WorldWideScience

Sample records for model zone sequence

  1. A generative Bezier curve model for surf-zone tracking in coastal image sequences

    CSIR Research Space (South Africa)

    Burke, Michael G

    2017-09-01

    Full Text Available This work introduces a generative Bezier curve model suitable for surf-zone curve tracking in coastal image sequences. The model combines an adaptive curve parametrised by control points governed by local random walks with a global sinusoidal motion...

  2. Nonparametric combinatorial sequence models.

    Science.gov (United States)

    Wauthier, Fabian L; Jordan, Michael I; Jojic, Nebojsa

    2011-11-01

    This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This article presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three biological sequence families which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution over sequence representations induced by the prior. By integrating out the posterior, our method compares favorably to leading binding predictors.

  3. THE HABITABLE ZONES OF PRE-MAIN-SEQUENCE STARS

    Energy Technology Data Exchange (ETDEWEB)

    Ramirez, Ramses M.; Kaltenegger, Lisa [Institute for Pale Blue Dots, Cornell University, Ithaca, NY (United States)

    2014-12-20

    We calculate the pre-main-sequence habitable zone (HZ) for stars of spectral classes F-M. The spatial distribution of liquid water and its change during the pre-main-sequence phase of protoplanetary systems is important for understanding how planets become habitable. Such worlds are interesting targets for future missions because the coolest stars could provide habitable conditions for up to 2.5 billion years post-accretion. Moreover, for a given star type, planetary systems are more easily resolved because of higher pre-main-sequence stellar luminosities, resulting in larger planet-star separation for cool stars than is the case for the traditional main-sequence (MS) HZ. We use one-dimensional radiative-convective climate and stellar evolutionary models to calculate pre-main-sequence HZ distances for F1-M8 stellar types. We also show that accreting planets that are later located in the traditional MS HZ orbiting stars cooler than a K5 (including the full range of M stars) receive stellar fluxes that exceed the runaway greenhouse threshold, and thus may lose substantial amounts of water initially delivered to them. We predict that M-star planets need to initially accrete more water than Earth did, or, alternatively, have additional water delivered later during the long pre-MS phase to remain habitable. Our findings are also consistent with recent claims that Venus lost its water during accretion.

  4. Habitable zone lifetimes of exoplanets around main sequence stars.

    Science.gov (United States)

    Rushby, Andrew J; Claire, Mark W; Osborn, Hugh; Watson, Andrew J

    2013-09-01

    The potential habitability of newly discovered exoplanets is initially assessed by determining whether their orbits fall within the circumstellar habitable zone of their star. However, the habitable zone (HZ) is not static in time or space, and its boundaries migrate outward at a rate proportional to the increase in luminosity of a star undergoing stellar evolution, possibly including or excluding planets over the course of the star's main sequence lifetime. We describe the time that a planet spends within the HZ as its "habitable zone lifetime." The HZ lifetime of a planet has strong astrobiological implications and is especially important when considering the evolution of complex life, which is likely to require a longer residence time within the HZ. Here, we present results from a simple model built to investigate the evolution of the "classic" HZ over time, while also providing estimates for the evolution of stellar luminosity over time in order to develop a "hybrid" HZ model. These models return estimates for the HZ lifetimes of Earth and 7 confirmed HZ exoplanets and 27 unconfirmed Kepler candidates. The HZ lifetime for Earth ranges between 6.29 and 7.79×10⁹ years (Gyr). The 7 exoplanets fall in a range between ∼1 and 54.72 Gyr, while the 27 Kepler candidate planets' HZ lifetimes range between 0.43 and 18.8 Gyr. Our results show that exoplanet HD 85512b is no longer within the HZ, assuming it has an Earth analog atmosphere. The HZ lifetime should be considered in future models of planetary habitability as setting an upper limit on the lifetime of any potential exoplanetary biosphere, and also for identifying planets of high astrobiological potential for continued observational or modeling campaigns.

  5. HABITABLE ZONES OF POST-MAIN SEQUENCE STARS

    Energy Technology Data Exchange (ETDEWEB)

    Ramirez, Ramses M.; Kaltenegger, Lisa [Carl Sagan Institute, Cornell University, Ithaca, NY (United States)

    2016-05-20

    Once a star leaves the main sequence and becomes a red giant, its Habitable Zone (HZ) moves outward, promoting detectable habitable conditions at larger orbital distances. We use a one-dimensional radiative-convective climate and stellar evolutionary models to calculate post-MS HZ distances for a grid of stars from 3700 to 10,000 K (∼M1 to A5 stellar types) for different stellar metallicities. The post-MS HZ limits are comparable to the distances of known directly imaged planets. We model the stellar as well as planetary atmospheric mass loss during the Red Giant Branch (RGB) and Asymptotic Giant Branch (AGB) phases for super-Moons to super-Earths. A planet can stay between 200 million years up to 9 Gyr in the post-MS HZ for our hottest and coldest grid stars, respectively, assuming solar metallicity. These numbers increase for increased stellar metallicity. Total atmospheric erosion only occurs for planets in close-in orbits. The post-MS HZ orbital distances are within detection capabilities of direct imaging techniques.

  6. Modelling passive margin sequence stratigraphy

    Science.gov (United States)

    Steckler, M.S.; Reynolds, D.; Coakley, B.; Swift, B.A.; Jarrard, R.D.

    1993-01-01

    We have modelled stratigraphic sequences to aid in deciphering the sedimentary response to sea-level change. Sequence geometry is found to be most sensitive to sea level, but other factors, including subsidence rate and sediment supply, can produce similar changes. Sediment loading and compaction also play a major role in generating accommodation, a factor often neglected in sequence-stratigraphic models. All of these parameters can control whether a type 1 or type 2 sequence boundary is produced. The models indicate that variations in margin characteristics produce systematic shifts in sequence boundary timing and systems tract distribution. The timing of the sequence boundary formation and systems tracts may differ by up to one-half of a sea-level cycle. Thus correlative sequence boundaries will not be synchronous. While rates of sea-level change may exceed the rate of thermal subsidence, isostasy and compaction may amplify the rate of total subsidence to several times greater than the thermal subsidence. Thus, total subsidence does not vary uniformly across the margin since it is modified by the sediment load. The amplitude of sea-level changes cannot be determined accurately without accounting for the major processes that affect sediment accumulation. Backstripping of a seismic line on the New Jersey margin is used to reconstruct continental margin geometry. The reconstructions show that the pre-existing ramp-margin geometry, rather than sea level, controls clinoform heights and slopes and sedimentary bypass. Backstripping also reveals progressive deformation of sequences due to compaction. Further work is still needed to understand quantitatively the role of sea level and the tectonic and sedimentary processes controlling sequence formation and influencing sequence architecture.

  7. Geochronological correlation of the late Precambrian sequences on and around the stable zones of Equatorial Africa

    International Nuclear Information System (INIS)

    Cahen, L.

    1982-01-01

    Very few radiometric age determinations have a bearing on the late Precambrian sequences of the stable zones of Equatorial Africa. A geochronological correlation of these sequences must therefore rest upon a compilation of ages from these stable zones and the corresponding mobile zones. About 15 ages of varying precision more or less well tied up with the stratigraphical sequences, together with results of the study of stromatolite assemblages allow a provisional correlation to be made. One conclusion of this correlation is that most mixtites surrounding the Congo basin are in a 950 +- 50 Ma age bracket and are presumably to be correlated. (Auth.)

  8. Site-Scale Saturated Zone Flow Model

    Energy Technology Data Exchange (ETDEWEB)

    G. Zyvoloski

    2003-12-17

    The purpose of this model report is to document the components of the site-scale saturated-zone flow model at Yucca Mountain, Nevada, in accordance with administrative procedure (AP)-SIII.lOQ, ''Models''. This report provides validation and confidence in the flow model that was developed for site recommendation (SR) and will be used to provide flow fields in support of the Total Systems Performance Assessment (TSPA) for the License Application. The output from this report provides the flow model used in the ''Site-Scale Saturated Zone Transport'', MDL-NBS-HS-000010 Rev 01 (BSC 2003 [162419]). The Site-Scale Saturated Zone Transport model then provides output to the SZ Transport Abstraction Model (BSC 2003 [164870]). In particular, the output from the SZ site-scale flow model is used to simulate the groundwater flow pathways and radionuclide transport to the accessible environment for use in the TSPA calculations. Since the development and calibration of the saturated-zone flow model, more data have been gathered for use in model validation and confidence building, including new water-level data from Nye County wells, single- and multiple-well hydraulic testing data, and new hydrochemistry data. In addition, a new hydrogeologic framework model (HFM), which incorporates Nye County wells lithology, also provides geologic data for corroboration and confidence in the flow model. The intended use of this work is to provide a flow model that generates flow fields to simulate radionuclide transport in saturated porous rock and alluvium under natural or forced gradient flow conditions. The flow model simulations are completed using the three-dimensional (3-D), finite-element, flow, heat, and transport computer code, FEHM Version (V) 2.20 (software tracking number (STN): 10086-2.20-00; LANL 2003 [161725]). Concurrently, process-level transport model and methodology for calculating radionuclide transport in the saturated zone at Yucca

  9. Site-Scale Saturated Zone Flow Model

    International Nuclear Information System (INIS)

    G. Zyvoloski

    2003-01-01

    The purpose of this model report is to document the components of the site-scale saturated-zone flow model at Yucca Mountain, Nevada, in accordance with administrative procedure (AP)-SIII.lOQ, ''Models''. This report provides validation and confidence in the flow model that was developed for site recommendation (SR) and will be used to provide flow fields in support of the Total Systems Performance Assessment (TSPA) for the License Application. The output from this report provides the flow model used in the ''Site-Scale Saturated Zone Transport'', MDL-NBS-HS-000010 Rev 01 (BSC 2003 [162419]). The Site-Scale Saturated Zone Transport model then provides output to the SZ Transport Abstraction Model (BSC 2003 [164870]). In particular, the output from the SZ site-scale flow model is used to simulate the groundwater flow pathways and radionuclide transport to the accessible environment for use in the TSPA calculations. Since the development and calibration of the saturated-zone flow model, more data have been gathered for use in model validation and confidence building, including new water-level data from Nye County wells, single- and multiple-well hydraulic testing data, and new hydrochemistry data. In addition, a new hydrogeologic framework model (HFM), which incorporates Nye County wells lithology, also provides geologic data for corroboration and confidence in the flow model. The intended use of this work is to provide a flow model that generates flow fields to simulate radionuclide transport in saturated porous rock and alluvium under natural or forced gradient flow conditions. The flow model simulations are completed using the three-dimensional (3-D), finite-element, flow, heat, and transport computer code, FEHM Version (V) 2.20 (software tracking number (STN): 10086-2.20-00; LANL 2003 [161725]). Concurrently, process-level transport model and methodology for calculating radionuclide transport in the saturated zone at Yucca Mountain using FEHM V 2.20 are being

  10. Retrosynthetic Reaction Prediction Using Neural Sequence-to-Sequence Models.

    Science.gov (United States)

    Liu, Bowen; Ramsundar, Bharath; Kawthekar, Prasad; Shi, Jade; Gomes, Joseph; Luu Nguyen, Quang; Ho, Stephen; Sloane, Jack; Wender, Paul; Pande, Vijay

    2017-10-25

    We describe a fully data driven model that learns to perform a retrosynthetic reaction prediction task, which is treated as a sequence-to-sequence mapping problem. The end-to-end trained model has an encoder-decoder architecture that consists of two recurrent neural networks, which has previously shown great success in solving other sequence-to-sequence prediction tasks such as machine translation. The model is trained on 50,000 experimental reaction examples from the United States patent literature, which span 10 broad reaction types that are commonly used by medicinal chemists. We find that our model performs comparably with a rule-based expert system baseline model, and also overcomes certain limitations associated with rule-based expert systems and with any machine learning approach that contains a rule-based expert system component. Our model provides an important first step toward solving the challenging problem of computational retrosynthetic analysis.

  11. Work zone lane closure analysis model.

    Science.gov (United States)

    2009-10-01

    At the Alabama Department of Transportation (ALDOT), the tool used by traffic engineers to predict whether a queue will form at a freeway work zone is the Excel-based "Lane Rental Model" developed at the Oklahoma Department of Transportation (OkDOT) ...

  12. Ice films follow structure zone model morphologies

    International Nuclear Information System (INIS)

    Cartwright, Julyan H.E.; Escribano, Bruno; Sainz-Diaz, C. Ignacio

    2010-01-01

    Ice films deposited at temperatures of 6-220 K and at low pressures in situ in a cryo-environmental scanning electron microscope show pronounced morphologies at the mesoscale consistent with the structure zone model of film growth. Water vapour was injected directly inside the chamber at ambient pressures ranging from 10 -4 Pa to 10 2 Pa. Several different substrates were used to exclude the influence of their morphology on the grown films. At the lowest temperatures the ice, which under these conditions is amorphous on the molecular scale, shows the mesoscale morphologies typical of the low-temperature zones of the structure zone model (SZM), including cauliflower, transition, spongelike and matchstick morphologies. Our experiments confirm that the SZM is independent of the chemical nature of the adsorbate, although the intermolecular interactions in water (hydrogen bonds) are different to those in ceramics or metals. At higher temperatures, on the other hand, where the ice is hexagonal crystalline on the molecular scale, it displays a complex palmlike morphology on the mesoscale.

  13. Ice films follow structure zone model morphologies

    Energy Technology Data Exchange (ETDEWEB)

    Cartwright, Julyan H.E. [Instituto Andaluz de Ciencias de la Tierra, CSIC-Universidad de Granada, E-18071 Granada (Spain); Escribano, Bruno, E-mail: bruno.escribano.salazar@gmail.co [Instituto Andaluz de Ciencias de la Tierra, CSIC-Universidad de Granada, E-18071 Granada (Spain); Sainz-Diaz, C. Ignacio [Instituto Andaluz de Ciencias de la Tierra, CSIC-Universidad de Granada, E-18071 Granada (Spain)

    2010-04-02

    Ice films deposited at temperatures of 6-220 K and at low pressures in situ in a cryo-environmental scanning electron microscope show pronounced morphologies at the mesoscale consistent with the structure zone model of film growth. Water vapour was injected directly inside the chamber at ambient pressures ranging from 10{sup -4} Pa to 10{sup 2} Pa. Several different substrates were used to exclude the influence of their morphology on the grown films. At the lowest temperatures the ice, which under these conditions is amorphous on the molecular scale, shows the mesoscale morphologies typical of the low-temperature zones of the structure zone model (SZM), including cauliflower, transition, spongelike and matchstick morphologies. Our experiments confirm that the SZM is independent of the chemical nature of the adsorbate, although the intermolecular interactions in water (hydrogen bonds) are different to those in ceramics or metals. At higher temperatures, on the other hand, where the ice is hexagonal crystalline on the molecular scale, it displays a complex palmlike morphology on the mesoscale.

  14. The Biomantle-Critical Zone Model

    Science.gov (United States)

    Johnson, D. L.; Lin, H.

    2006-12-01

    It is a fact that established fields, like geomorphology, soil science, and pedology, which treat near surface and surface processes, are undergoing conceptual changes. Disciplinary self examinations are rife. New practitioners are joining these fields, bringing novel and interdisciplinary ideas. Such new names as "Earth's critical zone," "near surface geophysics," and "weathering engine" are being coined for research groups. Their agendas reflect an effort to integrate and reenergize established fields and break new ground. The new discipline "hydropedology" integrates soil science with hydrologic principles, and recent biodynamic investigations have spawned "biomantle" concepts and principles. One force behind these sea shifts may be retrospectives whereby disciplines periodically re-invent themselves to meet new challenges. Such retrospectives may be manifest in the recent Science issue on "Soils, The Final Frontier" (11 June, 2004), and in recent National Research Council reports that have set challenges to science for the next three decades (Basic Research Opportunities in Earth Science, and Grand Challenges for the Environmental Sciences, both published in 2001). In keeping with such changes, we advocate the integration of biomantle and critical zone concepts into a general model of Earth's soil. (The scope of the model automatically includes the domain of hydropedology.) Our justification is that the integration makes for a more appealing holistic, and realistic, model for the domain of Earth's soil at any scale. The focus is on the biodynamics of the biomantle and water flow within the critical zone. In this general model the biomantle is the epidermis of the critical zone, which extends to the base of the aquifer. We define soil as the outer layer of landforms on planets and similar bodies altered by biological, chemical, and/or physical agents. Because Earth is the only planet with biological agents, as far as we know, it is the only one that has all

  15. Evolutionary sequence of models of planetary nebulae

    International Nuclear Information System (INIS)

    Vil'koviskij, Eh.Ya.; Kondrat'eva, L.N.; Tambovtseva, L.V.

    1983-01-01

    The evolutionary sequences of model planetary nebulae of different masses have been calculated. The computed emission line intensities are compared with the observed ones by means of the parameter ''reduced size of the nebula'', Rsub(n). It is shown that the evolution tracks of Schonberner for the central stars are consistent with the observed data. Part of ionized mass Mi in any nebulae does not not exceed 0.3 b and in the average Msu(i) 3 years at actual values of radius Rsub(i) <0.025 ps. Then the luminosity growth slows down to the maximum temperature which central star reaches and decreases with sharp decrease of the star luminosity. At that, the radius of ionized zone of greater mass nebulae can even decrease, inspite of the constant expansion of the nebula. As a result nebulae of great masses having undergone the evolution can be included in the number of observed compact objects (Rsub(n) < 0.1 ps)

  16. SATURATED ZONE FLOW AND TRANSPORT MODEL ABSTRACTION

    International Nuclear Information System (INIS)

    B.W. ARNOLD

    2004-01-01

    The purpose of the saturated zone (SZ) flow and transport model abstraction task is to provide radionuclide-transport simulation results for use in the total system performance assessment (TSPA) for license application (LA) calculations. This task includes assessment of uncertainty in parameters that pertain to both groundwater flow and radionuclide transport in the models used for this purpose. This model report documents the following: (1) The SZ transport abstraction model, which consists of a set of radionuclide breakthrough curves at the accessible environment for use in the TSPA-LA simulations of radionuclide releases into the biosphere. These radionuclide breakthrough curves contain information on radionuclide-transport times through the SZ. (2) The SZ one-dimensional (I-D) transport model, which is incorporated in the TSPA-LA model to simulate the transport, decay, and ingrowth of radionuclide decay chains in the SZ. (3) The analysis of uncertainty in groundwater-flow and radionuclide-transport input parameters for the SZ transport abstraction model and the SZ 1-D transport model. (4) The analysis of the background concentration of alpha-emitting species in the groundwater of the SZ

  17. A mathematical model and numerical method for thermoelectric DNA sequencing

    Science.gov (United States)

    Shi, Liwei; Guilbeau, Eric J.; Nestorova, Gergana; Dai, Weizhong

    2014-05-01

    Single nucleotide polymorphisms (SNPs) are single base pair variations within the genome that are important indicators of genetic predisposition towards specific diseases. This study explores the feasibility of SNP detection using a thermoelectric sequencing method that measures the heat released when DNA polymerase inserts a deoxyribonucleoside triphosphate into a DNA strand. We propose a three-dimensional mathematical model that governs the DNA sequencing device with a reaction zone that contains DNA template/primer complex immobilized to the surface of the lower channel wall. The model is then solved numerically. Concentrations of reactants and the temperature distribution are obtained. Results indicate that when the nucleoside is complementary to the next base in the DNA template, polymerization occurs lengthening the complementary polymer and releasing thermal energy with a measurable temperature change, implying that the thermoelectric conceptual device for sequencing DNA may be feasible for identifying specific genes in individuals.

  18. Comparisons of Source Characteristics between Recent Inland Crustal Earthquake Sequences inside and outside of Niigata-Kobe Tectonic Zone, Japan

    Science.gov (United States)

    Somei, K.; Asano, K.; Iwata, T.; Miyakoshi, K.

    2012-12-01

    After the 1995 Kobe earthquake, many M7-class inland earthquakes occurred in Japan. Some of those events (e.g., the 2004 Chuetsu earthquake) occurred in a tectonic zone which is characterized as a high strain rate zone by the GPS observation (Sagiya et al., 2000) or dense distribution of active faults. That belt-like zone along the coast in Japan Sea side of Tohoku and Chubu districts, and north of Kinki district, is called as the Niigata-Kobe tectonic zone (NKTZ, Sagiya et al, 2000). We investigate seismic scaling relationship for recent inland crustal earthquake sequences in Japan and compare source characteristics between events occurring inside and outside of NKTZ. We used S-wave coda part for estimating source spectra. Source spectral ratio is obtained by S-wave coda spectral ratio between the records of large and small events occurring close to each other from nation-wide strong motion network (K-NET and KiK-net) and broad-band seismic network (F-net) to remove propagation-path and site effects. We carefully examined the commonality of the decay of coda envelopes between event-pair records and modeled the observed spectral ratio by the source spectral ratio function with assuming omega-square source model for large and small events. We estimated the corner frequencies and seismic moment (ratio) from those modeled spectral ratio function. We determined Brune's stress drops of 356 events (Mw: 3.1-6.9) in ten earthquake sequences occurring in NKTZ and six sequences occurring outside of NKTZ. Most of source spectra obey omega-square source spectra. There is no obvious systematic difference between stress drops of events in NKTZ zone and others. We may conclude that the systematic tendency of seismic source scaling of the events occurred inside and outside of NKTZ does not exist and the average source scaling relationship can be effective for inland crustal earthquakes. Acknowledgements: Waveform data were provided from K-NET, KiK-net and F-net operated by

  19. Burrow casts from the Lystrosaurus-Procolophon Assemblage-zone, Karoo Sequence, South Africa

    Directory of Open Access Journals (Sweden)

    G.H. Groenewald

    1991-09-01

    Full Text Available Five types of burrow casts from the Lystrosaurus- Procolophon Assemblage-zone (Palingkloof Member and Katberg Formation, Triassic, Karoo sequence. South Africa are associated with casts of desiccation cracks and red mudstone. Vertebrate remains of Lystrosaurus sp. and Procolophon sp. indicate that these animals probably made the burrows during the Triassic. It is possible that burrowing was an adaptive advantage during periods of severe and unfavourable climatic conditions. Similar burrow casts were found in the Dicynodon-Theriognathus Assemblage-zone, suggesting a burrowing habit for fauna represented in this zone. In structure, the burrow casts resemble those of Scoyenia, Thalassinoides, Histioderma, Gyrolithes and Planolites reported from Germany, France, Asia, Ireland, Spain and the United States of America.

  20. Sequence modelling and an extensible data model for genomic database

    Energy Technology Data Exchange (ETDEWEB)

    Li, Peter Wei-Der [California Univ., San Francisco, CA (United States); Univ. of California, Berkeley, CA (United States)

    1992-01-01

    The Human Genome Project (HGP) plans to sequence the human genome by the beginning of the next century. It will generate DNA sequences of more than 10 billion bases and complex marker sequences (maps) of more than 100 million markers. All of these information will be stored in database management systems (DBMSs). However, existing data models do not have the abstraction mechanism for modelling sequences and existing DBMS`s do not have operations for complex sequences. This work addresses the problem of sequence modelling in the context of the HGP and the more general problem of an extensible object data model that can incorporate the sequence model as well as existing and future data constructs and operators. First, we proposed a general sequence model that is application and implementation independent. This model is used to capture the sequence information found in the HGP at the conceptual level. In addition, abstract and biological sequence operators are defined for manipulating the modelled sequences. Second, we combined many features of semantic and object oriented data models into an extensible framework, which we called the ``Extensible Object Model``, to address the need of a modelling framework for incorporating the sequence data model with other types of data constructs and operators. This framework is based on the conceptual separation between constructors and constraints. We then used this modelling framework to integrate the constructs for the conceptual sequence model. The Extensible Object Model is also defined with a graphical representation, which is useful as a tool for database designers. Finally, we defined a query language to support this model and implement the query processor to demonstrate the feasibility of the extensible framework and the usefulness of the conceptual sequence model.

  1. Sequence modelling and an extensible data model for genomic database

    Energy Technology Data Exchange (ETDEWEB)

    Li, Peter Wei-Der (California Univ., San Francisco, CA (United States) Lawrence Berkeley Lab., CA (United States))

    1992-01-01

    The Human Genome Project (HGP) plans to sequence the human genome by the beginning of the next century. It will generate DNA sequences of more than 10 billion bases and complex marker sequences (maps) of more than 100 million markers. All of these information will be stored in database management systems (DBMSs). However, existing data models do not have the abstraction mechanism for modelling sequences and existing DBMS's do not have operations for complex sequences. This work addresses the problem of sequence modelling in the context of the HGP and the more general problem of an extensible object data model that can incorporate the sequence model as well as existing and future data constructs and operators. First, we proposed a general sequence model that is application and implementation independent. This model is used to capture the sequence information found in the HGP at the conceptual level. In addition, abstract and biological sequence operators are defined for manipulating the modelled sequences. Second, we combined many features of semantic and object oriented data models into an extensible framework, which we called the Extensible Object Model'', to address the need of a modelling framework for incorporating the sequence data model with other types of data constructs and operators. This framework is based on the conceptual separation between constructors and constraints. We then used this modelling framework to integrate the constructs for the conceptual sequence model. The Extensible Object Model is also defined with a graphical representation, which is useful as a tool for database designers. Finally, we defined a query language to support this model and implement the query processor to demonstrate the feasibility of the extensible framework and the usefulness of the conceptual sequence model.

