive science, on the other hand, computational modelers typically advance de novo proposals for mechanisms to account for behavior. They offer indirect evidence that a proposed mechanism is adequate to produce particular behavioral data, but typically there is no direct empirical evidence for the hypothesized parts and operations. Models in these two fields differ in the extent of their empirical grounding, but they share the goal of achieving dynamic mechanistic explanation. That is, they augment a proposed mechanistic explanation with a computational model that enables exploration of the mechanism's dynamics. Using exemplars from circadian rhythm research, we extract six specific contributions provided by computational models. We then examine cognitive science models to determine how well they make the same types of contributions. We suggest that the modeling approach used in circadian research may prove useful in cognitive science as researchers develop procedures for experimentally decomposing cognitive mechanisms into parts and operations and begin to understand their nonlinear interactions.

  15. Experimental and Computational In Vitro Models of Left Ventricular Fluid Dynamics

    Science.gov (United States)

    Santhanakrishnan, Arvind; Samaee, Milad; Lee, Jae Ho; Bhalla, Amneet P. S.; Griffith, Boyce E.

    2015-11-01

    Computational fluid dynamics (CFD) and fluid-structure interaction (FSI) models of the heart promise to accelerate the design, testing, and regulatory approval of cardiovascular devices, but rigorous validation is required before such models can be used to design, optimize, or test device designs, or to customize patient treatment strategies. Obstacles to validation include difficulties in obtaining high-resolution in vivo data from healthy volunteers and patients and knowledge of in vivo loads and material parameters. In vitro platforms can provide a more controllable approach to obtaining high-resolution experimental data to use in the testing, development, and validation of cardiac and cardiovascular FSI models. We describe an experimental in vitro model of left ventricular fluid dynamics and progress towards using these models to validate computational models of left ventricular fluid dynamics based on the immersed boundary method.

  16. Dynamic Stall Measurements and Computations for a VR-12 Airfoil with a Variable Droop Leading Edge

    Science.gov (United States)

    Martin, P. B.; McAlister, K. W.; Chandrasekhara, M. S.; Geissler, W.

    2003-01-01

    High density-altitude operations of helicopters with advanced performance and maneuver capabilities have lead to fundamental research on active high-lift system concepts for rotor blades. The requirement for this type of system was to improve the sectional lift-to-drag ratio by alleviating dynamic stall on the retreating blade while simultaneously reducing the transonic drag rise of the advancing blade. Both measured and computational results showed that a Variable Droop Leading Edge (VDLE) airfoil is a viable concept for application to a rotor high-lift system. Results are presented for a series of 2D compressible dynamic stall wind tunnel tests with supporting CFD results for selected test cases. These measurements and computations show a dramatic decrease in the drag and pitching moment associated with severe dynamic stall when the VDLE concept is applied to the Boeing VR-12 airfoil. Test results also show an elimination of the negative pitch damping observed in the baseline moment hysteresis curves.

  17. Computational Analysis of the Transonic Dynamics Tunnel Using FUN3D

    Energy Technology Data Exchange (ETDEWEB)

    Chwalowski, Pawel; Quon, Eliot; Brynildsen, Scott E.

    2016-01-04

    This paper presents results from an explanatory two-year effort of applying Computational Fluid Dynamics (CFD) to analyze the empty-tunnel flow in the NASA Langley Research Center Transonic Dynamics Tunnel (TDT). The TDT is a continuous-flow, closed circuit, 16- x 16-foot slotted-test-section wind tunnel, with capabilities to use air or heavy gas as a working fluid. In this study, experimental data acquired in the empty tunnel using the R-134a test medium was used to calibrate the computational data. The experimental calibration data includes wall pressures, boundary-layer profiles, and the tunnel centerline Mach number profiles. Subsonic and supersonic flow regimes were considered, focusing on Mach 0.5, 0.7 and Mach 1.1 in the TDT test section. This study discusses the computational domain, boundary conditions, and initial conditions selected in the resulting steady-state analyses using NASA's FUN3D CFD software.

  18. Distribution, isomerization and enantiomer selectivity of hexabromocyclododecane (HBCD) diastereoisomers in different tissue and subcellular fractions of earthworms.

    Science.gov (United States)

    Li, Bing; Chen, Hao; Sun, Hongwen; Lan, Zhonghui

    2017-05-01

    In this study, earthworms Eisenia fetida (E. fetida) were exposed to a soil artificially contaminated with individual hexabromocyclododecane (HBCD) diastereoisomers (α-, β- and γ-HBCDs) to investigate the distribution, isomerization and enantiomer selectivity of HBCDs at tissue and subcellular levels. At the tissue level, the concentrations of HBCDs all followed the order of gut>bodyfluid>body wall, which suggested that earthworms accumulated HBCDs mainly via ingesting soil particles. At the subcellular level, the concentrations of HBCDs in an extracellular fraction consisting of granules, tissue fragment, cell membrane and intact cells (fraction A) were higher than those in an intracellular fractions consisting of the microsomal and cytosol (fraction B+C). This confirmed the passive diffusion during the distribution of HBCDs into the intracellular compartment. The distribution proportions of HBCDs varied among different tissue and subcellular fractions, and all changed over time within 14 days. The variable distributions of HBCDs in different fractions were a result of the comprehensive effects of dynamics and thermodynamics processes. The β- and γ-HBCDs were isomerized to α-HBCD in all tissue and subcellular fractions except for fraction C, and the isomerization ratios varied a lot, which seemed to be related to HBCDs residence time. The selective enrichment of (-) α-, (-) β and (-) γ-HBCDs was found in all fractions and this is consistent with that in the whole earthworm. Besides, the extents of enantio-selectivity did not change significantly among different tissue and subcellular fractions. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Computational Fluid Dynamics (CFD) Modeling And Analysis Delivery Order 0006: Cache-Aware Air Vehicles Unstructured Solver (AVUS)

    Science.gov (United States)

    2005-08-01

    AFRL-VA-WP-TM-2006-3009 COMPUTATIONAL FLUID DYNAMICS ( CFD ) MODELING AND ANALYSIS Delivery Order 0006: Cache-Aware Air Vehicles Unstructured...CONTRACT NUMBER F33615-03-D-3307-0006 5b. GRANT NUMBER 4. TITLE AND SUBTITLE COMPUTATIONAL FLUID DYNAMICS ( CFD ) MODELING AND ANALYSIS

  20. Differential subcellular distribution of ion channels and the diversity of neuronal function.

    Science.gov (United States)

    Nusser, Zoltan

    2012-06-01

    Following the astonishing molecular diversity of voltage-gated ion channels that was revealed in the past few decades, the ion channel repertoire expressed by neurons has been implicated as the major factor governing their functional heterogeneity. Although the molecular structure of ion channels is a key determinant of their biophysical properties, their subcellular distribution and densities on the surface of nerve cells are just as important for fulfilling functional requirements. Recent results obtained with high resolution quantitative localization techniques revealed complex, subcellular compartment-specific distribution patterns of distinct ion channels. Here I suggest that within a given neuron type every ion channel has a unique cell surface distribution pattern, with the functional consequence that this dramatically increases the computational power of nerve cells. Copyright © 2011 Elsevier Ltd. All rights reserved.

  1. DYNAMIC CONFIGURATION OF THE COMPUTING NODES OF THE ALICE O2 SYSTEM

    CERN Document Server

    Pugdeethosapol, Krittaphat

    2015-01-01

    The ALICE (A Large Ion Collider Experiment) Collaboration is preparing major upgrades for the detectors in 2020 in order to take advantage of the increase of collision rate at up to 50 KHz in the LHC for Pb-Pb beams. Together with these upgrades, the ALICE Online and Offline computing systems are being redesigned and upgraded to a new common system called O2. The O2 system is made of a software framework and a computing facility. The concept of the framework consists of implementing an online reconstruction and archiving of the data of all reconstructed collisions to permanent data storage. The main objective is to achieve a high-throughput system on heterogeneous computing platforms. Our KMUTT team has taken the responsibility of designing of accomplishing the design of the Control, Configuration, and Monitoring (CCM) of the computing infrastructure. This thesis is focusing on Configuration. The configuration module should allow dynamic configuration of processes and environment parameters during runtime. ...

  2. Purtscher retinopathy: an alternative etiology supported by computer fluid dynamic simulations.

    Science.gov (United States)

    Harrison, Thomas J; Abbasi, Cyrus O; Khraishi, Tariq A

    2011-10-11

    To explore an alternative etiology for Purtscher retinopathy by literature review and fluid dynamic computational simulations of wall shear stress (WSS) profiles. Computer simulations were developed, incorporating posterior pole retinal microvascular flow parameters, to demonstrate WSS profiles at 90° and 45° angle artery/arteriolar branching. Computer simulations reveal WSS profiles dependent on artery/arteriolar branching angles. At high flow rates an area of changed WSS and flow swirling and reversal was noted at the proximal fillet of the 90° arteriolar branching. These changes did not appear at the 45° arteriolar branching until the flow rate was increased an additional 30%. Computer simulation data, as well as review of the history and clinical findings of Purtscher and Purtscher-like retinopathy, present evidence that an additional etiology for Purtscher retinopathy may be a rheological event at a retinal posterior pole foci of vascular endothelial dysregulation, followed by downstream endothelin-induced vasculopathy.

  3. Dynamic Task Distribution Model for On-Chip Reconfigurable High Speed Computing System

    Directory of Open Access Journals (Sweden)

    Mahendra Vucha

    2015-01-01

    Full Text Available Modern embedded systems are being modeled as Reconfigurable High Speed Computing System (RHSCS where Reconfigurable Hardware, that is, Field Programmable Gate Array (FPGA, and softcore processors configured on FPGA act as computing elements. As system complexity increases, efficient task distribution methodologies are essential to obtain high performance. A dynamic task distribution methodology based on Minimum Laxity First (MLF policy (DTD-MLF distributes the tasks of an application dynamically onto RHSCS and utilizes available RHSCS resources effectively. The DTD-MLF methodology takes the advantage of runtime design parameters of an application represented as DAG and considers the attributes of tasks in DAG and computing resources to distribute the tasks of an application onto RHSCS. In this paper, we have described the DTD-MLF model and verified its effectiveness by distributing some of real life benchmark applications onto RHSCS configured on Virtex-5 FPGA device. Some benchmark applications are represented as DAG and are distributed to the resources of RHSCS based on DTD-MLF model. The performance of the MLF based dynamic task distribution methodology is compared with static task distribution methodology. The comparison shows that the dynamic task distribution model with MLF criteria outperforms the static task distribution techniques in terms of schedule length and effective utilization of available RHSCS resources.

  4. Adaptive workflow scheduling in grid computing based on dynamic resource availability

    Directory of Open Access Journals (Sweden)

    Ritu Garg

    2015-06-01

    Full Text Available Grid computing enables large-scale resource sharing and collaboration for solving advanced science and engineering applications. Central to the grid computing is the scheduling of application tasks to the resources. Various strategies have been proposed, including static and dynamic strategies. The former schedules the tasks to resources before the actual execution time and later schedules them at the time of execution. Static scheduling performs better but it is not suitable for dynamic grid environment. The lack of dedicated resources and variations in their availability at run time has made this scheduling a great challenge. In this study, we proposed the adaptive approach to schedule workflow tasks (dependent tasks to the dynamic grid resources based on rescheduling method. It deals with the heterogeneous dynamic grid environment, where the availability of computing nodes and links bandwidth fluctuations are inevitable due to existence of local load or load by other users. The proposed adaptive workflow scheduling (AWS approach involves initial static scheduling, resource monitoring and rescheduling with the aim to achieve the minimum execution time for workflow application. The approach differs from other techniques in literature as it considers the changes in resources (hosts and links availability and considers the impact of existing load over the grid resources. The simulation results using randomly generated task graphs and task graphs corresponding to real world problems (GE and FFT demonstrates that the proposed algorithm is able to deal with fluctuations of resource availability and provides overall optimal performance.

  5. Computational fluid dynamics evaluation of flow reversal treatment of giant basilar tip aneurysm.

    Science.gov (United States)

    Alnæs, Martin Sandve; Mardal, Kent-Andre; Bakke, Søren; Sorteberg, Angelika

    2015-10-01

    Therapeutic parent artery flow reversal is a treatment option for giant, partially thrombosed basilar tip aneurysms. The effectiveness of this treatment has been variable and not yet studied by applying computational fluid dynamics. Computed tomography images and blood flow velocities acquired with transcranial Doppler ultrasonography were obtained prior to and after bilateral endovascular vertebral artery occlusion for a giant basilar tip aneurysm. Patient-specific geometries and velocity waveforms were used in computational fluid dynamics simulations in order to determine the velocity and wall shear stress changes induced by treatment. Therapeutic parent artery flow reversal lead to a dramatic increase in aneurysm inflow and wall shear stress (30 to 170 Pa) resulting in an increase in intra-aneurysmal circulation. The enlargement of the circulated area within the aneurysm led to a re-normalization of the wall shear stress and the aneurysm remained stable for more than 8 years thereafter. Therapeutic parent artery flow reversal can lead to unintended, potentially harmful changes in aneurysm inflow which can be quantified and possibly predicted by applying computational fluid dynamics. © The Author(s) 2015.

  6. Estimation of changes in dynamic hydraulic force in a magnetically suspended centrifugal blood pump with transient computational fluid dynamics analysis.

    Science.gov (United States)

    Masuzawa, Toru; Ohta, Akiko; Tanaka, Nobuatu; Qian, Yi; Tsukiya, Tomonori

    2009-01-01

    The effect of the hydraulic force on magnetically levitated (maglev) pumps should be studied carefully to improve the suspension performance and the reliability of the pumps. A maglev centrifugal pump, developed at Ibaraki University, was modeled with 926 376 hexahedral elements for computational fluid dynamics (CFD) analyses. The pump has a fully open six-vane impeller with a diameter of 72.5 mm. A self-bearing motor suspends the impeller in the radial direction. The maximum pressure head and flow rate were 250 mmHg and 14 l/min, respectively. First, a steady-state analysis was performed using commercial code STAR-CD to confirm the model's suitability by comparing the results with the real pump performance. Second, transient analysis was performed to estimate the hydraulic force on the levitated impeller. The impeller was rotated in steps of 1 degrees using a sliding mesh. The force around the impeller was integrated at every step. The transient analysis revealed that the direction of the radial force changed dynamically as the vane's position changed relative to the outlet port during one circulation, and the magnitude of this force was about 1 N. The current maglev pump has sufficient performance to counteract this hydraulic force. Transient CFD analysis is not only useful for observing dynamic flow conditions in a centrifugal pump but is also effective for obtaining information about the levitation dynamics of a maglev pump.

  7. Structure and dynamics of amorphous polymers: computer simulations compared to experiment and theory

    Energy Technology Data Exchange (ETDEWEB)

    Paul, Wolfgang [Institut fuer Physik, Johannes Gutenberg-Universitaet, 55099 Mainz (Germany); Smith, Grant D [Department of Materials Science and Engineering and Department of Chemical and Fuels Engineering, University of Utah, Salt Lake City, UT 84112 (United States)

    2004-07-01

    This contribution considers recent developments in the computer modelling of amorphous polymeric materials. Progress in our capabilities to build models for the computer simulation of polymers from the detailed atomistic scale up to coarse-grained mesoscopic models, together with the ever-improving performance of computers, have led to important insights from computer simulations into the structural and dynamic properties of amorphous polymers. Structurally, chain connectivity introduces a range of length scales from that of the chemical bond to the radius of gyration of the polymer chain covering 2-4 orders of magnitude. Dynamically, this range of length scales translates into an even larger range of time scales observable in relaxation processes in amorphous polymers ranging from about 10{sup -13} to 10{sup -3} s or even to 10{sup 3} s when glass dynamics is concerned. There is currently no single simulation technique that is able to describe all these length and time scales efficiently. On large length and time scales basic topology and entropy become the governing properties and this fact can be exploited using computer simulations of coarse-grained polymer models to study universal aspects of the structure and dynamics of amorphous polymers. On the largest length and time scales chain connectivity is the dominating factor leading to the strong increase in longest relaxation times described within the reptation theory of polymer melt dynamics. Recently, many of the universal aspects of this behaviour have been further elucidated by computer simulations of coarse-grained polymer models. On short length scales the detailed chemistry and energetics of the polymer are important, and one has to be able to capture them correctly using chemically realistic modelling of specific polymers, even when the aim is to extract generic physical behaviour exhibited by the specific chemistry. Detailed studies of chemically realistic models highlight the central importance of

  8. Dynamic delamination buckling in composite laminates under impact loading: Computational simulation

    Science.gov (United States)

    Grady, Joseph E.; Chamis, Christos C.; Aiello, Robert A.

    1987-01-01

    A unique dynamic delamination buckling and delamination propagation analysis capability has been developed and incorporated into a finite element computer program. This capability consists of the following: (1) a modification of the direct time integration solution sequence which provides a new analysis algorithm that can be used to predict delamination buckling in a laminate subjected to dynamic loading, and (2) a new method of modeling the composite laminate using plate bending elements and multipoint constraints. This computer program is used to predict both impact induced buckling in composite laminates with initial delaminations and the strain energy release rate due to extension of the delamination. It is shown that delaminations near the outer surface of a laminate are susceptible to local buckling and buckling-induced delamination propagation when the laminate is subjected to transverse impact loading. The capability now exists to predict the time at which the onset of dynamic delamination buckling occurs, the dynamic buckling mode shape, and the dynamic delamination strain energy release rate.

  9. Dynamic delamination buckling in composite laminates under impact loading - Computational simulation

    Science.gov (United States)

    Grady, Joseph E.; Chamis, Christos C.; Aiello, Robert A.

    1989-01-01

    A unique dynamic delamination buckling and delamination propagation analysis capability has been developed and incorporated into a finite element computer program. This capability consists of the following: (1) a modification of the direct time integration solution sequence which provides a new analysis algorithm that can be used to predict delamination buckling in a laminate subjected to dynamic loading, and (2) a new method of modeling the composite laminate using plate bending elements and multipoint constraints. This computer program is used to predict both impact induced buckling in composite laminates with initial delaminations and the strain energy release rate due to extension of the delamination. It is shown that delaminations near the outer surface of a laminate are susceptible to local buckling and buckling-induced delamination propagation when the laminate is subjected to transverse impact loading. The capability now exists to predict the time at which the onset of dynamic delamination buckling occurs, the dynamic buckling mode shape, and the dynamic delamination strain energy release rate.

  10. Characterization of dynamic stall on 9-15 % thick airfoils using experiment and computation

    Science.gov (United States)

    Davidson, Phillip B.

    In recent years, the blade geometry on wind turbines and helicopters has been optimized for a particular span location. Unsteady flow phenomena like dynamic stall limit these designs and need to be better understood and correctly simulated. Currently, empirical and computational fluid dynamics (CFD) methods are used to simulate rotating wind turbine or helicopter blades, but each of these methods has limitations in predicting unsteady separated flows. To address these needs, the present work investigated oscillating airfoils over a range of conditions with an approach that provided fast, low-cost unsteady pressure data combined with a highly resolved flow field to better understand the physics of dynamic stall. An additional objective was to show how such data may be used to assess CFD simulations. This research has yielded interesting results showing characteristics of thin airfoil stall, leading edge stall, and trailing edge stall that were sorted and classified. Classification of the oscillating airfoil behavior with or without dynamic stall was performed using previous definitions for stall regime, separation characteristics, and other qualitative differences in stall pattern. After classifying the unsteady flow for each of the cases, comparison of experimental results and results obtained using an unsteady Reynolds Averaged Navier-Stokes (URANS) solver was performed to assess the ability of the solver to produce the same unsteady effects. Although both experiment and computation produced similar flow features, the timing and magnitude of the features in the dynamic stall and re-attachment process of the pitching cycle exhibited some significant differences.

  11. The accuracy of dynamic wedge dose computation in the ADAC Pinnacle RTP system.

    Science.gov (United States)

    Shao, H; Wu, X; Luo, C; Crooks, A; Bernstein, A; Markoe, A

    2004-01-01

    The nonphysical wedge is a modality that uses computer-controlled jaw motion to generate wedge-shaped dose distributions. There are Varian enhanced dynamic wedges (EDWs) and Siemens virtual wedges (VWs). We recently commissioned dynamic wedges on both Varian and Siemens LINACs. The beam data, acquired with a Wellhofer chamber array and a Sun Nuclear profiler, are used for modeling in the ADAC Pinnacle system. As recommended by ADAC, only a limited number of beam data is measured and used for beam modeling. Therefore, the dose distributions of dynamic wedges generated by Pinnacle must be examined. Following the commissioning of the dynamic wedges, we used Pinnacle to generate a number of dose distributions with different energies, wedge angles, field sizes, and depths. The computed data from Pinnacle are then compared with the measured data. The deviations of the output factor in all square and rectangular fields are mostly within 2.0% for both EDW and VW. For asymmetric fields, the deviations are within 3%. However, exceptions of differences more than 3% have been found in a larger field and large wedge combinations. The precision of the beam profiles generated by Pinnacle is also evaluated. As a result of this investigation, we present a scope of quality assurance tests that are necessary to ensure acceptable consistency between the delivered dose and the associated treatment plan when dynamic wedges are applied.

  12. Computation of accommodation coefficients and the use of velocity correlation profiles in molecular dynamics simulations

    Science.gov (United States)

    Spijker, Peter; Markvoort, Albert J.; Nedea, Silvia V.; Hilbers, Peter A. J.

    2010-01-01

    For understanding the behavior of a gas close to a channel wall it is important to model the gas-wall interactions as detailed as possible. When using molecular dynamics simulations these interactions can be modeled explicitly, but the computations are time consuming. Replacing the explicit wall with a wall model reduces the computational time but the same characteristics should still remain. Elaborate wall models, such as the Maxwell-Yamamoto model or the Cercignani-Lampis model need a phenomenological parameter (the accommodation coefficient) for the description of the gas-wall interaction as an input. Therefore, computing these accommodation coefficients in a reliable way is very important. In this paper, two systems (platinum walls with either argon or xenon gas confined between them) are investigated and are used for comparison of the accommodation coefficients for the wall models and the explicit molecular dynamics simulations. Velocity correlations between incoming and outgoing particles colliding with the wall have been used to compare explicit simulations and wall models even further. Furthermore, based on these velocity correlations, a method to compute the accommodation coefficients is presented, and these newly computed accommodation coefficients are used to show improved correlation behavior for the wall models.

  13. Neural dynamics as sampling: a model for stochastic computation in recurrent networks of spiking neurons.

    Directory of Open Access Journals (Sweden)

    Lars Buesing

    2011-11-01

    Full Text Available The organization of computations in networks of spiking neurons in the brain is still largely unknown, in particular in view of the inherently stochastic features of their firing activity and the experimentally observed trial-to-trial variability of neural systems in the brain. In principle there exists a powerful computational framework for stochastic computations, probabilistic inference by sampling, which can explain a large number of macroscopic experimental data in neuroscience and cognitive science. But it has turned out to be surprisingly difficult to create a link between these abstract models for stochastic computations and more detailed models of the dynamics of networks of spiking neurons. Here we create such a link and show that under some conditions the stochastic firing activity of networks of spiking neurons can be interpreted as probabilistic inference via Markov chain Monte Carlo (MCMC sampling. Since common methods for MCMC sampling in distributed systems, such as Gibbs sampling, are inconsistent with the dynamics of spiking neurons, we introduce a different approach based on non-reversible Markov chains that is able to reflect inherent temporal processes of spiking neuronal activity through a suitable choice of random variables. We propose a neural network model and show by a rigorous theoretical analysis that its neural activity implements MCMC sampling of a given distribution, both for the case of discrete and continuous time. This provides a step towards closing the gap between abstract functional models of cortical computation and more detailed models of networks of spiking neurons.

  14. Neural dynamics as sampling: a model for stochastic computation in recurrent networks of spiking neurons.

    Science.gov (United States)

    Buesing, Lars; Bill, Johannes; Nessler, Bernhard; Maass, Wolfgang

    2011-11-01

    The organization of computations in networks of spiking neurons in the brain is still largely unknown, in particular in view of the inherently stochastic features of their firing activity and the experimentally observed trial-to-trial variability of neural systems in the brain. In principle there exists a powerful computational framework for stochastic computations, probabilistic inference by sampling, which can explain a large number of macroscopic experimental data in neuroscience and cognitive science. But it has turned out to be surprisingly difficult to create a link between these abstract models for stochastic computations and more detailed models of the dynamics of networks of spiking neurons. Here we create such a link and show that under some conditions the stochastic firing activity of networks of spiking neurons can be interpreted as probabilistic inference via Markov chain Monte Carlo (MCMC) sampling. Since common methods for MCMC sampling in distributed systems, such as Gibbs sampling, are inconsistent with the dynamics of spiking neurons, we introduce a different approach based on non-reversible Markov chains that is able to reflect inherent temporal processes of spiking neuronal activity through a suitable choice of random variables. We propose a neural network model and show by a rigorous theoretical analysis that its neural activity implements MCMC sampling of a given distribution, both for the case of discrete and continuous time. This provides a step towards closing the gap between abstract functional models of cortical computation and more detailed models of networks of spiking neurons.

  15. Modeling Potential Carbon Monoxide Exposure Due to Operation of a Major Rocket Engine Altitude Test Facility Using Computational Fluid Dynamics

    Science.gov (United States)

    Blotzer, Michael J.; Woods, Jody L.

    2009-01-01

    This viewgraph presentation reviews computational fluid dynamics as a tool for modelling the dispersion of carbon monoxide at the Stennis Space Center's A3 Test Stand. The contents include: 1) Constellation Program; 2) Constellation Launch Vehicles; 3) J2X Engine; 4) A-3 Test Stand; 5) Chemical Steam Generators; 6) Emission Estimates; 7) Located in Existing Test Complex; 8) Computational Fluid Dynamics; 9) Computational Tools; 10) CO Modeling; 11) CO Model results; and 12) Next steps.

  16. A new way of estimating compute-boundedness and its application to dynamic voltage scaling

    DEFF Research Database (Denmark)

    Venkatachalam, Vasanth; Franz, Michael; Probst, Christian W.

    2007-01-01

    Many dynamic voltage scaling algorithms rely on measuring hardware events (such as cache misses) for predicting how much a workload can be slowed down with acceptable performance loss. The events measured, however, are at best indirectly related to execution time and clock frequency. By relating...... these two indicators logically, we propose a new way of predicting a workload's compute-boundedness that is based on direct observation, and only requires measuring the total execution cycles for the two highest clock frequencies. Our predictor can be used to develop dynamic voltage scaling algorithms...

  17. Evolution of perturbed dynamical systems: analytical computation with time independent accuracy

    Energy Technology Data Exchange (ETDEWEB)

    Gurzadyan, A.V. [Russian-Armenian (Slavonic) University, Department of Mathematics and Mathematical Modelling, Yerevan (Armenia); Kocharyan, A.A. [Monash University, School of Physics and Astronomy, Clayton (Australia)

    2016-12-15

    An analytical method for investigation of the evolution of dynamical systems with independent on time accuracy is developed for perturbed Hamiltonian systems. The error-free estimation using of computer algebra enables the application of the method to complex multi-dimensional Hamiltonian and dissipative systems. It also opens principal opportunities for the qualitative study of chaotic trajectories. The performance of the method is demonstrated on perturbed two-oscillator systems. It can be applied to various non-linear physical and astrophysical systems, e.g. to long-term planetary dynamics. (orig.)

  18. Computational Fluid Dynamics Modelling of Hydraulics and Sedimentation in Process Reactors during Aeration Tank Settling

    DEFF Research Database (Denmark)

    Jensen, M.D.; Ingildsen, P.; Rasmussen, Michael R.

    2006-01-01

    Aeration tank settling is a control method allowing settling in the process tank during highhydraulic load. The control method is patented. Aeration tank settling has been applied in several wastewater treatment plants using the present design of the process tanks. Some process tank designs...... haveshown to be more effective than others. To improve the design of less effective plants, computational fluiddynamics (CFD) modelling of hydraulics and sedimentation has been applied. This paper discusses theresults at one particular plant experiencing problems with partly short-circuiting of the inlet...... suggested andtested by means of computational fluid dynamics modelling. The most promising design changes have beenfound and reported....

  19. Numerical computation of soliton dynamics for NLS equations in a driving potential

    Directory of Open Access Journals (Sweden)

    Marco Caliari

    2010-06-01

    Full Text Available We provide numerical computations for the soliton dynamics of the nonlinear Schrodinger equation with an external potential. After computing the ground state solution r of a related elliptic equation we show that, in the semi-classical regime, the center of mass of the solution with initial datum built upon r is driven by the solution to $ddot x=- abla V(x$. Finally, we provide examples and analyze the numerical errors in the two dimensional case when V is a harmonic potential.

  20. Advances in computational dynamics of particles, materials and structures a unified approach

    CERN Document Server

    Har, Jason

    2012-01-01

    Computational methods for the modeling and simulation of the dynamic response and behavior of particles, materials and structural systems have had a profound influence on science, engineering and technology. Complex science and engineering applications dealing with complicated structural geometries and materials that would be very difficult to treat using analytical methods have been successfully simulated using computational tools. With the incorporation of quantum, molecular and biological mechanics into new models, these methods are poised to play an even bigger role in the future. Ad

  1. Linear stability analysis of detonations via numerical computation and dynamic mode decomposition

    KAUST Repository

    Kabanov, Dmitry I.

    2017-12-08

    We introduce a new method to investigate linear stability of gaseous detonations that is based on an accurate shock-fitting numerical integration of the linearized reactive Euler equations with a subsequent analysis of the computed solution via the dynamic mode decomposition. The method is applied to the detonation models based on both the standard one-step Arrhenius kinetics and two-step exothermic-endothermic reaction kinetics. Stability spectra for all cases are computed and analyzed. The new approach is shown to be a viable alternative to the traditional normal-mode analysis used in detonation theory.

  2. Dynamic gas temperature measurements using a personal computer for data acquisition and reduction

    Science.gov (United States)

    Fralick, Gustave C.; Oberle, Lawrence G.; Greer, Lawrence C., III

    1993-01-01

    This report describes a dynamic gas temperature measurement system. It has frequency response to 1000 Hz, and can be used to measure temperatures in hot, high pressure, high velocity flows. A personal computer is used for collecting and processing data, which results in a much shorter wait for results than previously. The data collection process and the user interface are described in detail. The changes made in transporting the software from a mainframe to a personal computer are described in appendices, as is the overall theory of operation.

  3. Global dynamics of a novel multi-group model for computer worms

    Science.gov (United States)

    Gong, Yong-Wang; Song, Yu-Rong; Jiang, Guo-Ping

    2013-04-01

    In this paper, we study worm dynamics in computer networks composed of many autonomous systems. A novel multi-group SIQR (susceptible-infected-quarantined-removed) model is proposed for computer worms by explicitly considering anti-virus measures and the network infrastructure. Then, the basic reproduction number of worm R0 is derived and the global dynamics of the model are established. It is shown that if R0 is less than or equal to 1, the disease-free equilibrium is globally asymptotically stable and the worm dies out eventually, whereas, if R0 is greater than 1, one unique endemic equilibrium exists and it is globally asymptotically stable, thus the worm persists in the network. Finally, numerical simulations are given to illustrate the theoretical results.

  4. Computational Fluid Dynamics (CFD) Simulations of a Finned Projectile with Microflaps for Flow Control

    Science.gov (United States)

    2016-04-01

    Sciences Meeting; 2003 Jan 6– 9; Reno, NV. AIAA Paper No.: 2003-1352. 2. DeSpirito J. Transient lateral jet interaction effects on a generic fin- stabilized ...Microflaps for Flow Control by Jubaraj Sahu Approved for public release; distribution is unlimited. NOTICES...Computational Fluid Dynamics (CFD) Simulations of a Finned Projectile with Microflaps for Flow Control by Jubaraj Sahu Weapons and Materials Research

  5. Characterization and optimization of single-use bioreactors and biopharmaceutical production processes using computational fluid dynamics

    OpenAIRE

    Kaiser, Stephan Christian

    2015-01-01

    Durch die örtliche und zeitliche Modellierung der auftretenden Strömungen bietet die numerische Fluiddynamik (engl. Computational Fluid Dynamics, CFD) das Potenzial detaillierte Untersuchungen der Hydrodynamik in Bioreaktoren durchzuführen. Allerdings sind bisher nur wenige Studien in Verbindung mit Einwegbioreaktoren, die sich durch konstruktiven Besonderheiten von ihren klassischen Gegenspielern aus Glas und/oder Edelstahl unterscheiden, publiziert. Die vorliegende Arbeit soll daher geeigne...

  6. The NASA Computational Fluid Dynamics (CFD) program - Building technology to solve future challenges

    Science.gov (United States)

    Richardson, Pamela F.; Dwoyer, Douglas L.; Kutler, Paul; Povinelli, Louis A.

    1993-01-01

    This paper presents the NASA Computational Fluid Dynamics program in terms of a strategic vision and goals as well as NASA's financial commitment and personnel levels. The paper also identifies the CFD program customers and the support to those customers. In addition, the paper discusses technical emphasis and direction of the program and some recent achievements. NASA's Ames, Langley, and Lewis Research Centers are the research hubs of the CFD program while the NASA Headquarters Office of Aeronautics represents and advocates the program.

  7. A simplified and improved modeling approach for the structural fumigation process using computational fluid dynamics

    OpenAIRE

    Chayaprasert, W.; Maier, D. E.; Subramanyam, B.

    2010-01-01

    A 3D Computational fluid dynamics (CFD) model of the fumigation process in the Hal Ross Flour Mill of Kansas State University, Manhattan, Kansas, USA, was formulated for prediction of the gas leakage rate to approximate the gas Half-loss time (HLT) during fumigation with Methyl bromide (MB) and Sulfuryl fluoride (SF). The model consisted of external and internal flow domains. The external domain was used to predict stagnation pressures generated by wind impinging on the mill’s walls. The inte...

  8. Computational fluid dynamics analysis to assess performance variability of in-duct UV-C systems

    OpenAIRE

    Capetillo, A; Noakes, CJ; Sleigh, PA

    2015-01-01

    UV-C is becoming a mainstream air sterilisation technology, and is marketed in the form of energy saving and infection reduction devices. An accurate rating of device performance is essential to ensure appropriate microbial reduction yet avoid wastage of energy due to over performance. This paper demonstrates the potential benefits from using computational fluid dynamics (CFD) to assess performance. A CFD model was developed using discrete ordinate (DO) irradiation modeling and Lagrangian par...

  9. Computational fluid dynamics analysis of the Canadian deuterium uranium moderator tests at the Stern Laboratories Inc.

    OpenAIRE

    Kim, Hyoung Tae; Chang, Se-Myong

    2015-01-01

    A numerical calculation with the commercial computational fluid dynamics code CFX-14.0 was conducted for a test facility simulating the Canadian deuterium uranium moderator thermal–hydraulics. Two kinds of moderator thermal–hydraulic tests at Stern Laboratories Inc. were performed in the full geometric configuration of the Canadian deuterium uranium moderator circulating vessel, which is called a calandria tank, housing a matrix of horizontal rod bundles simulating calandria tubes. The first ...