  2. Near-field/altered-zone models report

    Energy Technology Data Exchange (ETDEWEB)

    Hardin, E. L., LLNL

    1998-03-01

    The U.S. Department of Energy is studying Yucca Mountain as the possible site for the first underground repository for permanent disposal of spent fuel from commercial nuclear reactors as well as for other types high-level nuclear waste. Emplacement of high-level radioactive waste, especially commercial spent nuclear fuel (CSNF), in Yucca Mountain will release a large amount of heat into the rock above and below the repository. The heating rate will decrease with time, creating a thermal pulse. Over a period of several thousand years, the rock temperature will rise initially, then drop when the production of decay heat falls below the rate at which heat escapes from the hot zone. Besides raising the rock temperature, much of this heat will vaporize water, which will then condense in cooler regions. The condensate is likely to form a gravity-driven heat pipe above the repository, creating the possibility that water may drain back onto the waste packages (WPs) or that it may ''shed'' through the pillars between emplacement drifts. The long-term importance of these effects has been investigated through the development, testing, and application of thermohydrologic (TH) models. Other effects, such coupled chemical and mechanical processes, may also influence the movement of water above, within, and below the emplacement drifts. A recent report on thermally driven coupled processes (Hardin and Chesnut, 1997) provides a qualitative assessment of the probable significance of these processes for the Yucca Mountain Site Characterization Project (YMSCP) and is the phenomenological framework for the present report. This report describes the conceptual and numerical models that have been developed to predict the thermal, mechanical, hydrologic, and chemical responses to the cumulative heat production of the potential host rock at Yucca Mountain. As proposed, the repository horizon will be situated within the Topopah Spring tuff, in the adjacent middle

  3. Hidden Markov models for labeled sequences

    DEFF Research Database (Denmark)

    Krogh, Anders Stærmose

    1994-01-01

    A hidden Markov model for labeled observations, called a class HMM, is introduced and a maximum likelihood method is developed for estimating the parameters of the model. Instead of training it to model the statistics of the training sequences it is trained to optimize recognition. It resembles MMI...

  4. The Cohesive Zone Model for Fatigue Crack Growth

    Directory of Open Access Journals (Sweden)

    Jinxiang Liu

    2013-01-01

    Full Text Available In the past decade, the cohesive zone model has been receiving increasing attention as a powerful tool for the simulation of fatigue crack growth. When applying cohesive zone model to fatigue fracture problem, three aspects should generally be taken into account, that is, unloading-reloading path, damage evolution during cyclic loading, and crack surface contact and friction behavior. This paper addresses the critical views of these aspects. Before that, the formulation of cohesive zone model and identification of cohesive zone model parameters and its numerical implementation have been reviewed.

  5. A neurocomputational model of automatic sequence production.

    Science.gov (United States)

    Helie, Sebastien; Roeder, Jessica L; Vucovich, Lauren; Rünger, Dennis; Ashby, F Gregory

    2015-07-01

    Most behaviors unfold in time and include a sequence of submovements or cognitive activities. In addition, most behaviors are automatic and repeated daily throughout life. Yet, relatively little is known about the neurobiology of automatic sequence production. Past research suggests a gradual transfer from the associative striatum to the sensorimotor striatum, but a number of more recent studies challenge this role of the BG in automatic sequence production. In this article, we propose a new neurocomputational model of automatic sequence production in which the main role of the BG is to train cortical-cortical connections within the premotor areas that are responsible for automatic sequence production. The new model is used to simulate four different data sets from human and nonhuman animals, including (1) behavioral data (e.g., RTs), (2) electrophysiology data (e.g., single-neuron recordings), (3) macrostructure data (e.g., TMS), and (4) neurological circuit data (e.g., inactivation studies). We conclude with a comparison of the new model with existing models of automatic sequence production and discuss a possible new role for the BG in automaticity and its implication for Parkinson's disease.

  6. Clustering metagenomic sequences with interpolated Markov models

    Directory of Open Access Journals (Sweden)

    Kelley David R

    2010-11-01

    Full Text Available Abstract Background Sequencing of environmental DNA (often called metagenomics has shown tremendous potential to uncover the vast number of unknown microbes that cannot be cultured and sequenced by traditional methods. Because the output from metagenomic sequencing is a large set of reads of unknown origin, clustering reads together that were sequenced from the same species is a crucial analysis step. Many effective approaches to this task rely on sequenced genomes in public databases, but these genomes are a highly biased sample that is not necessarily representative of environments interesting to many metagenomics projects. Results We present SCIMM (Sequence Clustering with Interpolated Markov Models, an unsupervised sequence clustering method. SCIMM achieves greater clustering accuracy than previous unsupervised approaches. We examine the limitations of unsupervised learning on complex datasets, and suggest a hybrid of SCIMM and supervised learning method Phymm called PHYSCIMM that performs better when evolutionarily close training genomes are available. Conclusions SCIMM and PHYSCIMM are highly accurate methods to cluster metagenomic sequences. SCIMM operates entirely unsupervised, making it ideal for environments containing mostly novel microbes. PHYSCIMM uses supervised learning to improve clustering in environments containing microbial strains from well-characterized genera. SCIMM and PHYSCIMM are available open source from http://www.cbcb.umd.edu/software/scimm.

  7. HABITABLE ZONES AROUND MAIN-SEQUENCE STARS: DEPENDENCE ON PLANETARY MASS

    Energy Technology Data Exchange (ETDEWEB)

    Kopparapu, Ravi Kumar; Ramirez, Ramses M.; Kasting, James F. [Department of Geosciences, Penn State University, 443 Deike Building, University Park, PA 16802 (United States); SchottelKotte, James [Department of Astronomy and Astrophysics, The Pennsylvania State University, 525 Davey Laboratory, University Park, PA 16802 (United States); Domagal-Goldman, Shawn [NASA Astrobiology Institute' s Virtual Planetary Laboratory, P.O. Box 351580, Seattle, WA 98195 (United States); Eymet, Vincent, E-mail: ruk15@psu.edu [Laboratoire d' Astrophysique de Bordeaux, Universite de Bordeaux 1, UMR 5804, F-33270 Floirac (France)

    2014-06-01

    The ongoing discoveries of extra-solar planets are unveiling a wide range of terrestrial mass (size) planets around their host stars. In this Letter, we present estimates of habitable zones (HZs) around stars with stellar effective temperatures in the range 2600 K-7200 K, for planetary masses between 0.1 M {sub ⊕} and 5 M {sub ⊕}. Assuming H{sub 2}O-(inner HZ) and CO{sub 2}-(outer HZ) dominated atmospheres, and scaling the background N{sub 2} atmospheric pressure with the radius of the planet, our results indicate that larger planets have wider HZs than do smaller ones. Specifically, with the assumption that smaller planets will have less dense atmospheres, the inner edge of the HZ (runaway greenhouse limit) moves outward (∼10% lower than Earth flux) for low mass planets due to larger greenhouse effect arising from the increased H{sub 2}O column depth. For larger planets, the H{sub 2}O column depth is smaller, and higher temperatures are needed before water vapor completely dominates the outgoing longwave radiation. Hence the inner edge moves inward (∼7% higher than Earth's flux). The outer HZ changes little due to the competing effects of the greenhouse effect and an increase in albedo. New, three-dimensional climate model results from other groups are also summarized, and we argue that further, independent studies are needed to verify their predictions. Combined with our previous work, the results presented here provide refined estimates of HZs around main-sequence stars and provide a step toward a more comprehensive analysis of HZs.

  8. Modeling of prepregs during automated draping sequences

    Science.gov (United States)

    Krogh, Christian; Glud, Jens A.; Jakobsen, Johnny

    2017-10-01

    The behavior of wowen prepreg fabric during automated draping sequences is investigated. A drape tool under development with an arrangement of grippers facilitates the placement of a woven prepreg fabric in a mold. It is essential that the draped configuration is free from wrinkles and other defects. The present study aims at setting up a virtual draping framework capable of modeling the draping process from the initial flat fabric to the final double curved shape and aims at assisting the development of an automated drape tool. The virtual draping framework consists of a kinematic mapping algorithm used to generate target points on the mold which are used as input to a draping sequence planner. The draping sequence planner prescribes the displacement history for each gripper in the drape tool and these displacements are then applied to each gripper in a transient model of the draping sequence. The model is based on a transient finite element analysis with the material's constitutive behavior currently being approximated as linear elastic orthotropic. In-plane tensile and bias-extension tests as well as bending tests are conducted and used as input for the model. The virtual draping framework shows a good potential for obtaining a better understanding of the drape process and guide the development of the drape tool. However, results obtained from using the framework on a simple test case indicate that the generation of draping sequences is non-trivial.

  9. Whole-genome sequencing identifies recurrent somatic NOTCH2 mutations in splenic marginal zone lymphoma.

    Science.gov (United States)

    Kiel, Mark J; Velusamy, Thirunavukkarasu; Betz, Bryan L; Zhao, Lili; Weigelin, Helmut G; Chiang, Mark Y; Huebner-Chan, David R; Bailey, Nathanael G; Yang, David T; Bhagat, Govind; Miranda, Roberto N; Bahler, David W; Medeiros, L Jeffrey; Lim, Megan S; Elenitoba-Johnson, Kojo S J

    2012-08-27

    Splenic marginal zone lymphoma (SMZL), the most common primary lymphoma of spleen, is poorly understood at the genetic level. In this study, using whole-genome DNA sequencing (WGS) and confirmation by Sanger sequencing, we observed mutations identified in several genes not previously known to be recurrently altered in SMZL. In particular, we identified recurrent somatic gain-of-function mutations in NOTCH2, a gene encoding a protein required for marginal zone B cell development, in 25 of 99 (∼25%) cases of SMZL and in 1 of 19 (∼5%) cases of nonsplenic MZLs. These mutations clustered near the C-terminal proline/glutamate/serine/threonine (PEST)-rich domain, resulting in protein truncation or, rarely, were nonsynonymous substitutions affecting the extracellular heterodimerization domain (HD). NOTCH2 mutations were not present in other B cell lymphomas and leukemias, such as chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL; n = 15), mantle cell lymphoma (MCL; n = 15), low-grade follicular lymphoma (FL; n = 44), hairy cell leukemia (HCL; n = 15), and reactive lymphoid hyperplasia (n = 14). NOTCH2 mutations were associated with adverse clinical outcomes (relapse, histological transformation, and/or death) among SMZL patients (P = 0.002). These results suggest that NOTCH2 mutations play a role in the pathogenesis and progression of SMZL and are associated with a poor prognosis.

  10. Relative role of transfer zones in controlling sequence stacking patterns and facies distribution: insights from the Fushan Depression, South China Sea

    Science.gov (United States)

    Liu, Entao; Wang, Hua; Li, Yuan; Huang, Chuanyan

    2015-04-01

    In sedimentary basins, a transfer zone can be defined as a coordinated system of deformational features which has good prospects for hydrocarbon exploration. Although the term 'transfer zone' has been widely applied to the study of extensional basins, little attention has been paid to its controlling effect on sequence tracking pattern and depositional facies distribution. Fushan Depression is a half-graben rift sub-basin, located in the southeast of the Beibuwan Basin, South China Sea. In this study, comparative analysis of seismic reflection, palaeogeomorphology, fault activity and depositional facies distribution in the southern slope indicates that three different types of sequence stacking patterns (i.e. multi-level step-fault belt in the western area, flexure slope belt in the central area, gentle slope belt in the eastern area) were developed along the southern slope, together with a large-scale transfer zone in the central area, at the intersection of the western and eastern fault systems. Further analysis shows that the transfer zone played an important role in the diversity of sequence stacking patterns in the southern slope by dividing the Fushan Depression into two non-interfering tectonic systems forming different sequence patterns, and leading to the formation of the flexure slope belt in the central area. The transfer zone had an important controlling effect on not only the diversity of sequence tracking patterns, but also the facies distribution on the relay ramp. During the high-stand stage, under the controlling effect of the transfer zone, the sediments contain a significant proportion of coarser material accumulated and distributed along the ramp axis. By contrast, during the low-stand stage, the transfer zone did not seem to contribute significantly to the low-stand fan distribution which was mainly controlled by the slope gradient (palaeogeomorphology). Therefore, analysis of the transfer zone can provide a new perspective for basin analysis

  11. Modeling of formation of precipitate free zone

    Czech Academy of Sciences Publication Activity Database

    Svoboda, Jiří; Maier, G.

    2010-01-01

    Roč. 101, č. 8 (2010), s. 997-1002 ISSN 1862-5282 R&D Projects: GA ČR GAP108/10/1781 Institutional research plan: CEZ:AV0Z20410507 Keywords : Precipitate free zone * Diffusion * Coarsening Subject RIV: BJ - Thermodynamic s Impact factor: 0.860, year: 2010

  12. Modeling alternative zoning strategies in forest management

    NARCIS (Netherlands)

    Krcmar, E.; Vertinsky, I.; Kooten, van G.C.

    2003-01-01

    To satisfy public demands for environmental values, forest companies are facing the prospect of a reduction in wood supply and increases in costs. Some Canadian provincial governments have proposed intensifying silviculture in special zones dedicated to timber production as the means for pushing out

  13. Multicoil2: Predicting Coiled Coils and Their Oligomerization States from Sequence in the Twilight Zone

    Science.gov (United States)

    Trigg, Jason; Gutwin, Karl; Keating, Amy E.; Berger, Bonnie

    2011-01-01

    The alpha-helical coiled coil can adopt a variety of topologies, among the most common of which are parallel and antiparallel dimers and trimers. We present Multicoil2, an algorithm that predicts both the location and oligomerization state (two versus three helices) of coiled coils in protein sequences. Multicoil2 combines the pairwise correlations of the previous Multicoil method with the flexibility of Hidden Markov Models (HMMs) in a Markov Random Field (MRF). The resulting algorithm integrates sequence features, including pairwise interactions, through multinomial logistic regression to devise an optimized scoring function for distinguishing dimer, trimer and non-coiled-coil oligomerization states; this scoring function is used to produce Markov Random Field potentials that incorporate pairwise correlations localized in sequence. Multicoil2 significantly improves both coiled-coil detection and dimer versus trimer state prediction over the original Multicoil algorithm retrained on a newly-constructed database of coiled-coil sequences. The new database, comprised of 2,105 sequences containing 124,088 residues, includes reliable structural annotations based on experimental data in the literature. Notably, the enhanced performance of Multicoil2 is evident when tested in stringent leave-family-out cross-validation on the new database, reflecting expected performance on challenging new prediction targets that have minimal sequence similarity to known coiled-coil families. The Multicoil2 program and training database are available for download from http://multicoil2.csail.mit.edu. PMID:21901122

  14. Multicoil2: predicting coiled coils and their oligomerization states from sequence in the twilight zone.

    Directory of Open Access Journals (Sweden)

    Jason Trigg

    Full Text Available The alpha-helical coiled coil can adopt a variety of topologies, among the most common of which are parallel and antiparallel dimers and trimers. We present Multicoil2, an algorithm that predicts both the location and oligomerization state (two versus three helices of coiled coils in protein sequences. Multicoil2 combines the pairwise correlations of the previous Multicoil method with the flexibility of Hidden Markov Models (HMMs in a Markov Random Field (MRF. The resulting algorithm integrates sequence features, including pairwise interactions, through multinomial logistic regression to devise an optimized scoring function for distinguishing dimer, trimer and non-coiled-coil oligomerization states; this scoring function is used to produce Markov Random Field potentials that incorporate pairwise correlations localized in sequence. Multicoil2 significantly improves both coiled-coil detection and dimer versus trimer state prediction over the original Multicoil algorithm retrained on a newly-constructed database of coiled-coil sequences. The new database, comprised of 2,105 sequences containing 124,088 residues, includes reliable structural annotations based on experimental data in the literature. Notably, the enhanced performance of Multicoil2 is evident when tested in stringent leave-family-out cross-validation on the new database, reflecting expected performance on challenging new prediction targets that have minimal sequence similarity to known coiled-coil families. The Multicoil2 program and training database are available for download from http://multicoil2.csail.mit.edu.

  15. A viscoplastic shear-zone model for episodic slow slip events in oceanic subduction zones

    Science.gov (United States)

    Yin, A.; Meng, L.

    2016-12-01

    Episodic slow slip events occur widely along oceanic subduction zones at the brittle-ductile transition depths ( 20-50 km). Although efforts have been devoted to unravel their mechanical origins, it remains unclear about the physical controls on the wide range of their recurrence intervals and slip durations. In this study we present a simple mechanical model that attempts to account for the observed temporal evolution of slow slip events. In our model we assume that slow slip events occur in a viscoplastic shear zone (i.e., Bingham material), which has an upper static and a lower dynamic plastic yield strength. We further assume that the hanging wall deformation is approximated as an elastic spring. We envision the shear zone to be initially locked during forward/landward motion but is subsequently unlocked when the elastic and gravity-induced stress exceeds the static yield strength of the shear zone. This leads to backward/trenchward motion damped by viscous shear-zone deformation. As the elastic spring progressively loosens, the hanging wall velocity evolves with time and the viscous shear stress eventually reaches the dynamic yield strength. This is followed by the termination of the trenchward motion when the elastic stress is balanced by the dynamic yield strength of the shear zone and the gravity. In order to account for the zig-saw slip-history pattern of typical repeated slow slip events, we assume that the shear zone progressively strengthens after each slow slip cycle, possibly caused by dilatancy as commonly assumed or by progressive fault healing through solution-transport mechanisms. We quantify our conceptual model by obtaining simple analytical solutions. Our model results suggest that the duration of the landward motion increases with the down-dip length and the static yield strength of the shear zone, but decreases with the ambient loading velocity and the elastic modulus of the hanging wall. The duration of the backward/trenchward motion depends

  16. Modeling biogechemical reactive transport in a fracture zone

    Energy Technology Data Exchange (ETDEWEB)

    Molinero, Jorge; Samper, Javier; Yang, Chan Bing, and Zhang, Guoxiang; Guoxiang, Zhang

    2005-01-14

    A coupled model of groundwater flow, reactive solute transport and microbial processes for a fracture zone of the Aspo site at Sweden is presented. This is the model of the so-called Redox Zone Experiment aimed at evaluating the effects of tunnel construction on the geochemical conditions prevailing in a fracture granite. It is found that a model accounting for microbially-mediated geochemical processes is able to reproduce the unexpected measured increasing trends of dissolved sulfate and bicarbonate. The model is also useful for testing hypotheses regarding the role of microbial processes and evaluating the sensitivity of model results to changes in biochemical parameters.

  17. Modeling biogeochemical reactive transport in a fracture zone

    International Nuclear Information System (INIS)

    Molinero, Jorge; Samper, Javier; Yang, Chan Bing; Zhang, Guoxiang; Guoxiang, Zhang

    2005-01-01

    A coupled model of groundwater flow, reactive solute transport and microbial processes for a fracture zone of the Aspo site at Sweden is presented. This is the model of the so-called Redox Zone Experiment aimed at evaluating the effects of tunnel construction on the geochemical conditions prevailing in a fracture granite. It is found that a model accounting for microbially-mediated geochemical processes is able to reproduce the unexpected measured increasing trends of dissolved sulfate and bicarbonate. The model is also useful for testing hypotheses regarding the role of microbial processes and evaluating the sensitivity of model results to changes in biochemical parameters

  18. Relating Cohesive Zone Model to Linear Elastic Fracture Mechanics

    Science.gov (United States)

    Wang, John T.

    2010-01-01

    The conditions required for a cohesive zone model (CZM) to predict a failure load of a cracked structure similar to that obtained by a linear elastic fracture mechanics (LEFM) analysis are investigated in this paper. This study clarifies why many different phenomenological cohesive laws can produce similar fracture predictions. Analytical results for five cohesive zone models are obtained, using five different cohesive laws that have the same cohesive work rate (CWR-area under the traction-separation curve) but different maximum tractions. The effect of the maximum traction on the predicted cohesive zone length and the remote applied load at fracture is presented. Similar to the small scale yielding condition for an LEFM analysis to be valid. the cohesive zone length also needs to be much smaller than the crack length. This is a necessary condition for a CZM to obtain a fracture prediction equivalent to an LEFM result.

  19. Modeling Spatial and Temporal Fault Zone Evolution in Basement Rocks

    Science.gov (United States)

    Lunn, R. J.; Moir, H.; Shipton, Z. K.; Willson, J. P.

    2007-05-01

    There is considerable industrial interest in assessing the permeability of faults for the purpose of oil and gas production, deep well injection of waste liquids, underground storage of natural gas and disposal of radioactive waste. Deterministic prior estimation of fault hydraulic properties is highly error prone. Faults zones are formed through a complex interaction of mechanical, hydraulic and chemical processes and their permeability varies considerably over both space and time. Algorithms for predicting fault seal potential using throw and host rock property data exist for clay-rich fault seals but are contentious. In the case of crystalline rocks and sand-sand contacts, no such algorithms exist. In any case, the study of fault growth processes does not suggest that there is a clear or simple relationship between fault throw and the fault zone permeability. To improve estimates of fault zone permeability, it is important to understand the underlying hydro-mechanical processes of fault zone formation. In this research, we explore the spatial and temporal evolution of fault zones through development and application of a 2D hydro-mechanical finite element model. The temporal development of fault zone damage is simulated perpendicular to the main slip surface using Navier's equation for mechanical deformation. The model is applied to study development of fault zones in basement rocks. We simulate the evolution of fault zones from pre-existing joints and explore controls on the growth rate and locations of multiple splay fractures which link-up to form complex damage zones. We explore the temporal evolution of the stress field surrounding the fault tip for both propagation of isolated small faults and for fault linkage Results from these simulations have been validated using outcrop data.

  20. Nonlinear wave energy modelling in the surf zone

    Directory of Open Access Journals (Sweden)

    Th. V. Karambas

    1996-01-01

    Full Text Available Breaking wave energy in the surf zone is modelled through the incorporation of the time dependent energy balance equation in a non linear dispersive wave propagation model. The energy equations solved simultaneously with the momentum and continuity equation. Turbulence effects and the non uniform horizontal velocity distribution due to breaking is introduced in both the energy and momentum equations. The dissipation term is a function of the velocity defect derived from a turbulent analysis. The resulting system predicts both wave characteristics (surface elevation and velocity and the energy distribution inside surf zone. The model is validated against experimental data and analytical expressions.

  1. Modelling flow through unsaturated zones: Sensitivity to unsaturated ...

    Indian Academy of Sciences (India)

    A numerical model to simulate moisture flow through unsaturated zones is developed using the finite element method, and is validated by comparing the model results with those available in the literature. The sensitivities of different processes such as gravity drainage and infiltration to the variations in the unsaturated soil ...

  2. Modelling flow through unsaturated zones: Sensitivity to unsaturated ...

    Indian Academy of Sciences (India)

    M. Senthilkumar (Newgen Imaging) 1461 1996 Oct 15 13:05:22

    MS received 13 October 1997; revised 20 November 2001. Abstract. A numerical model to simulate moisture flow through unsaturated zones is developed using the finite element method, and is validated by comparing the model results with those available in the literature. The sensitivities of different processes such as ...

  3. Sustainable Street Vendors Spatial Zoning Models in Surakarta

    Science.gov (United States)

    Rahayu, M. J.; Putri, R. A.; Rini, E. F.

    2018-02-01

    Various strategies that have been carried out by Surakarta’s government to organize street vendors have not achieved the goal of street vendors’ arrangement comprehensively. The street vendors arrangement strategy consists of physical (spatial) and non-physical. One of the physical arrangements is to define the street vendor’s zoning. Based on the street vendors’ characteristics, there are two alternative locations of stabilization (as one kind of street vendors’ arrangement) that can be used. The aim of this study is to examine those alternative locations to set the street vendor’s zoning models. Quatitative method is used to formulate the spatial zoning model. The street vendor’s zoning models are formulated based on two approaches, which are the distance to their residences and previous trading locations. Geographic information system is used to indicate all street vendors’ residences and trading locations based on their type of goods. Through proximity point distance tool on ArcGIS, we find the closeness of residential location and previous trading location with the alternative location of street vendors’ stabilization. The result shows that the location was chosen by the street vendors to sell their goods mainly consider the proximity to their homes. It also shows street vendor’s zoning models which based on the type of street vendor’s goods.

  4. Unsaturated zone flow modeling for GWTT-95

    International Nuclear Information System (INIS)

    Ho, C.K.; Altman, S.J.; McKenna, S.A.; Arnold, B.W.