  10. Computational strong-field quantum dynamics. Intense light-matter interactions

    Energy Technology Data Exchange (ETDEWEB)

    Bauer, Dieter (ed.) [Rostock Univ. (Germany). Inst. fuer Physik

    2017-09-01

    This graduate textbook introduces the computational techniques to study ultra-fast quantum dynamics of matter exposed to strong laser fields. Coverage includes methods to propagate wavefunctions according to the time dependent Schroedinger, Klein-Gordon or Dirac equation, the calculation of typical observables, time-dependent density functional theory, multi configurational time-dependent Hartree-Fock, time-dependent configuration interaction singles, the strong-field approximation, and the microscopic particle-in-cell approach.

  11. Computational strong-field quantum dynamics intense light-matter interactions

    CERN Document Server

    2017-01-01

    This graduate textbook introduces the computational techniques to study ultra-fast quantum dynamics of matter exposed to strong laser fields. Coverage includes methods to propagate wavefunctions according to the time-dependent Schrödinger, Klein-Gordon or Dirac equation, the calculation of typical observables, time-dependent density functional theory, multi-configurational time-dependent Hartree-Fock, time-dependent configuration interaction singles, the strong-field approximation, and the microscopic particle-in-cell approach.

  12. Developing a computationally efficient dynamic multilevel hybrid optimization scheme using multifidelity model interactions.

    Energy Technology Data Exchange (ETDEWEB)

    Hough, Patricia Diane (Sandia National Laboratories, Livermore, CA); Gray, Genetha Anne (Sandia National Laboratories, Livermore, CA); Castro, Joseph Pete Jr. (; .); Giunta, Anthony Andrew

    2006-01-01

    Many engineering application problems use optimization algorithms in conjunction with numerical simulators to search for solutions. The formulation of relevant objective functions and constraints dictate possible optimization algorithms. Often, a gradient based approach is not possible since objective functions and constraints can be nonlinear, nonconvex, non-differentiable, or even discontinuous and the simulations involved can be computationally expensive. Moreover, computational efficiency and accuracy are desirable and also influence the choice of solution method. With the advent and increasing availability of massively parallel computers, computational speed has increased tremendously. Unfortunately, the numerical and model complexities of many problems still demand significant computational resources. Moreover, in optimization, these expenses can be a limiting factor since obtaining solutions often requires the completion of numerous computationally intensive simulations. Therefore, we propose a multifidelity optimization algorithm (MFO) designed to improve the computational efficiency of an optimization method for a wide range of applications. In developing the MFO algorithm, we take advantage of the interactions between multi fidelity models to develop a dynamic and computational time saving optimization algorithm. First, a direct search method is applied to the high fidelity model over a reduced design space. In conjunction with this search, a specialized oracle is employed to map the design space of this high fidelity model to that of a computationally cheaper low fidelity model using space mapping techniques. Then, in the low fidelity space, an optimum is obtained using gradient or non-gradient based optimization, and it is mapped back to the high fidelity space. In this paper, we describe the theory and implementation details of our MFO algorithm. We also demonstrate our MFO method on some example problems and on two applications: earth penetrators and

  13. Dynamic computer model for the metallogenesis and tectonics of the Circum-North Pacific

    Science.gov (United States)

    Scotese, Christopher R.; Nokleberg, Warren J.; Monger, James W.H.; Norton, Ian O.; Parfenov, Leonid M.; Khanchuk, Alexander I.; Bundtzen, Thomas K.; Dawson, Kenneth M.; Eremin, Roman A.; Frolov, Yuri F.; Fujita, Kazuya; Goryachev, Nikolai A.; Pozdeev, Anany I.; Ratkin, Vladimir V.; Rodinov, Sergey M.; Rozenblum, Ilya S.; Scholl, David W.; Shpikerman, Vladimir I.; Sidorov, Anatoly A.; Stone, David B.

    2001-01-01

    The digital files on this report consist of a dynamic computer model of the metallogenesis and tectonics of the Circum-North Pacific, and background articles, figures, and maps. The tectonic part of the dynamic computer model is derived from a major analysis of the tectonic evolution of the Circum-North Pacific which is also contained in directory tectevol. The dynamic computer model and associated materials on this CD-ROM are part of a project on the major mineral deposits, metallogenesis, and tectonics of the Russian Far East, Alaska, and the Canadian Cordillera. The project provides critical information on bedrock geology and geophysics, tectonics, major metalliferous mineral resources, metallogenic patterns, and crustal origin and evolution of mineralizing systems for this region. The major scientific goals and benefits of the project are to: (1) provide a comprehensive international data base on the mineral resources of the region that is the first, extensive knowledge available in English; (2) provide major new interpretations of the origin and crustal evolution of mineralizing systems and their host rocks, thereby enabling enhanced, broad-scale tectonic reconstructions and interpretations; and (3) promote trade and scientific and technical exchanges between North America and Eastern Asia.

  14. CFD (Computational Fluid Dynamics) simulators and thermal cracking of heavy oil and ultraheavy residues using microreactor

    Energy Technology Data Exchange (ETDEWEB)

    Jardini, Andre L.; Bineli, Aulus R.R.; Viadana, Adriana M.; Maciel, Maria Regina Wolf; Maciel Filho, Rubens [State University of Campinas (UNICAMP), SP (Brazil). School of Chemical Engineering; Medina, Lilian C.; Gomes, Alexandre de O. [PETROBRAS S.A., Rio de Janeiro, RJ (Brazil). Centro de Pesquisas (CENPES); Barros, Ricardo S. [University Foundation Jose Bonifacio (FUJB), Rio de Janeiro, RJ (Brazil)

    2008-07-01

    In this paper, the design of microreactor with microfluidics channels has been carried out in Computer Aided Design Software (CAD) and constructed in rapid prototyping system to be used in chemical reaction processing of the heavy oil fractions. The flow pattern properties of microreactor (fluid dynamics, mixing behavior) have been considered through CFD (computational fluid dynamics) simulations. CFD calculations are also used to study the design and specification of new microreactor developments. The potential advantages of using a microreactor include better control of reaction conditions, improved safety and portability. A more detailed crude assay of the raw national oil, whose importance was evidenced by PETROBRAS/CENPES allows establishing the optimum strategies and processing conditions, aiming at a maximum utilization of the heavy oil fractions, towards valuable products. These residues are able to be processed in microreactor, in which conventional process like as hydrotreating, catalytic and thermal cracking may be carried out in a much more intensified fashion. The whole process development involves a prior thermal study to define the possible operating conditions for a particular task, the microreactor design through computational fluid dynamics and construction using rapid prototyping. This gives high flexibility for process development, shorter time, and costumer/task oriented process/product development. (author)

  15. A Novel Iterative and Dynamic Trust Computing Model for Large Scaled P2P Networks

    Directory of Open Access Journals (Sweden)

    Zhenhua Tan

    2016-01-01

    Full Text Available Trust management has been emerging as an essential complementary part to security mechanisms of P2P systems, and trustworthiness is one of the most important concepts driving decision making and establishing reliable relationships. Collusion attack is a main challenge to distributed P2P trust model. Large scaled P2P systems have typical features, such as large scaled data with rapid speed, and this paper presented an iterative and dynamic trust computation model named IDTrust (Iterative and Dynamic Trust model according to these properties. First of all, a three-layered distributed trust communication architecture was presented in IDTrust so as to separate evidence collector and trust decision from P2P service. Then an iterative and dynamic trust computation method was presented to improve efficiency, where only latest evidences were enrolled during one iterative computation. On the basis of these, direct trust model, indirect trust model, and global trust model were presented with both explicit and implicit evidences. We consider multifactors in IDTrust model according to different malicious behaviors, such as similarity, successful transaction rate, and time decay factors. Simulations and analysis proved the rightness and efficiency of IDTrust against attacks with quick respond and sensitiveness during trust decision.

  16. Subcellular drug targeting, pharmacokinetics and bioavailability.

    Science.gov (United States)

    Leucuta, Sorin Emilian

    2014-02-01

    Effective treatment of diseases at the molecular level is possible by directing the drug substance (micromolecular, protein or peptide drugs, DNA, oligonucleotides, siRNA) with the aid of a specialized nanoparticulate carrier, for safe and effective transport to the specific site of action in the cytosol and its organelles including nuclear targeting. To achieve efficient cytosolic delivery of therapeutics or nuclear targeting, different drug delivery systems (DDS) have been developed (macromolecular drug conjugates, chemically or genetically modified proteins, and particulate drug carriers) capable of subcellular internalization overcoming the biological barriers, by passive targeting and especially by active targeting (receptor-targeted delivery). The success depends on the physicochemical nature of DDS, intracellular barriers that these systems need to overcome, the bioavailability of the bioactive drug, biodistribution, the intracellular pharmacokinetics and its influence on the pharmacodynamic effect. Models necessary for this purpose exist but they need to be more developed especially with quantitative treatments, after the development of the means of highlighting the evolution of the drug substance in biophase or at the level of the target cellular organelle by quantitative assays. It is expected that intracellularly targeted drug delivery approaches will be clinically useful using specialized DDSs belonging to the pharmaceutical nanotechnologies.

  17. cAMP signaling in subcellular compartments.

    Science.gov (United States)

    Lefkimmiatis, Konstantinos; Zaccolo, Manuela

    2014-09-01

    In the complex microcosm of a cell, information security and its faithful transmission are critical for maintaining internal stability. To achieve a coordinated response of all its parts to any stimulus the cell must protect the information received from potentially confounding signals. Physical segregation of the information transmission chain ensures that only the entities able to perform the encoded task have access to the relevant information. The cAMP intracellular signaling pathway is an important system for signal transmission responsible for the ancestral 'flight or fight' response and involved in the control of critical functions including frequency and strength of heart contraction, energy metabolism and gene transcription. It is becoming increasingly apparent that the cAMP signaling pathway uses compartmentalization as a strategy for coordinating the large number of key cellular functions under its control. Spatial confinement allows the formation of cAMP signaling "hot spots" at discrete subcellular domains in response to specific stimuli, bringing the information in proximity to the relevant effectors and their recipients, thus achieving specificity of action. In this report we discuss how the different constituents of the cAMP pathway are targeted and participate in the formation of cAMP compartmentalized signaling events. We illustrate a few examples of localized cAMP signaling, with a particular focus on the nucleus, the sarcoplasmic reticulum and the mitochondria. Finally, we discuss the therapeutic potential of interventions designed to perturb specific cAMP cascades locally. Copyright © 2014 Elsevier Inc. All rights reserved.

  18. Tau regulates the subcellular localization of calmodulin

    Energy Technology Data Exchange (ETDEWEB)

    Barreda, Elena Gomez de [Centro de Biologia Molecular ' Severo Ochoa' , CSIC/UAM, Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid (Spain); Avila, Jesus, E-mail: javila@cbm.uam.es [Centro de Biologia Molecular ' Severo Ochoa' , CSIC/UAM, Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid (Spain); CIBER de Enfermedades Neurodegenerativas, 28031 Madrid (Spain)

    2011-05-13

    Highlights: {yields} In this work we have tried to explain how a cytoplasmic protein could regulate a cell nuclear function. We have tested the role of a cytoplasmic protein (tau) in regulating the expression of calbindin gene. We found that calmodulin, a tau-binding protein with nuclear and cytoplasmic localization, increases its nuclear localization in the absence of tau. Since nuclear calmodulin regulates calbindin expression, a decrease in nuclear calmodulin, due to the presence of tau that retains it at the cytoplasm, results in a change in calbindin expression. -- Abstract: Lack of tau expression in neuronal cells results in a change in the expression of few genes. However, little is known about how tau regulates gene expression. Here we show that the presence of tau could alter the subcellular localization of calmodulin, a protein that could be located at the cytoplasm or in the nucleus. Nuclear calmodulin binds to co-transcription factors, regulating the expression of genes like calbindin. In this work, we have found that in neurons containing tau, a higher proportion of calmodulin is present in the cytoplasm compared with neurons lacking tau and that an increase in cytoplasmic calmodulin correlates with a higher expression of calbindin.

  19. Multimodal subcellular imaging with microcavity photoacoustic transducer.

    Science.gov (United States)

    Tan, Zhiliang; Tang, Zhilie; Wu, Yongbo; Liao, Yanfei; Dong, Wei; Guo, Lina

    2011-01-31

    Photoacoustic microscopy (PAM) is dominantly sensitive to the endogenous optical absorption compared with the confocal microscopy which images with scattering photons. PAM has similar structure such as optical transportation system, the optical scanning, and light source with the laser scanning confocal microscopy (LSCM). In order to match the PAM with LSCM, a special design microcavity photoacoustic (PA) transducer with high sensitivity is developed to detect the photoacoustic signals induced by modulated continuous wave (CW) laser. By employing a microcavity PA transducer, a PAM can be integrated with LSCM. Thus a simultaneous multimodal imaging can be obtained with the same laser source and optical system. The lateral resolutions of the PAM and the LSCM are both tested to be better than 1.25 μm. Then subcellular multimodal imaging can be achieved. Images from the two modes are corresponding with each other but functionally complementary. Combining PAM and LSCM provides more comprehensive information for the cytological test. This technique is demonstrated for imaging red-blood cells and meristematic cells.

  20. Flexible Launch Vehicle Stability Analysis Using Steady and Unsteady Computational Fluid Dynamics

    Science.gov (United States)

    Bartels, Robert E.

    2012-01-01

    Launch vehicles frequently experience a reduced stability margin through the transonic Mach number range. This reduced stability margin can be caused by the aerodynamic undamping one of the lower-frequency flexible or rigid body modes. Analysis of the behavior of a flexible vehicle is routinely performed with quasi-steady aerodynamic line loads derived from steady rigid aerodynamics. However, a quasi-steady aeroelastic stability analysis can be unconservative at the critical Mach numbers, where experiment or unsteady computational aeroelastic analysis show a reduced or even negative aerodynamic damping.Amethod of enhancing the quasi-steady aeroelastic stability analysis of a launch vehicle with unsteady aerodynamics is developed that uses unsteady computational fluid dynamics to compute the response of selected lower-frequency modes. The response is contained in a time history of the vehicle line loads. A proper orthogonal decomposition of the unsteady aerodynamic line-load response is used to reduce the scale of data volume and system identification is used to derive the aerodynamic stiffness, damping, and mass matrices. The results are compared with the damping and frequency computed from unsteady computational aeroelasticity and from a quasi-steady analysis. The results show that incorporating unsteady aerodynamics in this way brings the enhanced quasi-steady aeroelastic stability analysis into close agreement with the unsteady computational aeroelastic results.

  1. Dynamic Context-Aware and Limited Resources-Aware Service Adaptation for Pervasive Computing

    Directory of Open Access Journals (Sweden)

    Moeiz Miraoui

    2011-01-01

    Full Text Available A pervasive computing system (PCS requires that devices be context aware in order to provide proactively adapted services according to the current context. Because of the highly dynamic environment of a PCS, the service adaptation task must be performed during device operation. Most of the proposed approaches do not deal with the problem in depth, because they are either not really context aware or the problem itself is not thought to be dynamic. Devices in a PCS are generally hand-held, that is, they have limited resources, and so, in the effort to make them more reliable, the service adaptation must take into account this constraint. In this paper, we propose a dynamic service adaptation approach for a device operating in a PCS that is both context aware and limited resources aware. The approach is then modeled using colored Petri Nets and simulated using the CPN Tools, an important step toward its validation.

  2. Temporal and Spatio-Temporal Dynamic Instabilities: Novel Computational and Experimental approaches

    Science.gov (United States)

    Doedel, Eusebius J.; Panayotaros, Panayotis; Lambruschini, Carlos L. Pando

    2016-11-01

    This special issue contains a concise account of significant research results presented at the international workshop on Advanced Computational and Experimental Techniques in Nonlinear Dynamics, which was held in Cusco, Peru in August 2015. The meeting gathered leading experts, as well as new researchers, who have contributed to different aspects of Nonlinear Dynamics. Particularly significant was the presence of many active scientists from Latin America. The topics covered in this special issue range from advanced numerical techniques to novel physical experiments, and reflect the present state of the art in several areas of Nonlinear Dynamics. It contains seven review articles, followed by twenty-one regular papers that are organized in five categories, namely (1) Nonlinear Evolution Equations and Applications, (2) Numerical Continuation in Self-sustained Oscillators, (3) Synchronization, Control and Data Analysis, (4) Hamiltonian Systems, and (5) Scaling Properties in Maps.

  3. Cloud Computing as an Alternative IT Solution for SMEs: A System Dynamic Approach

    Directory of Open Access Journals (Sweden)

    Mochamad Arief Abdillah

    2014-12-01

    Full Text Available Small medium enterprises (SMEs play a big role for GDP in Indonesia. In 2012, SMEs made contribution 59,08 % for GDP Indonesia. The amount of SMEs in Indonesia is 99,99 % from total company in Indonesia. From that data, we know that SMEs is very big market in Indonesia. However, despite many big contributions that SMEs gave, SMEs also have challenges for themselves. The limitation of capital is one of challenges that SMEs have to face. The limit of capital make SMEs spend their capital wisely. They have to think very carefully how to expand their business. Is it profitable or not. In this paper we want to understand about the phenomenon why SMEs are hard to implement information and system technology. We used observation and secondary data to construct the variables. After that, we use the variables to build the model using system dynamics. And then we simulate it to know the impact implementation of information technology to flow business of SMEs. To propose new alternative technology (cloud computing, we modified the variables in the model and simulated it. We compared the result between own information technology and cloud computing. The result shows that cloud computing is suitable to be implemented in SMEs.Keywords : Cloud computing, SME, System Dynamic, Information Technology, Model

  4. Dynamic Load Balancing Strategy for Cloud Computing with Ant Colony Optimization

    Directory of Open Access Journals (Sweden)

    Ren Gao

    2015-11-01

    Full Text Available How to distribute and coordinate tasks in cloud computing is a challenging issue, in order to get optimal resource utilization and avoid overload. In this paper, we present a novel approach on load balancing via ant colony optimization (ACO, for balancing the workload in a cloud computing platform dynamically. Two strategies, forward-backward ant mechanism and max-min rules, are introduced to quickly find out the candidate nodes for load balancing. We formulate pheromone initialization and pheromone update according to physical resources under the cloud computing environment, including pheromone evaporation, incentive, and punishment rules, etc. Combined with task execution prediction, we define the moving probability of ants in two ways, that is, whether the forward ant meets the backward ant, or not, in the neighbor node, with the aim of accelerating searching processes. Simulations illustrate that the proposed strategy can not only provide dynamic load balancing for cloud computing with less searching time, but can also get high network performance under medium and heavily loaded contexts.