    1995-01-01

    In accordance with the Nuclear Regulatory Commission regulation regarding groundwater travel times at geologic repositories, various models of unsaturated flow in fractured tuff have been developed and implemented to assess groundwater travel times at the potential repository at Yucca Mountain, Nevada. Kaplan used one-dimensional models to describe the uncertainty and sensitivity of travel times to various processes at Yucca Mountain. Robey and Arnold et al. used a two-dimensional equivalent continuum model (ECM) with inter- and intra-unit heterogeneity in an attempt to assess fast-flow paths through the unsaturated, fractured tuff at Yucca Mountain (GWTT-94). However, significant flow through the fractures in previous models was not simulated due to the characteristics of the ECM, which requires the matrix to be nearly saturated before flow through the fractures is initiated. In the current study (GWTT-95), four two-dimensional cross-sections at Yucca Mountain are simulated using both the ECM and dual-permeability (DK) models. The properties of both the fracture and matrix domains are geostatistically simulated, yielding completely heterogeneous continua. Then, simulations of flow through the four cross-sections are performed using spatially nonuniform infiltration boundary conditions. Steady-state groundwater travel times from the potential repository to the water table are calculated

  5. Modelling Wind Turbine Inflow: The Induction Zone

    DEFF Research Database (Denmark)

    Meyer Forsting, Alexander Raul

    to the rotor, but requires exact knowledge of the flow deceleration to estimate the available, undis- turbed kinetic energy. Thus this thesis explores, mostly numerically, any wind turbine or environmental dependencies of this deceleration. The computational fluid dynamics model (CFD) employed is validated......A wind turbine decelerates the wind in front of its rotor by extracting kinetic energy. The wind speed reduction is maximal at the rotor and negligible more than five rotor radii upfront. By measuring wind speed this far from the rotor, the turbine’s performance is determined without any rotor bias...... significant parameter. Exploiting this singu- lar dependency, a fast semi-empirical model is devised that accurately predicts the velocity deficit upstream of a single turbine. Near-rotor mea-surements in combination with this model are able to retrieve the kinetic energy available to the turbine in flat...

  6. `Dhara': An Open Framework for Critical Zone Modeling

    Science.gov (United States)

    Le, P. V.; Kumar, P.

    2016-12-01

    Processes in the Critical Zone, which sustain terrestrial life, are tightly coupled across hydrological, physical, biological, chemical, pedological, geomorphological and ecological domains over both short and long timescales. Observations and quantification of the Earth's surface across these domains using emerging high resolution measurement technologies such as light detection and ranging (lidar) and hyperspectral remote sensing are enabling us to characterize fine scale landscape attributes over large spatial areas. This presents a unique opportunity to develop novel approaches to model the Critical Zone that can capture fine scale intricate dependencies across the different processes in 3D. The development of interdisciplinary tools that transcend individual disciplines and capture new levels of complexity and emergent properties is at the core of Critical Zone science. Here we introduce an open framework for high-performance computing model (`Dhara') for modeling complex processes in the Critical Zone. The framework is designed to be modular in structure with the aim to create uniform and efficient tools to facilitate and leverage process modeling. It also provides flexibility to maintain, collaborate, and co-develop additional components by the scientific community. We show the essential framework that simulates ecohydrologic dynamics, and surface - sub-surface coupling in 3D using hybrid parallel CPU-GPU. We demonstrate that the open framework in Dhara is feasible for detailed, multi-processes, and large-scale modeling of the Critical Zone, which opens up exciting possibilities. We will also present outcomes from a Modeling Summer Institute led by Intensively Managed Critical Zone Observatory (IMLCZO) with representation from several CZOs and international representatives.

  7. Models of auroral-zone conductances

    Science.gov (United States)

    Reiff, P. H.

    1984-01-01

    The magnetosphere-ionosphere system is strongly coupled, with magnetospheric Birkeland currents feeding ionospheric Pedersen and Hall currents. Central to any computer simulation of this system is a detailed, valid conductivity model. An accurate conductivity model is also vital in order to infer Birkeland currents and electric field patterns from inversions of magnetometer chain data. Several recent attempts at constructing conductivity models are presented and their strengths and weaknesses discussed. Incoherent scatter radar measurements can determine height profiles of electron content, from which Pedersen and Hall conductances may be calculated. These yield excellent spatial and good temporal resolution; however, they are limited in field of view. A global pattern requires either 24 hours of data or a chain of stations. Synoptic empirical models (quantized by indices such as Kp or AE) typically are limited by their large bin size (1 deg invariant latitude x 1 hour MLT), and cannot reproduce arcs. Estimating conductivity globally from Dynamics Explorer auroral images is promising, and can yield reasonable time scales (of about 10 minutes); however, this procedure is still only now being tested.

  8. Modelling Spatial and Temporal Fault Zone Evolution in Basement Rocks

    Science.gov (United States)

    Lunn, R. J.; Willson, J. P.; Shipton, Z. K.

    2006-12-01

    There is considerable industrial interest in assessing the permeability of faults for the purpose of oil and gas production, deep well injection of waste liquids, underground storage of natural gas and disposal of radioactive waste. Prior estimation of fault hydraulic properties is highly error prone. Faults zones are formed through a complex interaction of mechanical, hydraulic and chemical processes and their permeability varies considerably over both space and time. Algorithms for predicting fault seal potential using throw and host rock property data exist for clay-rich fault seals but are contentious. In the case of crystalline rocks and sand-sand contacts, no such algorithms exist. In any case, the study of fault growth processes does not suggest that there is a clear or simple relationship between fault throw and the fault zone permeability. To improve estimates of fault zone permeability, it is important to understand the underlying hydro-mechanical processes of fault zone formation. In this research, we explore the spatial and temporal evolution of fault zones through development and application of a 2D hydro-mechanical finite element model. The development of fault zone damage is simulated perpendicular to the main slip surface using a fully coupled solution of Navier's equation for mechanical deformation and Darcy's Law/conservation of fluid mass for subsurface fluid flow. The model is applied to study development of fault zones in basement rocks, based on the conceptual model of S. J. Martell, J. Struct. Geol. 12(7):869-882, 1990. We simulate the evolution of fault zones from pre-existing joints and explore controls on the growth rate and locations of multiple splay fractures which link-up to form complex damage zones. We are the first researchers to successfully simulate the temporal and spatial evolution of multiple wing cracks, tertiary fracturing, antithetic fractures propagating into the compressive region, infill fracturing between faults and

  9. MODELLING OF POSTSEISMIC PROCESSES IN SUBDUCTION ZONES

    Directory of Open Access Journals (Sweden)

    Irina S. Vladimirova

    2012-01-01

    Full Text Available Large intraplate subduction earthquakes are generally accompanied by prolonged and intense postseismic anomalies. In the present work, viscoelastic relaxation in the upper mantle and the asthenosphere is considered as a main mechanism responsible for the occurrence of such postseismic effects. The study of transient processes is performed on the basis of data on postseismic processes accompanying the first Simushir earthquake on 15 November 2006 and Maule earthquake on 27 February 2010.The methodology of modelling a viscoelastic relaxation process after a large intraplate subduction earthquake is presented. A priori parameters of the selected model describing observed postseismic effects are adjusted by minimizing deviations between modeled surface displacements and actual surface displacements recorded by geodetic methods through solving corresponding inverse problems.The presented methodology yielded estimations of Maxwell’s viscosity of the asthenosphere of the central Kuril Arc and also of the central Chile. Besides, postseismic slip distribution patterns were obtained for the focus of the Simushir earthquake of 15 November 2006 (Mw=8.3 (Figure 3, and distribution patterns of seismic and postseismic slip were determined for the focus of the Maule earthquake of 27 February 2010 (Mw=8.8 (Figure 6. These estimations and patterns can provide for prediction of the intensity of viscoelastic stress attenuation in the asthenosphere; anomalous values should be taken into account as adjustment factors when analyzing inter-seismic deformation in order to ensure correct estimation of the accumulated elastic seismogenic potential.

  10. Mixing effects on nitrogen and oxygen concentrations and the relationship to mean residence time in a hyporheic zone of a riffle-pool sequence

    Science.gov (United States)

    Naranjo, Ramon C.; Niswonger, Richard G.; Clinton Davis,

    2015-01-01

    Flow paths and residence times in the hyporheic zone are known to influence biogeochemical processes such as nitrification and denitrification. The exchange across the sediment-water interface may involve mixing of surface water and groundwater through complex hyporheic flow paths that contribute to highly variable biogeochemically active zones. Despite the recognition of these patterns in the literature, conceptualization and analysis of flow paths and nitrogen transformations beneath riffle-pool sequences often neglect to consider bed form driven exchange along the entire reach. In this study, the spatial and temporal distribution of dissolved oxygen (DO), nitrate (NO3-) and ammonium (NH4+) were monitored in the hyporheic zone beneath a riffle-pool sequence on a losing section of the Truckee River, NV. Spatially-varying hyporheic exchange and the occurrence of multi-scale hyporheic mixing cells are shown to influence concentrations of DO and NO3- and the mean residence time (MRT) of riffle and pool areas. Distinct patterns observed in piezometers are shown to be influenced by the first large flow event following a steady 8 month period of low flow conditions. Increases in surface water discharge resulted in reversed hydraulic gradients and production of nitrate through nitrification at small vertical spatial scales (0.10 to 0.25 m) beneath the sediment-water interface. In areas with high downward flow rates and low MRT, denitrification may be limited. The use of a longitudinal two-dimensional flow model helped identify important mechanisms such as multi-scale hyporheic mixing cells and spatially varying MRT, an important driver for nitrogen transformation in the riverbed. Our observations of DO and NO3- concentrations and model simulations highlight the role of multi-scale hyporheic mixing cells on MRT and nitrogen transformations in the hyporheic zone of riffle-pool sequences. This article is protected by copyright. All rights reserved.

  11. PROBABILISTIC ZONING OF ADJACENT CATCHMENTS BY PHYSICAL MODELING

    Directory of Open Access Journals (Sweden)

    Yu. B. Andreev

    2012-01-01

    Full Text Available Now the probabilistic zoning of avalanche sites is being made either on the basis of the available field data, or using the mathematical and physical modeling of avalanche dynamics processes. The work purpose consisted in research of interaction and compiling probabilistic zoning maps of two adjacent avalanche sites by a physical modeling method. For the two adjacent sites № 9 and 10 on the slope of northern exposition ofTchegetMountain(Elbrus region,Caucasus the model of this slope with the scale of 1: 2 500 was created. The model dimension is 0,82 × 1,1 ×0,57 m. This model was produced using the 4-mm plywood sheets imposed against each other. The model horizontals correspond to the10 mnatural ones. The model slope was also surfaced by thin gypsum lay and then varnished. The fine-grained sawdust (0.1 mm with a natural friction angle of 43º has been chosen as the loose material modeling snow. A series of experiments on modeling avalanche releases from the two sites were carried out resulted in the measurements of avalanche deposit parameters such as run-out distance and length, width and thickness of deposits. The similarity criteria were used during the experiments. The morphometric features of adjacent sites interaction are revealed. The basic result of the carried out work will consist in the probabilistic zoning map of two adjacent sites № 9 and 10.

  12. Modelling flow through unsaturated zones: Sensitivity to unsaturated ...

    Indian Academy of Sciences (India)

    M. Senthilkumar (Newgen Imaging) 1461 1996 Oct 15 13:05:22

    water flow through unsaturated zones and study the effect of unsaturated soil parameters on water movement during different processes such as gravity drainage and infiltration. 2. Modelling Richards equation for vertical unsaturated flow. For one-dimensional vertical flow in unsaturated soil, the pressure-head based ...

  13. Internal tectonic structure of the Central American Wadati-Benioff zone based on analysis of aftershock sequences

    Czech Academy of Sciences Publication Activity Database

    Špičák, Aleš; Hanuš, Václav; Vaněk, Jiří; Běhounková, Marie

    2007-01-01

    Roč. 112, B9 (2007), B09304/1-B09304/18 ISSN 0148-0227 R&D Projects: GA ČR GA205/03/1203 Institutional research plan: CEZ:AV0Z30120515 Keywords : Wadati-Benioff zone * aftershocks sequences * internal tectonic structure Subject RIV: DC - Siesmology, Volcanology, Earth Structure Impact factor: 2.953, year: 2007

  14. Stochastic modelling of daily rainfall sequences

    NARCIS (Netherlands)

    Buishand, T.A.

    1977-01-01

    Rainfall series of different climatic regions were analysed with the aim of generating daily rainfall sequences. A survey of the data is given in I, 1. When analysing daily rainfall sequences one must be aware of the following points:
    a. Seasonality. Because of seasonal variation

  15. Biostratigraphy, facies and sequence stratigraphy of the Sarvak Formation in the Ahwaz Oil Field, North Dezful Embayment Zone

    Directory of Open Access Journals (Sweden)

    Mohammad Hasan Kazemzadeh

    2016-08-01

    Full Text Available Paleontological studies lead to recognition of 21 genera and 16 species of benthic foraminifera, 5 genera and 6 species of planktonic foraminifera and 3 genera and 3 species of oligosteginids. The vertical distribution of fauna lead to identification of 5 biozones including: Favusella washitensis Range Zone, Oligostegina Assemblage Zone, Rudist debris Zone, Nezzazata-Alveolinids Assemblage Zone, Nezzazatinella-Dicyclina Assemblage Zone. Based on the indicated biozones, the age of the Sarvak Formation is Late Albian to Early Turonian in the study area. Eleven carbonate facies belonging to four environments including tidal flat, restricted and semi-restricted lagoon, shoal and open marine are recognized. The identified facies are deposited on the homoclinal ramp setting. Based on the vertical changes of facies and recognized depositional environments, four third-order depositional sequences are represented. The transgressive systems tracts mainly comprises of open marine facies including sponge spicule, oligosteginid, echinoid and benthic foraminifera, while the highstand systems tracts mainly consists of shoal facies rich in bioclast, and restricted and semi-restricted lagoon facies rich in porcellaneous and hyaline benthic foraminifera and peloid. The maximum flooding surface represented by open marine facies including echinoid and planktonic foraminifera

  16. Calibration of the Site-Scale Saturated Zone Flow Model

    Energy Technology Data Exchange (ETDEWEB)

    G. A. Zyvoloski

    2001-06-28

    The purpose of the flow calibration analysis work is to provide Performance Assessment (PA) with the calibrated site-scale saturated zone (SZ) flow model that will be used to make radionuclide transport calculations. As such, it is one of the most important models developed in the Yucca Mountain project. This model will be a culmination of much of our knowledge of the SZ flow system. The objective of this study is to provide a defensible site-scale SZ flow and transport model that can be used for assessing total system performance. A defensible model would include geologic and hydrologic data that are used to form the hydrogeologic framework model; also, it would include hydrochemical information to infer transport pathways, in-situ permeability measurements, and water level and head measurements. In addition, the model should include information on major model sensitivities. Especially important are those that affect calibration, the direction of transport pathways, and travel times. Finally, if warranted, alternative calibrations representing different conceptual models should be included. To obtain a defensible model, all available data should be used (or at least considered) to obtain a calibrated model. The site-scale SZ model was calibrated using measured and model-generated water levels and hydraulic head data, specific discharge calculations, and flux comparisons along several of the boundaries. Model validity was established by comparing model-generated permeabilities with the permeability data from field and laboratory tests; by comparing fluid pathlines obtained from the SZ flow model with those inferred from hydrochemical data; and by comparing the upward gradient generated with the model with that observed in the field. This analysis is governed by the Office of Civilian Radioactive Waste Management (OCRWM) Analysis and Modeling Report (AMR) Development Plan ''Calibration of the Site-Scale Saturated Zone Flow Model'' (CRWMS M&O 1999

  17. Calibration of the Site-Scale Saturated Zone Flow Model

    International Nuclear Information System (INIS)

    Zyvoloski, G. A.

    2001-01-01

    The purpose of the flow calibration analysis work is to provide Performance Assessment (PA) with the calibrated site-scale saturated zone (SZ) flow model that will be used to make radionuclide transport calculations. As such, it is one of the most important models developed in the Yucca Mountain project. This model will be a culmination of much of our knowledge of the SZ flow system. The objective of this study is to provide a defensible site-scale SZ flow and transport model that can be used for assessing total system performance. A defensible model would include geologic and hydrologic data that are used to form the hydrogeologic framework model; also, it would include hydrochemical information to infer transport pathways, in-situ permeability measurements, and water level and head measurements. In addition, the model should include information on major model sensitivities. Especially important are those that affect calibration, the direction of transport pathways, and travel times. Finally, if warranted, alternative calibrations representing different conceptual models should be included. To obtain a defensible model, all available data should be used (or at least considered) to obtain a calibrated model. The site-scale SZ model was calibrated using measured and model-generated water levels and hydraulic head data, specific discharge calculations, and flux comparisons along several of the boundaries. Model validity was established by comparing model-generated permeabilities with the permeability data from field and laboratory tests; by comparing fluid pathlines obtained from the SZ flow model with those inferred from hydrochemical data; and by comparing the upward gradient generated with the model with that observed in the field. This analysis is governed by the Office of Civilian Radioactive Waste Management (OCRWM) Analysis and Modeling Report (AMR) Development Plan ''Calibration of the Site-Scale Saturated Zone Flow Model'' (CRWMS M and O 1999a)

  18. The Cascadia Subduction Zone: two contrasting models of lithospheric structure

    Science.gov (United States)

    Romanyuk, T.V.; Blakely, R.; Mooney, W.D.

    1998-01-01

    The Pacific margin of North America is one of the most complicated regions in the world in terms of its structure and present day geodynamic regime. The aim of this work is to develop a better understanding of lithospheric structure of the Pacific Northwest, in particular the Cascadia subduction zone of Southwest Canada and Northwest USA. The goal is to compare and contrast the lithospheric density structure along two profiles across the subduction zone and to interpet the differences in terms of active processes. The subduction of the Juan de Fuca plate beneath North America changes markedly along the length of the subduction zone, notably in the angle of subduction, distribution of earthquakes and volcanism, goelogic and seismic structure of the upper plate, and regional horizontal stress. To investigate these characteristics, we conducted detailed density modeling of the crust and mantle along two transects across the Cascadia subduction zone. One crosses Vancouver Island and the Canadian margin, the other crosses the margin of central Oregon.

  19. Composite Binary Sequences with a Large Ensemble and Zero Correlation Zone

    Directory of Open Access Journals (Sweden)

    S. S. Yudachev

    2015-01-01

    Full Text Available The article considers a proposed class of derived signals such as composite binary sequences for application in advanced spread spectrum radio systems of various purposes, using signals based on spectrum spreading by direct sequence method. Considered composite sequences, having a representative set of lengths and unique correlation properties, compares favorably with the widely used at present large ensembles formed on a single algorithmic basis. To evaluate the properties of the composite sequences generated on the basis of two components - the Barker code and Kerdock sequences, expressions of periodic and aperiodic correlation functions are given.An algorithm for generating practical ensembles of composite sequences is presented. On the basis of the algorithm and its software implementation in C #, the samples of the sequence ensembles of various lengths were obtained and their periodic and aperiodic correlation functions and statistical characteristics were studied in detail. As an illustration, some of the most typical correlation functions are presented. The most remarkable characteristics allowing a ssessing the feasibility of using this type of sequences in the design of specific types of radio systems are considered.On the basis of the proposed program and the performed calculations the conclusions can be drawn about the possibility of using the sequences of these classes, with the aim of reducing intra-system disturbance in the projected spread spectrum CDMA.

  20. Predicting Biological Information Flow in a Model Oxygen Minimum Zone

    Science.gov (United States)

    Louca, S.; Hawley, A. K.; Katsev, S.; Beltran, M. T.; Bhatia, M. P.; Michiels, C.; Capelle, D.; Lavik, G.; Doebeli, M.; Crowe, S.; Hallam, S. J.

    2016-02-01

    Microbial activity drives marine biochemical fluxes and nutrient cycling at global scales. Geochemical measurements as well as molecular techniques such as metagenomics, metatranscriptomics and metaproteomics provide great insight into microbial activity. However, an integration of molecular and geochemical data into mechanistic biogeochemical models is still lacking. Recent work suggests that microbial metabolic pathways are, at the ecosystem level, strongly shaped by stoichiometric and energetic constraints. Hence, models rooted in fluxes of matter and energy may yield a holistic understanding of biogeochemistry. Furthermore, such pathway-centric models would allow a direct consolidation with meta'omic data. Here we present a pathway-centric biogeochemical model for the seasonal oxygen minimum zone in Saanich Inlet, a fjord off the coast of Vancouver Island. The model considers key dissimilatory nitrogen and sulfur fluxes, as well as the population dynamics of the genes that mediate them. By assuming a direct translation of biocatalyzed energy fluxes to biosynthesis rates, we make predictions about the distribution and activity of the corresponding genes. A comparison of the model to molecular measurements indicates that the model explains observed DNA, RNA, protein and cell depth profiles. This suggests that microbial activity in marine ecosystems such as oxygen minimum zones is well described by DNA abundance, which, in conjunction with geochemical constraints, determines pathway expression and process rates. Our work further demonstrates how meta'omic data can be mechanistically linked to environmental redox conditions and biogeochemical processes.

  1. Biological sequence analysis: probabilistic models of proteins and nucleic acids

    National Research Council Canada - National Science Library

    Durbin, Richard

    1998-01-01

    ... analysis methods are now based on principles of probabilistic modelling. Examples of such methods include the use of probabilistically derived score matrices to determine the significance of sequence alignments, the use of hidden Markov models as the basis for profile searches to identify distant members of sequence families, and the inference...

  2. Modelling of two-zone accelerator-driven systems

    Directory of Open Access Journals (Sweden)

    V. A. Babenko

    2012-09-01

    Full Text Available Neutron-physical modelings of two-zone subcritical reactor driven by high-intensity neutron generator are considered. The cascade principle in subcritical reactors, the use of which can hypothetically substantially amplify the neutron flux from the external source is discussed in this article. The theoretical preconditions of the cascade principle are discussed, and the directions of practical realization of the cascade subcritical system are considered, namely the possible methods of neutron feedback between reactor sections elimination. The results of Monte Carlo neutron-physical modeling of the cascade subcritical systems are presented and discussed.

  3. Numerical modeling of continental lithospheric weak zone over plume

    Science.gov (United States)

    Perepechko, Y. V.; Sorokin, K. E.

    2011-12-01

    The work is devoted to the development of magmatic systems in the continental lithosphere over diffluent mantle plumes. The areas of tension originating over them are accompanied by appearance of fault zones, and the formation of permeable channels, which are distributed magmatic melts. The numerical simulation of the dynamics of deformation fields in the lithosphere due to convection currents in the upper mantle, and the formation of weakened zones that extend up to the upper crust and create the necessary conditions for the formation of intermediate magma chambers has been carried out. Thermodynamically consistent non-isothermal model simulates the processes of heat and mass transfer of a wide class of magmatic systems, as well as the process of strain localization in the lithosphere and their influence on the formation of high permeability zones in the lower crust. The substance of the lithosphere is a rheologic heterophase medium, which is described by a two-velocity hydrodynamics. This makes it possible to take into account the process of penetration of the melt from the asthenosphere into the weakened zone. The energy dissipation occurs mainly due to interfacial friction and inelastic relaxation of shear stresses. The results of calculation reveal a nonlinear process of the formation of porous channels and demonstrate the diversity of emerging dissipative structures which are determined by properties of both heterogeneous lithosphere and overlying crust. Mutual effect of a permeable channel and the corresponding filtration process of the melt on the mantle convection and the dynamics of the asthenosphere have been studied. The formation of dissipative structures in heterogeneous lithosphere above mantle plumes occurs in accordance with the following scenario: initially, the elastic behavior of heterophase lithosphere leads to the formation of the narrow weakened zone, though sufficiently extensive, with higher porosity. Further, the increase in the width of

  4. An elastic plate model for interseismic deformation in subduction zones

    Science.gov (United States)

    Kanda, Ravi V. S.; Simons, Mark

    2010-03-01

    Geodetic observations of interseismic surface deformation in the vicinity of subduction zones are frequently interpreted using simple kinematic elastic dislocation models (EDM). In this theoretical study, we develop a kinematic EDM that simulates plate subduction over the interseismic period (the elastic subducting plate model (ESPM)) having only 2 more degrees of freedom than the well-established back slip model (BSM): an elastic plate thickness and the fraction of flexural stresses due to bending at the trench that are released continuously. Unlike the BSM, in which steady state deformation in both plates is assumed to be negligible, the ESPM includes deformation in the subducting and overriding plates (owing to plate thickness), while still preserving the correct sense of convergence velocity between the subducting and overriding plates, as well as zero net steady state vertical offset between the two plates when integrated over many seismic cycles. The ESPM links elastic plate flexure processes to interseismic deformation and helps clarify under what conditions the BSM is appropriate for fitting interseismic geodetic data at convergent margins. We show that the ESPM is identical to the BSM in the limiting case of zero plate thickness, thereby providing an alternative motivation for the BSM. The ESPM also provides a consistent convention for applying the BSM to any megathrust interface geometry. Even in the case of nonnegligible plate thickness, the deformation field predicted by the ESPM reduces to that of the BSM if stresses related to plate flexure at the trench are released either continuously and completely at shallow depths during the interseismic period or deep in the subduction zone (below ˜100 km). However, if at least a portion of these stresses are not continuously released in the shallow portion of the subduction zone (via seismic or aseismic events), then the predicted surface velocities of these two models can differ significantly at horizontal

  5. Quantum Rabi model in the Brillouin zone with ultracold atoms

    Science.gov (United States)

    Felicetti, Simone; Rico, Enrique; Sabin, Carlos; Ockenfels, Till; Koch, Johannes; Leder, Martin; Grossert, Christopher; Weitz, Martin; Solano, Enrique

    2017-01-01

    The quantum Rabi model describes the interaction between a two-level quantum system and a single bosonic mode. We propose a method to perform a quantum simulation of the quantum Rabi model, introducing an implementation of the two-level system provided by the occupation of Bloch bands in the first Brillouin zone by ultracold atoms in tailored optical lattices. The effective qubit interacts with a quantum harmonic oscillator implemented in an optical dipole trap. Our realistic proposal allows one to experimentally investigate the quantum Rabi model for extreme parameter regimes, which are not achievable with natural light-matter interactions. When the simulated wave function exceeds the validity region of the simulation, we identify a generalized version of the quantum Rabi model in a periodic phase space.