  5. Dynamics of seated computer work before and after prolonged constrained sitting.

    Science.gov (United States)

    Madeleine, Pascal

    2012-07-01

    This laboratory study investigated seated computer work before and after prolonged constrained sitting. Discomfort ratings and kinetic and kinematics data were recorded in nine healthy males performing computer work for 5 min before and after 96 min of sitting. The displacement of the center of pressure (CoP) in anterior-posterior and medial-lateral directions and lumbar curvature (LC) were calculated. The root mean square, standard deviation, and sample entropy values were computed from the CoPs and LC signals to assess the magnitude, amount of variability, and regularity of sitting dynamics, respectively. The discomfort increased for the buttocks (p = .02).The standard deviation and sample entropy values of the CoPs and LC signals, respectively, increased (p .15) after prolonged constrained sitting compared with before. This present study showed that during seated computer work, prolonged constrained sitting affected the amount of variability and the regularity of sitting postural control, whereas the magnitude was not affected. The importance of the dynamics of sitting control may challenge the idea of a static and ideal seated posture at work.

  6. SYSTEM DYNAMICS MODEL FOR EVALUATION OF REUSE OF ELECTRONIC WASTE ORIGINATED FROM PERSONAL COMPUTERS

    Directory of Open Access Journals (Sweden)

    Eugênio Simonetto

    2016-11-01

    Full Text Available Information and Communication Technologies (ICT are part of the day to day activities of a large part of world population, however its use involves a growing generation of electronic waste (ewaste. Due to the increasing technological innovation, it occurs that in a short time, the products become obsolete and have their life cycle reduced. The article aims to present the development, verification and validation of models of computational simulation for assessment of environmental and financial impacts caused by the extension of the life cycle of personal computers (PC through their remanufacturing. For the system modeling the System Dynamics theory was used. Results generated by the simulation model, show that the remanufacturing is a viable alternative for the reutilization of discarded computers and that it is possible, in advance, to discuss, assess and decide necessary measures for a better financial and environmental performance in the acquisition and use of ICT.

  7. Molecular dynamics-based virtual screening: accelerating the drug discovery process by high-performance computing.

    Science.gov (United States)

    Ge, Hu; Wang, Yu; Li, Chanjuan; Chen, Nanhao; Xie, Yufang; Xu, Mengyan; He, Yingyan; Gu, Xinchun; Wu, Ruibo; Gu, Qiong; Zeng, Liang; Xu, Jun

    2013-10-28

    High-performance computing (HPC) has become a state strategic technology in a number of countries. One hypothesis is that HPC can accelerate biopharmaceutical innovation. Our experimental data demonstrate that HPC can significantly accelerate biopharmaceutical innovation by employing molecular dynamics-based virtual screening (MDVS). Without using HPC, MDVS for a 10K compound library with tens of nanoseconds of MD simulations requires years of computer time. In contrast, a state of the art HPC can be 600 times faster than an eight-core PC server is in screening a typical drug target (which contains about 40K atoms). Also, careful design of the GPU/CPU architecture can reduce the HPC costs. However, the communication cost of parallel computing is a bottleneck that acts as the main limit of further virtual screening improvements for drug innovations.

  8. HECTAR: a method to predict subcellular targeting in heterokonts

    National Research Council Canada - National Science Library

    Gschloessl, Bernhard; Guermeur, Yann; Cock, J Mark

    2008-01-01

    .... To understand the biology of these organisms, it is necessary to be able to predict the subcellular localisation of their proteins but this is not straightforward, particularly in photosynthetic...

  9. Subcellular Localization of Class I Histone Deacetylases in the Developing Xenopus tectum.

    Science.gov (United States)

    Guo, Xia; Ruan, Hangze; Li, Xia; Qin, Liming; Tao, Yi; Qi, Xianjie; Gao, Juanmei; Gan, Lin; Duan, Shumin; Shen, Wanhua

    2015-01-01

    Histone deacetylases (HDACs) are thought to localize in the nucleus to regulate gene transcription and play pivotal roles in neurogenesis, apoptosis, and plasticity. However, the subcellular distribution of class I HDACs in the developing brain remains unclear. Here, we show that HDAC1 and HDAC2 are located in both the mitochondria and the nucleus in the Xenopus laevis stage 34 tectum and are mainly restricted to the nucleus following further brain development. HDAC3 is widely present in the mitochondria, nucleus, and cytoplasm during early tectal development and is mainly distributed in the nucleus in stage 45 tectum. In contrast, HDAC8 is broadly located in the mitochondria, nucleus, and cytoplasm during tectal development. These data demonstrate that HDAC1, HDAC2, and HDAC3 are transiently localized in the mitochondria and that the subcellular distribution of class I HDACs in the Xenopus tectum is heterogeneous. Furthermore, we observed that spherical mitochondria accumulate in the cytoplasm at earlier stages, whereas elongated mitochondria are evenly distributed in the tectum at later stages. The activity of histone acetylation (H4K12) remains low in mitochondria during tectal development. Pharmacological blockades of HDACs using a broad spectrum HDAC inhibitor of Trichostatin A (TSA) or specific class I HDAC inhibitors of MS-275 and MGCD0103 decrease the number of mitochondria in the tectum at stage 34. These findings highlight a link between the subcellular distribution of class I HDACs and mitochondrial dynamics in the developing optic tectum of Xenopus laevis.

  10. Subcellular localization of class I histone deacetylases in the developing Xenopus tectum

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    Xia eGuo

    2016-01-01

    Full Text Available Histone deacetylases (HDACs are thought to localize in the nucleus to regulate gene transcription and play pivotal roles in neurogenesis, apoptosis and plasticity. However, the subcellular distribution of class I HDACs in the developing brain remains unclear. Here, we show that HDAC1 and HDAC2 are located in both the mitochondria and the nucleus in the Xenopus laevis stage 34 tectum and are mainly restricted to the nucleus following further brain development. HDAC3 is widely present in the mitochondria, nucleus and cytoplasm during early tectal development and is mainly distributed in the nucleus in stage 45 tectum. In contrast, HDAC8 is broadly located in the mitochondria, nucleus and cytoplasm during tectal development. These data demonstrate that HDAC1, HDAC2 and HDAC3 are transiently localized in the mitochondria and that the subcellular distribution of class I HDACs in the Xenopus tectum is heterogeneous. Furthermore, we observed that spherical mitochondria accumulate in the cytoplasm at earlier stages, whereas elongated mitochondria are evenly distributed in the tectum at later stages. The activity of histone acetylation (H4K12 remains low in mitochondria during tectal development. Pharmacological blockades of HDACs using a broad spectrum HDAC inhibitor of Trichostatin A (TSA or specific class I HDAC inhibitors of MS-275 and MGCD0103 decrease the number of mitochondria in the tectum at stage 34. These findings highlight a link between the subcellular distribution of class I HDACs and mitochondrial dynamics in the developing optic tectum of Xenopus laevis.

  11. Subcellular distribution of non-muscle myosin IIb is controlled by FILIP through Hsc70.

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    Hideshi Yagi

    Full Text Available The neuronal spine is a small, actin-rich dendritic or somatic protrusion that serves as the postsynaptic compartment of the excitatory synapse. The morphology of the spine reflects the activity of the synapse and is regulated by the dynamics of the actin cytoskeleton inside, which is controlled by actin binding proteins such as non-muscle myosin. Previously, we demonstrated that the subcellular localization and function of myosin IIb are regulated by its binding partner, filamin-A interacting protein (FILIP. However, how the subcellular distribution of myosin IIb is controlled by FILIP is not yet known. The objective of this study was to identify potential binding partners of FILIP that contribute to its regulation of non-muscle myosin IIb. Pull-down assays detected a 70-kDa protein that was identified by mass spectrometry to be the chaperone protein Hsc70. The binding of Hsc70 to FILIP was controlled by the adenosine triphosphatase (ATPase activity of Hsc70. Further, FILIP bound to Hsc70 via a domain that was not required for binding non-muscle myosin IIb. Inhibition of ATPase activity of Hsc70 impaired the effect of FILIP on the subcellular distribution of non-muscle myosin IIb. Further, in primary cultured neurons, an inhibitor of Hsc70 impeded the morphological change in spines induced by FILIP. Collectively, these results demonstrate that Hsc70 interacts with FILIP to mediate its effects on non-muscle myosin IIb and to regulate spine morphology.

  12. Chaotic dynamics in nanoscale NbO2 Mott memristors for analogue computing

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    Kumar, Suhas; Strachan, John Paul; Williams, R. Stanley

    2017-08-01

    At present, machine learning systems use simplified neuron models that lack the rich nonlinear phenomena observed in biological systems, which display spatio-temporal cooperative dynamics. There is evidence that neurons operate in a regime called the edge of chaos that may be central to complexity, learning efficiency, adaptability and analogue (non-Boolean) computation in brains. Neural networks have exhibited enhanced computational complexity when operated at the edge of chaos, and networks of chaotic elements have been proposed for solving combinatorial or global optimization problems. Thus, a source of controllable chaotic behaviour that can be incorporated into a neural-inspired circuit may be an essential component of future computational systems. Such chaotic elements have been simulated using elaborate transistor circuits that simulate known equations of chaos, but an experimental realization of chaotic dynamics from a single scalable electronic device has been lacking. Here we describe niobium dioxide (NbO2) Mott memristors each less than 100 nanometres across that exhibit both a nonlinear-transport-driven current-controlled negative differential resistance and a Mott-transition-driven temperature-controlled negative differential resistance. Mott materials have a temperature-dependent metal-insulator transition that acts as an electronic switch, which introduces a history-dependent resistance into the device. We incorporate these memristors into a relaxation oscillator and observe a tunable range of periodic and chaotic self-oscillations. We show that the nonlinear current transport coupled with thermal fluctuations at the nanoscale generates chaotic oscillations. Such memristors could be useful in certain types of neural-inspired computation by introducing a pseudo-random signal that prevents global synchronization and could also assist in finding a global minimum during a constrained search. We specifically demonstrate that incorporating such

  13. KCC2-dependent subcellular ECl difference of ON-OFF retinal ganglion cells in larval zebrafish

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    Rongwei eZhang

    2013-05-01

    Full Text Available Subcellular difference in the reversal potential of Cl- (ECl has been found in many types of neurons. As local ECl largely determines the action of nearby GABAergic/glycinergic synapses, subcellular ECl difference can effectively regulate neuronal computation. The ON-OFF retinal ganglion cell (RGC processes both ON and OFF visual signals via its ON and OFF dendrites, respectively. It is thus interesting to investigate whether the ON and OFF dendrites of single RGCs exhibit different local ECl. Here, using in vivo gramicidin-perforated patch recording in larval zebrafish ON-OFF RGCs, we examine local ECl at the ON and OFF dendrites, and soma through measuring light-evoked ON and OFF inhibitory responses, and GABA-induced response at the soma, respectively. We find there are subcellular ECl differences between the soma and dendrite, as well as between the ON and OFF dendrites of single RGCs. These somato-dendritic and inter-dendritic ECl differences are dependent on the Cl- extruder, K+/Cl- co-transporter (KCC2, because they are largely diminished by down-regulating kcc2 expression with morpholino oligonucleotides or by blocking KCC2 function with furosemide. Thus, our findings indicate that there exists KCC2-dependent ECl difference between the ON and OFF dendrites of individual ON-OFF RGCs that may differentially affect visual processing in the ON and OFF pathways.

  14. A multiple information fusion method for predicting subcellular locations of two different types of bacterial protein simultaneously.

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    Chen, Jing; Xu, Huimin; He, Ping-An; Dai, Qi; Yao, Yuhua

    2016-01-01

    Subcellular localization prediction of bacterial protein is an important component of bioinformatics, which has great importance for drug design and other applications. For the prediction of protein subcellular localization, as we all know, lots of computational tools have been developed in the recent decades. In this study, we firstly introduce three kinds of protein sequences encoding schemes: physicochemical-based, evolutionary-based, and GO-based. The original and consensus sequences were combined with physicochemical properties. And elements information of different rows and columns in position-specific scoring matrix were taken into consideration simultaneously for more core and essence information. Computational methods based on gene ontology (GO) have been demonstrated to be superior to methods based on other features. Then principal component analysis (PCA) is applied for feature selection and reduced vectors are input to a support vector machine (SVM) to predict protein subcellular localization. The proposed method can achieve a prediction accuracy of 98.28% and 97.87% on a stringent Gram-positive (Gpos) and Gram-negative (Gneg) dataset with Jackknife test, respectively. At last, we calculate "absolute true overall accuracy (ATOA)", which is stricter than overall accuracy. The ATOA obtained from the proposed method is also up to 97.32% and 93.06% for Gpos and Gneg. From both the rationality of testing procedure and the success rates of test results, the current method can improve the prediction quality of protein subcellular localization. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  15. Subcellular targeting strategies for drug design and delivery.

    Science.gov (United States)

    Rajendran, Lawrence; Knölker, Hans-Joachim; Simons, Kai

    2010-01-01

    Many drug targets are localized to particular subcellular compartments, yet current drug design strategies are focused on bioavailability and tissue targeting and rarely address drug delivery to specific intracellular compartments. Insights into how the cell traffics its constituents to these different cellular locations could improve drug design. In this Review, we explore the fundamentals of membrane trafficking and subcellular organization, as well as strategies used by pathogens to appropriate these mechanisms and the implications for drug design and delivery.

  16. Subcellular analysis by laser ablation electrospray ionization mass spectrometry

    Science.gov (United States)

    Vertes, Akos; Stolee, Jessica A; Shrestha, Bindesh

    2014-12-02

    In various embodiments, a method of laser ablation electrospray ionization mass spectrometry (LAESI-MS) may generally comprise micro-dissecting a cell comprising at least one of a cell wall and a cell membrane to expose at least one subcellular component therein, ablating the at least one subcellular component by an infrared laser pulse to form an ablation plume, intercepting the ablation plume by an electrospray plume to form ions, and detecting the ions by mass spectrometry.

  17. Alternative splicing and differential subcellular localization of the rat FGF antisense gene product

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    Casson Alan G

    2008-01-01

    Full Text Available Abstract Background GFG/NUDT is a nudix hydrolase originally identified as the product of the fibroblast growth factor-2 antisense (FGF-AS gene. While the FGF-AS RNA has been implicated as an antisense regulator of FGF-2 expression, the expression and function of the encoded GFG protein is largely unknown. Alternative splicing of the primary FGF-AS mRNA transcript predicts multiple GFG isoforms in many species including rat. In the present study we focused on elucidating the expression and subcellular distribution of alternatively spliced rat GFG isoforms. Results RT-PCR and immunohistochemistry revealed tissue-specific GFG mRNA isoform expression and subcellular distribution of GFG immunoreactivity in cytoplasm and nuclei of a wide range of normal rat tissues. FGF-2 and GFG immunoreactivity were co-localized in some, but not all, tissues examined. Computational analysis identified a mitochondrial targeting sequence (MTS in the N-terminus of three previously described rGFG isoforms. Confocal laser scanning microscopy and subcellular fractionation analysis revealed that all rGFG isoforms bearing the MTS were specifically targeted to mitochondria whereas isoforms and deletion mutants lacking the MTS were localized in the cytoplasm and nucleus. Mutation and deletion analysis confirmed that the predicted MTS was necessary and sufficient for mitochondrial compartmentalization. Conclusion Previous findings strongly support a role for the FGF antisense RNA as a regulator of FGF2 expression. The present study demonstrates that the antisense RNA itself is translated, and that protein isoforms resulting form alternative RNA splicing are sorted to different subcellular compartments. FGF-2 and its antisense protein are co-expressed in many tissues and in some cases in the same cells. The strong conservation of sequence and genomic organization across animal species suggests important functional significance to the physical association of these transcript

  18. ngLOC: software and web server for predicting protein subcellular localization in prokaryotes and eukaryotes

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    King Brian R

    2012-07-01

    Full Text Available Abstract Background Understanding protein subcellular localization is a necessary component toward understanding the overall function of a protein. Numerous computational methods have been published over the past decade, with varying degrees of success. Despite the large number of published methods in this area, only a small fraction of them are available for researchers to use in their own studies. Of those that are available, many are limited by predicting only a small number of organelles in the cell. Additionally, the majority of methods predict only a single location for a sequence, even though it is known that a large fraction of the proteins in eukaryotic species shuttle between locations to carry out their function. Findings We present a software package and a web server for predicting the subcellular localization of protein sequences based on the ngLOC method. ngLOC is an n-gram-based Bayesian classifier that predicts subcellular localization of proteins both in prokaryotes and eukaryotes. The overall prediction accuracy varies from 89.8% to 91.4% across species. This program can predict 11 distinct locations each in plant and animal species. ngLOC also predicts 4 and 5 distinct locations on gram-positive and gram-negative bacterial datasets, respectively. Conclusions ngLOC is a generic method that can be trained by data from a variety of species or classes for predicting protein subcellular localization. The standalone software is freely available for academic use under GNU GPL, and the ngLOC web server is also accessible at http://ngloc.unmc.edu.

  19. A sub-cellular viscoelastic model for cell population mechanics.

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    Yousef Jamali

    Full Text Available Understanding the biomechanical properties and the effect of biomechanical force on epithelial cells is key to understanding how epithelial cells form uniquely shaped structures in two or three-dimensional space. Nevertheless, with the limitations and challenges posed by biological experiments at this scale, it becomes advantageous to use mathematical and 'in silico' (computational models as an alternate solution. This paper introduces a single-cell-based model representing the cross section of a typical tissue. Each cell in this model is an individual unit containing several sub-cellular elements, such as the elastic plasma membrane, enclosed viscoelastic elements that play the role of cytoskeleton, and the viscoelastic elements of the cell nucleus. The cell membrane is divided into segments where each segment (or point incorporates the cell's interaction and communication with other cells and its environment. The model is capable of simulating how cells cooperate and contribute to the overall structure and function of a particular tissue; it mimics many aspects of cellular behavior such as cell growth, division, apoptosis and polarization. The model allows for investigation of the biomechanical properties of cells, cell-cell interactions, effect of environment on cellular clusters, and how individual cells work together and contribute to the structure and function of a particular tissue. To evaluate the current approach in modeling different topologies of growing tissues in distinct biochemical conditions of the surrounding media, we model several key cellular phenomena, namely monolayer cell culture, effects of adhesion intensity, growth of epithelial cell through interaction with extra-cellular matrix (ECM, effects of a gap in the ECM, tensegrity and tissue morphogenesis and formation of hollow epithelial acini. The proposed computational model enables one to isolate the effects of biomechanical properties of individual cells and the

  20. Synthetic tetracycline-inducible regulatory networks: computer-aided design of dynamic phenotypes

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    Kaznessis Yiannis N

    2007-01-01

    Full Text Available Abstract Background Tightly regulated gene networks, precisely controlling the expression of protein molecules, have received considerable interest by the biomedical community due to their promising applications. Among the most well studied inducible transcription systems are the tetracycline regulatory expression systems based on the tetracycline resistance operon of Escherichia coli, Tet-Off (tTA and Tet-On (rtTA. Despite their initial success and improved designs, limitations still persist, such as low inducer sensitivity. Instead of looking at these networks statically, and simply changing or mutating the promoter and operator regions with trial and error, a systematic investigation of the dynamic behavior of the network can result in rational design of regulatory gene expression systems. Sophisticated algorithms can accurately capture the dynamical behavior of gene networks. With computer aided design, we aim to improve the synthesis of regulatory networks and propose new designs that enable tighter control of expression. Results In this paper we engineer novel networks by recombining existing genes or part of genes. We synthesize four novel regulatory networks based on the Tet-Off and Tet-On systems. We model all the known individual biomolecular interactions involved in transcription, translation, regulation and induction. With multiple time-scale stochastic-discrete and stochastic-continuous models we accurately capture the transient and steady state dynamics of these networks. Important biomolecular interactions are identified and the strength of the interactions engineered to satisfy design criteria. A set of clear design rules is developed and appropriate mutants of regulatory proteins and operator sites are proposed. Conclusion The complexity of biomolecular interactions is accurately captured through computer simulations. Computer simulations allow us to look into the molecular level, portray the dynamic behavior of gene regulatory

  1. Distributed Algorithm for Computing the Vehicle Launch Dynamics under Interaction with the Medium

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    G. A. Shcheglov

    2015-01-01

    Full Text Available The paper describes a distributed algorithm and a structure of the software package for its implementation in which a program for computing the vehicle launch dynamics under interaction with the medium flow is complemented with a program to determine the unsteady hydrodynamic loads by the vortex element method.A distinctive feature of the developed system is that its local (running on a single computing core LEAVING program to calculate the launch dynamics runs together with concurrent (running on multiple computing cores MDVDD program to compute the unsteady vortex flow and hydrodynamic loads. The LEAVING program is the main one. It is launched app and then runs the MDVDD program in concurrent mode on the specified number of cores. Using MPI technology allows you to use a multiprocessor PC or a local network of multiple PCs to perform calculations. The equations of launcher spring-mass model dynamics and equations of vortex elements parameters evolution are integrated with the same time step. The interprogram communiaction in the step is provided asynchronously using the OS Windows Event mechanism (Events. Interfacing between LEAVING and MDVDD programs is built using the OS Windows FileMapping technology, which allows a specified data structure to be displayed and read to the fixed memory area.The paper provides analysis of acceleration achieved with parallel processing on different numbers of cores, and defines a parallelization degree of various operations. It shows that the parallelization efficiency of the developed algorithm is slower than in case of calculation of the rigid body flow. The causes of reduced efficiency are discussed.It is shown that the developed algorithm can be effectively used to solve problems on a small number of cores, e.g. on PC based on one or two quad-core processors.

  2. Studies on variable swirl intake system for DI diesel engine using computational fluid dynamics

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    Jebamani Rathnaraj David

    2008-01-01

    Full Text Available It is known that a helical port is more effective than a tangential port to attain the required swirl ratio with minimum sacrifice in the volumetric efficiency. The swirl port is designed for lesser swirl ratio to reduce emissions at higher speeds. But this condition increases the air fuel mixing time and particulate smoke emissions at lower speeds. Optimum swirl ratio is necessary according to the engine operating condition for optimum combustion and emission reduction. Hence the engine needs variable swirl to enhance the combustion in the cylinder according to its operating conditions, for example at partial load or low speed condition it requires stronger swirl, while the air quantity is more important than the swirl under very high speed or full load and maximum torque conditions. The swirl and charging quantity can easily trade off and can be controlled by the opening of the valve. Hence in this study the steady flow rig experiment is used to evaluate the swirl of a helical intake port design for different operating conditions. The variable swirl plate set up of the W06DTIE2 engine is used to experimentally study the swirl variation for different openings of the valve. The sliding of the swirl plate results in the variation of the area of inlet port entry. Therefore in this study a swirl optimized combustion system varying according to the operating conditions by a variable swirl plate mechanism is studied experimentally and compared with the computational fluid dynamics predictions. In this study the fluent computational fluid dynamics code has been used to evaluate the flow in the port-cylinder system of a DI diesel engine in a steady flow rig. The computational grid is generated directly from 3-D CAD data and in cylinder flow simulations, with inflow boundary conditions from experimental measurements, are made using the fluent computational fluid dynamics code. The results are in very good agreement with experimental results.

  3. Analysis of subcellular metabolite distributions within Arabidopsis thaliana leaf tissue: a primer for subcellular metabolomics.

    Science.gov (United States)

    Krueger, Stephan; Steinhauser, Dirk; Lisec, Jan; Giavalisco, Patrick

    2014-01-01

    Every biological organism relies for its proper function on interactions between a multitude of molecular entities like RNA, proteins, and metabolites. The comprehensive measurement and the analysis of all these entities would therefore provide the basis for our functional and mechanistic understanding of most biological processes. Next to their amount and identity, it is most crucial to also gain information about the subcellular distribution and the flux of the measured compounds between the cellular compartments. That is, we want to understand not only the individual functions of cellular components but also their functional implications within the whole organism. While the analysis of macromolecules like DNA, RNA, and proteins is quite established and robust, analytical techniques for small metabolites, which are prone to diffusion and degradation processes, provide a host of unsolved challenges. The major limitations here are the metabolite conversion and relocation processes. In this protocol we describe a methodological workflow which includes a nonaqueous fractionation method, a fractionated two-phase liquid/liquid extraction protocol, and a software package, which together allow extracting and analyzing starch, proteins, and especially polar and lipophilic metabolites from a single sample towards the estimation of their subcellular distributions.

  4. Coupled contagion dynamics of fear and disease: mathematical and computational explorations.

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    Joshua M Epstein

    Full Text Available BACKGROUND: In classical mathematical epidemiology, individuals do not adapt their contact behavior during epidemics. They do not endogenously engage, for example, in social distancing based on fear. Yet, adaptive behavior is well-documented in true epidemics. We explore the effect of including such behavior in models of epidemic dynamics. METHODOLOGY/PRINCIPAL FINDINGS: Using both nonlinear dynamical systems and agent-based computation, we model two interacting contagion processes: one of disease and one of fear of the disease. Individuals can "contract" fear through contact with individuals who are infected with the disease (the sick, infected with fear only (the scared, and infected with both fear and disease (the sick and scared. Scared individuals--whether sick or not--may remove themselves from circulation with some probability, which affects the contact dynamic, and thus the disease epidemic proper. If we allow individuals to recover from fear and return to circulation, the coupled dynamics become quite rich, and can include multiple waves of infection. We also study flight as a behavioral response. CONCLUSIONS/SIGNIFICANCE: In a spatially extended setting, even relatively small levels of fear-inspired flight can have a dramatic impact on spatio-temporal epidemic dynamics. Self-isolation and spatial flight are only two of many possible actions that fear-infected individuals may take. Our main point is that behavioral adaptation of some sort must be considered.

  5. Open Quantum Dynamics Calculations with the Hierarchy Equations of Motion on Parallel Computers.

    Science.gov (United States)

    Strümpfer, Johan; Schulten, Klaus

    2012-08-14

    Calculating the evolution of an open quantum system, i.e., a system in contact with a thermal environment, has presented a theoretical and computational challenge for many years. With the advent of supercomputers containing large amounts of memory and many processors, the computational challenge posed by the previously intractable theoretical models can now be addressed. The hierarchy equations of motion present one such model and offer a powerful method that remained under-utilized so far due to its considerable computational expense. By exploiting concurrent processing on parallel computers the hierarchy equations of motion can be applied to biological-scale systems. Herein we introduce the quantum dynamics software PHI, that solves the hierarchical equations of motion. We describe the integrator employed by PHI and demonstrate PHI's scaling and efficiency running on large parallel computers by applying the software to the calculation of inter-complex excitation transfer between the light harvesting complexes 1 and 2 of purple photosynthetic bacteria, a 50 pigment system.

  6. Automation of multi-agent control for complex dynamic systems in heterogeneous computational network

    Science.gov (United States)

    Oparin, Gennady; Feoktistov, Alexander; Bogdanova, Vera; Sidorov, Ivan

    2017-01-01

    The rapid progress of high-performance computing entails new challenges related to solving large scientific problems for various subject domains in a heterogeneous distributed computing environment (e.g., a network, Grid system, or Cloud infrastructure). The specialists in the field of parallel and distributed computing give the special attention to a scalability of applications for problem solving. An effective management of the scalable application in the heterogeneous distributed computing environment is still a non-trivial issue. Control systems that operate in networks, especially relate to this issue. We propose a new approach to the multi-agent management for the scalable applications in the heterogeneous computational network. The fundamentals of our approach are the integrated use of conceptual programming, simulation modeling, network monitoring, multi-agent management, and service-oriented programming. We developed a special framework for an automation of the problem solving. Advantages of the proposed approach are demonstrated on the parametric synthesis example of the static linear regulator for complex dynamic systems. Benefits of the scalable application for solving this problem include automation of the multi-agent control for the systems in a parallel mode with various degrees of its detailed elaboration.

  7. Gigaflop performance on a CRAY-2: Multitasking a computational fluid dynamics application

    Science.gov (United States)

    Tennille, Geoffrey M.; Overman, Andrea L.; Lambiotte, Jules J.; Streett, Craig L.

    1991-01-01

    The methodology is described for converting a large, long-running applications code that executed on a single processor of a CRAY-2 supercomputer to a version that executed efficiently on multiple processors. Although the conversion of every application is different, a discussion of the types of modification used to achieve gigaflop performance is included to assist others in the parallelization of applications for CRAY computers, especially those that were developed for other computers. An existing application, from the discipline of computational fluid dynamics, that had utilized over 2000 hrs of CPU time on CRAY-2 during the previous year was chosen as a test case to study the effectiveness of multitasking on a CRAY-2. The nature of dominant calculations within the application indicated that a sustained computational rate of 1 billion floating-point operations per second, or 1 gigaflop, might be achieved. The code was first analyzed and modified for optimal performance on a single processor in a batch environment. After optimal performance on a single CPU was achieved, the code was modified to use multiple processors in a dedicated environment. The results of these two efforts were merged into a single code that had a sustained computational rate of over 1 gigaflop on a CRAY-2. Timings and analysis of performance are given for both single- and multiple-processor runs.

  8. Ideal Particle Sizes for Inhaled Steroids Targeting Vocal Granulomas: Preliminary Study Using Computational Fluid Dynamics.

    Science.gov (United States)

    Perkins, Elizabeth L; Basu, Saikat; Garcia, Guilherme J M; Buckmire, Robert A; Shah, Rupali N; Kimbell, Julia S

    2017-11-01

    Objectives Vocal fold granulomas are benign lesions of the larynx commonly caused by gastroesophageal reflux, intubation, and phonotrauma. Current medical therapy includes inhaled corticosteroids to target inflammation that leads to granuloma formation. Particle sizes of commonly prescribed inhalers range over 1 to 4 µm. The study objective was to use computational fluid dynamics to investigate deposition patterns over a range of particle sizes of inhaled corticosteroids targeting the larynx and vocal fold granulomas. Study Design Retrospective, case-specific computational study. Setting Tertiary academic center. Subjects/Methods A 3-dimensional anatomically realistic computational model of a normal adult airway from mouth to trachea was constructed from 3 computed tomography scans. Virtual granulomas of varying sizes and positions along the vocal fold were incorporated into the base model. Assuming steady-state, inspiratory, turbulent airflow at 30 L/min, computational fluid dynamics was used to simulate respiratory transport and deposition of inhaled corticosteroid particles ranging over 1 to 20 µm. Results Laryngeal deposition in the base model peaked for particle sizes 8 to 10 µm (2.8%-3.5%). Ideal sizes ranged over 6 to 10, 7 to 13, and 7 to 14 µm for small, medium, and large granuloma sizes, respectively. Glottic deposition was maximal at 10.8% for 9-µm-sized particles for the large posterior granuloma, 3 times the normal model (3.5%). Conclusion As the virtual granuloma size increased and the location became more posterior, glottic deposition and ideal particle size generally increased. This preliminary study suggests that inhalers with larger particle sizes, such as fluticasone propionate dry-powder inhaler, may improve laryngeal drug deposition. Most commercially available inhalers have smaller particles than suggested here.

  9. Computational fluid dynamics simulation and geometric design of hydraulic turbine draft tube

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    JB Sosa

    2015-10-01

    Full Text Available Any hydraulic reaction turbine is installed with a draft tube that impacts widely the entire turbine performance, on which its functions are as follows: drive the flux in appropriate manner after it releases its energy to the runner; recover the suction head by a suction effect; and improve the dynamic energy in the runner outlet. All these functions are strongly linked to the geometric definition of the draft tube. This article proposes a geometric parametrization and analysis of a Francis turbine draft tube. Based on the parametric definition, geometric changes in the draft tube are proposed and the turbine performance is modeled by computational fluid dynamics; the boundary conditions are set by measurements performed in a hydroelectric power plant. This modeling allows us to see the influence of the draft tube shape on the entire turbine performance. The numerical analysis is based on the steady-state solution of the turbine component flows for different guide vanes opening and multiple modified draft tubes. The computational fluid dynamics predictions are validated using hydroelectric plant measurements. The prediction of the turbine performance is successful and it is linked to the draft tube geometric features; therefore, it is possible to obtain a draft tube parameter value that results in a desired turbine performance.

  10. Computer Algebra Study of Structural and Symmetry Properties of Discrete Dynamical Systems

    Science.gov (United States)

    Kornyak, V. V.

    2010-06-01

    To study structural and symmetry properties of discrete dynamical systems of different types -- deterministic, mesoscopic statistical and quantum -- we develope various approaches based essentially on the computer algebra and computational group theory methods. We introduce the concept of a system of discrete relations on an abstract simplicial complex and develope algorithms for analysis of compatibility and construction of canonical decompositions of such systems. We describe application of these techniques to some cellular automata. Much attention is paid to study symmetries of the systems. In the case of deterministic systems we reveale some important relations between symmetries and dynamics. In particular, we demonstrate that moving soliton-like structures -- like "spaceships" in cellular automata, "traveling waves" in mathematical physics and "generalized coherent states" in quantum physics -- arise inevitably in deterministic dynamical system whose symmetry group splits the set of states into finite number of group orbits. We propose an approach to quantization of discrete systems based on introduction of gauge connection with values in unitary representations of some finite quantizing groups -- the elements of the connection are interpreted as amplitudes of quantum transitions. To study properties of the suggested quantization we introduce a class of simple models -- local quantum models on regular graphs.

  11. Petascale molecular dynamics simulation using the fast multipole method on K computer

    KAUST Repository

    Ohno, Yousuke

    2014-10-01

    In this paper, we report all-atom simulations of molecular crowding - a result from the full node simulation on the "K computer", which is a 10-PFLOPS supercomputer in Japan. The capability of this machine enables us to perform simulation of crowded cellular environments, which are more realistic compared to conventional MD simulations where proteins are simulated in isolation. Living cells are "crowded" because macromolecules comprise ∼30% of their molecular weight. Recently, the effects of crowded cellular environments on protein stability have been revealed through in-cell NMR spectroscopy. To measure the performance of the "K computer", we performed all-atom classical molecular dynamics simulations of two systems: target proteins in a solvent, and target proteins in an environment of molecular crowders that mimic the conditions of a living cell. Using the full system, we achieved 4.4 PFLOPS during a 520 million-atom simulation with cutoff of 28 Å. Furthermore, we discuss the performance and scaling of fast multipole methods for molecular dynamics simulations on the "K computer", as well as comparisons with Ewald summation methods. © 2014 Elsevier B.V. All rights reserved.