  6. DISCRETE DEFORMATION WAVE DYNAMICS IN SHEAR ZONES: PHYSICAL MODELLING RESULTS

    Directory of Open Access Journals (Sweden)

    S. A. Bornyakov

    2016-01-01

    Full Text Available Observations of earthquake migration along active fault zones [Richter, 1958; Mogi, 1968] and related theoretical concepts [Elsasser, 1969] have laid the foundation for studying the problem of slow deformation waves in the lithosphere. Despite the fact that this problem has been under study for several decades and discussed in numerous publications, convincing evidence for the existence of deformation waves is still lacking. One of the causes is that comprehensive field studies to register such waves by special tools and equipment, which require sufficient organizational and technical resources, have not been conducted yet.The authors attempted at finding a solution to this problem by physical simulation of a major shear zone in an elastic-viscous-plastic model of the lithosphere. The experiment setup is shown in Figure 1 (A. The model material and boundary conditions were specified in accordance with the similarity criteria (described in detail in [Sherman, 1984; Sherman et al., 1991; Bornyakov et al., 2014]. The montmorillonite clay-and-water paste was placed evenly on two stamps of the installation and subject to deformation as the active stamp (1 moved relative to the passive stamp (2 at a constant speed. The upper model surface was covered with fine sand in order to get high-contrast photos. Photos of an emerging shear zone were taken every second by a Basler acA2000-50gm digital camera. Figure 1 (B shows an optical image of a fragment of the shear zone. The photos were processed by the digital image correlation method described in [Sutton et al., 2009]. This method estimates the distribution of components of displacement vectors and strain tensors on the model surface and their evolution over time [Panteleev et al., 2014, 2015].Strain fields and displacements recorded in the optical images of the model surface were estimated in a rectangular box (220.00×72.17 mm shown by a dot-and-dash line in Fig. 1, A. To ensure a sufficient level of

  7. Multiobjective Fuzzy Mixed Assembly Line Sequencing Optimization Model

    OpenAIRE

    Tahriri, Farzad; Zawiah Md Dawal, Siti; Taha, Zahari

    2014-01-01

    It can be deduced from previous studies that there exists a research gap in assembly line sequencing optimization model for mixed-model production lines. In particular, there is a lack of studies which focus on the integration between job shop and assembly lines using fuzzy techniques. Hence, this paper is aimed at addressing the multiobjective mixed-model assembly line sequencing problem by integrating job shop and assembly production lines for factories with modular layouts. The primary go...

  8. Slab2 - Updated Subduction Zone Geometries and Modeling Tools

    Science.gov (United States)

    Moore, G.; Hayes, G. P.; Portner, D. E.; Furtney, M.; Flamme, H. E.; Hearne, M. G.

    2017-12-01

    The U.S. Geological Survey database of global subduction zone geometries (Slab1.0), is a highly utilized dataset that has been applied to a wide range of geophysical problems. In 2017, these models have been improved and expanded upon as part of the Slab2 modeling effort. With a new data driven approach that can be applied to a broader range of tectonic settings and geophysical data sets, we have generated a model set that will serve as a more comprehensive, reliable, and reproducible resource for three-dimensional slab geometries at all of the world's convergent margins. The newly developed framework of Slab2 is guided by: (1) a large integrated dataset, consisting of a variety of geophysical sources (e.g., earthquake hypocenters, moment tensors, active-source seismic survey images of the shallow slab, tomography models, receiver functions, bathymetry, trench ages, and sediment thickness information); (2) a dynamic filtering scheme aimed at constraining incorporated seismicity to only slab related events; (3) a 3-D data interpolation approach which captures both high resolution shallow geometries and instances of slab rollback and overlap at depth; and (4) an algorithm which incorporates uncertainties of contributing datasets to identify the most probable surface depth over the extent of each subduction zone. Further layers will also be added to the base geometry dataset, such as historic moment release, earthquake tectonic providence, and interface coupling. Along with access to several queryable data formats, all components have been wrapped into an open source library in Python, such that suites of updated models can be released as further data becomes available. This presentation will discuss the extent of Slab2 development, as well as the current availability of the model and modeling tools.

  9. Petrology, chronology and sequence of vein systems: Systematic magmatic and hydrothermal history of a major intracontinental shear zone, Canadian Appalachians

    Science.gov (United States)

    Pe-Piper, Georgia; Piper, David J. W.; McFarlane, Chris R. M.; Sangster, Chris; Zhang, Yuanyuan; Boucher, Brandon

    2018-04-01

    Intra-continental shear zones developed during continental collision may experience prolonged magmatism and mineralization. The Cobequid Shear Zone formed part of a NE-SW-trending, orogen-parallel shear system in the late Devonian-early Carboniferous, where syn-tectonic granite-gabbro plutons and volcanic rocks 4 km thick were progressively deformed. In late Carboniferous to Permian, Alleghanian collision of Africa with Laurentia formed the E-W trending Minas Fault Zone, reactivating parts of the Cobequid Shear Zone. The 50 Ma history of hydrothermal mineralization following pluton emplacement is difficult to resolve from field relationships of veins, but SEM study of thin sections provides clear detail on the sequence of mineralization. The general paragenesis is: albite ± quartz ± chlorite ± monazite → biotite → calcite, allanite, pyrite → Fe-carbonates, Fe-oxides, minor sulfides, calcite and synchysite. Chronology was determined from literature reports and new U-Pb LA-ICPMS dating of monazite and allanite in veins. Vein mineralization was closely linked to magmatic events. Vein emplacement occurred preferentially during fault movement recognised from basin-margin inversion, as a result of fractures opening in the damage zone of master faults. The sequence of mineralization, from ca. 355 Ma riebeckite and albite veins to ca. 327 (-305?) Ma siderite-magnetite and sulfide mineralization, resembles Precambrian iron-oxide-copper-gold (IOCG) systems in the literature. The abundant magmatic Na, halogens and CO2 in veins and some magmatic bodies, characteristic of IOCG systems, were derived from the deeply subducted Rheic Ocean slab with little terrigenous sediment. Regional extension of the Magdalen Basin caused asthenospheric upwelling and melting of the previously metasomatized sub-continental lithospheric mantle. Crustal scale strike-slip faulting facilitated the rise of magmas, resulting in high heat flow driving an active hydrothermal system. Table S2

  10. Thermodynamics-based models of transcriptional regulation with gene sequence.

    Science.gov (United States)

    Wang, Shuqiang; Shen, Yanyan; Hu, Jinxing

    2015-12-01

    Quantitative models of gene regulatory activity have the potential to improve our mechanistic understanding of transcriptional regulation. However, the few models available today have been based on simplistic assumptions about the sequences being modeled or heuristic approximations of the underlying regulatory mechanisms. In this work, we have developed a thermodynamics-based model to predict gene expression driven by any DNA sequence. The proposed model relies on a continuous time, differential equation description of transcriptional dynamics. The sequence features of the promoter are exploited to derive the binding affinity which is derived based on statistical molecular thermodynamics. Experimental results show that the proposed model can effectively identify the activity levels of transcription factors and the regulatory parameters. Comparing with the previous models, the proposed model can reveal more biological sense.

  11. Definition of zones with different levels of productivity within an agricultural field using fuzzy modeling

    Science.gov (United States)

    Zoning of agricultural fields is an important task for utilization of precision farming technology. One method for the definition of zones with different levels of productivity is based on fuzzy indicator model. Fuzzy indicator model for identification of zones with different levels of productivit...

  12. Discrete shear-transformation-zone plasticity modeling of notched bars

    Science.gov (United States)

    Kondori, Babak; Amine Benzerga, A.; Needleman, Alan

    2018-02-01

    Plane strain tension analyses of un-notched and notched bars are carried out using discrete shear transformation zone plasticity. In this framework, the carriers of plastic deformation are shear transformation zones (STZs) which are modeled as Eshelby inclusions. Superposition is used to represent a boundary value problem solution in terms of discretely modeled Eshelby inclusions, given analytically for an infinite elastic medium, and an image solution that enforces the prescribed boundary conditions. The image problem is a standard linear elastic boundary value problem that is solved by the finite element method. Potential STZ activation sites are randomly distributed in the bars and constitutive relations are specified for their evolution. Results are presented for un-notched bars, for bars with blunt notches and for bars with sharp notches. The computed stress-strain curves are serrated with the magnitude of the associated stress-drops depending on bar size, notch acuity and STZ evolution. Cooperative deformation bands (shear bands) emerge upon straining and, in some cases, high stress levels occur within the bands. Effects of specimen geometry and size on the stress-strain curves are explored. Depending on STZ kinetics, notch strengthening, notch insensitivity or notch weakening are obtained. The analyses provide a rationale for some conflicting findings regarding notch effects on the mechanical response of metallic glasses.

  13. Validating a perceptual distraction model in a personal two-zone sound system

    DEFF Research Database (Denmark)

    Rämö, Jussi; Christensen, Lasse; Bech, Søren

    2017-01-01

    using a simple loudspeaker setup, consisting of only two loudspeakers, one for the target sound source and the other for the interfering sound source. Recently, the model was successfully validated in a complex personal sound-zone system with speech-on-music stimuli. Second round of validations were...... conducted by physically altering the sound-zone system and running a set of new listening experiments utilizing two sound zones within the sound-zone system. Thus, validating the model using a different sound-zone system with both speech-on-music and music-on-speech stimuli sets. Preliminary results show...... the performance of personal sound-zone systems....

  14. Using heat as a tracer to estimate spatially distributed mean residence times in the hyporheic zone of a riffle-pool sequence

    Science.gov (United States)

    Naranjo, Ramon C.

    2013-01-01

    Biochemical reactions that occur in the hyporheic zone are highly dependent on the time solutes that are in contact with sediments of the riverbed. In this investigation, we developed a 2-D longitudinal flow and solute-transport model to estimate the spatial distribution of mean residence time in the hyporheic zone. The flow model was calibrated using observations of temperature and pressure, and the mean residence times were simulated using the age-mass approach for steady-state flow conditions. The approach used in this investigation includes the mixing of different ages and flow paths of water through advection and dispersion. Uncertainty of flow and transport parameters was evaluated using standard Monte Carlo and the generalized likelihood uncertainty estimation method. Results of parameter estimation support the presence of a low-permeable zone in the riffle area that induced horizontal flow at a shallow depth within the riffle area. This establishes shallow and localized flow paths and limits deep vertical exchange. For the optimal model, mean residence times were found to be relatively long (9–40.0 days). The uncertainty of hydraulic conductivity resulted in a mean interquartile range (IQR) of 13 days across all piezometers and was reduced by 24% with the inclusion of temperature and pressure observations. To a lesser extent, uncertainty in streambed porosity and dispersivity resulted in a mean IQR of 2.2 and 4.7 days, respectively. Alternative conceptual models demonstrate the importance of accounting for the spatial distribution of hydraulic conductivity in simulating mean residence times in a riffle-pool sequence.

  15. Multivariate models to classify Tuscan virgin olive oils by zone.

    Directory of Open Access Journals (Sweden)

    Alessandri, Stefano

    1999-10-01

    Full Text Available In order to study and classify Tuscan virgin olive oils, 179 samples were collected. They were obtained from drupes harvested during the first half of November, from three different zones of the Region. The sampling was repeated for 5 years. Fatty acids, phytol, aliphatic and triterpenic alcohols, triterpenic dialcohols, sterols, squalene and tocopherols were analyzed. A subset of variables was considered. They were selected in a preceding work as the most effective and reliable, from the univariate point of view. The analytical data were transformed (except for the cycloartenol to compensate annual variations, the mean related to the East zone was subtracted from each value, within each year. Univariate three-class models were calculated and further variables discarded. Then multivariate three-zone models were evaluated, including phytol (that was always selected and all the combinations of palmitic, palmitoleic and oleic acid, tetracosanol, cycloartenol and squalene. Models including from two to seven variables were studied. The best model shows by-zone classification errors less than 40%, by-zone within-year classification errors that are less than 45% and a global classification error equal to 30%. This model includes phytol, palmitic acid, tetracosanol and cycloartenol.

    Para estudiar y clasificar aceites de oliva vírgenes Toscanos, se utilizaron 179 muestras, que fueron obtenidas de frutos recolectados durante la primera mitad de Noviembre, de tres zonas diferentes de la Región. El muestreo fue repetido durante 5 años. Se analizaron ácidos grasos, fitol, alcoholes alifáticos y triterpénicos, dialcoholes triterpénicos, esteroles, escualeno y tocoferoles. Se consideró un subconjunto de variables que fueron seleccionadas en un trabajo anterior como el más efectivo y fiable, desde el punto de vista univariado. Los datos analíticos se transformaron (excepto para el cicloartenol para compensar las variaciones anuales, rest

  16. Velocity Structure in the West Bohemia Seismic Zone: Velocity Models Retrieved from different Earthquake Swarms

    Science.gov (United States)

    Alexandrakis, C.; Löberich, E.; Kieslich, A.; Calo, M.; Vavrycuk, V.; Buske, S.

    2015-12-01

    Earthquake swarms, fluid migration and gas springs are indications of the ongoing geodynamic processes within the West Bohemia seismic zone located at the Czech-German border. The possible relationship between the fluids, gas and seismicity is of particular interest and has motivated numerous past, ongoing and future studies, including a multidisciplinary monitoring proposal through the International Continental Scientific Drilling Program (ICDP). The most seismically active area within the West Bohemia seismic zone is located at the Czech town Nový Kostel. The Nový Kostel zone experiences frequent swarms of several hundreds to thousands of earthquakes over a period of weeks to several months. The seismicity is always located in the same area and depth range (~5-15 km), however the activated fault segments and planes differ. For example, the 2008 swarm activated faults along the southern end of the seismic zone, the 2011 swarm activated the northern segment, and the recent 2014 swarm activated the middle of the seismic zone. This indicates changes to the local stress field, and may relate to fluid migration and/or the complicated tectonic situation. The West Bohemia Seismic Network (WEBNET) is ideally located for studying the Nový Kostel swarm area and provides good azimuthal coverage. Here, we use the high quality P- and S-wave arrival picks recorded by WEBNET to calculate swarm-dependent velocity models for the 2008 and 2011 swarms, and an averaged (swarm independent) model using earthquakes recorded between 1991 and 2011. To this end, we use double-difference tomography to calculate P- and S-wave velocity models. The models are compared and examined in terms of swarm-dependent velocities and structures. Since the P-to-S velocity ratio is particularly sensitive to the presence of pore fluids, we derive ratio models directly from the inverted P- and S-wave models in order to investigate the potential influence of fluids on the seismicity. Finally, clustering

  17. Modeling of Prepregs during Automated Draping Sequences

    DEFF Research Database (Denmark)

    Krogh, Christian; Glud, Jens Ammitzbøll; Jakobsen, Johnny

    2017-01-01

    significant quality variations in the final part. Thus, an automated layup solution is under development where a robot can manipulate and drape the prepregs into the mold. The success of this implementation relies on both accurate and computationally efficient models describing the mechanical behavior...... aspect of the draping must be taken into account. The accurate modeling is accomplished with an explicit Finite Element (FE) scheme with shell elements. Material characterization in the form of uniaxial tensile tests, bias-extension tests (45 ° tensile test) and bending tests provide input for the model...

  18. Static stress transfer within the Cephalonia Transfer Fault Zone (CTFZ) during the 2014 seismic sequence in Cephalonia and the 2015 earthquake in Lefkada

    Science.gov (United States)

    Sboras, Sotiris; Chatzipetros, Alexandros; Pavlides, Spyros; Karastathis, Vassilis; Papadopoulos, Gerassimos

    2017-04-01

    The 2014 seismic sequence in Cephalonia and the following 2015 earthquake in Lefkada Islands, Greece, showed that the Cephalonia Transfer Fault Zone (CTFZ), which runs along the western coasts of both islands, comprises a wide fault zone of parallel to sub-parallel fault segments. The January-February 2014 sequence of Cephalonia consisted of three moderate to strong events. According to published focal mechanisms, the first strongest shock (January 26, Mw 6.1) was produced by a W-dipping, oblique (right-lateral reverse) fault, the second (January 26, Mw 5.3) by a ENE-dipping, pure reverse fault and the third by a ESE-dipping, almost pure right-lateral strike slip fault. The November 17 2015 (Mw 6.4) Lefkada earthquake was produced by a WNW-dipping, roughly vertical, almost pure right-lateral strike-slip fault. None of the shocks above produced any direct coseismic ground rupture, while published relocated hypocentral locations for the Cephalonia sequence revealed various depths indicating a complex fault pattern. Based on published seismological, geological and satellite data (i.e. InSAR), the respective seismic sources were modelled in order to calculate the static stress changes i) during the Cephalonia and Lefkada sequences, and ii) after the sequences for the surrounding faults from the Greek Database of Seismogenic Sources (GreDaSS). Results showed that the February 3 2014 Cephalonia fault was variously affected by the rupture of the two January 26 faults. Stress change distribution on the fault plane showed that both stress drop and rise occurred. The November 17 2015 Lefkada fault was slightly loaded after the rupture of the whole Cephalonia fault system due to the great distance. The post-sequence stress changes variously affect the surrounding faults: the southern segment of the CTFZ is relieved from stresses, while the central ones show a mixed situation. The large northern segment, offshore from Lefkada Island, is mainly under stress drop. Stress drop is

  19. Parameterizing sequence alignment with an explicit evolutionary model.

    Science.gov (United States)

    Rivas, Elena; Eddy, Sean R

    2015-12-10

    Inference of sequence homology is inherently an evolutionary question, dependent upon evolutionary divergence. However, the insertion and deletion penalties in the most widely used methods for inferring homology by sequence alignment, including BLAST and profile hidden Markov models (profile HMMs), are not based on any explicitly time-dependent evolutionary model. Using one fixed score system (BLOSUM62 with some gap open/extend costs, for example) corresponds to making an unrealistic assumption that all sequence relationships have diverged by the same time. Adoption of explicit time-dependent evolutionary models for scoring insertions and deletions in sequence alignments has been hindered by algorithmic complexity and technical difficulty. We identify and implement several probabilistic evolutionary models compatible with the affine-cost insertion/deletion model used in standard pairwise sequence alignment. Assuming an affine gap cost imposes important restrictions on the realism of the evolutionary models compatible with it, as single insertion events with geometrically distributed lengths do not result in geometrically distributed insert lengths at finite times. Nevertheless, we identify one evolutionary model compatible with symmetric pair HMMs that are the basis for Smith-Waterman pairwise alignment, and two evolutionary models compatible with standard profile-based alignment. We test different aspects of the performance of these "optimized branch length" models, including alignment accuracy and homology coverage (discrimination of residues in a homologous region from nonhomologous flanking residues). We test on benchmarks of both global homologies (full length sequence homologs) and local homologies (homologous subsequences embedded in nonhomologous sequence). Contrary to our expectations, we find that for global homologies a single long branch parameterization suffices both for distant and close homologous relationships. In contrast, we do see an advantage in

  20. IDENTIFICATION OF EARTHQUAKE AFTERSHOCK AND SWARM SEQUENCES IN THE BAIKAL RIFT ZONE

    Directory of Open Access Journals (Sweden)

    N. A. Radziminovich

    2013-01-01

    Full Text Available The catalog of earthquakes (КR³6.6 which occurred in the Baikal rift zone (BRZ was declastered, and the results are presented in the article. Aftershocks of seismic events (КR³12.5 were determined by the software developed by V.B. Smirnov (Lomonosov Moscow State University with application of the algorithm co-authored by G.M. Molchan and O.E. Dmitrieva. To ensure proper control of the software application, aftershocks were also selected manually. The results of declustering show that aftershocks of the earthquakes (КR³12.5 account for about 25 per cent of all seismic events in the regional catalog. Aftershocks accompanied 90 per cent of all the earthquakes considered as main shocks. Besides, earthquake swarms, including events with КR³11, were identified. The results of this study show that, in the BRZ, the swarms and strong events with aftershocks are not spatially separated, and this conclusion differs from the views of the previous studies that reviewed data from a shorter observation period. Moreover, it is noted that the swarms may consist of several main shocks accompanied by aftershocks. The data accumulated over the last fifty years of instrumental observations support the conclusion made earlier that the swarms in BRZ occur mainly in the north-eastward direction from Lake Baikal and also confirm the trend of a small number of aftershocks accompanying earthquakes in the south-western part of the Baikal rift zone.

  1. Modeling of Prepregs during Automated Draping Sequences

    DEFF Research Database (Denmark)

    Krogh, Christian; Glud, Jens Ammitzbøll; Jakobsen, Johnny

    pockets and other defects. The models must, among other things, account for the nonlinear anisotropic constitutive behavior, viscoelasticity, possible plasticity, and contact which includes friction between the ply-mold and ply-end effector interfaces. The problem is path dependent and thus the transient...

  2. Model morphing and sequence assignment after molecular replacement

    International Nuclear Information System (INIS)

    Terwilliger, Thomas C.; Read, Randy J.; Adams, Paul D.; Brunger, Axel T.; Afonine, Pavel V.; Hung, Li-Wei

    2013-01-01

    A procedure for model building is described that combines morphing a model to match a density map, trimming the morphed model and aligning the model to a sequence. A procedure termed ‘morphing’ for improving a model after it has been placed in the crystallographic cell by molecular replacement has recently been developed. Morphing consists of applying a smooth deformation to a model to make it match an electron-density map more closely. Morphing does not change the identities of the residues in the chain, only their coordinates. Consequently, if the true structure differs from the working model by containing different residues, these differences cannot be corrected by morphing. Here, a procedure that helps to address this limitation is described. The goal of the procedure is to obtain a relatively complete model that has accurate main-chain atomic positions and residues that are correctly assigned to the sequence. Residues in a morphed model that do not match the electron-density map are removed. Each segment of the resulting trimmed morphed model is then assigned to the sequence of the molecule using information about the connectivity of the chains from the working model and from connections that can be identified from the electron-density map. The procedure was tested by application to a recently determined structure at a resolution of 3.2 Å and was found to increase the number of correctly identified residues in this structure from the 88 obtained using phenix.resolve sequence assignment alone (Terwilliger, 2003 ▶) to 247 of a possible 359. Additionally, the procedure was tested by application to a series of templates with sequence identities to a target structure ranging between 7 and 36%. The mean fraction of correctly identified residues in these cases was increased from 33% using phenix.resolve sequence assignment to 47% using the current procedure. The procedure is simple to apply and is available in the Phenix software package

  3. Model morphing and sequence assignment after molecular replacement

    Energy Technology Data Exchange (ETDEWEB)

    Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov [Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87545 (United States); Read, Randy J. [University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY (United Kingdom); Adams, Paul D. [Lawrence Berkeley National Laboratory, One Cyclotron Road, Bldg 64R0121, Berkeley, CA 94720 (United States); Brunger, Axel T. [Stanford University, 318 Campus Drive West, Stanford, CA 94305 (United States); Afonine, Pavel V. [Lawrence Berkeley National Laboratory, One Cyclotron Road, Bldg 64R0121, Berkeley, CA 94720 (United States); Hung, Li-Wei [Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87545 (United States)

    2013-11-01

    A procedure for model building is described that combines morphing a model to match a density map, trimming the morphed model and aligning the model to a sequence. A procedure termed ‘morphing’ for improving a model after it has been placed in the crystallographic cell by molecular replacement has recently been developed. Morphing consists of applying a smooth deformation to a model to make it match an electron-density map more closely. Morphing does not change the identities of the residues in the chain, only their coordinates. Consequently, if the true structure differs from the working model by containing different residues, these differences cannot be corrected by morphing. Here, a procedure that helps to address this limitation is described. The goal of the procedure is to obtain a relatively complete model that has accurate main-chain atomic positions and residues that are correctly assigned to the sequence. Residues in a morphed model that do not match the electron-density map are removed. Each segment of the resulting trimmed morphed model is then assigned to the sequence of the molecule using information about the connectivity of the chains from the working model and from connections that can be identified from the electron-density map. The procedure was tested by application to a recently determined structure at a resolution of 3.2 Å and was found to increase the number of correctly identified residues in this structure from the 88 obtained using phenix.resolve sequence assignment alone (Terwilliger, 2003 ▶) to 247 of a possible 359. Additionally, the procedure was tested by application to a series of templates with sequence identities to a target structure ranging between 7 and 36%. The mean fraction of correctly identified residues in these cases was increased from 33% using phenix.resolve sequence assignment to 47% using the current procedure. The procedure is simple to apply and is available in the Phenix software package.