  12. Cortico-striatal language pathways dynamically adjust for syntactic complexity: A computational study.

    Science.gov (United States)

    Szalisznyó, Krisztina; Silverstein, David; Teichmann, Marc; Duffau, Hugues; Smits, Anja

    2017-01-01

    A growing body of literature supports a key role of fronto-striatal circuits in language perception. It is now known that the striatum plays a role in engaging attentional resources and linguistic rule computation while also serving phonological short-term memory capabilities. The ventral semantic and the dorsal phonological stream dichotomy assumed for spoken language processing also seems to play a role in cortico-striatal perception. Based on recent studies that correlate deep Broca-striatal pathways with complex syntax performance, we used a previously developed computational model of frontal-striatal syntax circuits and hypothesized that different parallel language pathways may contribute to canonical and non-canonical sentence comprehension separately. We modified and further analyzed a thematic role assignment task and corresponding reservoir computing model of language circuits, as previously developed by Dominey and coworkers. We examined the models performance under various parameter regimes, by influencing how fast the presented language input decays and altering the temporal dynamics of activated word representations. This enabled us to quantify canonical and non-canonical sentence comprehension abilities. The modeling results suggest that separate cortico-cortical and cortico-striatal circuits may be recruited differently for processing syntactically more difficult and less complicated sentences. Alternatively, a single circuit would need to dynamically and adaptively adjust to syntactic complexity. Copyright © 2016. Published by Elsevier Inc.

  13. ADDRESSING HUMAN EXPOSURE TO AIR POLLUTANTS AROUND BUILDINGS IN URBAN AREAS WITH COMPUTATIONAL FLUID DYNAMICS (CFD) MODELS

    Science.gov (United States)

    Computational Fluid Dynamics (CFD) simulations provide a number of unique opportunities for expanding and improving capabilities for modeling exposures to environmental pollutants. The US Environmental Protection Agency's National Exposure Research Laboratory (NERL) has been c...

  14. Combined application of computational fluid dynamics (CFD) and design of experiments (DOE) to hydrodynamic simulation of a coal classifier

    National Research Council Canada - National Science Library

    Hamid Khoshdast; Vahideh Shojaei; Hami Khoshdast

    2017-01-01

    Combining the computational fluid dynamics (CFD) and the design of experiments (DOE) methods, as a mixed approach in modeling was proposed so that to simultaneously benefit from the advantages of both modeling methods...

  15. Belavkin-Kolkoltsov watch-dog effects in interactively controlled stochastic computer-graphic dynamic systems a mathematical study

    CERN Document Server

    Juriev, D V

    1995-01-01

    Stochastic properties of the long-time behaviour of a continuously observed (and interactively controlled) quantum-field top are investigated mathematically. Applications to interactively controlled stochastic computer-graphic dynamic systems are discussed.

  16. Impact of Side Branches on the Computation of Fractional Flow in Intracranial Arterial Stenosis Using the Computational Fluid Dynamics Method.

    Science.gov (United States)

    Liu, Haipeng; Lan, Linfang; Leng, Xinyi; Ip, Hing Lung; Leung, Thomas W H; Wang, Defeng; Wong, Ka Sing

    2018-01-01

    Computational fluid dynamics (CFD) allows noninvasive fractional flow (FF) computation in intracranial arterial stenosis. Removal of small artery branches is necessary in CFD simulation. The consequent effects on FF value needs to be judged. An idealized vascular model was built with 70% focal luminal stenosis. A branch with one third or one half of the radius of the parent vessel was added at a distance of 5, 10, 15 and 20 mm to the lesion. With pressure and flow rate applied as inlet and outlet boundary conditions, CFD simulations were performed. Flow distribution at bifurcations followed Murray's law. By including or removing side branches, five patient-specific intracranial artery models were simulated. Transient simulation was performed on a patient-specific model, with a larger branch for validation. Branching effect was considered trivial if the FF difference between paired models (branches included or removed) was within 5%. Compared with the control model without a branch, in all idealized models the relative differences of FF was within 2%. In five pairs of cerebral arteries (branches included/removed), FFs were 0.876 and 0.877, 0.853 and 0.858, 0.874 and 0.869, 0.865 and 0.858, 0.952 and 0.948. The relative difference in each pair was less than 1%. In transient model, the relative difference of FF was 3.5%. The impact of removing side branches with radius less than 50% of the parent vessel on FF measurement accuracy is negligible in static CFD simulations, and minor in transient CFD simulation. Copyright © 2018. Published by Elsevier Inc.

  17. Irrigation dynamics associated with positive pressure, apical negative pressure and passive ultrasonic irrigations: a computational fluid dynamics analysis.

    Science.gov (United States)

    Chen, José Enrique; Nurbakhsh, Babak; Layton, Gillian; Bussmann, Markus; Kishen, Anil

    2014-08-01

    Complexities in root canal anatomy and surface adherent biofilm structures remain as challenges in endodontic disinfection. The ability of an irrigant to penetrate into the apical region of a canal, along with its interaction with the root canal walls, will aid in endodontic disinfection. The aim of this study was to qualitatively examine the irrigation dynamics of syringe irrigation with different needle tip designs (open-ended and closed-ended), apical negative pressure irrigation with the EndoVac® system, and passive ultrasonic-assisted irrigation, using a computational fluid dynamics model. Syringe-based irrigation with a side-vented needle showed a higher wall shear stress than the open-ended but was localised to a small region of the canal wall. The apical negative pressure mode of irrigation generated the lowest wall shear stress, while the passive-ultrasonic irrigation group showed the highest wall shear stress along with the greatest magnitude of velocity. © 2013 The Authors. Australian Endodontic Journal © 2013 Australian Society of Endodontology.

  18. The dynamics of discrete-time computation, with application to recurrent neural networks and finite state machine extraction.

    Science.gov (United States)

    Casey, M

    1996-08-15

    Recurrent neural networks (RNNs) can learn to perform finite state computations. It is shown that an RNN performing a finite state computation must organize its state space to mimic the states in the minimal deterministic finite state machine that can perform that computation, and a precise description of the attractor structure of such systems is given. This knowledge effectively predicts activation space dynamics, which allows one to understand RNN computation dynamics in spite of complexity in activation dynamics. This theory provides a theoretical framework for understanding finite state machine (FSM) extraction techniques and can be used to improve training methods for RNNs performing FSM computations. This provides an example of a successful approach to understanding a general class of complex systems that has not been explicitly designed, e.g., systems that have evolved or learned their internal structure.

  19. Computational fluid dynamics and particle image velocimetry assisted design tools for a new generation of trochoidal gear pumps

    OpenAIRE

    García Vilchez, Mercedes; Gámez Montero, Pedro Javier; Codina Macià, Esteban; Castilla López, Roberto; Raush Alviach, Gustavo Adolfo; Freire Venegas, Francisco Javier; Río Cano, Carlos

    2015-01-01

    Trochoidal gear pumps produce significant flow pulsations that result in pressure pulsations, which interact with the system where they are connected, shortening the life of both the pump and circuit components. The complicated aspects of the operation of a gerotor pump make computational fluid dynamics the proper tool for modelling and simulating its flow characteristics. A three-dimensional model with deforming mesh computational fluid dynamics is presented, including the effects of the man...

  20. A computational fluid dynamics simulation framework for ventricular catheter design optimization.

    Science.gov (United States)

    Weisenberg, Sofy H; TerMaath, Stephanie C; Barbier, Charlotte N; Hill, Judith C; Killeffer, James A

    2017-11-10

    OBJECTIVE Cerebrospinal fluid (CSF) shunts are the primary treatment for patients suffering from hydrocephalus. While proven effective in symptom relief, these shunt systems are plagued by high failure rates and often require repeated revision surgeries to replace malfunctioning components. One of the leading causes of CSF shunt failure is obstruction of the ventricular catheter by aggregations of cells, proteins, blood clots, or fronds of choroid plexus that occlude the catheter's small inlet holes or even the full internal catheter lumen. Such obstructions can disrupt CSF diversion out of the ventricular system or impede it entirely. Previous studies have suggested that altering the catheter's fluid dynamics may help to reduce the likelihood of complete ventricular catheter failure caused by obstruction. However, systematic correlation between a ventricular catheter's design parameters and its performance, specifically its likelihood to become occluded, still remains unknown. Therefore, an automated, open-source computational fluid dynamics (CFD) simulation framework was developed for use in the medical community to determine optimized ventricular catheter designs and to rapidly explore parameter influence for a given flow objective. METHODS The computational framework was developed by coupling a 3D CFD solver and an iterative optimization algorithm and was implemented in a high-performance computing environment. The capabilities of the framework were demonstrated by computing an optimized ventricular catheter design that provides uniform flow rates through the catheter's inlet holes, a common design objective in the literature. The baseline computational model was validated using 3D nuclear imaging to provide flow velocities at the inlet holes and through the catheter. RESULTS The optimized catheter design achieved through use of the automated simulation framework improved significantly on previous attempts to reach a uniform inlet flow rate distribution using

  1. A meta-model for computer executable dynamic clinical safety checklists.

    Science.gov (United States)

    Nan, Shan; Van Gorp, Pieter; Lu, Xudong; Kaymak, Uzay; Korsten, Hendrikus; Vdovjak, Richard; Duan, Huilong

    2017-12-12

    Safety checklist is a type of cognitive tool enforcing short term memory of medical workers with the purpose of reducing medical errors caused by overlook and ignorance. To facilitate the daily use of safety checklists, computerized systems embedded in the clinical workflow and adapted to patient-context are increasingly developed. However, the current hard-coded approach of implementing checklists in these systems increase the cognitive efforts of clinical experts and coding efforts for informaticists. This is due to the lack of a formal representation format that is both understandable by clinical experts and executable by computer programs. We developed a dynamic checklist meta-model with a three-step approach. Dynamic checklist modeling requirements were extracted by performing a domain analysis. Then, existing modeling approaches and tools were investigated with the purpose of reusing these languages. Finally, the meta-model was developed by eliciting domain concepts and their hierarchies. The feasibility of using the meta-model was validated by two case studies. The meta-model was mapped to specific modeling languages according to the requirements of hospitals. Using the proposed meta-model, a comprehensive coronary artery bypass graft peri-operative checklist set and a percutaneous coronary intervention peri-operative checklist set have been developed in a Dutch hospital and a Chinese hospital, respectively. The result shows that it is feasible to use the meta-model to facilitate the modeling and execution of dynamic checklists. We proposed a novel meta-model for the dynamic checklist with the purpose of facilitating creating dynamic checklists. The meta-model is a framework of reusing existing modeling languages and tools to model dynamic checklists. The feasibility of using the meta-model is validated by implementing a use case in the system.

  2. Computer modelling of the cerebrospinal fluid flow dynamics of aqueduct stenosis.

    Science.gov (United States)

    Jacobson, E E; Fletcher, D F; Morgan, M K; Johnston, I H

    1999-01-01

    As the craniospinal space is a pressure loaded system it is difficult to conceptualize and understand the flow dynamics through the ventricular system. Aqueduct stenosis compromises flow, increasing the pressure required to move cerebrospinal fluid (CSF) through the ventricles. Under normal circumstances, less than one pascal (1 Pa) of pressure is required to move a physiological flow of CSF through the aqueduct. This is too small to measure using clinical pressure transducers. A computational fluid dynamics (CFD) program, CFX, has been used to model two forms of aqueduct stenosis: simple narrowing and forking of the aqueduct. This study shows that with mild stenoses, the increase in pressure required to drive flow becomes significant (86-125 Pa), which may result in an increased transmantle pressure difference but not necessarily an increased intraventricular pressure. Severe stenoses will result in both. Wall shear stresses increase concomitantly and may contribute to local damage of the aqueduct wall and further gliosis with narrowing.

  3. A Computation Fluid Dynamic Model for Gas Lift Process Simulation in a Vertical Oil Well

    Directory of Open Access Journals (Sweden)

    Kadivar Arash

    2017-03-01

    Full Text Available Continuous gas-lift in a typical oil well was simulated using computational fluid dynamic (CFD technique. A multi fluid model based on the momentum transfer between liquid and gas bubbles was employed to simulate two-phase flow in a vertical pipe. The accuracy of the model was investigated through comparison of numerical predictions with experimental data. The model then was used to study the dynamic behaviour of the two-phase flow around injection point in details. The predictions by the model were compared with other empirical correlations, as well. To obtain an optimum condition of gas-lift, the influence of the effective parameters including the quantity of injected gas, tubing diameter and bubble size distribution were investigated. The results revealed that increasing tubing diameter, the injected gas rate and decreasing bubble diameter improve gas-lift performance.

  4. Finite element solution techniques for large-scale problems in computational fluid dynamics

    Science.gov (United States)

    Liou, J.; Tezduyar, T. E.

    1987-01-01

    Element-by-element approximate factorization, implicit-explicit and adaptive implicit-explicit approximation procedures are presented for the finite-element formulations of large-scale fluid dynamics problems. The element-by-element approximation scheme totally eliminates the need for formation, storage and inversion of large global matrices. Implicit-explicit schemes, which are approximations to implicit schemes, substantially reduce the computational burden associated with large global matrices. In the adaptive implicit-explicit scheme, the implicit elements are selected dynamically based on element level stability and accuracy considerations. This scheme provides implicit refinement where it is needed. The methods are applied to various problems governed by the convection-diffusion and incompressible Navier-Stokes equations. In all cases studied, the results obtained are indistinguishable from those obtained by the implicit formulations.

  5. The Modeling and Complexity of Dynamical Systems by Means of Computation and Information Theories

    Directory of Open Access Journals (Sweden)

    Robert Logozar

    2011-12-01

    Full Text Available We present the modeling of dynamical systems and finding of their complexity indicators by the use of concepts from computation and information theories, within the framework of J. P. Crutchfield's theory of  ε-machines. A short formal outline of the  ε-machines is given. In this approach, dynamical systems are analyzed directly from the time series that is received from a properly adjusted measuring instrument. The binary strings are parsed through the parse tree, within which morphologically and probabilistically unique subtrees or morphs are recognized as system states. The outline and precise interrelation of the information-theoretic entropies and complexities emanating from the model is given. The paper serves also as a theoretical foundation for the future presentation of the DSA program that implements the  ε-machines modeling up to the stochastic finite automata level.

  6. Computational fluid dynamics analysis for a combustion chamber in an industrial gas turbine

    Energy Technology Data Exchange (ETDEWEB)

    Anzai, Thiago Koichi; Fontes, Carlo Eduardo; Ropelato, Karolline [Engineering Simulation and Scientic Software (ESSS), Florianopolis, SC (Brazil)], E-mails: anzai@esss.com.br, carlos.fontes@esss.com.br, ropelato@esss.com.br; Silva, Luis Fernando Figueira da; Alva Huapaya, Luis Enrique [Pontificia Universidade Catolica do Rio de Janeiro (PUC-Rio), RJ (Brazil). Dept. de Engenharia Mecanica], E-mails: luisfer@esp.puc-rio.br, luisalva@esp.puc-rio.br

    2011-04-15

    The accurate prediction of pollutant emissions from a gas turbine combustion chamber is a major concern when the equipment is subjected to long operational periods beyond its design point. Under such conditions, the flow field itself might also show big differences from the design point, leading, for instance, to undesirable hot spots or instabilities in the combustion process. A study of all possible operational conditions is economically unfeasible. Also a Direct Numerical Simulation of industrial combustors is beyond the capacity of the foreseeable computational resources, therefore models must be used to analyze such issues. This study presents the results for an industrial gas turbine combustion chamber using Computational Fluid Dynamics. The model used contained an ad-hoc parameter for which a new formulation is proposed. The influence of this new formulation is examined both in terms of the flow field structure and the combustion stabilization mechanism. (author)

  7. Facilitation and Coherence Between the Dynamic and Retrospective Perception of Segmentation in Computer-Generated Music

    Directory of Open Access Journals (Sweden)

    Freya Bailes

    2007-08-01

    Full Text Available We examined the impact of listening context (sound duration and prior presentation on the human perception of segmentation in sequences of computer music. This research extends previous work by the authors (Bailes & Dean, 2005, which concluded that context-dependent effects such as the asymmetrical detection of an increase in timbre compared to a decrease of the same magnitude have a significant bearing on the cognition of sound structure. The current study replicated this effect, and demonstrated that listeners (N = 14 are coherent in their detection of segmentation between real-time and retrospective tasks. In addition, response lag was reduced from a first hearing to a second hearing, and following long (7 s rather than short (1 or 3 s segments. These findings point to the role of short-term memory in dynamic structural perception of computer music.

  8. A computational fluid dynamic modelling approach to assess the representativeness of urban monitoring stations.

    Science.gov (United States)

    Santiago, Jose Luis; Martín, Fernando; Martilli, Alberto

    2013-06-01

    Air quality measurements of urban monitoring stations have a limited spatial representativeness due to the complexity of urban meteorology and emissions distribution. In this work, a methodology based on a set of computational fluid dynamics simulations based on Reynolds-Averaged Navier-Stokes equations (RANS-CFD) for different meteorological conditions covering several months is developed in order to analyse the spatial representativeness of urban monitoring stations and to complement their measured concentrations. The methodology has been applied to two urban areas nearby air quality traffic-oriented stations in Pamplona and Madrid (Spain) to analyse nitrogen oxides concentrations. The computed maps of pollutant concentrations around each station show strong spatial variability being very difficult to comply with the European legislation concerning the spatial representativeness of traffic-oriented air quality stations. Copyright © 2013 Elsevier B.V. All rights reserved.