  4. TSPA Model for the Yucca Mountain Unsaturated Zone

    Energy Technology Data Exchange (ETDEWEB)

    M.L. Wilson; C.K. Ho

    2001-12-12

    Yucca Mountain, Nevada, is being considered as a potential site for a repository for spent nuclear fuel and high-level radioactive waste. Total-system performance-assessment (TSPA) calculations are performed to evaluate the safety of the site. Such calculations require submodels for all important engineered and natural components of the disposal system. There are five submodels related to the unsaturated zone: climate, infiltration, mountain-scale flow of water, seepage into emplacement drifts, and radionuclide transport. For each of these areas, models have been developed and implemented for use in TSPA. The climate model is very simple (a set of climate states have been deduced from paleoclimate data, and the times when climate changes occur in the future have been estimated), but the other four models make use of complex process models involving time-consuming computer runs. An important goal is to evaluate the impact of uncertainties (e.g., incomplete knowledge of the site) on the estimates of potential repository performance, so particular attention is given to the key uncertainties for each area. Uncertainties in climate, infiltration, and mountain-scale flow are represented in TSPA simulations by means of discrete high, medium, and low cases, Uncertainties in seepage and radionuclide transport are represented by means of continuous probability distributions for several key parameters.

  5. TSPA Model for the Yucca Mountain Unsaturated Zone

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, M. L.; Ho, C. K.

    2002-02-26

    Yucca Mountain, Nevada, is being considered as a potential site for a repository for spent nuclear fuel and high-level radioactive waste. Total-system performance-assessment (TSPA) calculations are performed to evaluate the safety of the site. Such calculations require submodels for all important engineered and natural components of the disposal system. There are five submodels related to the unsaturated zone: climate, infiltration, mountain-scale flow of water, seepage into emplacement drifts, and radionuclide transport. For each of these areas, models have been developed and implemented for use in TSPA. The climate model is very simple (a set of climate states have been deduced from paleoclimate data, and the times when climate changes occur in the future have been estimated), but the other four models make use of complex process models involving time-consuming computer runs. An important goal is to evaluate the impact of uncertainties (e.g., incomplete knowledge of the site) on the estimates of potential repository performance, so particular attention is given to the key uncertainties for each area. Uncertainties in climate, infiltration, and mountain-scale flow are represented in TSPA simulations by means of discrete high, medium, and low cases. Uncertainties in seepage and radionuclide transport are represented by means of continuous probability distributions for several key parameters.

  6. Modeling of particle coarsening and precipitation free zones

    Science.gov (United States)

    Yang, N.; Saidi, P.; Daymond, M. R.; Hoyt, J. J.

    2017-12-01

    Previous simulation studies of the effect of volume fraction on the precipitate coarsening process have treated precipitates as point sources or sinks of solute atoms. These studies have demonstrated that, although the average particle size varying with time as {t}1/3 is still valid, the coarsening rate constant is an increasing function of volume fraction. In this study we extend these simulation methods to model particle coarsening near grain boundaries. An essential feature of the new model is the solute depletion that occurs at grain boundaries. The simulation results are shown to quantitatively reproduce the following aspects of particle coarsening near grain boundaries in certain alloys: (a) precipitate free zones (PFZs) form near grain boundaries, (b) the width of PFZs increases with time and is proportional to the square root of time, (c) particles at the edge of PFZs are larger than those inside the grain. This novel model is shown to be well suited to describe particle coarsening near grain boundaries. In addition, it reinforces the credibility of the theories built into our mathematical model, i.e., the formation of PFZs near grain boundaries is caused by diffusion of solute atoms.

  7. Clustering-neural network models for freeway work zone capacity estimation.

    Science.gov (United States)

    Jiang, Xiaomo; Adeli, Hojjat

    2004-06-01

    Two neural network models, called clustering-RBFNN and clustering-BPNN models, are created for estimating the work zone capacity in a freeway work zone as a function of seventeen different factors through judicious integration of the subtractive clustering approach with the radial basis function (RBF) and the backpropagation (BP) neural network models. The clustering-RBFNN model has the attractive characteristics of training stability, accuracy, and quick convergence. The results of validation indicate that the work zone capacity can be estimated by clustering-neural network models in general with an error of less than 10%, even with limited data available to train the models. The clustering-RBFNN model is used to study several main factors affecting work zone capacity. The results of such parametric studies can assist work zone engineers and highway agencies to create effective traffic management plans (TMP) for work zones quantitatively and objectively.

  8. Statistical approaches to use a model organism for regulatory sequences annotation of newly sequenced species.

    Directory of Open Access Journals (Sweden)

    Pietro Liò

    Full Text Available A major goal of bioinformatics is the characterization of transcription factors and the transcriptional programs they regulate. Given the speed of genome sequencing, we would like to quickly annotate regulatory sequences in newly-sequenced genomes. In such cases, it would be helpful to predict sequence motifs by using experimental data from closely related model organism. Here we present a general algorithm that allow to identify transcription factor binding sites in one newly sequenced species by performing Bayesian regression on the annotated species. First we set the rationale of our method by applying it within the same species, then we extend it to use data available in closely related species. Finally, we generalise the method to handle the case when a certain number of experiments, from several species close to the species on which to make inference, are available. In order to show the performance of the method, we analyse three functionally related networks in the Ascomycota. Two gene network case studies are related to the G2/M phase of the Ascomycota cell cycle; the third is related to morphogenesis. We also compared the method with MatrixReduce and discuss other types of validation and tests. The first network is well known and provides a biological validation test of the method. The two cell cycle case studies, where the gene network size is conserved, demonstrate an effective utility in annotating new species sequences using all the available replicas from model species. The third case, where the gene network size varies among species, shows that the combination of information is less powerful but is still informative. Our methodology is quite general and could be extended to integrate other high-throughput data from model organisms.

  9. Optimization and evaluation of probabilistic-logic sequence models

    DEFF Research Database (Denmark)

    Christiansen, Henning; Lassen, Ole Torp

    Analysis of biological sequence data demands more and more sophisticated and fine-grained models, but these in turn introduce hard computational problems. A class of probabilistic-logic models is considered, which increases the expressibility from HMM's and SCFG's regular and context-free languages...

  10. A Probabilistic Genome-Wide Gene Reading Frame Sequence Model

    DEFF Research Database (Denmark)

    Have, Christian Theil; Mørk, Søren

    as output. The model can be used to obtain the most probable genome annotation based on a combination of i: a gene finder score of each gene candidate and ii: the sequence of the reading frames of gene candidates through a genome. The model --- as well as a higher order variant --- is developed and tested......We introduce a new type of probabilistic sequence model, that model the sequential composition of reading frames of genes in a genome. Our approach extends gene finders with a model of the sequential composition of genes at the genome-level -- effectively producing a sequential genome annotation...... using the probabilistic logic programming language and machine learning system PRISM - a fast and efficient model prototyping environment, using bacterial gene finding performance as a benchmark of signal strength. The model is used to prune a set of gene predictions from an underlying gene finder...

  11. Vadose Zone Modeling Workshop proceedings, March 29--30, 1993

    International Nuclear Information System (INIS)

    Khaleel, R.

    1993-08-01

    At the Hanford Site, the record of decision for remediation of CERCLA sites is largely based on results of the baseline risk and performance assessment of the remedial action alternatives. These assessments require the ability to predict the fate and transport of contaminants along appropriate exposure pathways which, in case of the Hanford Site, includes the migration of contaminants through the vadose zone to the water table. Listed below are some of the requirements, as prescribed by the regulators, relative to CERCLA risk and performance assessment at Hanford. A workshop was organized by the Environmental Risk and Performance Assessment Group, Westinghouse Hanford Company on March 29--30, 1993 at the Richland Best Western Tower Inn. During the workshop, an assessment was made of the need for and scope of various tasks being conducted or planned as part of the Hanford Site waste isolation performance assessment/risk assessment activities. Three external, nationally-recognized experts served as part of a review panel for the workshop: (a) Professor Lynn Gelhar of MIT; (b) Professor Peter Wierenga of University of Arizona; and (c) Dr. Rien van Genuchten of US Salinity Laboratory, Riverside, California. The technical experts provided their perspectives on the current state-of-the-art in vadose zone flow and transport modeling. In addition, the technical experts provided an outside independent assessment of the work being performed or planned in support of various activities identified in TPA Milestone M-29-02. This document includes the following: Recommendations from the three peer reviewers; areas of expertise of the three peer reviewers; workshop agenda; copies of viewgraphs (where available) from presenters at the workshop; workshop minutes; and list of workshop attendees

  12. An Integrative Wave Model for the Marginal Ice Zone Based on a Rheological Parameterization

    Science.gov (United States)

    2015-09-30

    1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. An Integrative Wave model for the Marginal Ice Zone...people.clarkson.edu/~hhshen LONG-TERM GOALS To enhance wave forecasting models such as WAVEWATCH III (WW3) so that they can predict the marginal ice zone (MIZ...Antarctic marginal ice zone were used to evaluate the viscoelastic ice damping models. The 2012 data came from two buoys separated by over 100km

  13. Analysis of Sequence Diagram Layout in Advanced UML Modelling Tools

    Directory of Open Access Journals (Sweden)

    Ņikiforova Oksana

    2016-05-01

    Full Text Available System modelling using Unified Modelling Language (UML is the task that should be solved for software development. The more complex software becomes the higher requirements are stated to demonstrate the system to be developed, especially in its dynamic aspect, which in UML is offered by a sequence diagram. To solve this task, the main attention is devoted to the graphical presentation of the system, where diagram layout plays the central role in information perception. The UML sequence diagram due to its specific structure is selected for a deeper analysis on the elements’ layout. The authors research represents the abilities of modern UML modelling tools to offer automatic layout of the UML sequence diagram and analyse them according to criteria required for the diagram perception.

  14. Cohesive zone modelling of interface fracture near flaws in adhesive joints

    DEFF Research Database (Denmark)

    Hansen, Peter Feraren; Jensen, Henrik Myhre

    2004-01-01

    A cohesive zone model is suggested for modelling of interface fracture near flaws in adhesive joints. A shear-loaded adhesive joint bonded with a planar circular bond region is modelled using both the cohesive zone model and a fracture mechanical model. Results from the models show good agreement...... of crack propagation on the location and shape of the crack front and on the initial joint strength. Subsequently, the cohesive zone model is used to model interface fracture through a planar adhesive layer containing a periodic array of elliptical flaws. The effects of flaw shape are investigated, as well...

  15. Modeling Zone-3 Protection with Generic Relay Models for Dynamic Contingency Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Qiuhua; Vyakaranam, Bharat GNVSR; Diao, Ruisheng; Makarov, Yuri V.; Samaan, Nader A.; Vallem, Mallikarjuna R.; Pajuelo, Eli

    2017-10-02

    This paper presents a cohesive approach for calculating and coordinating the settings of multiple zone-3 protections for dynamic contingency analysis. The zone-3 protections are represented by generic distance relay models. A two-step approach for determining zone-3 relay settings is proposed. The first step is to calculate settings, particularly, the reach, of each zone-3 relay individually by iteratively running line open-end fault short circuit analysis; the blinder is also employed and properly set to meet the industry standard under extreme loading conditions. The second step is to systematically coordinate the protection settings of the zone-3 relays. The main objective of this coordination step is to address the over-reaching issues. We have developed a tool to automate the proposed approach and generate the settings of all distance relays in a PSS/E dyr format file. The calculated zone-3 settings have been tested on a modified IEEE 300 system using a dynamic contingency analysis tool (DCAT).

  16. 3D vadose zone modeling using geostatistical inferences

    International Nuclear Information System (INIS)

    Knutson, C.F.; Lee, C.B.

    1991-01-01

    In developing a 3D model of the 600 ft thick interbedded basalt and sediment complex that constitutes the vadose zone at the Radioactive Waste Management Complex (RWMC) at the Idaho National Engineering Laboratory (INEL) geostatistical data were captured for 12--15 parameters (e.g. permeability, porosity, saturation, etc. and flow height, flow width, flow internal zonation, etc.). This two scale data set was generated from studies of subsurface core and geophysical log suites at RWMC and from surface outcrop exposures located at the Box Canyon of the Big Lost River and from Hell's Half Acre lava field all located in the general RWMC area. Based on these currently available data, it is possible to build a 3D stochastic model that utilizes: cumulative distribution functions obtained from the geostatistical data; backstripping and rebuilding of stratigraphic units; an ''expert'' system that incorporates rules based on expert geologic analysis and experimentally derived geostatistics for providing: (a) a structural and isopach map of each layer, (b) a realization of the flow geometry of each basalt flow unit, and (c) a realization of the internal flow parameters (eg permeability, porosity, and saturation) for each flow. 10 refs., 4 figs., 1 tab

  17. EIA modelling for coastal zone management. Part 2

    Digital Repository Service at National Institute of Oceanography (India)

    Babu, M.T.; Vethamony, P.

    stream_size 15 stream_content_type text/plain stream_name Summer_Sch_EIA_Manage_Coast_Zone_2001_95.pdf.txt stream_source_info Summer_Sch_EIA_Manage_Coast_Zone_2001_95.pdf.txt Content-Encoding ISO-8859-1 Content-Type text...

  18. Modeling Diverse Pathways to Age Progressive Volcanism in Subduction Zones.

    Science.gov (United States)

    Kincaid, C. R.; Szwaja, S.; Sylvia, R. T.; Druken, K. A.

    2015-12-01

    One of the best, and most challenging clues to unraveling mantle circulation patterns in subduction zones comes in the form of age progressive volcanic and geochemical trends. Hard fought geological data from many subduction zones, like Tonga-Lau, the Cascades and Costa-Rica/Nicaragua, reveal striking temporal patterns used in defining mantle flow directions and rates. We summarize results from laboratory subduction models showing a range in circulation and thermal-chemical transport processes. These interaction styles are capable of producing such trends, often reflecting apparent instead of actual mantle velocities. Lab experiments use a glucose working fluid to represent Earth's upper mantle and kinematically driven plates to produce a range in slab sinking and related wedge transport patterns. Kinematic forcing assumes most of the super-adiabatic temperature gradient available to drive major downwellings is in the tabular slabs. Moreover, sinking styles for fully dynamic subduction depend on many complicating factors that are only poorly understood and which can vary widely even for repeated parameter combinations. Kinematic models have the benefit of precise, repeatable control of slab motions and wedge flow responses. Results generated with these techniques show the evolution of near-surface thermal-chemical-rheological heterogeneities leads to age progressive surface expressions in a variety of ways. One set of experiments shows that rollback and back-arc extension combine to produce distinct modes of linear, age progressive melt delivery to the surface through a) erosion of the rheological boundary layer beneath the overriding plate, and deformation and redistribution of both b) mantle residuum produced from decompression melting and c) formerly active, buoyant plumes. Additional experiments consider buoyant diapirs rising in a wedge under the influence of rollback, back-arc spreading and slab-gaps. Strongly deflected diapirs, experiencing variable rise

  19. Main sequence models for massive zero-metal stars

    Science.gov (United States)

    Cary, N.

    1974-01-01

    Zero-age main-sequence models for stars of 20, 10, 5, and 2 solar masses with no heavy elements are constructed for three different possible primordial helium abundances: Y=0.00, Y=0.23, and Y=0.30. The latter two values of Y bracket the range of primordial helium abundances cited by Wagoner. With the exceptions of the two 20 solar mass models that contain helium, these models are found to be self-consistent in the sense that the formation of carbon through the triple-alpha process during premain sequence contraction is not sufficient to bring the CN cycle into competition with the proton-proton chain on the ZAMS. The zero-metal models of the present study have higher surface and central temperatures, higher central densities, smaller radii, and smaller convective cores than do the population I models with the same masses.

  20. Model morphing and sequence assignment after molecular replacement.

    Science.gov (United States)

    Terwilliger, Thomas C; Read, Randy J; Adams, Paul D; Brunger, Axel T; Afonine, Pavel V; Hung, Li-Wei

    2013-11-01

    A procedure termed `morphing' for improving a model after it has been placed in the crystallographic cell by molecular replacement has recently been developed. Morphing consists of applying a smooth deformation to a model to make it match an electron-density map more closely. Morphing does not change the identities of the residues in the chain, only their coordinates. Consequently, if the true structure differs from the working model by containing different residues, these differences cannot be corrected by morphing. Here, a procedure that helps to address this limitation is described. The goal of the procedure is to obtain a relatively complete model that has accurate main-chain atomic positions and residues that are correctly assigned to the sequence. Residues in a morphed model that do not match the electron-density map are removed. Each segment of the resulting trimmed morphed model is then assigned to the sequence of the molecule using information about the connectivity of the chains from the working model and from connections that can be identified from the electron-density map. The procedure was tested by application to a recently determined structure at a resolution of 3.2 Å and was found to increase the number of correctly identified residues in this structure from the 88 obtained using phenix.resolve sequence assignment alone (Terwilliger, 2003) to 247 of a possible 359. Additionally, the procedure was tested by application to a series of templates with sequence identities to a target structure ranging between 7 and 36%. The mean fraction of correctly identified residues in these cases was increased from 33% using phenix.resolve sequence assignment to 47% using the current procedure. The procedure is simple to apply and is available in the Phenix software package.

  1. Modeling critical zone processes in intensively managed environments

    Science.gov (United States)

    Kumar, Praveen; Le, Phong; Woo, Dong; Yan, Qina

    2017-04-01

    Processes in the Critical Zone (CZ), which sustain terrestrial life, are tightly coupled across hydrological, physical, biochemical, and many other domains over both short and long timescales. In addition, vegetation acclimation resulting from elevated atmospheric CO2 concentration, along with response to increased temperature and altered rainfall pattern, is expected to result in emergent behaviors in ecologic and hydrologic functions, subsequently controlling CZ processes. We hypothesize that the interplay between micro-topographic variability and these emergent behaviors will shape complex responses of a range of ecosystem dynamics within the CZ. Here, we develop a modeling framework ('Dhara') that explicitly incorporates micro-topographic variability based on lidar topographic data with coupling of multi-layer modeling of the soil-vegetation continuum and 3-D surface-subsurface transport processes to study ecological and biogeochemical dynamics. We further couple a C-N model with a physically based hydro-geomorphologic model to quantify (i) how topographic variability controls the spatial distribution of soil moisture, temperature, and biogeochemical processes, and (ii) how farming activities modify the interaction between soil erosion and soil organic carbon (SOC) dynamics. To address the intensive computational demand from high-resolution modeling at lidar data scale, we use a hybrid CPU-GPU parallel computing architecture run over large supercomputing systems for simulations. Our findings indicate that rising CO2 concentration and air temperature have opposing effects on soil moisture, surface water and ponding in topographic depressions. Further, the relatively higher soil moisture and lower soil temperature contribute to decreased soil microbial activities in the low-lying areas due to anaerobic conditions and reduced temperatures. The decreased microbial relevant processes cause the reduction of nitrification rates, resulting in relatively lower nitrate

  2. Reactive symbol sequences for a model of hydrogen combustion.

    Science.gov (United States)

    Alaghemandi, Mohammad; Green, Jason R

    2016-01-28

    Transient, macroscopic states of chemical disequilibrium are born out of the microscopic dynamics of molecules. As a reaction mixture evolves, the temporal patterns of chemical species encodes some of this dynamical information, while their statistics are a manifestation of the bulk kinetics. Here, we define a chemically-informed symbolic dynamics as a coarse-grained representation of classical molecular dynamics, and analyze the sequences of chemical species for a model of hydrogen combustion. We use reactive molecular dynamics simulations to generate the sequences and derive probability distributions for sequence observables: the reaction time scales and the chain length - the total number of reactions between initiation of a reactant and termination at products. The time scales and likelihood of the sequences depend strongly on the chain length, temperature, and density. Temperature suppresses the uncertainty in chain length for hydrogen sequences, but enhances the uncertainty in oxygen sequence chain lengths. This method of analyzing a surrogate chemical symbolic dynamics reduces the complexity of the chemistry from the atomistic to the molecular level and has the potential for extension to more complicated reaction systems.

  3. Plantagora: modeling whole genome sequencing and assembly of plant genomes.

    Directory of Open Access Journals (Sweden)

    Roger Barthelson

    Full Text Available BACKGROUND: Genomics studies are being revolutionized by the next generation sequencing technologies, which have made whole genome sequencing much more accessible to the average researcher. Whole genome sequencing with the new technologies is a developing art that, despite the large volumes of data that can be produced, may still fail to provide a clear and thorough map of a genome. The Plantagora project was conceived to address specifically the gap between having the technical tools for genome sequencing and knowing precisely the best way to use them. METHODOLOGY/PRINCIPAL FINDINGS: For Plantagora, a platform was created for generating simulated reads from several different plant genomes of different sizes. The resulting read files mimicked either 454 or Illumina reads, with varying paired end spacing. Thousands of datasets of reads were created, most derived from our primary model genome, rice chromosome one. All reads were assembled with different software assemblers, including Newbler, Abyss, and SOAPdenovo, and the resulting assemblies were evaluated by an extensive battery of metrics chosen for these studies. The metrics included both statistics of the assembly sequences and fidelity-related measures derived by alignment of the assemblies to the original genome source for the reads. The results were presented in a website, which includes a data graphing tool, all created to help the user compare rapidly the feasibility and effectiveness of different sequencing and assembly strategies prior to testing an approach in the lab. Some of our own conclusions regarding the different strategies were also recorded on the website. CONCLUSIONS/SIGNIFICANCE: Plantagora provides a substantial body of information for comparing different approaches to sequencing a plant genome, and some conclusions regarding some of the specific approaches. Plantagora also provides a platform of metrics and tools for studying the process of sequencing and assembly

  4. Modeling ChIP sequencing in silico with applications.

    Directory of Open Access Journals (Sweden)

    Zhengdong D Zhang

    2008-08-01

    Full Text Available ChIP sequencing (ChIP-seq is a new method for genomewide mapping of protein binding sites on DNA. It has generated much excitement in functional genomics. To score data and determine adequate sequencing depth, both the genomic background and the binding sites must be properly modeled. To develop a computational foundation to tackle these issues, we first performed a study to characterize the observed statistical nature of this new type of high-throughput data. By linking sequence tags into clusters, we show that there are two components to the distribution of tag counts observed in a number of recent experiments: an initial power-law distribution and a subsequent long right tail. Then we develop in silico ChIP-seq, a computational method to simulate the experimental outcome by placing tags onto the genome according to particular assumed distributions for the actual binding sites and for the background genomic sequence. In contrast to current assumptions, our results show that both the background and the binding sites need to have a markedly nonuniform distribution in order to correctly model the observed ChIP-seq data, with, for instance, the background tag counts modeled by a gamma distribution. On the basis of these results, we extend an existing scoring approach by using a more realistic genomic-background model. This enables us to identify transcription-factor binding sites in ChIP-seq data in a statistically rigorous fashion.

  5. Modelling and control design for SHARON/Anammox reactor sequence

    DEFF Research Database (Denmark)

    Valverde Perez, Borja; Mauricio Iglesias, Miguel; Sin, Gürkan

    2012-01-01

    With the perspective of investigating a suitable control design for autotrophic nitrogen removal, this work presents a complete model of the SHARON/Anammox reactor sequence. The dynamics of the reactor were explored pointing out the different scales of the rates in the system: slow microbial...

  6. Fast, Sequence Adaptive Parcellation of Brain MR Using Parametric Models

    DEFF Research Database (Denmark)

    Puonti, Oula; Iglesias, Juan Eugenio; Van Leemput, Koen

    2013-01-01

    -of-the-art segmentation performance in both cortical and subcortical structures, while retaining all the benefits of generative parametric models, including high computational speed, automatic adaptiveness to changes in image contrast when different scanner platforms and pulse sequences are used, and the ability...

  7. Seismo-thermo-mechanical modeling of subduction zone seismicity

    International Nuclear Information System (INIS)

    Dinther van, Y.

    2013-01-01

    The catastrophic occurrence of the 2004 M9.2 Sumatra and 2011 M9.0 Tohoku earthquakes illustrated the disastrous impact of megathrust earthquakes on society. They also emphasized our limited understanding of where and when these 'big ones' may strike. The necessary improvement of long-term seismic hazard assessment requires a better physical understanding of the seismic cycle at these seismically active subduction zones. Models have the potential to overcome the restricted, direct observations in space and time. Currently, however, no model exists to explore the relation between long-term subduction dynamics and relating deformation and short-term seismogenesis. The development, validation and initial application of such a physically consistent seismo-thermo-mechanical numerical model is the main objective of this thesis. First, I present a novel analog modeling tool that simulates cycling of megathrust earthquakes in a visco-elastic gelatin wedge. A comparison with natural observations shows interseismic and coseismic physics are captured in a robust, albeit simplified, way. This tool is used to validate that a continuum-mechanics based, visco-elasto-plastic numerical approach, typically used for large-scale geodynamic problems, can be extended to study the short-term seismogenesis of megathrust earthquakes. To generate frictional instabilities and match laboratory source parameters, a local invariant implementation of a strongly slip rate-dependent friction formulation is required. The resulting continuum approach captures several interesting dynamic features, including inter-, co- and postseismic deformation that agrees qualitatively with GPS measurements and dynamic rupture features, including cracks, self-healing pulses and fault re-rupturing. To facilitate a comparison to natural settings, I consider a more realistic setup of the Southern Chilean margin in terms of geometry and physical processes. Results agree with seismological, geodetic and

  8. Multiobjective Fuzzy Mixed Assembly Line Sequencing Optimization Model

    Directory of Open Access Journals (Sweden)

    Farzad Tahriri

    2014-01-01

    Full Text Available It can be deduced from previous studies that there exists a research gap in assembly line sequencing optimization model for mixed-model production lines. In particular, there is a lack of studies which focus on the integration between job shop and assembly lines using fuzzy techniques. Hence, this paper is aimed at addressing the multiobjective mixed-model assembly line sequencing problem by integrating job shop and assembly production lines for factories with modular layouts. The primary goal is to minimize the make-span, setup time, and cost simultaneously in mixed-model assembly lines. Such conflicting goals arise when switching between different products. A genetic algorithm (GA approach is used to solve this problem, in which trapezoidal fuzzy numbers are implemented for variables such as operation and travelling time in order to generate results with higher accuracy and representative of real-case data.

  9. An applied model for the height of the daytime mixed layer and the entrainment zone

    DEFF Research Database (Denmark)

    Batchvarova, E.; Gryning, Sven-Erik

    1994-01-01

    A model is presented for the height of the mixed layer and the depth of the entrainment zone under near-neutral and unstable atmospheric conditions. It is based on the zero-order mixed layer height model of Batchvarova and Gryning (1991) and the parameterization of the entrainment zone depth prop...

  10. Cohesive zone model and GTN model collation for ductile crack growth

    Czech Academy of Sciences Publication Activity Database

    Kozák, Vladislav; Dlouhý, Ivo; Chlup, Zdeněk

    2008-01-01

    Roč. 567-568, - (2008), s. 145-148 ISSN 0255-5476. [MSMF /5./. Brno, 27.06.2007-29.06.2007] R&D Projects: GA ČR(CZ) GA101/05/0493; GA AV ČR IAA200410502 Institutional research plan: CEZ:AV0Z20410507 Keywords : cohesive zone model * GTN model * J-R curve prediction Subject RIV: JG - Metallurgy

  11. A Novel Scheme of Fast-frequency Hopping Optical CDMA System with No-hit-zone Sequence

    Science.gov (United States)

    Ji, Jianhua; liu, Ling; Wang, Ke; Zhang, Zhipeng; Xu, Ming

    2013-09-01

    In traditional fast frequency-hopping OCDMA (FFH-OCDMA) system, beat noise and multiple-access interference are the main performance limitations, and complicated power control must be employed to eliminate the near-far effect. In this paper, a novel scheme of FFH-OCDMA with no-hit-zone sequence is proposed, which is named NHZ FFH-OCDMA. In NHZ FFH-OCDMA, the synchronization among users can be controlled within permissible time delay, and the code cross-correlation for different users equals zero. Therefore, near-far effect can be eliminated. Furthermore, beat noise and multiple-access interference also can be removed. Simulation of eight simultaneous users with dada rate 100 Mbit/s is demonstrated, where the fiber link consists of 50 km single-mode fiber, plus 5 km dispersion compensating fiber. Simulation results show that the near-far problem of NHZ FFH-OCDMA can be eliminated, and complicated power control can be removed. Therefore, this scheme is a good candidate for optical access network.

  12. Genome sequence of the model medicinal mushroom Ganoderma lucidum

    Science.gov (United States)

    Chen, Shilin; Xu, Jiang; Liu, Chang; Zhu, Yingjie; Nelson, David R.; Zhou, Shiguo; Li, Chunfang; Wang, Lizhi; Guo, Xu; Sun, Yongzhen; Luo, Hongmei; Li, Ying; Song, Jingyuan; Henrissat, Bernard; Levasseur, Anthony; Qian, Jun; Li, Jianqin; Luo, Xiang; Shi, Linchun; He, Liu; Xiang, Li; Xu, Xiaolan; Niu, Yunyun; Li, Qiushi; Han, Mira V.; Yan, Haixia; Zhang, Jin; Chen, Haimei; Lv, Aiping; Wang, Zhen; Liu, Mingzhu; Schwartz, David C.; Sun, Chao

    2012-01-01

    Ganoderma lucidum is a widely used medicinal macrofungus in traditional Chinese medicine that creates a diverse set of bioactive compounds. Here we report its 43.3-Mb genome, encoding 16,113 predicted genes, obtained using next-generation sequencing and optical mapping approaches. The sequence analysis reveals an impressive array of genes encoding cytochrome P450s (CYPs), transporters and regulatory proteins that cooperate in secondary metabolism. The genome also encodes one of the richest sets of wood degradation enzymes among all of the sequenced basidiomycetes. In all, 24 physical CYP gene clusters are identified. Moreover, 78 CYP genes are coexpressed with lanosterol synthase, and 16 of these show high similarity to fungal CYPs that specifically hydroxylate testosterone, suggesting their possible roles in triterpenoid biosynthesis. The elucidation of the G. lucidum genome makes this organism a potential model system for the study of secondary metabolic pathways and their regulation in medicinal fungi. PMID:22735441

  13. PSA modeling of long-term accident sequences

    International Nuclear Information System (INIS)

    Georgescu, Gabriel; Corenwinder, Francois; Lanore, Jeanne-Marie

    2014-01-01

    In the context of the extension of PSA scope to include external hazards, in France, both operator (EDF) and IRSN work for the improvement of methods to better take into account in the PSA the accident sequences induced by initiators which affect a whole site containing several nuclear units (reactors, fuel pools,...). These methodological improvements represent an essential prerequisite for the development of external hazards PSA. However, it has to be noted that in French PSA, even before Fukushima, long term accident sequences were taken into account: many insight were therefore used, as complementary information, to enhance the safety level of the plants. IRSN proposed an external events PSA development program. One of the first steps of the program is the development of methods to model in the PSA the long term accident sequences, based on the experience gained. At short term IRSN intends to enhance the modeling of the 'long term' accident sequences induced by the loss of the heat sink or/and the loss of external power supply. The experience gained by IRSN and EDF from the development of several probabilistic studies treating long term accident sequences shows that the simple extension of the mission time of the mitigation systems from 24 hours to longer times is not sufficient to realistically quantify the risk and to obtain a correct ranking of the risk contributions and that treatment of recoveries is also necessary. IRSN intends to develop a generic study which can be used as a general methodology for the assessment of the long term accident sequences, mainly generated by external hazards and their combinations. This first attempt to develop this generic study allowed identifying some aspects, which may be hazard (or combinations of hazards) or related to initial boundary conditions, which should be taken into account for further developments. (authors)

  14. Hydrogeological characterisation and modelling of deformation zones and fracture domains, Forsmark modelling stage 2.2

    Energy Technology Data Exchange (ETDEWEB)

    Follin, Sven (SF GeoLogic AB, Taeby (SE)); Leven, Jakob (Swedish Nuclear Fuel and Waste Management Co., Stockholm (SE)); Hartley, Lee; Jackson, Peter; Joyce, Steve; Roberts, David; Swift, Ben (Serco Assurance, Harwell (GB))

    2007-09-15

    The work reported here collates the structural-hydraulic information gathered in 21 cored boreholes and 32 percussion-drilled boreholes belonging to Forsmark site description, modelling stage 2.2. The analyses carried out provide the hydrogeological input descriptions of the bedrock in Forsmark needed by the end users Repository Engineering, Safety Assessment and Environmental Impact Assessment; that is, hydraulic properties of deformation zones and fracture domains. The same information is also needed for constructing 3D groundwater flow models of the Forsmark site and surrounding area. The analyses carried out render the following conceptual model regarding the observed heterogeneity in deformation zone transmissivity: We find the geological division of the deterministically modelled deformation zones into eight categories (sets) useful from a hydrogeological point of view. Seven of the eight categories are steeply dipping, WNW, NW, NNW, NNE, NE, ENE and EW, and on is gently dipping, G. All deformation zones, regardless of orientation (strike and dip), are subjected to a substantial decrease in transmissivity with depth. The data gathered suggest a contrast of c. 20,000 times for the uppermost one kilometre of bedrock, i.e. more than four orders of magnitude. The hydraulic properties below this depth are not investigated. The lateral heterogeneity is also substantial but more irregular in its appearance. For instance, for a given elevation and deformation zone category (orientation), the spatial variability in transmissivity within a particular deformation zone appears to be as large as the variability between all deformation zones. This suggests that the lateral correlation length is shorter than the shortest distance between two adjacent observation points and shorter than the category spacing. The observation that the mean transmissivity of the gently-dipping deformation zones is c. one to two orders of magnitude greater than the mean transmissivities of all

  15. Development of geoinformation zoning model of urban territories for use in urban cadaster systems

    Directory of Open Access Journals (Sweden)

    Денис Вікторович Горковчук

    2016-12-01

    Full Text Available The structure and composition of zoning spatial resources is explored. Geoinformation mode of geospatial zoning data on the basis of object-relational database management system is developed. Developed zoning model is tested in the environment of open-source database management system PostgreSQL. Applied SQL-function for automatic creation of build conditions and restrictions of land development is implemented

  16. Validating a perceptual distraction model in a personal two-zone sound system

    DEFF Research Database (Denmark)

    Rämö, Jussi; Christensen, Lasse; Bech, Søren

    2017-01-01

    This paper focuses on validating a perceptual distraction model, which aims to predict user’s perceived distraction caused by audio-on-audio interference, e.g., two competing audio sources within the same listening space. Originally, the distraction model was trained with music-on-music stimuli...... using a simple loudspeaker setup, consisting of only two loudspeakers, one for the target sound source and the other for the interfering sound source. Recently, the model was successfully validated in a complex personal sound-zone system with speech-on-music stimuli. Second round of validations were...... conducted by physically altering the sound-zone system and running a set of new listening experiments utilizing two sound zones within the sound-zone system. Thus, validating the model using a different sound-zone system with both speech-on-music and music-on-speech stimuli sets. Preliminary results show...

  17. An analytical model for non-conservative pollutants mixing in the surf zone.

    Science.gov (United States)

    Ki, Seo Jin; Hwang, Jin Hwan; Kang, Joo-Hyon; Kim, Joon Ha

    2009-01-01

    Accurate simulation of the surf zone is a prerequisite to improve beach management as well as to understand the fundamentals of fate and transport of contaminants. In the present study, a diagnostic model modified from a classic solute model is provided to illuminate non-conservative pollutants behavior in the surf zone. To readily understand controlling processes in the surf zone, a new dimensionless quantity is employed with index of kappa number (K, a ratio of inactivation rate to transport rate of microbial pollutant in the surf zone), which was then evaluated under different environmental frames during a week simulation period. The sensitivity analysis showed that hydrodynamics and concentration gradients in the surf zone mostly depend on n (number of rip currents), indicating that n should be carefully adjusted in the model. The simulation results reveal, furthermore, that large deviation typically occurs in the daytime, signifying inactivation of fecal indicator bacteria is the main process to control surf zone water quality during the day. Overall, the analytical model shows a good agreement between predicted and synthetic data (R(2) = 0.51 and 0.67 for FC and ENT, respectively) for the simulated period, amplifying its potential use in the surf zone modelling. It is recommended that when the dimensionless index is much larger than 0.5, the present modified model can predict better than the conventional model, but if index is smaller than 0.5, the conventional model is more efficient with respect to time and cost.

  18. A Comparison of Freeway Work Zone Capacity Prediction Models

    NARCIS (Netherlands)

    Zheng, N.; Hegyi, A.; Hoogendoorn, S.P.; Van Zuylen, H.J.; Peters, D.

    2011-01-01

    To keep the freeway networks in a good condition, road works such as maintenance and reconstruction are carried out regularly. The resulting work zones including the related traffic management measures, give different traffic capacities of the infrastructures, which determines the travel time for

  19. Modeling and Simulation for a Surf Zone Robot

    Science.gov (United States)

    2012-12-14

    Figure 1.6: A picture Carmel River State Beach near Monterey, California showing a typical surf zone enviroment . Features include submerged and exposed...picture of the enviroment [34]. Another benefit that will be gained from the use of ROS for navigation is the direct integration of Gazebo and the

  20. Hydrogeologic Framework Model for the Saturated-Zone Site-Scale Flow

    Energy Technology Data Exchange (ETDEWEB)

    Z. Peterman

    2003-03-05

    Yucca Mountain is being evaluated as a potential site for development of a geologic repository for the permanent disposal of spent nuclear fuel and high-level radioactive waste. Ground water is considered to be the principal means for transporting radionuclides that may be released from the potential repository to the accessible environment, thereby possibly affecting public health and safety. The ground-water hydrology of the region is a result of both the arid climatic conditions and the complex geology. Ground-water flow in the Yucca Mountain region generally can be described as consisting of two main components: a series of relatively shallow and localized flow paths that are superimposed on deeper regional flow paths. A significant component of the regional ground-water flow is through a thick, generally deep-lying, Paleozoic carbonate rock sequence. Locally within the potential repository area, the flow is through a vertical sequence of welded and nonwelded tuffs that overlie the carbonate aquifer. Downgradient from the site, these tuffs terminate in basin fill deposits that are dominated by alluvium. Throughout the system, extensive and prevalent faults and fractures may control ground-water flow. The purpose of this Analysis/Modeling Report (AMR) is to document the three-dimensional (3D) hydrogeologic framework model (HFM) that has been constructed specifically to support development of a site-scale ground-water flow and transport model. Because the HFM provides the fundamental geometric framework for constructing the site-scale 3D ground-water flow model that will be used to evaluate potential radionuclide transport through the saturated zone (SZ) from beneath the potential repository to down-gradient compliance points, the HFM is important for assessing potential repository system performance. This AMR documents the progress of the understanding of the site-scale SZ ground-water flow system framework at Yucca Mountain based on data through July 1999. The

  1. From Field- to Landscape-Scale Vadose Zone Processes: Scale Issues, Modeling, and Monitoring

    NARCIS (Netherlands)

    Corwin, D.L.; Hopmans, J.; Rooij, de G.H.

    2006-01-01

    Modeling and monitoring vadose zone processes across multiple scales is a fundamental component of many environmental and natural resource issues including nonpoint source (NPS) pollution, watershed management, and nutrient management, to mention just a few. In this special section in Vadose Zone

  2. A parametric investigation of hydrogen hcci combustion using a multi-zone model approach

    International Nuclear Information System (INIS)

    Komninos, N.P.; Hountalas, D.T.; Rakopoulos, C.D.

    2007-01-01

    The purpose of the present study is to examine the effect of various operating variables of a homogeneous charge compression ignition (HCCI) engine fueled with hydrogen, using a multi-zone model developed by the authors. The multi-zone model consists of zones, which are allotted spatial locations within the combustion chamber. The model takes into account heat transfer between the zones and the combustion chamber walls, providing a spatial temperature distribution during the closed part of the engine cycle, i.e. compression, combustion and expansion. Mass transfer between zones is also accounted for, based on the geometric configuration of the zones, and includes the flow of mass in and out of the crevice regions, represented by the crevice zone. Combustion is incorporated using chemical kinetics based on a chemical reaction mechanism for the oxidation of hydrogen. This chemical reaction mechanism also includes the reactions for nitrogen oxides formation. Using the multi-zone model a parametric investigation is conducted, in order to determine the effect of engine speed, equivalence ratio, compression ratio, inlet pressure and inlet temperature, on the performance, combustion characteristics and emissions of an HCCI engine fueled with hydrogen

  3. Explorative study on management model of tourism business zone at Kuta, Bali

    Science.gov (United States)

    Astawa, I. K.; Suardani, A. A. P.; Harmini, A. A. A. N.

    2018-01-01

    Business activities through asset management of indigenous village of Kuta provide an opportunity for the community to participate in improving their welfare. This study aims to analyze the management model of Kuta’s tourism business zone, the involvement of stakeholders in the management of Kuta’s tourism business zone in indigenous village of Kuta and the implications of each business tourism zone in indigenous village of Kuta in the level of community welfare in each zone. Data collection was done by observation, interview, questionnaire, and documentation. The main instrument of this study is the researchers themselves assisted with interview guideline. The results showed that the management model has been arranged in 5 tourism business zones in indigenous village of Kuta. The involvement of all stakeholders in the management of the tourism business zone follows the procedure of execution of duties and provides security, comfort and certainty of doing business activities at each zone. The implications of the tourism business in the level of community welfare in each zone in indigenous village of Kuta have been able to bring happiness in business and all community are satisfied with the income they earned from work in each business zone.

  4. Vegetation root zone storage and rooting depth, derived from local calibration of a global hydrological model

    Science.gov (United States)

    van der Ent, R.; Van Beek, R.; Sutanudjaja, E.; Wang-Erlandsson, L.; Hessels, T.; Bastiaanssen, W.; Bierkens, M. F.

    2017-12-01

    The storage and dynamics of water in the root zone control many important hydrological processes such as saturation excess overland flow, interflow, recharge, capillary rise, soil evaporation and transpiration. These processes are parameterized in hydrological models or land-surface schemes and the effect on runoff prediction can be large. Root zone parameters in global hydrological models are very uncertain as they cannot be measured directly at the scale on which these models operate. In this paper we calibrate the global hydrological model PCR-GLOBWB using a state-of-the-art ensemble of evaporation fields derived by solving the energy balance for satellite observations. We focus our calibration on the root zone parameters of PCR-GLOBWB and derive spatial patterns of maximum root zone storage. We find these patterns to correspond well with previous research. The parameterization of our model allows for the conversion of maximum root zone storage to root zone depth and we find that these correspond quite well to the point observations where available. We conclude that climate and soil type should be taken into account when regionalizing measured root depth for a certain vegetation type. We equally find that using evaporation rather than discharge better allows for local adjustment of root zone parameters within a basin and thus provides orthogonal data to diagnose and optimize hydrological models and land surface schemes.

  5. A Coupled Groundwater-Surface Water Modeling Framework for Simulating Transition Zone Processes.

    Science.gov (United States)

    Mugunthan, Pradeep; Russell, Kevin T; Gong, Binglei; Riley, Michael J; Chin, Arthur; McDonald, Blair G; Eastcott, Linda J

    2017-05-01

    There is an identified need for fully representing groundwater-surface water transition zone (i.e., the sediment zone that connects groundwater and surface water) processes in modeling fate and transport of contaminants to assist with management of contaminated sediments. Most existing groundwater and surface water fate and transport models are not dynamically linked and do not consider transition zone processes such as bioturbation and deposition and erosion of sediments. An interface module is developed herein to holistically simulate the fate and transport by coupling two commonly used models, Environmental Fluid Dynamics Code (EFDC) and SEAWAT, to simulate surface water and groundwater hydrodynamics, while providing an enhanced representation of the processes in the transition zone. Transition zone and surface water contaminant processes were represented through an enhanced version of the EFDC model, AQFATE. AQFATE also includes SEDZLJ, a state-of-the-science surface water sediment transport model. The modeling framework was tested on a published test problem and applied to evaluate field-scale two- and three-dimensional contaminant transport. The model accurately simulated concentrations of salinity from a published test case. For the field-scale applications, the model showed excellent mass balance closure for the transition zone and provided accurate simulations of all transition zone processes represented in the modeling framework. The model predictions for the two-dimensional field case were consistent with site-specific observations of contaminant migration. This modeling framework represents advancement in the simulation of transition zone processes and can help inform risk assessment at sites where contaminant sources from upland areas have the potential to impact sediments and surface water. © 2016, National Ground Water Association.

  6. Model Package Report: Central Plateau Vadose Zone Geoframework Version 1.0

    Energy Technology Data Exchange (ETDEWEB)

    Springer, Sarah D.

    2018-03-27

    The purpose of the Central Plateau Vadose Zone (CPVZ) Geoframework model (GFM) is to provide a reasonable, consistent, and defensible three-dimensional (3D) representation of the vadose zone beneath the Central Plateau at the Hanford Site to support the Composite Analysis (CA) vadose zone contaminant fate and transport models. The GFM is a 3D representation of the subsurface geologic structure. From this 3D geologic model, exported results in the form of point, surface, and/or volumes are used as inputs to populate and assemble the various numerical model architectures, providing a 3D-layered grid that is consistent with the GFM. The objective of this report is to define the process used to produce a hydrostratigraphic model for the vadose zone beneath the Hanford Site Central Plateau and the corresponding CA domain.

  7. A stochastic model for EEG microstate sequence analysis.

    Science.gov (United States)

    Gärtner, Matthias; Brodbeck, Verena; Laufs, Helmut; Schneider, Gaby

    2015-01-01

    The analysis of spontaneous resting state neuronal activity is assumed to give insight into the brain function. One noninvasive technique to study resting state activity is electroencephalography (EEG) with a subsequent microstate analysis. This technique reduces the recorded EEG signal to a sequence of prototypical topographical maps, which is hypothesized to capture important spatio-temporal properties of the signal. In a statistical EEG microstate analysis of healthy subjects in wakefulness and three stages of sleep, we observed a simple structure in the microstate transition matrix. It can be described with a first order Markov chain in which the transition probability from the current state (i.e., map) to a different map does not depend on the current map. The resulting transition matrix shows a high agreement with the observed transition matrix, requiring only about 2% of mass transport (1/2 L1-distance). In the second part, we introduce an extended framework in which the simple Markov chain is used to make inferences on a potential underlying time continuous process. This process cannot be directly observed and is therefore usually estimated from discrete sampling points of the EEG signal given by the local maxima of the global field power. Therefore, we propose a simple stochastic model called sampled marked intervals (SMI) model that relates the observed sequence of microstates to an assumed underlying process of background intervals and thus, complements approaches that focus on the analysis of observable microstate sequences. Copyright © 2014 Elsevier Inc. All rights reserved.

  8. Modelling of composite concrete block pavement systems applying a cohesive zone model

    DEFF Research Database (Denmark)

    Skar, Asmus; Poulsen, Peter Noe

    This paper presents a numerical analysis of the fracture behaviour of the cement bound base material in composite concrete block pavement systems, using a cohesive zone model. The functionality of the proposed model is tested on experimental and numerical investigations of beam bending tests....... The pavement is modelled as a simple slab on grade structure and parameters influencing the response, such as analysis technique, geometry and material parameters are studied. Moreover, the analysis is extended to a real scale example, modelling the pavement as a three-layered structure. It is found...... that the cohesive model is suitable for simulation of crack propagation in cement bound materials subjected to monotonic loading. The methodology implemented gives a new understanding of the mechanical behaviour of cement bound materials which can be used in further refinements of mechanical models for composite...

  9. Effects of Aftershock Declustering in Risk Modeling: Case Study of a Subduction Sequence in Mexico

    Science.gov (United States)

    Kane, D. L.; Nyst, M.

    2014-12-01

    Earthquake hazard and risk models often assume that earthquake rates can be represented by a stationary Poisson process, and that aftershocks observed in historical seismicity catalogs represent a deviation from stationarity that must be corrected before earthquake rates are estimated. Algorithms for classifying individual earthquakes as independent mainshocks or as aftershocks vary widely, and analysis of a single catalog can produce considerably different earthquake rates depending on the declustering method implemented. As these rates are propagated through hazard and risk models, the modeled results will vary due to the assumptions implied by these choices. In particular, the removal of large aftershocks following a mainshock may lead to an underestimation of the rate of damaging earthquakes and potential damage due to a large aftershock may be excluded from the model. We present a case study based on the 1907 - 1911 sequence of nine 6.9 Mexico in order to illustrate the variability in risk under various declustering approaches. Previous studies have suggested that subduction zone earthquakes in Mexico tend to occur in clusters, and this particular sequence includes events that would be labeled as aftershocks in some declustering approaches yet are large enough to produce significant damage. We model the ground motion for each event, determine damage ratios using modern exposure data, and then compare the variability in the modeled damage from using the full catalog or one of several declustered catalogs containing only "independent" events. We also consider the effects of progressive damage caused by each subsequent event and how this might increase or decrease the total losses expected from this sequence.

  10. Groundwater suitability recharge zones modelling - A GIS application

    Science.gov (United States)

    Dabral, S.; Bhatt, B.; Joshi, J. P.; Sharma, N.

    2014-11-01

    Groundwater quality in Gujarat state is highly variable and due to multiplicity of factors viz. influenced by direct sea water encroachment, inherent sediment salinity, water logging, overexploitation leading to overall deterioration in ground water quality, coupled with domestic and industrial pollution etc. The groundwater scenario in the state is not very encouraging due to imbalance between recharge and groundwater exploitation. Further, the demand for water has increased manifold owing to agricultural, industrial and domestic requirement and this has led to water scarcity in many parts of the state, which is likely to become more severe in coming future due to both natural and manmade factors. Therefore, sustainable development of groundwater resource requires precise quantitative assessment based on reasonably valid scientific principles. Hence, delineation of groundwater potential zones (GWPZ), has acquired great significance. The present study focuses on the integrated Geospatial and Multi-Criteria Decision Making (MCDM) techniques to determine the most important contributing factors that affect the groundwater resources and also to delineate the potential zones for groundwater recharge. The multiple thematic layers of influencing parameters viz. geology, geomorphology, soil, slope, drainage density and land use, weightages were assigned to the each factor according to their relative importance as per subject experts opinion owing to the natural setup of the region. The Analytical Hierarchy Process (AHP) was applied to these factors and potential recharge zones were identified. The study area for the assessment of groundwater recharge potential zones is Mahi-Narmada inter-stream region of Gujarat state. The study shows that around 28 % region has the excellent suitability of the ground water recharge.