  9. A Computational Fluid Dynamic Model for a Novel Flash Ironmaking Process

    Science.gov (United States)

    Perez-Fontes, Silvia E.; Sohn, Hong Yong; Olivas-Martinez, Miguel

    A computational fluid dynamic model for a novel flash ironmaking process based on the direct gaseous reduction of iron oxide concentrates is presented. The model solves the three-dimensional governing equations including both gas-phase and gas-solid reaction kinetics. The turbulence-chemistry interaction in the gas-phase is modeled by the eddy dissipation concept incorporating chemical kinetics. The particle cloud model is used to track the particle phase in a Lagrangian framework. A nucleation and growth kinetics rate expression is adopted to calculate the reduction rate of magnetite concentrate particles. Benchmark experiments reported in the literature for a nonreacting swirling gas jet and a nonpremixed hydrogen jet flame were simulated for validation. The model predictions showed good agreement with measurements in terms of gas velocity, gas temperature and species concentrations. The relevance of the computational model for the analysis of a bench reactor operation and the design of an industrial-pilot plant is discussed.

  10. Finite-element-model updating using computational intelligence techniques applications to structural dynamics

    CERN Document Server

    Marwala, Tshilidzi

    2010-01-01

    Finite element models (FEMs) are widely used to understand the dynamic behaviour of various systems. FEM updating allows FEMs to be tuned better to reflect measured data and may be conducted using two different statistical frameworks: the maximum likelihood approach and Bayesian approaches. Finite Element Model Updating Using Computational Intelligence Techniques applies both strategies to the field of structural mechanics, an area vital for aerospace, civil and mechanical engineering. Vibration data is used for the updating process. Following an introduction a number of computational intelligence techniques to facilitate the updating process are proposed; they include: • multi-layer perceptron neural networks for real-time FEM updating; • particle swarm and genetic-algorithm-based optimization methods to accommodate the demands of global versus local optimization models; • simulated annealing to put the methodologies into a sound statistical basis; and • response surface methods and expectation m...

  11. Dynamic stepping information process method in mobile bio-sensing computing environments.

    Science.gov (United States)

    Lee, Tae-Gyu; Lee, Seong-Hoon

    2014-01-01

    Recently, the interest toward human longevity free from diseases is being converged as one system frame along with the development of mobile computing environment, diversification of remote medical system and aging society. Such converged system enables implementation of a bioinformatics system created as various supplementary information services by sensing and gathering health conditions and various bio-information of mobile users to set up medical information. The existing bio-information system performs static and identical process without changes after the bio-information process defined at the initial system configuration executes the system. However, such static process indicates ineffective execution in the application of mobile bio-information system performing mobile computing. Especially, an inconvenient duty of having to perform initialization of new definition and execution is accompanied during the process configuration of bio-information system and change of method. This study proposes a dynamic process design and execution method to overcome such ineffective process.

  12. Overview of ICE Project: Integration of Computational Fluid Dynamics and Experiments

    Science.gov (United States)

    Stegeman, James D.; Blech, Richard A.; Babrauckas, Theresa L.; Jones, William H.

    2001-01-01

    Researchers at the NASA Glenn Research Center have developed a prototype integrated environment for interactively exploring, analyzing, and validating information from computational fluid dynamics (CFD) computations and experiments. The Integrated CFD and Experiments (ICE) project is a first attempt at providing a researcher with a common user interface for control, manipulation, analysis, and data storage for both experiments and simulation. ICE can be used as a live, on-tine system that displays and archives data as they are gathered; as a postprocessing system for dataset manipulation and analysis; and as a control interface or "steering mechanism" for simulation codes while visualizing the results. Although the full capabilities of ICE have not been completely demonstrated, this report documents the current system. Various applications of ICE are discussed: a low-speed compressor, a supersonic inlet, real-time data visualization, and a parallel-processing simulation code interface. A detailed data model for the compressor application is included in the appendix.

  13. Computational fluid dynamics analysis of the Canadian deuterium uranium moderator tests at the Stern Laboratories Inc.

    Directory of Open Access Journals (Sweden)

    Hyoung Tae Kim

    2015-04-01

    Full Text Available A numerical calculation with the commercial computational fluid dynamics code CFX-14.0 was conducted for a test facility simulating the Canadian deuterium uranium moderator thermal–hydraulics. Two kinds of moderator thermal–hydraulic tests at Stern Laboratories Inc. were performed in the full geometric configuration of the Canadian deuterium uranium moderator circulating vessel, which is called a calandria tank, housing a matrix of horizontal rod bundles simulating calandria tubes. The first of these tests is the pressure drop measurement of a cross flow in the horizontal rod bundles. The other is the local temperature measurement on the cross section of the horizontal cylinder vessel simulating the calandria system. In the present study, the full geometric details of the calandria tank are incorporated in the grid generation of the computational domain to which the boundary conditions for each experiment are applied. The numerical solutions are reviewed and compared with the available test data.

  14. The comparisons of computational models of pavement due to the dynamic load act

    Directory of Open Access Journals (Sweden)

    Valašková Veronika

    2017-01-01

    Full Text Available Finite element method (FEM is frequently used to solve current problems of the structural mechanics in engineering practice. The dynamic interaction of the two systems is one of the topics that can be solved using FEM. To simplify the solution of the interaction, it is possible to divide the system in two independent subsystems, vehicle and pavement. Computing software ADINA, based on the principles of the finite element modelling, was adopted to solve the given problem. The results from the first computational model can be used as the inputs for the second model. To analyse stress state of the pavement with different composition, three specific types of pavements were selected – concrete pavement, semi-rigid pavement and flexible pavement. The pavements represent the typical pavement types used for the regular road structures. This article is focused on the analysis of the stress state and the displacements of the pavement induced by the moving load from the traffic.

  15. Computational fluid dynamics applied to flows in an internal combustion engine

    Science.gov (United States)

    Griffin, M. D.; Diwakar, R.; Anderson, J. D., Jr.; Jones, E.

    1978-01-01

    The reported investigation is a continuation of studies conducted by Diwakar et al. (1976) and Griffin et al. (1976), who reported the first computational fluid dynamic results for the two-dimensional flowfield for all four strokes of a reciprocating internal combustion (IC) engine cycle. An analysis of rectangular and cylindrical three-dimensional engine models is performed. The working fluid is assumed to be inviscid air of constant specific heats. Calculations are carried out of a four-stroke IC engine flowfield wherein detailed finite-rate chemical combustion of a gasoline-air mixture is included. The calculations remain basically inviscid, except that in some instances thermal conduction is included to allow a more realistic model of the localized sparking of the mixture. All the results of the investigation are obtained by means of an explicity time-dependent finite-difference technique, using a high-speed digital computer.

  16. A discrete force allocation algorithm for modelling wind turbines in computational fluid dynamics

    DEFF Research Database (Denmark)

    Réthoré, Pierre-Elouan; Sørensen, Niels N.

    2012-01-01

    , this algorithm does not address the specific cases where discrete forces are present. The velocities and pressure exhibit some significant numerical fluctuations at the position where the body forces are applied. While this issue is limited in space, it is usually critical to accurately estimate the velocity...... the possibility of coarsening the mesh where the forces are applied and have a considerable effect in reducing the computational cost of modelling wind turbines, wind farms and forests. This approach gives excellent results with three test cases where an analytical solution is known. This correction is also......This paper describes an algorithm for allocating discrete forces in computational fluid dynamics (CFD). Discrete forces are useful in wind energy CFD. They are used as an approximation of the wind turbine blades’ action on the wind (actuator disc/line), to model forests and to model turbulent...

  17. Adrenal glands in hypovolemic shock: preservation of contrast enhancement at dynamic computed tomography.

    Science.gov (United States)

    Ito, Katsuyoshi; Higashi, Hiroki; Kanki, Akihiko; Tamada, Tsutomu; Yamashita, Takenori; Yamamoto, Akira; Watanabe, Shigeru

    2010-07-01

    To evaluate contrast enhancement effects of the adrenal glands at dynamic computed tomography (CT) in adult severe trauma patients with hypovolemic shock in comparison with patients without hypovolemic shock. This study population included a total of 74 patients with (n = 24) and without (n = 50) blunt trauma and hypovolemic shock. Measurement of CT attenuation values of the adrenal gland and calculation of the enhancement washout percentages were performed. The mean +/- SD CT attenuation values of the adrenal glands in the arterial phase of dynamic CT in patients with hypovolemic shock (137.3 +/- 41.7 Hounsfield unit [HU]) were not significantly different (P = 0.16) from those in control subjects (127.3 +/- 19.6 HU). The mean CT attenuation values of the adrenal glands in the delayed phase of dynamic CT in patients with hypovolemic shock (82.0 +/- 14.7 HU) were also not significantly different (P = 0.89) from those in control subjects (82.4 +/- 10.0 HU). The mean percentage (35%) of enhancement washout of the adrenal glands in patients with hypovolemic shock was not significantly different (P = 0.81) from that (34%) in control subjects. Contrast enhancement effects of the adrenal glands at contrast-enhanced dynamic CT in patients with hypovolemic shock were similar to those in control subjects, indicating the preserved enhancement and perfusion of the adrenal gland rather than intense and persistent enhancement in patients with hypovolemic shock.

  18. Evaluation of static and dynamic perfusion cardiac computed tomography for quantitation and classification tasks

    Science.gov (United States)

    Bindschadler, Michael; Modgil, Dimple; Branch, Kelley R.; La Riviere, Patrick J.; Alessio, Adam M.

    2016-01-01

    Abstract. Cardiac computed tomography (CT) acquisitions for perfusion assessment can be performed in a dynamic or static mode. Either method may be used for a variety of clinical tasks, including (1) stratifying patients into categories of ischemia and (2) using a quantitative myocardial blood flow (MBF) estimate to evaluate disease severity. In this simulation study, we compare method performance on these classification and quantification tasks for matched radiation dose levels and for different flow states, patient sizes, and injected contrast levels. Under conditions simulated, the dynamic method has low bias in MBF estimates (0 to 0.1  ml/min/g) compared to linearly interpreted static assessment (0.45 to 0.48  ml/min/g), making it more suitable for quantitative estimation. At matched radiation dose levels, receiver operating characteristic analysis demonstrated that the static method, with its high bias but generally lower variance, had superior performance (pstatic assessment with a correctly tuned exponential relationship between the apparent CT number and MBF has superior quantification performance to static assessment with a linear relationship and to dynamic assessment. However, tuning the exponential relationship to the patient and scan characteristics will likely prove challenging. This study demonstrates that the selection and optimization of static or dynamic acquisition modes should depend on the specific clinical task. PMID:27175377

  19. Dynamic X-ray computed tomography; Tomographie dynamique a rayons X

    Energy Technology Data Exchange (ETDEWEB)

    Grangeat, P

    2003-07-01

    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)

  20. Computer vision profiling of neurite outgrowth dynamics reveals spatiotemporal modularity of Rho GTPase signaling.

    Science.gov (United States)

    Fusco, Ludovico; Lefort, Riwal; Smith, Kevin; Benmansour, Fethallah; Gonzalez, German; Barillari, Caterina; Rinn, Bernd; Fleuret, Francois; Fua, Pascal; Pertz, Olivier

    2016-01-04

    Rho guanosine triphosphatases (GTPases) control the cytoskeletal dynamics that power neurite outgrowth. This process consists of dynamic neurite initiation, elongation, retraction, and branching cycles that are likely to be regulated by specific spatiotemporal signaling networks, which cannot be resolved with static, steady-state assays. We present NeuriteTracker, a computer-vision approach to automatically segment and track neuronal morphodynamics in time-lapse datasets. Feature extraction then quantifies dynamic neurite outgrowth phenotypes. We identify a set of stereotypic neurite outgrowth morphodynamic behaviors in a cultured neuronal cell system. Systematic RNA interference perturbation of a Rho GTPase interactome consisting of 219 proteins reveals a limited set of morphodynamic phenotypes. As proof of concept, we show that loss of function of two distinct RhoA-specific GTPase-activating proteins (GAPs) leads to opposite neurite outgrowth phenotypes. Imaging of RhoA activation dynamics indicates that both GAPs regulate different spatiotemporal Rho GTPase pools, with distinct functions. Our results provide a starting point to dissect spatiotemporal Rho GTPase signaling networks that regulate neurite outgrowth. © 2016 Fusco et al.

  1. Use of computational fluid dynamics simulations for design of a pretreatment screw conveyor reactor.

    Science.gov (United States)

    Berson, R Eric; Hanley, Thomas R

    2005-01-01

    Computational fluid dynamics simulations were employed to compare performance of various designs of a pretreatment screw conveyor reactor. The reactor consisted of a vertical screw used to create cross flow between the upward conveying solids and the downward flow of acid. Simulations were performed with the original screw design and a modified design in which the upper flights of the screw were removed. Results of the simulations show visually that the modified design provided favorable plug flow behavior within the reactor. Pressure drop across the length of the reactor without the upper screws in place was predicted by the simulations to be 5 vs 40 kPa for the original design.

  2. Computational fluid dynamics in ventilation. 4: Commercial application of CFD in ventilation

    Science.gov (United States)

    Nielsen, Peter V.

    In considering the commercial applications of Computational Fluid Dynamics (CFD) in ventilation, the following are addressed: typical markets (airport centers, large theaters, atria, shopping malls, etc.); typical problems to be solved (energy flow, draft, ventilation effectiveness, pressure distribution, etc.); and high priority areas, activities and quantities (fast preprocessing, effective visualization software, etc.). It is stated that the commercial application of CFD may be looked upon as an advanced 'zonal' model. The 'zonal' model concept is outlined and CFD with large control volumes is considered. An illustrated example of air flow simulation in a theater is given.

  3. Investigation of acceleration effects on missile aerodynamics using computational fluid dynamics

    CSIR Research Space (South Africa)

    Gledhill, Irvy MA

    2009-01-01

    Full Text Available aeroelastic models, moving control surfaces, helicopter blades and store release. However, in order to be able to predict the behaviour of accelerating and manoeuvring flying bodies correctly, one must be able to treat arbitrarily moving reference frames... and Applied Mechanics, Cape Town (2006) pp. 268-275. [10] L.L. Green, A.M. Spence, P.C. Murphy, Computational methods for dynamic stability and control derivatives, AIAA 2004-0015 (2004). [11] H.P. Greenspan, The Theory of Rotating Fluids, Cambridge...

  4. Optimization of a new flow design for solid oxide cells using computational fluid dynamics modelling

    DEFF Research Database (Denmark)

    Duhn, Jakob Dragsbæk; Jensen, Anker Degn; Wedel, Stig

    2016-01-01

    Design of a gas distributor to distribute gas flow into parallel channels for Solid Oxide Cells (SOC) is optimized, with respect to flow distribution, using Computational Fluid Dynamics (CFD) modelling. The CFD model is based on a 3d geometric model and the optimized structural parameters include...... conversion is found to be directly proportional to the flow uniformity. Finally the effect of manufacturing errors is investigated. The design is shown to be robust towards deviations from design dimensions of at least ±0.1 mm which is well within obtainable tolerances....

  5. Computing and Visualizing Dynamic Time Warping Alignments in R: The dtw Package

    Directory of Open Access Journals (Sweden)

    Toni Giorgino

    2009-08-01

    Full Text Available Dynamic time warping is a popular technique for comparing time series, providing both a distance measure that is insensitive to local compression and stretches and the warping which optimally deforms one of the two input series onto the other. A variety of algorithms and constraints have been discussed in the literature. The dtw package provides an unification of them; it allows R users to compute time series alignments mixing freely a variety of continuity constraints, restriction windows, endpoints, local distance definitions, and so on. The package also provides functions for visualizing alignments and constraints using several classic diagram types.

  6. Computationally Efficient Modelling of Dynamic Soil-Structure Interaction of Offshore Wind Turbines on Gravity Footings

    DEFF Research Database (Denmark)

    Damgaard, Mads; Andersen, Lars Vabbersgaard; Ibsen, Lars Bo

    2014-01-01

    The formulation and quality of a computationally efficient model of offshore wind turbine surface foundations is examined. The aim is to establish a model, workable in the frequency and time domain, that can be applied in aeroelastic codes for fast and reliable evaluation of the dynamic structural...... to wave propagating in the subsoil–even for soil stratifications with low cut-in frequencies. In this regard, utilising discrete second-order models for the physical interpretation of a rational filter puts special demands on the Newmark β-scheme, where the time integration in most cases only provides...

  7. Computational fluid dynamics simulations of flow and concentration polarization in forward osmosis membrane systems

    DEFF Research Database (Denmark)

    Gruber, M.F.; Johnson, C.J.; Tang, C.Y.

    2011-01-01

    Forward osmosis is an osmotically driven membrane separation process that relies on the utilization of a large osmotic pressure differential generated across a semi-permeable membrane. In recent years forward osmosis has shown great promise in the areas of wastewater treatment, seawater...... the understanding of membrane systems, models that can accurately encapsulate all significant physical processes occurring in the systems are required. The present study demonstrates a computational fluid dynamics (CFD) model capable of simulating forward osmosis systems with asymmetric membranes. The model...

  8. Final Project Report: Data Locality Enhancement of Dynamic Simulations for Exascale Computing

    Energy Technology Data Exchange (ETDEWEB)

    Shen, Xipeng [North Carolina State Univ., Raleigh, NC (United States)

    2016-04-27

    The goal of this project is to develop a set of techniques and software tools to enhance the matching between memory accesses in dynamic simulations and the prominent features of modern and future manycore systems, alleviating the memory performance issues for exascale computing. In the first three years, the PI and his group have achieves some significant progress towards the goal, producing a set of novel techniques for improving the memory performance and data locality in manycore systems, yielding 18 conference and workshop papers and 4 journal papers and graduating 6 Ph.Ds. This report summarizes the research results of this project through that period.