  11. Genome sequencing and population genomics in non-model organisms.

    Science.gov (United States)

    Ellegren, Hans

    2014-01-01

    High-throughput sequencing technologies are revolutionizing the life sciences. The past 12 months have seen a burst of genome sequences from non-model organisms, in each case representing a fundamental source of data of significant importance to biological research. This has bearing on several aspects of evolutionary biology, and we are now beginning to see patterns emerging from these studies. These include significant heterogeneity in the rate of recombination that affects adaptive evolution and base composition, the role of population size in adaptive evolution, and the importance of expansion of gene families in lineage-specific adaptation. Moreover, resequencing of population samples (population genomics) has enabled the identification of the genetic basis of critical phenotypes and cast light on the landscape of genomic divergence during speciation. Copyright © 2013 Elsevier Ltd. All rights reserved.

  12. Maar-diatreme volcanism relating to the pyroclastic sequence of a newly discovered high-alumina basalt in the Maroa Volcanic Centre, Taupo Volcanic Zone, New Zealand

    Science.gov (United States)

    Kósik, S.; Németh, K.; Procter, J. N.; Zellmer, G. F.

    2017-07-01

    Diatreme sequences have previously been described from drill holes within the Taupo Volcanic Zone. The newly discovered Te Hukui Basalt exhibits deep excavation of country rocks that do not appear elsewhere at the surface. The basalt is characterized by proximal deposition of pyroclastic deposits relating to phreatomagmatism. The geochemical composition classifies these rocks as high-alumina basalts. They erupted along the Orakeikorako Fault at the same location where rhyolitic activity of Puketerata occurred at a later point in time. The petrological characteristics of the basalts indicate the mixing of mafic melt with crystalline mush relating to more evolved magmas. The new basaltic occurrence supports frequent mafic recharge of shallow magma reservoirs, inducing basaltic eruptions, in this case the mafic magma intruding into highly crystallized mush zones. This may explain why basaltic eruptions mostly occur on the edge of the central extensional part of the Taupo Volcanic Zone.

  13. Mapping the Habitable Zone of Exoplanets with a 2D Energy Balance Model

    Science.gov (United States)

    Moon, Nicole Taylor; Dr. Lisa Kaltenegger, Dr. Ramses Ramirez

    2018-01-01

    Traditionally, the habitable zone has been defined as the distance at which liquid water could exist on the surface of a rocky planet. However, different complexity models (simplified and fast:1D, and complex and time-intense:3D) models derive different boundaries for the habitable zone. The goal of this project was to test a new intermediate complexity 2D Energy Balance model, add a new ice albedo feedback mechanism, and derive the habitable zone boundaries. After completing this first project, we also studied how other feedback mechanisms, such as the presence of clouds and the carbonate-silicate cycle, effected the location of the habitable zone boundaries using this 2D model. This project was completed as part of a 2017 summer REU program hosted by Cornell's Center for Astrophysics and Plantary Sciecne and in partnership with the Carl Sagan Institute.

  14. An empirical exploration of the world oil price under the target zone model

    International Nuclear Information System (INIS)

    Tang, Linghui; Hammoudeh, Shawkat

    2002-01-01

    This paper investigates the behavior of the world oil price based on the first-generation target zone model. Using anecdotal data during the period of 1988-1999, we found that OPEC has tried to maintain a weak target zone regime for the oil price. Our econometric tests suggest that the movement of the oil price is not only manipulated by actual and substantial interventions by OPEC but also tempered by market participants' expectations of interventions. As a consequence, the non-linear model based on the target zone theory has very good forecasting ability when the oil price approaches the upper or lower limit of the band

  15. An empirical exploration of the world oil price under the target zone model

    International Nuclear Information System (INIS)

    Linghui Tang; Shawkat Hammoudeh

    2002-01-01

    This paper investigates the behavior of the world oil price based on the first-generation target zone model. Using anecdotal data during the period of 1988-1999, we found that OPEC has tried to maintain a weak target zone regime for the oil price. Our econometric tests suggest that the movement of the oil price is not only manipulated by actual and substantial interventions by OPEC but also tempered by market participants' expectations of interventions. As a consequence, the non-linear model based on the target zone theory has very good forecasting ability when the oil price approaches the upper or lower limit of the band. (author)

  16. Comprehensive Information Retrieval and Model Input Sequence (CIRMIS)

    Energy Technology Data Exchange (ETDEWEB)

    Friedrichs, D.R.

    1977-04-01

    The Comprehensive Information Retrieval and Model Input Sequence (CIRMIS) was developed to provide the research scientist with man--machine interactive capabilities in a real-time environment, and thereby produce results more quickly and efficiently. The CIRMIS system was originally developed to increase data storage and retrieval capabilities and ground-water model control for the Hanford site. The overall configuration, however, can be used in other areas. The CIRMIS system provides the user with three major functions: retrieval of well-based data, special application for manipulating surface data or background maps, and the manipulation and control of ground-water models. These programs comprise only a portion of the entire CIRMIS system. A complete description of the CIRMIS system is given in this report. 25 figures, 7 tables. (RWR)

  17. Calibrating vadose zone models with time-lapse gravity data

    DEFF Research Database (Denmark)

    Christiansen, Lars; Binning, Philip John; Rosbjerg, Dan

    2011-01-01

    The vadose zone plays an important role in the hydrologic cycle. Various geophysical methods can determine soil water content variations in time and space in volumes ranging from a few cubic centimeters to several cubic meters. In contrast to the established methods, time-lapse gravity measurements...... hydrologic information. In this study, changes in the soil water content gave rise to a measurable signal in a forced infiltration experiment on a 107-m2 grassland area. Time-lapse gravity data were able to constrain the van Genuchten soil hydraulic parameters in both a synthetic example and a field...

  18. Protein model discrimination using mutational sensitivity derived from deep sequencing.

    Science.gov (United States)

    Adkar, Bharat V; Tripathi, Arti; Sahoo, Anusmita; Bajaj, Kanika; Goswami, Devrishi; Chakrabarti, Purbani; Swarnkar, Mohit K; Gokhale, Rajesh S; Varadarajan, Raghavan

    2012-02-08

    A major bottleneck in protein structure prediction is the selection of correct models from a pool of decoys. Relative activities of ∼1,200 individual single-site mutants in a saturation library of the bacterial toxin CcdB were estimated by determining their relative populations using deep sequencing. This phenotypic information was used to define an empirical score for each residue (RankScore), which correlated with the residue depth, and identify active-site residues. Using these correlations, ∼98% of correct models of CcdB (RMSD ≤ 4Å) were identified from a large set of decoys. The model-discrimination methodology was further validated on eleven different monomeric proteins using simulated RankScore values. The methodology is also a rapid, accurate way to obtain relative activities of each mutant in a large pool and derive sequence-structure-function relationships without protein isolation or characterization. It can be applied to any system in which mutational effects can be monitored by a phenotypic readout. Copyright © 2012 Elsevier Ltd. All rights reserved.

  19. Next-Generation Sequence Analysis of Cancer Xenograft Models

    Science.gov (United States)

    Rossello, Fernando J.; Tothill, Richard W.; Britt, Kara; Marini, Kieren D.; Falzon, Jeanette; Thomas, David M.; Peacock, Craig D.; Marchionni, Luigi; Li, Jason; Bennett, Samara; Tantoso, Erwin; Brown, Tracey; Chan, Philip; Martelotto, Luciano G.; Watkins, D. Neil

    2013-01-01

    Next-generation sequencing (NGS) studies in cancer are limited by the amount, quality and purity of tissue samples. In this situation, primary xenografts have proven useful preclinical models. However, the presence of mouse-derived stromal cells represents a technical challenge to their use in NGS studies. We examined this problem in an established primary xenograft model of small cell lung cancer (SCLC), a malignancy often diagnosed from small biopsy or needle aspirate samples. Using an in silico strategy that assign reads according to species-of-origin, we prospectively compared NGS data from primary xenograft models with matched cell lines and with published datasets. We show here that low-coverage whole-genome analysis demonstrated remarkable concordance between published genome data and internal controls, despite the presence of mouse genomic DNA. Exome capture sequencing revealed that this enrichment procedure was highly species-specific, with less than 4% of reads aligning to the mouse genome. Human-specific expression profiling with RNA-Seq replicated array-based gene expression experiments, whereas mouse-specific transcript profiles correlated with published datasets from human cancer stroma. We conclude that primary xenografts represent a useful platform for complex NGS analysis in cancer research for tumours with limited sample resources, or those with prominent stromal cell populations. PMID:24086345

  20. Next-generation sequence analysis of cancer xenograft models.

    Directory of Open Access Journals (Sweden)

    Fernando J Rossello

    Full Text Available Next-generation sequencing (NGS studies in cancer are limited by the amount, quality and purity of tissue samples. In this situation, primary xenografts have proven useful preclinical models. However, the presence of mouse-derived stromal cells represents a technical challenge to their use in NGS studies. We examined this problem in an established primary xenograft model of small cell lung cancer (SCLC, a malignancy often diagnosed from small biopsy or needle aspirate samples. Using an in silico strategy that assign reads according to species-of-origin, we prospectively compared NGS data from primary xenograft models with matched cell lines and with published datasets. We show here that low-coverage whole-genome analysis demonstrated remarkable concordance between published genome data and internal controls, despite the presence of mouse genomic DNA. Exome capture sequencing revealed that this enrichment procedure was highly species-specific, with less than 4% of reads aligning to the mouse genome. Human-specific expression profiling with RNA-Seq replicated array-based gene expression experiments, whereas mouse-specific transcript profiles correlated with published datasets from human cancer stroma. We conclude that primary xenografts represent a useful platform for complex NGS analysis in cancer research for tumours with limited sample resources, or those with prominent stromal cell populations.

  1. Gravity Modeling of the Cerro Goden fault zone, NW Puerto Rico

    Science.gov (United States)

    Mattei, G. A.; Keranen, K. M.; Asencio, E.

    2010-12-01

    The 2010 M7.0 Haiti earthquake served as a reminder of potential earthquake hazards on upper-crustal fault systems along the northern boundary of the Carribean plate. In this study we modeled the structure of the Cerro Goden and subparallel fault zones in northwestern Puerto Rico, which cross through densely populated areas, using existing and newly collected gravity data. The fault zone had previously been mapped at the surface, but the details of the fault zone in the subsurface and the detailed structure remain poorly constrained. We used our gravity data to extend surface geologic models to greater depth. Specifically, we modeled and interpreted a north-to-south 2-D model perpendicular to the Cerro Goden fault zone. We used horizontal derivative and residual anomaly maps to emphasize edges of subsurface bodies and shallow structures of interest. Our preliminary 2D model constrains the width and depth extent of serpentinite bodies along the fault zones, the relationship of the faults with the Cerro Goden anticline in central Puerto Rico, and confirms the steep NE dip of the faults extrapolated from surface data. Additional data will be collected in the future across the Cerro Goden fault zone to laterally extend our models of subsurface structural features.

  2. Hydrogeologic Framework Model for the Saturated Zone Site Scale flow and Transport Model

    International Nuclear Information System (INIS)

    Miller, T.

    2004-01-01

    The purpose of this report is to document the 19-unit, hydrogeologic framework model (19-layer version, output of this report) (HFM-19) with regard to input data, modeling methods, assumptions, uncertainties, limitations, and validation of the model results in accordance with AP-SIII.10Q, Models. The HFM-19 is developed as a conceptual model of the geometric extent of the hydrogeologic units at Yucca Mountain and is intended specifically for use in the development of the ''Saturated Zone Site-Scale Flow Model'' (BSC 2004 [DIRS 170037]). Primary inputs to this model report include the GFM 3.1 (DTN: MO9901MWDGFM31.000 [DIRS 103769]), borehole lithologic logs, geologic maps, geologic cross sections, water level data, topographic information, and geophysical data as discussed in Section 4.1. Figure 1-1 shows the information flow among all of the saturated zone (SZ) reports and the relationship of this conceptual model in that flow. The HFM-19 is a three-dimensional (3-D) representation of the hydrogeologic units surrounding the location of the Yucca Mountain geologic repository for spent nuclear fuel and high-level radioactive waste. The HFM-19 represents the hydrogeologic setting for the Yucca Mountain area that covers about 1,350 km2 and includes a saturated thickness of about 2.75 km. The boundaries of the conceptual model were primarily chosen to be coincident with grid cells in the Death Valley regional groundwater flow model (DTN: GS960808312144.003 [DIRS 105121]) such that the base of the site-scale SZ flow model is consistent with the base of the regional model (2,750 meters below a smoothed version of the potentiometric surface), encompasses the exploratory boreholes, and provides a framework over the area of interest for groundwater flow and radionuclide transport modeling. In depth, the model domain extends from land surface to the base of the regional groundwater flow model (D'Agnese et al. 1997 [DIRS 100131], p 2). For the site-scale SZ flow model, the HFM

  3. Hydrogeologic Framework Model for the Saturated Zone Site Scale flow and Transport Model

    Energy Technology Data Exchange (ETDEWEB)

    T. Miller

    2004-11-15

    The purpose of this report is to document the 19-unit, hydrogeologic framework model (19-layer version, output of this report) (HFM-19) with regard to input data, modeling methods, assumptions, uncertainties, limitations, and validation of the model results in accordance with AP-SIII.10Q, Models. The HFM-19 is developed as a conceptual model of the geometric extent of the hydrogeologic units at Yucca Mountain and is intended specifically for use in the development of the ''Saturated Zone Site-Scale Flow Model'' (BSC 2004 [DIRS 170037]). Primary inputs to this model report include the GFM 3.1 (DTN: MO9901MWDGFM31.000 [DIRS 103769]), borehole lithologic logs, geologic maps, geologic cross sections, water level data, topographic information, and geophysical data as discussed in Section 4.1. Figure 1-1 shows the information flow among all of the saturated zone (SZ) reports and the relationship of this conceptual model in that flow. The HFM-19 is a three-dimensional (3-D) representation of the hydrogeologic units surrounding the location of the Yucca Mountain geologic repository for spent nuclear fuel and high-level radioactive waste. The HFM-19 represents the hydrogeologic setting for the Yucca Mountain area that covers about 1,350 km2 and includes a saturated thickness of about 2.75 km. The boundaries of the conceptual model were primarily chosen to be coincident with grid cells in the Death Valley regional groundwater flow model (DTN: GS960808312144.003 [DIRS 105121]) such that the base of the site-scale SZ flow model is consistent with the base of the regional model (2,750 meters below a smoothed version of the potentiometric surface), encompasses the exploratory boreholes, and provides a framework over the area of interest for groundwater flow and radionuclide transport modeling. In depth, the model domain extends from land surface to the base of the regional groundwater flow model (D'Agnese et al. 1997 [DIRS 100131], p 2). For the site

  4. One-dimensional flow model of the river-hyporheic zone system

    Science.gov (United States)

    Pokrajac, D.

    2016-12-01

    The hyporheic zone is a shallow layer beneath natural streams that is characterized by intense exchange of water, nutrients, pollutants and thermal energy. Understanding these exchange processes is crucial for successful modelling of the river hydrodynamics and morphodynamics at various scales from the river corridor up to the river network scale (Cardenas, 2015). Existing simulation models of hyporheic exchange processes are either idealized models of the tracer movement through the river-hyporheic zone system (e.g. TSM, Bencala and Walters, 1983) or detailed models of turbulent flow in a stream, coupled with a conventional 2D Darcian groundwater model (e.g. Cardenas and Wilson, 2007). This paper presents an alternative approach which involves a simple 1-D simulation model of the hyporheic zone system based on the classical SWE equations coupled with the newly developed porous media analogue. This allows incorporating the effects of flow unsteadiness and non-Darcian parameterization od the drag term in the hyporheic zone model. The conceptual model of the stream-hyporheic zone system consists of a 1D model of the open channel flow in the river, coupled with a 1D model of the flow in the hyporheic zone via volume flux due to the difference in the water level in the river and the hyporheic zone. The interaction with the underlying groundwater aquifer is neglected, but coupling the present model with any conventional groundwater model is straightforward. The paper presents the derivation of the 1D flow equations for flow in the hyporheic zone, the details of the numerical scheme used for solving them and the model validation by comparison with published experimental data. References Bencala, K. E., and R. A. Walters (1983) "Simulation of solute transport in a mountain pool-and-riffle stream- a transient storage model", Water Resources Reseach 19(3): 718-724. Cardenas, M. B. (2015) "Hyporheic zone hydrologic science: A historical account of its emergence and a

  5. Universal sequence replication, reversible polymerization and early functional biopolymers: a model for the initiation of prebiotic sequence evolution.

    Directory of Open Access Journals (Sweden)

    Sara Imari Walker

    Full Text Available Many models for the origin of life have focused on understanding how evolution can drive the refinement of a preexisting enzyme, such as the evolution of efficient replicase activity. Here we present a model for what was, arguably, an even earlier stage of chemical evolution, when polymer sequence diversity was generated and sustained before, and during, the onset of functional selection. The model includes regular environmental cycles (e.g. hydration-dehydration cycles that drive polymers between times of replication and functional activity, which coincide with times of different monomer and polymer diffusivity. Template-directed replication of informational polymers, which takes place during the dehydration stage of each cycle, is considered to be sequence-independent. New sequences are generated by spontaneous polymer formation, and all sequences compete for a finite monomer resource that is recycled via reversible polymerization. Kinetic Monte Carlo simulations demonstrate that this proposed prebiotic scenario provides a robust mechanism for the exploration of sequence space. Introduction of a polymer sequence with monomer synthetase activity illustrates that functional sequences can become established in a preexisting pool of otherwise non-functional sequences. Functional selection does not dominate system dynamics and sequence diversity remains high, permitting the emergence and spread of more than one functional sequence. It is also observed that polymers spontaneously form clusters in simulations where polymers diffuse more slowly than monomers, a feature that is reminiscent of a previous proposal that the earliest stages of life could have been defined by the collective evolution of a system-wide cooperation of polymer aggregates. Overall, the results presented demonstrate the merits of considering plausible prebiotic polymer chemistries and environments that would have allowed for the rapid turnover of monomer resources and for

  6. Ranking zones model – a multicriterial approach to the spatial management of urban areas

    Directory of Open Access Journals (Sweden)

    Ivan Marović

    2015-03-01

    Full Text Available Urban investment planning is highly complex and different views are provided by stakeholders and experts as to the scope, scale and potential solutions. The evaluation of such investments requires explicit consideration of multiple, conflicting and incommensurate criteria that have an important social, economic, and environmental influence on various stakeholders in different ways. To take into account all the dimensions, the proposed model is the Ranking Zones Model (RZM, based on PROMETHEE methods. The RZM comprises several steps providing a rank-list of all observed zones. It helps decision-makers come up with consistent decisions as to which zones to invest in and, at the same time, provides reassurance that the decision was based on a proper comparison of all relevant urban zone areas. The advantage of this approach is that even with a change in the decision-making structure, the actual procedure remains consistent.

  7. EFFECT OF METALLICITY ON THE EVOLUTION OF THE HABITABLE ZONE FROM THE PRE-MAIN SEQUENCE TO THE ASYMPTOTIC GIANT BRANCH AND THE SEARCH FOR LIFE

    International Nuclear Information System (INIS)

    Danchi, William C.; Lopez, Bruno

    2013-01-01

    During the course of stellar evolution, the location and width of the habitable zone changes as the luminosity and radius of the star evolves. The duration of habitability for a planet located at a given distance from a star is greatly affected by the characteristics of the host star. A quantification of these effects can be used observationally in the search for life around nearby stars. The longer the duration of habitability, the more likely it is that life has evolved. The preparation of observational techniques aimed at detecting life would benefit from the scientific requirements deduced from the evolution of the habitable zone. We present a study of the evolution of the habitable zone around stars of 1.0, 1.5, and 2.0 M ☉ for metallicities ranging from Z = 0.0001 to Z = 0.070. We also consider the evolution of the habitable zone from the pre-main sequence until the asymptotic giant branch is reached. We find that metallicity strongly affects the duration of the habitable zone for a planet as well as the distance from the host star where the duration is maximized. For a 1.0 M ☉ star with near solar metallicity, Z = 0.017, the duration of the habitable zone is >10 Gyr at distances 1.2-2.0 AU from the star, whereas the duration is >20 Gyr for high-metallicity stars (Z = 0.070) at distances of 0.7-1.8 AU, and ∼4 Gyr at distances of 1.8-3.3 AU for low-metallicity stars (Z = 0.0001). Corresponding results have been obtained for stars of 1.5 and 2.0 solar masses.

  8. Quasi-3D modelling of surf zone dynamics

    NARCIS (Netherlands)

    Luijendijk, A.; Henrotte, J.; Walstra, D.J.R.; van Ormondt, M.

    2010-01-01

    A quasi-three-dimensional model (quasi-3D) has been developed through the implementation of an analytical 1DV flow model in existing depth-averaged shallow water equations. The model includes the effects of waves and wind on the vertical distribution of the horizontal velocities. Comparisons with

  9. [Biomarker screening of rat pulmonary hypertension model by transcriptome sequencing].

    Science.gov (United States)

    Hu, F; Xie, L; Yu, L; Chen, J; Liu, H M

    2016-04-01

    To screen relative gene and pathway of rat severe pulmonary hypertension by transcriptome sequencing. Pulmonary hypertension animal model of SD rats was established by left lung resection and hypodermic injection of monocrotaline.Monocrotaline was injected subcutaneously one week after left lung resection.Eight rats at 1, 3, 5 weeks after the injection of monocrotaline respectively were named group M1, group M2 and group M3.Eight normal rats were assigned into control group (group C). The right lung tissue was used for transcriptome sequencing to screen the differentially expressed genes.KEGG pathway analysis was performed to screen the pathways with enriched differentially expressed genes. The animal model was established successfully.The pulmonary artery pressure was as follows: group C (28.6±3.0) mmHg(1 mmHg=0.133 kPa), group M1 (38.9±3.3) mmHg, group M2 (50.8±3.9) mmHg, group M3 (51.5±3.5) mmHg.The pressure elevated in group M1 compared with group C (P=0.007). The pressure in M2 and M3 elevated compared with M1(P=0.002 and Ppulmonary hypertension were epithelial specific receptor tyrosine kinase(Tie2) and thrombospondin-1(TSP-1). Tie2 was down-regulated (qpulmonary hypertension and up-regulated (qpulmonary hypertension.TSP-1 was up-regulated (qpulmonary hypertension and down-regulated (qpulmonary hypertension.In the stage of severe pulmonary hypertension, the differentially expressed genes were enriched mainly in the pathways of phosphatidylinostitol 3-kinase, focal adhesion kinase and extracellular matrix receptor interaction. The study provides transcriptome information of rat pulmonary hypertension model and normal rat.Possible mechanisms of pulmonary hypertension are found.These genes and pathways might be new precursor for the diagnosis and treatment of pulmonary hypertension.

  10. Slab1.0: A three-dimensional model of global subduction zone geometries

    Science.gov (United States)

    Hayes, Gavin P.; Wald, David J.; Johnson, Rebecca L.

    2012-01-01

    We describe and present a new model of global subduction zone geometries, called Slab1.0. An extension of previous efforts to constrain the two-dimensional non-planar geometry of subduction zones around the focus of large earthquakes, Slab1.0 describes the detailed, non-planar, three-dimensional geometry of approximately 85% of subduction zones worldwide. While the model focuses on the detailed form of each slab from their trenches through the seismogenic zone, where it combines data sets from active source and passive seismology, it also continues to the limits of their seismic extent in the upper-mid mantle, providing a uniform approach to the definition of the entire seismically active slab geometry. Examples are shown for two well-constrained global locations; models for many other regions are available and can be freely downloaded in several formats from our new Slab1.0 website, http://on.doi.gov/d9ARbS. We describe improvements in our two-dimensional geometry constraint inversion, including the use of ‘average’ active source seismic data profiles in the shallow trench regions where data are otherwise lacking, derived from the interpolation between other active source seismic data along-strike in the same subduction zone. We include several analyses of the uncertainty and robustness of our three-dimensional interpolation methods. In addition, we use the filtered, subduction-related earthquake data sets compiled to build Slab1.0 in a reassessment of previous analyses of the deep limit of the thrust interface seismogenic zone for all subduction zones included in our global model thus far, concluding that the width of these seismogenic zones is on average 30% larger than previous studies have suggested.

  11. A simple model of the wind turbine induction zone derived from numerical simulations

    DEFF Research Database (Denmark)

    Troldborg, Niels; Meyer Forsting, Alexander Raul

    2017-01-01

    The induction zone in front of different wind turbine rotors is studied by means of steady-state Navier-Stokes simulations combined with an actuator disk approach. It is shown that, for distances beyond 1 rotor radius upstream of the rotors, the induced velocity is self-similar and independent of...... of the rotor geometry. On the basis of these findings, a simple analytical model of the induction zone of wind turbines is proposed....