  9. COMPUTATIONAL FLUID DYNAMICS MODELING OF SCALED HANFORD DOUBLE SHELL TANK MIXING - CFD MODELING SENSITIVITY STUDY RESULTS

    Energy Technology Data Exchange (ETDEWEB)

    JACKSON VL

    2011-08-31

    The primary purpose of the tank mixing and sampling demonstration program is to mitigate the technical risks associated with the ability of the Hanford tank farm delivery and celtification systems to measure and deliver a uniformly mixed high-level waste (HLW) feed to the Waste Treatment and Immobilization Plant (WTP) Uniform feed to the WTP is a requirement of 24590-WTP-ICD-MG-01-019, ICD-19 - Interface Control Document for Waste Feed, although the exact definition of uniform is evolving in this context. Computational Fluid Dynamics (CFD) modeling has been used to assist in evaluating scaleup issues, study operational parameters, and predict mixing performance at full-scale.

  10. INTRODUCING CAFein, A NEW COMPUTATIONAL TOOL FOR STELLAR PULSATIONS AND DYNAMIC TIDES

    Energy Technology Data Exchange (ETDEWEB)

    Valsecchi, F.; Farr, W. M.; Willems, B.; Rasio, F. A.; Kalogera, V., E-mail: francesca@u.northwestern.edu [Department of Physics and Astronomy and Center for Interdisciplinary Exploration and Research in Astrophysics (CIERA), Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 (United States)

    2013-08-10

    Here we present CAFein, a new computational tool for investigating radiative dissipation of dynamic tides in close binaries and of non-adiabatic, non-radial stellar oscillations in isolated stars in the linear regime. For the latter, CAFein computes the non-adiabatic eigenfrequencies and eigenfunctions of detailed stellar models. The code is based on the so-called Riccati method, a numerical algorithm that has been successfully applied to a variety of stellar pulsators, and which does not suffer from the major drawbacks of commonly used shooting and relaxation schemes. Here we present an extension of the Riccati method to investigate dynamic tides in close binaries. We demonstrate CAFein's capabilities as a stellar pulsation code both in the adiabatic and non-adiabatic regimes, by reproducing previously published eigenfrequencies of a polytrope, and by successfully identifying the unstable modes of a stellar model in the {beta} Cephei/SPB region of the Hertzsprung-Russell diagram. Finally, we verify CAFein's behavior in the dynamic tides regime by investigating the effects of dynamic tides on the eigenfunctions and orbital and spin evolution of massive main sequence stars in eccentric binaries, and of hot Jupiter host stars. The plethora of asteroseismic data provided by NASA's Kepler satellite, some of which include the direct detection of tidally excited stellar oscillations, make CAFein quite timely. Furthermore, the increasing number of observed short-period detached double white dwarfs (WDs) and the observed orbital decay in the tightest of such binaries open up a new possibility of investigating WD interiors through the effects of tides on their orbital evolution.

  11. Transient computation fluid dynamics modeling of a single proton exchange membrane fuel cell with serpentine channel

    Science.gov (United States)

    Hu, Guilin; Fan, Jianren

    The proton exchange membrane fuel cell (PEMFC) has become a promising candidate for the power source of electrical vehicles because of its low pollution, low noise and especially fast startup and transient responses at low temperatures. A transient, three-dimensional, non-isothermal and single-phase mathematical model based on computation fluid dynamics has been developed to describe the transient process and the dynamic characteristics of a PEMFC with a serpentine fluid channel. The effects of water phase change and heat transfer, as well as electrochemical kinetics and multicomponent transport on the cell performance are taken into account simultaneously in this comprehensive model. The developed model was employed to simulate a single laboratory-scale PEMFC with an electrode area about 20 cm 2. The dynamic behavior of the characteristic parameters such as reactant concentration, pressure loss, temperature on the membrane surface of cathode side and current density during start-up process were computed and are discussed in detail. Furthermore, transient responses of the fuel cell characteristics during step changes and sinusoidal changes in the stoichiometric flow ratio of the cathode inlet stream, cathode inlet stream humidity and cell voltage are also studied and analyzed and interesting undershoot/overshoot behavior of some variables was found. It was also found that the startup and transient response time of a PEM fuel cell is of the order of a second, which is similar to the simulation results predicted by most models. The result is an important guide for the optimization of PEMFC designs and dynamic operation.

  12. Investigating methods of supporting dynamically linked executables on high performance computing platforms.

    Energy Technology Data Exchange (ETDEWEB)

    Kelly, Suzanne Marie; Laros, James H., III; Pedretti, Kevin Thomas Tauke; Levenhagen, Michael J.

    2009-09-01

    Shared libraries have become ubiquitous and are used to achieve great resource efficiencies on many platforms. The same properties that enable efficiencies on time-shared computers and convenience on small clusters prove to be great obstacles to scalability on large clusters and High Performance Computing platforms. In addition, Light Weight operating systems such as Catamount have historically not supported the use of shared libraries specifically because they hinder scalability. In this report we will outline the methods of supporting shared libraries on High Performance Computing platforms using Light Weight kernels that we investigated. The considerations necessary to evaluate utility in this area are many and sometimes conflicting. While our initial path forward has been determined based on this evaluation we consider this effort ongoing and remain prepared to re-evaluate any technology that might provide a scalable solution. This report is an evaluation of a range of possible methods of supporting dynamically linked executables on capability class1 High Performance Computing platforms. Efforts are ongoing and extensive testing at scale is necessary to evaluate performance. While performance is a critical driving factor, supporting whatever method is used in a production environment is an equally important and challenging task.

  13. Haemodynamic simulation of aneurysm coiling in an anatomically accurate computational fluid dynamics model: technical note

    Energy Technology Data Exchange (ETDEWEB)

    Mitsos, Aristotelis P. [University of Oxford, Department of Neuroradiology, John Radcliffe Hospital, Oxford (United Kingdom); University of Oxford, Wolfson College, Oxford (United Kingdom); Kakalis, Nikolaos M.P.; Ventikos, Yiannis P. [University of Oxford, Department of Engineering Science, Oxford (United Kingdom); Byrne, James V. [University of Oxford, Department of Neuroradiology, John Radcliffe Hospital, Oxford (United Kingdom)

    2008-04-15

    Computational fluid dynamics (CFD) is a numerical technique that is used for studying haemodynamic parameters in cerebral aneurysms. As it is now possible to represent an anatomically accurate intracranial aneurysm in a computational model, we have attempted to simulate its endosaccular occlusion with coils and demonstrate the haemodynamic changes induced. This is the first attempt to use this particular porous medium-based method for coiling simulation in a CFD model, to our knowledge. Datasets from a rotational 3-D digital subtraction angiogram of a recently ruptured anterior communicating aneurysm were converted into a 3-D geometric model and the discretized data were processed using the computational technique developed. Coiling embolisation simulation was achieved by impediment of flow through a porous medium with characteristics following a series of embolisation coils. Haemodynamic parameters studied were: pressure distribution on the vessel wall, blood velocity and blood flow patterns. Significant haemodynamic changes were detected after deployment of the first coil. Similar, but less dramatic changes occurred during subsequent stages of coiling. The blood flow patterns became less vortical in the aneurysm sac as velocity decreased to stagnation and the wall pressure at the fundus was gradually reduced. Furthermore, the haemodynamic characteristics developed at the area of the neck remnant could form the basis for assessing the likelihood of delayed coil compaction and aneurysm regrowth. Appropriate computational techniques show great promise in simulating the haemodynamic behaviour of the various stages in coil embolisation and may be a potentially valuable tool in interventional planning and procedural decision-making. (orig.)

  14. New imaging tools in cardiovascular medicine: computational fluid dynamics and 4D flow MRI.

    Science.gov (United States)

    Itatani, Keiichi; Miyazaki, Shohei; Furusawa, Tokoki; Numata, Satoshi; Yamazaki, Sachiko; Morimoto, Kazuki; Makino, Rina; Morichi, Hiroko; Nishino, Teruyasu; Yaku, Hitoshi

    2017-11-01

    Blood flow imaging is a novel technology in cardiovascular medicine and surgery. Today, two types of blood flow imaging tools are available: measurement-based flow visualization including 4D flow MRI (or 3D cine phase-contrast magnetic resonance imaging), or echocardiography flow visualization software, and computer flow simulation modeling based on computational fluid dynamics (CFD). MRI and echocardiography flow visualization provide measured blood flow but have limitations in temporal and spatial resolution, whereas CFD flow calculates the flow according to assumptions instead of flow measurement, and it has sufficiently fine resolution up to the computer memory limit, and it enables even virtual surgery when combined with computer graphics. Blood flow imaging provides profound insight into the pathophysiology of cardiovascular diseases, because it quantifies and visualizes mechanical stress on the vessel walls or heart ventricle. Wall shear stress (WSS) is a stress on the endothelial wall caused by the near wall blood flow, and it is thought to be a predictor of atherosclerosis progression in coronary or aortic diseases. Flow energy loss (EL) is the loss of blood flow energy caused by viscous friction of turbulent diseased flow, and it is expected to be a predictor of ventricular workload on various heart diseases including heart valve disease, cardiomyopathy, and congenital heart diseases. Blood flow imaging can provide useful information for developing predictive medicine in cardiovascular diseases, and may lead to breakthroughs in cardiovascular surgery, especially in the decision-making process.

  15. Computational Fluid Dynamics (CFD-Based Droplet Size Estimates in Emulsification Equipment

    Directory of Open Access Journals (Sweden)

    Jo Janssen

    2016-12-01

    Full Text Available While academic literature shows steady progress in combining multi-phase computational fluid dynamics (CFD and population balance modelling (PBM of emulsification processes, the computational burden of this approach is still too large for routine use in industry. The challenge, thus, is to link a sufficiently detailed flow analysis to the droplet behavior in a way that is both physically relevant and computationally manageable. In this research article we propose the use of single-phase CFD to map out the local maximum stable droplet diameter within a given device, based on well-known academic droplet break-up studies in quasi-steady 2D linear flows. The results of the latter are represented by analytical correlations for the critical capillary number, which are valid across a wide viscosity ratio range. Additionally, we suggest a parameter to assess how good the assumption of quasi-steady 2D flow is locally. The approach is demonstrated for a common lab-scale rotor-stator device (Ultra-Turrax, IKA-Werke GmbH, Staufen, Germany. It is found to provide useful insights with minimal additional user coding and little increase in computational effort compared to the single-phase CFD simulations of the flow field, as such. Some suggestions for further development are briefly discussed.

  16. A distributed, dynamic, parallel computational model: the role of noise in velocity storage.

    Science.gov (United States)

    Karmali, Faisal; Merfeld, Daniel M

    2012-07-01

    Networks of neurons perform complex calculations using distributed, parallel computation, including dynamic "real-time" calculations required for motion control. The brain must combine sensory signals to estimate the motion of body parts using imperfect information from noisy neurons. Models and experiments suggest that the brain sometimes optimally minimizes the influence of noise, although it remains unclear when and precisely how neurons perform such optimal computations. To investigate, we created a model of velocity storage based on a relatively new technique--"particle filtering"--that is both distributed and parallel. It extends existing observer and Kalman filter models of vestibular processing by simulating the observer model many times in parallel with noise added. During simulation, the variance of the particles defining the estimator state is used to compute the particle filter gain. We applied our model to estimate one-dimensional angular velocity during yaw rotation, which yielded estimates for the velocity storage time constant, afferent noise, and perceptual noise that matched experimental data. We also found that the velocity storage time constant was Bayesian optimal by comparing the estimate of our particle filter with the estimate of the Kalman filter, which is optimal. The particle filter demonstrated a reduced velocity storage time constant when afferent noise increased, which mimics what is known about aminoglycoside ablation of semicircular canal hair cells. This model helps bridge the gap between parallel distributed neural computation and systems-level behavioral responses like the vestibuloocular response and perception.

  17. Distributed dynamical computation in neural circuits with propagating coherent activity patterns.

    Directory of Open Access Journals (Sweden)

    Pulin Gong

    2009-12-01

    Full Text Available Activity in neural circuits is spatiotemporally organized. Its spatial organization consists of multiple, localized coherent patterns, or patchy clusters. These patterns propagate across the circuits over time. This type of collective behavior has ubiquitously been observed, both in spontaneous activity and evoked responses; its function, however, has remained unclear. We construct a spatially extended, spiking neural circuit that generates emergent spatiotemporal activity patterns, thereby capturing some of the complexities of the patterns observed empirically. We elucidate what kind of fundamental function these patterns can serve by showing how they process information. As self-sustained objects, localized coherent patterns can signal information by propagating across the neural circuit. Computational operations occur when these emergent patterns interact, or collide with each other. The ongoing behaviors of these patterns naturally embody both distributed, parallel computation and cascaded logical operations. Such distributed computations enable the system to work in an inherently flexible and efficient way. Our work leads us to propose that propagating coherent activity patterns are the underlying primitives with which neural circuits carry out distributed dynamical computation.

  18. Dynamic load balancing of matrix-vector multiplications on roadrunner compute nodes

    Energy Technology Data Exchange (ETDEWEB)

    Sancho Pitarch, Jose Carlos [Los Alamos National Laboratory

    2009-01-01

    Hybrid architectures that combine general purpose processors with accelerators are being adopted in several large-scale systems such as the petaflop Roadrunner supercomputer at Los Alamos. In this system, dual-core Opteron host processors are tightly coupled with PowerXCell 8i processors within each compute node. In this kind of hybrid architecture, an accelerated mode of operation is typically used to offload performance hotspots in the computation to the accelerators. In this paper we explore the suitability of a variant of this acceleration mode in which the performance hotspots are actually shared between the host and the accelerators. To achieve this we have designed a new load balancing algorithm, which is optimized for the Roadrunner compute nodes, to dynamically distribute computation and associated data between the host and the accelerators at runtime. Results are presented using this approach for sparse and dense matrix-vector multiplications that show load-balancing can improve performance by up to 24% over solely using the accelerators.

  19. Applied & Computational MathematicsChallenges for the Design and Control of Dynamic Energy Systems

    Energy Technology Data Exchange (ETDEWEB)

    Brown, D L; Burns, J A; Collis, S; Grosh, J; Jacobson, C A; Johansen, H; Mezic, I; Narayanan, S; Wetter, M

    2011-03-10

    consumption. In addition the finding was that there are tools and technologies that can be assembled and deployed in the short term - the next 3-5 years - that can be used to significantly reduce the cost and time effective delivery of moderate energy savings in the U.S. building stock. Simulation tools, which are a core strength of current DOE computational research programs, provide only a part of the answer by providing a basis for simulation enabled design. New investments will be required within a broad dynamics and control research agenda which must focus on dynamics, control, optimization and simulation of multi-scale energy systems during design and operation. U.S. investments in high performance and high productivity computing (HP2C) should be leveraged and coupled with advances in dynamics and control to impact both the existing building stock through retrofits and also new construction. The essential R&D areas requiring investment are: (1) Characterizing the Dynamics of Multi-scale Energy Systems; (2) Control and Optimization Methodologies of Multi-scale Energy Systems Under Uncertainty; and (3) Multiscale Modeling and Simulation Enabled Design and Operation. The concept of using design and control specific computational tools is a new idea for the building industry. The potential payoffs in terms of accelerated design cycle times, performance optimization and optimal supervisory control to obtain and maintain energy savings are huge. Recent advances in computational power, computer science, and mathematical algorithms offer the foundations to address the control problems presented by the complex dynamics of whole building systems. The key areas for focus and associated metrics with targets for establishing competitiveness in energy efficient building design and operation are: (1) Scalability - Current methodology and tools can provide design guidance for very low energy buildings in weeks to months; what is needed is hours to days. A 50X improvement is needed. (2

  20. Design of a three-dimensional hand/forearm model to apply computational fluid dynamics

    Directory of Open Access Journals (Sweden)

    Daniel Almeida Marinho

    2010-04-01

    Full Text Available The purpose of this study was to develop a three-dimensional digital model of a human hand and forearm to apply Computational Fluid Dynamics to propulsion analysis in swimming. Computer tomography scans of the hand and forearm of an Olympic swimmer were applied. The data were converted, using image processing techniques, into relevant coordinate input, which could be used in Computational Fluid Dynamics software. From that analysis, it was possible to verify an almost perfect agreement between the true human segment and the digital model. This technique could be used as a means to overcome the difficulties in developing a true three-dimensional model of a specific segment of the human body. Additionally, it could be used to improve the use of Computational Fluid Dynamics generally in sports and specifically in swimming studies, decreasing the gap between the experimental and the computational data.O objetivo do presente estudo foi desenvolver um modelo digital tridimensional de uma mão e um antebraço humano para aplicar a Dinâmica Computacional de Fluidos ao estudo da propulsão em natação. Foram aplicados procedimentos computorizados de tomografia axial na mão e antebraço de um nadador Olímpico. Através de técnicas de processamento de imagem, os dados foram convertidos em coordenadas tridimensionais, que podem ser utilizadas em programas de simulação computacional. Através dos resultados encontrados, foi possível verificar uma semelhança quase perfeita entre o segmento humano e o modelo digital. Esta técnica pode ser utilizada como uma forma de ultrapassar as dificuldades em desenvolver um modelo digital tridimensional de um segmento específico do corpo humano. Complementarmente, pode ser bastante útil na melhoria da utilização da Dinâmica Computacional de Fluidos no Desporto, de uma forma geral, e, mais especificamente, nos estudos em natação, diminuindo a diferença entre a investigação experimental e a investiga