  12. The combined effect of attraction and orientation zones in 2D flocking models

    Science.gov (United States)

    Iliass, Tarras; Cambui, Dorilson

    2016-01-01

    In nature, many animal groups, such as fish schools or bird flocks, clearly display structural order and appear to move as a single coherent entity. In order to understand the complex motion of these systems, we study the Vicsek model of self-propelled particles (SPP) which is an important tool to investigate the behavior of collective motion of live organisms. This model reproduces the biological behavior patterns in the two-dimensional (2D) space. Within the framework of this model, the particles move with the same absolute velocity and interact locally in the zone of orientation by trying to align their direction with that of the neighbors. In this paper, we model the collective movement of SPP using an agent-based model which follows biologically motivated behavioral rules, by adding a second region called the attraction zone, where each particles move towards each other avoiding being isolated. Our main goal is to present a detailed numerical study on the effect of the zone of attraction on the kinetic phase transition of our system. In our study, the consideration of this zone seems to play an important role in the cohesion. Consequently, in the directional orientation, the zone that we added forms the compact particle group. In our simulation, we show clearly that the model proposed here can produce two collective behavior patterns: torus and dynamic parallel group. Implications of these findings are discussed.

  13. Variable-intercept panel model for deformation zoning of a super-high arch dam.

    Science.gov (United States)

    Shi, Zhongwen; Gu, Chongshi; Qin, Dong

    2016-01-01

    This study determines dam deformation similarity indexes based on an analysis of deformation zoning features and panel data clustering theory, with comprehensive consideration to the actual deformation law of super-high arch dams and the spatial-temporal features of dam deformation. Measurement methods of these indexes are studied. Based on the established deformation similarity criteria, the principle used to determine the number of dam deformation zones is constructed through entropy weight method. This study proposes the deformation zoning method for super-high arch dams and the implementation steps, analyzes the effect of special influencing factors of different dam zones on the deformation, introduces dummy variables that represent the special effect of dam deformation, and establishes a variable-intercept panel model for deformation zoning of super-high arch dams. Based on different patterns of the special effect in the variable-intercept panel model, two panel analysis models were established to monitor fixed and random effects of dam deformation. Hausman test method of model selection and model effectiveness assessment method are discussed. Finally, the effectiveness of established models is verified through a case study.

  14. Sequence Stratigraphy of lower zones of Asmari Formation in Marun Oilfield by using of microfacies analysis, isolith maps and γ- Ray log

    Directory of Open Access Journals (Sweden)

    Jalil Jafari

    2015-01-01

    Full Text Available The Oligo- Miocene Asmari Formation is one of the most important reservoir units of the Marun Oilfield in Dezful Embayment SW Iran, deposited in Zagros foreland basin. The goal of this study is to interpret depositional environment and sequence stratigraphy of lower zones of the Asmari Formation in Well No.281, 342 and 312in Marun Oilfield based on changes in the shape of γ- Ray, isolith maps and microfacies properties. Accordingly, identification of 9 carbonate microfacies and 2 siliciclastic petrofacies were identified that are deposited in four depositional environment including open marine, barrier, lagoon and tidal flat in a homoclinal ramp (consisting of outer, middle and inner ramp. Also, based on the shape of γ- Ray log, There sediment were deposited in marine environment. In open marine and barrier environments, The shape of γ- Ray log is serrated bell-shaped, serrated funnel-shaped, left bow-shaped, serrated shape and right boxcar shape, Whole in the beach environment it is cylinder and funnel shape and in lagoon and tidal flat environment can be seen on right bow to cylinder-shaped. Based on the isolith maps, sandstone of lower zones of the Asmari Formation in Marun Oilfield expanded by deltaic system along the southwestern margin of the basin and influenced by changes in sea level constantly. Sequence stratigraphic analysis led to identification of three third- order (DS1, DS2 and DS3 depositional sequences.

  15. The effect of adipose derived stromal vascular fraction on stasis zone in an experimental burn model.

    Science.gov (United States)

    Eyuboglu, Atilla Adnan; Uysal, Cagri A; Ozgun, Gonca; Coskun, Erhan; Markal Ertas, Nilgun; Haberal, Mehmet

    2018-03-01

    Stasis zone is the surrounding area of the coagulation zone which is an important part determining the extent of the necrosis in burn patients. In our study we aim to salvage the stasis zone by injecting adipose derived stromal vascular fraction (ADSVF). Thermal injury was applied on dorsum of Sprague-Dawley rats (n=20) by the "comb burn" model as described previously. When the burn injury was established on Sprague-Dawley rats (30min); rat dorsum was separated into 2 equal parts consisting of 4 burn zones (3 stasis zone) on each pair. ADSVF cells harvested from inguinal fat pads of Sprague-Dawley rats (n=5) were injected on the right side while same amount of phosphate buffered saline (PBS) injected on the left side of the same animal. One week later, average vital tissue on the statis zone was determined by macroscopy, angiography and microscopy. Vascular density, inflammatory cell density, gradient of fibrosis and epithelial thickness were determined via immunohistochemical assay. Macroscopic stasis zone tissue viability (32±3.28%, 57±4.28%) (p51, 1.50±0.43) (pzone on acute burn injuries. Copyright © 2017 Elsevier Ltd and ISBI. All rights reserved.

  16. Human Inferences about Sequences: A Minimal Transition Probability Model.

    Directory of Open Access Journals (Sweden)

    Florent Meyniel

    2016-12-01

    Full Text Available The brain constantly infers the causes of the inputs it receives and uses these inferences to generate statistical expectations about future observations. Experimental evidence for these expectations and their violations include explicit reports, sequential effects on reaction times, and mismatch or surprise signals recorded in electrophysiology and functional MRI. Here, we explore the hypothesis that the brain acts as a near-optimal inference device that constantly attempts to infer the time-varying matrix of transition probabilities between the stimuli it receives, even when those stimuli are in fact fully unpredictable. This parsimonious Bayesian model, with a single free parameter, accounts for a broad range of findings on surprise signals, sequential effects and the perception of randomness. Notably, it explains the pervasive asymmetry between repetitions and alternations encountered in those studies. Our analysis suggests that a neural machinery for inferring transition probabilities lies at the core of human sequence knowledge.

  17. Audio-Magnetotelluric Modeling of Cimandiri Fault Zone at Cibeber, Cianjur

    Directory of Open Access Journals (Sweden)

    Lina Handayani

    2016-12-01

    Full Text Available DOI: 10.17014/ijog.4.1.39-47The characteristic of Cimandiri Fault Zone has not been completely defined despite plenty of studies had already been accomplished. Therefore, an audio-magnetotelluric modeling was carried out. An audiomagnetotelluric survey was conducted at two parallel lines (N166oE that intersected Cimandiri Fault Zone in Cibeber area, Cianjur. The distance between those two lines was 4.5 km and each line consisted of twenty-one stations with the distance between stations was 500 m. From the acquired forty-two apparent resistivity curves, inversion was executed to obtain two models. The models indicate layers with resistivity value of > 1000 ohm.m at about 500 m depth at both lines, which are associated to the basement layer. Columns of low resistivity zones in about the middle of each model represent fault zones as the weak zones of the area, and both models displayed them slightly dip southward as thrust faults.

  18. Sequencing batch-reactor control using Gaussian-process models.

    Science.gov (United States)

    Kocijan, Juš; Hvala, Nadja

    2013-06-01

    This paper presents a Gaussian-process (GP) model for the design of sequencing batch-reactor (SBR) control for wastewater treatment. The GP model is a probabilistic, nonparametric model with uncertainty predictions. In the case of SBR control, it is used for the on-line optimisation of the batch-phases duration. The control algorithm follows the course of the indirect process variables (pH, redox potential and dissolved oxygen concentration) and recognises the characteristic patterns in their time profile. The control algorithm uses GP-based regression to smooth the signals and GP-based classification for the pattern recognition. When tested on the signals from an SBR laboratory pilot plant, the control algorithm provided a satisfactory agreement between the proposed completion times and the actual termination times of the biodegradation processes. In a set of tested batches the final ammonia and nitrate concentrations were below 1 and 0.5 mg L(-1), respectively, while the aeration time was shortened considerably. Copyright © 2013 Elsevier Ltd. All rights reserved.

  19. A Two-Zone Multigrid Model for SI Engine Combustion Simulation Using Detailed Chemistry

    Directory of Open Access Journals (Sweden)

    Hai-Wen Ge

    2010-01-01

    Full Text Available An efficient multigrid (MG model was implemented for spark-ignited (SI engine combustion modeling using detailed chemistry. The model is designed to be coupled with a level-set-G-equation model for flame propagation (GAMUT combustion model for highly efficient engine simulation. The model was explored for a gasoline direct-injection SI engine with knocking combustion. The numerical results using the MG model were compared with the results of the original GAMUT combustion model. A simpler one-zone MG model was found to be unable to reproduce the results of the original GAMUT model. However, a two-zone MG model, which treats the burned and unburned regions separately, was found to provide much better accuracy and efficiency than the one-zone MG model. Without loss in accuracy, an order of magnitude speedup was achieved in terms of CPU and wall times. To reproduce the results of the original GAMUT combustion model, either a low searching level or a procedure to exclude high-temperature computational cells from the grouping should be applied to the unburned region, which was found to be more sensitive to the combustion model details.

  20. Numerical modeling of the productivity of vertical to shallowly dipping fractured zones in crystalline rocks

    Science.gov (United States)

    Leray, S.; de Dreuzy, J.-R.; Bour, O.; Bresciani, E.

    2013-02-01

    SummaryGroundwater resources in crystalline rock are typically associated with the weathered zone and regional sub-vertical faults that are well connected to the surface. However, some sub-horizontal and shallowly dipping fractured zones can also be highly-productive aquifers. In this paper, numerical simulations of a conceptual hydrogeological model show that the flow to such strongly transmissive fractured zones is controlled by their transmissivity or by their deepening structure. While leakage through the overlying rock units is generally the limiting factor, recharge always occurs at least close to the outcrop of the fractured zone where the overlying rock is thinner and guarantees the availability of some groundwater. At small dip angles, recharge extends spatially and the flow within the fractured zone may even become the limiting factor when the hydraulic conductivity of the overlying rock is not less than two orders of magnitude smaller than the fractured zone transmissivity. This is precisely the case of the Plœmeur aquifer (Brittany, France) located in a crystalline rock geologic setting, where groundwater in a shallowly dipping fractured zone is used as the source of water supply for a nearby city of 20,000 people. Simulation results show that the fractured zones may represent potential aquifers under a large variety of hydrogeological conditions. Aquifers in shallowly dipping structures differ strongly from those located in regional sub-vertical fault zones in terms of flow patterns, and thus supposedly in terms of management of the groundwater resource. They are more local than regional in scale, and consequently do not require regional fracture connectivity. The leakage through the overlying rock unit enhances water quality. Finally, we argue that the potential widespread occurrence of these alternative and possibly less accessible resources should promote the development of appropriate identification methods.

  1. Multi-Zone hybrid model for failure detection of the stable ventilation systems

    DEFF Research Database (Denmark)

    Gholami, Mehdi; Schiøler, Henrik; Soltani, Mohsen

    2010-01-01

    In this paper, a conceptual multi-zone model for climate control of a live stock building is elaborated. The main challenge of this research is to estimate the parameters of a nonlinear hybrid model. A recursive estimation algorithm, the Extended Kalman Filter (EKF) is implemented for estimation...

  2. Dynamic Model of Basic Oxygen Steelmaking Process Based on Multi-zone Reaction Kinetics: Model Derivation and Validation

    Science.gov (United States)

    Rout, Bapin Kumar; Brooks, Geoff; Rhamdhani, M. Akbar; Li, Zushu; Schrama, Frank N. H.; Sun, Jianjun

    2018-04-01

    A multi-zone kinetic model coupled with a dynamic slag generation model was developed for the simulation of hot metal and slag composition during the basic oxygen furnace (BOF) operation. The three reaction zones (i) jet impact zone, (ii) slag-bulk metal zone, (iii) slag-metal-gas emulsion zone were considered for the calculation of overall refining kinetics. In the rate equations, the transient rate parameters were mathematically described as a function of process variables. A micro and macroscopic rate calculation methodology (micro-kinetics and macro-kinetics) were developed to estimate the total refining contributed by the recirculating metal droplets through the slag-metal emulsion zone. The micro-kinetics involves developing the rate equation for individual droplets in the emulsion. The mathematical models for the size distribution of initial droplets, kinetics of simultaneous refining of elements, the residence time in the emulsion, and dynamic interfacial area change were established in the micro-kinetic model. In the macro-kinetics calculation, a droplet generation model was employed and the total amount of refining by emulsion was calculated by summing the refining from the entire population of returning droplets. A dynamic FetO generation model based on oxygen mass balance was developed and coupled with the multi-zone kinetic model. The effect of post-combustion on the evolution of slag and metal composition was investigated. The model was applied to a 200-ton top blowing converter and the simulated value of metal and slag was found to be in good agreement with the measured data. The post-combustion ratio was found to be an important factor in controlling FetO content in the slag and the kinetics of Mn and P in a BOF process.

  3. Dynamic Model of Basic Oxygen Steelmaking Process Based on Multi-zone Reaction Kinetics: Model Derivation and Validation

    Science.gov (United States)

    Rout, Bapin Kumar; Brooks, Geoff; Rhamdhani, M. Akbar; Li, Zushu; Schrama, Frank N. H.; Sun, Jianjun

    2018-01-01

    A multi-zone kinetic model coupled with a dynamic slag generation model was developed for the simulation of hot metal and slag composition during the basic oxygen furnace (BOF) operation. The three reaction zones (i) jet impact zone, (ii) slag-bulk metal zone, (iii) slag-metal-gas emulsion zone were considered for the calculation of overall refining kinetics. In the rate equations, the transient rate parameters were mathematically described as a function of process variables. A micro and macroscopic rate calculation methodology (micro-kinetics and macro-kinetics) were developed to estimate the total refining contributed by the recirculating metal droplets through the slag-metal emulsion zone. The micro-kinetics involves developing the rate equation for individual droplets in the emulsion. The mathematical models for the size distribution of initial droplets, kinetics of simultaneous refining of elements, the residence time in the emulsion, and dynamic interfacial area change were established in the micro-kinetic model. In the macro-kinetics calculation, a droplet generation model was employed and the total amount of refining by emulsion was calculated by summing the refining from the entire population of returning droplets. A dynamic FetO generation model based on oxygen mass balance was developed and coupled with the multi-zone kinetic model. The effect of post-combustion on the evolution of slag and metal composition was investigated. The model was applied to a 200-ton top blowing converter and the simulated value of metal and slag was found to be in good agreement with the measured data. The post-combustion ratio was found to be an important factor in controlling FetO content in the slag and the kinetics of Mn and P in a BOF process.

  4. Modeling subgrid-scale turbulent fluxes in the "Grey Zone"

    Science.gov (United States)

    De Roode, S. R.; Jonker, H. J.; Siebesma, P.

    2017-12-01

    The ever increasing computational power nowadays allows both weather and climate models to operate at a horizontal grid resolution that is high enough to resolve some part of the turbulent transport. Some of these models apply a Smagorinsky type TKE closure model including a buoyancy production term to compute the subgrid turbulent fluxes of heat, momentum and moisture. For a stable stratification an analytical solution for the eddy viscosity can be derived. From a comparison with similarity relations from field observations it is concluded that an anistropic grid, as measured by the ratio of the horizontal to the vertical grid mesh sizes (r=Dx/Dz>1), will yield excessive subgrid mixing and an erroneous dependency on the grid resolution. Secondly, in contrast to what is being used in many LES models, field observations suggest that for a stable boundary layer the turbulent Prandtl number is close to unity. The effect of grid anistropy is also investigated for the CONSTRAIN cold air outbreak model intercomparison case. Here opposite results are found. In the presence of convective stratocumulus clouds the Smagorinsky model appears to be well capable of compensating the gradual reduction of the resolved vertical fluxes with coarsening horizontal grid resolution, up to values Dx>3 km, in such a way that the total turbulent fluxes are hardly affected.

  5. A probabilistic quantitative risk assessment model for the long-term work zone crashes.

    Science.gov (United States)

    Meng, Qiang; Weng, Jinxian; Qu, Xiaobo

    2010-11-01

    Work zones especially long-term work zones increase traffic conflicts and cause safety problems. Proper casualty risk assessment for a work zone is of importance for both traffic safety engineers and travelers. This paper develops a novel probabilistic quantitative risk assessment (QRA) model to evaluate the casualty risk combining frequency and consequence of all accident scenarios triggered by long-term work zone crashes. The casualty risk is measured by the individual risk and societal risk. The individual risk can be interpreted as the frequency of a driver/passenger being killed or injured, and the societal risk describes the relation between frequency and the number of casualties. The proposed probabilistic QRA model consists of the estimation of work zone crash frequency, an event tree and consequence estimation models. There are seven intermediate events--age (A), crash unit (CU), vehicle type (VT), alcohol (AL), light condition (LC), crash type (CT) and severity (S)--in the event tree. Since the estimated value of probability for some intermediate event may have large uncertainty, the uncertainty can thus be characterized by a random variable. The consequence estimation model takes into account the combination effects of speed and emergency medical service response time (ERT) on the consequence of work zone crash. Finally, a numerical example based on the Southeast Michigan work zone crash data is carried out. The numerical results show that there will be a 62% decrease of individual fatality risk and 44% reduction of individual injury risk if the mean travel speed is slowed down by 20%. In addition, there will be a 5% reduction of individual fatality risk and 0.05% reduction of individual injury risk if ERT is reduced by 20%. In other words, slowing down speed is more effective than reducing ERT in the casualty risk mitigation. 2010 Elsevier Ltd. All rights reserved.

  6. Root zone water quality model (RZWQM2): Model use, calibration and validation

    Science.gov (United States)

    Ma, Liwang; Ahuja, Lajpat; Nolan, B.T.; Malone, Robert; Trout, Thomas; Qi, Z.

    2012-01-01

    The Root Zone Water Quality Model (RZWQM2) has been used widely for simulating agricultural management effects on crop production and soil and water quality. Although it is a one-dimensional model, it has many desirable features for the modeling community. This article outlines the principles of calibrating the model component by component with one or more datasets and validating the model with independent datasets. Users should consult the RZWQM2 user manual distributed along with the model and a more detailed protocol on how to calibrate RZWQM2 provided in a book chapter. Two case studies (or examples) are included in this article. One is from an irrigated maize study in Colorado to illustrate the use of field and laboratory measured soil hydraulic properties on simulated soil water and crop production. It also demonstrates the interaction between soil and plant parameters in simulated plant responses to water stresses. The other is from a maize-soybean rotation study in Iowa to show a manual calibration of the model for crop yield, soil water, and N leaching in tile-drained soils. Although the commonly used trial-and-error calibration method works well for experienced users, as shown in the second example, an automated calibration procedure is more objective, as shown in the first example. Furthermore, the incorporation of the Parameter Estimation Software (PEST) into RZWQM2 made the calibration of the model more efficient than a grid (ordered) search of model parameters. In addition, PEST provides sensitivity and uncertainty analyses that should help users in selecting the right parameters to calibrate.

  7. Numerical modeling of dispersion of pollutant in the coastal zone of the Western Black Sea

    International Nuclear Information System (INIS)

    Daniel, P.; Mungov, G.; Kortchev, G.

    1999-01-01

    During the last years in NIMH numerical models were used for forecasting the sea state in the Western Black Sea. The recent developments in this field include a numerical model for computation the dispersion of pollutants in the coastal zone first of all the adaptation of the operational oil-spill model of Meteo-France for the hydrological conditions of the Black Sea and under verification is numerical model for transportation of radionuclides as specific conservative tracers

  8. Prediction and Validation of Heat Release Direct Injection Diesel Engine Using Multi-Zone Model

    Science.gov (United States)

    Anang Nugroho, Bagus; Sugiarto, Bambang; Prawoto; Shalahuddin, Lukman

    2014-04-01

    The objective of this study is to develop simulation model which capable to predict heat release of diesel combustion accurately in efficient computation time. A multi-zone packet model has been applied to solve the combustion phenomena inside diesel cylinder. The model formulations are presented first and then the numerical results are validated on a single cylinder direct injection diesel engine at various engine speed and timing injections. The model were found to be promising to fulfill the objective above.

  9. Zone-specific logistic regression models improve classification of prostate cancer on multi-parametric MRI

    Energy Technology Data Exchange (ETDEWEB)

    Dikaios, Nikolaos; Halligan, Steve; Taylor, Stuart; Atkinson, David; Punwani, Shonit [University College London, Centre for Medical Imaging, London (United Kingdom); University College London Hospital, Departments of Radiology, London (United Kingdom); Alkalbani, Jokha; Sidhu, Harbir Singh [University College London, Centre for Medical Imaging, London (United Kingdom); Abd-Alazeez, Mohamed; Ahmed, Hashim U.; Emberton, Mark [University College London, Research Department of Urology, Division of Surgery and Interventional Science, London (United Kingdom); Kirkham, Alex [University College London Hospital, Departments of Radiology, London (United Kingdom); Freeman, Alex [University College London Hospital, Department of Histopathology, London (United Kingdom)

    2015-09-15

    To assess the interchangeability of zone-specific (peripheral-zone (PZ) and transition-zone (TZ)) multiparametric-MRI (mp-MRI) logistic-regression (LR) models for classification of prostate cancer. Two hundred and thirty-one patients (70 TZ training-cohort; 76 PZ training-cohort; 85 TZ temporal validation-cohort) underwent mp-MRI and transperineal-template-prostate-mapping biopsy. PZ and TZ uni/multi-variate mp-MRI LR-models for classification of significant cancer (any cancer-core-length (CCL) with Gleason > 3 + 3 or any grade with CCL ≥ 4 mm) were derived from the respective cohorts and validated within the same zone by leave-one-out analysis. Inter-zonal performance was tested by applying TZ models to the PZ training-cohort and vice-versa. Classification performance of TZ models for TZ cancer was further assessed in the TZ validation-cohort. ROC area-under-curve (ROC-AUC) analysis was used to compare models. The univariate parameters with the best classification performance were the normalised T2 signal (T2nSI) within the TZ (ROC-AUC = 0.77) and normalized early contrast-enhanced T1 signal (DCE-nSI) within the PZ (ROC-AUC = 0.79). Performance was not significantly improved by bi-variate/tri-variate modelling. PZ models that contained DCE-nSI performed poorly in classification of TZ cancer. The TZ model based solely on maximum-enhancement poorly classified PZ cancer. LR-models dependent on DCE-MRI parameters alone are not interchangeable between prostatic zones; however, models based exclusively on T2 and/or ADC are more robust for inter-zonal application. (orig.)

  10. Development of a modular vapor intrusion model with variably saturated and non-isothermal vadose zone.

    Science.gov (United States)

    Bekele, Dawit N; Naidu, Ravi; Chadalavada, Sreenivasulu

    2017-10-12

    Human health risk assessment at hydrocarbon-contaminated sites requires a critical evaluation of the exposure pathways of volatile organic compounds including assessments of vapor exposure in indoor air. Although there are a number of vapor intrusion models (VIM) currently available, they rarely reproduce actual properties of soils in the vadose zone. At best, users of such models assume averaged parameters for the vadose zone based on information generated elsewhere. The objective of this study was to develop a one-dimensional steady-state VIM, indoorCARE™ model, that considers vertical spatial variations of the degree of saturation (or effective air-filled porosity) and temperature of the vadose zone. The indoorCARE™ model was developed using a quasi-analytical equation that (1) solves the coupled equations governing soil-water movement driven by pressure head and a soil heat transport module describing conduction of heat and (2) provides a VIM that accommodates various types of conceptual site model (CSM) scenarios. The indoorCARE™ model is applicable to both chlorinated hydrocarbon and petroleum hydrocarbon (PHC) contaminated sites. The model incorporates biodegradations of PHCs at a range of CSM scenarios. The results demonstrate that predictions of indoor vapor concentrations made with the indoorCARE™ model are close to those of the J&E and BioVapor models under homogeneous vadose zone conditions. The newly developed model under heterogeneous vadose zone conditions demonstrated improved predictions of indoor vapor concentrations. The research study presented a more accurate and more realistic way to evaluate potential human health risks associated with the soil-vapor-to-indoor-air pathways.

  11. Modeling Swash zone sediment transport at Truc Vert beach

    NARCIS (Netherlands)

    Van Rooijen, A.; Reniers, A.; Van Thiel de Vries, J.S.M.; Blenkinsopp, C.; McCall, R.

    2012-01-01

    A one-dimensional hydrostatic version of the XBeach model (Roelvink et al., 2009) is applied to hindcast swash morphodynamics measured during an accretive, and an erosive tide at Le Truc Vert beach (France) in early spring 2008 (Masselink et. al, 2009; Blenkinsopp et al., 2011). Swash hydrodynamics

  12. Parameter Estimation of Dynamic Multi-zone Models for Livestock Indoor Climate Control

    DEFF Research Database (Denmark)

    Wu, Zhuang; Stoustrup, Jakob; Heiselberg, Per

    2008-01-01

    and winter at a real scale livestock building in Denmark. The obtained comparative results between the measured data and the simulated output confirm that a very simple multi-zone model can capture the salient dynamical features of the climate dynamics which are needed for control purposes......., the livestock, the ventilation system and the building on the dynamic performance of indoor climate. Some significant parameters employed in the climate model as well as the airflow interaction between each conceptual zone are identified with the use of experimental time series data collected during spring...

  13. Numerical modeling for saturated-zone groundwater travel time analysis at Yucca Mountain

    International Nuclear Information System (INIS)

    Arnold, B.W.; Barr, G.E.

    1996-01-01

    A three-dimensional, site-scale numerical model of groundwater flow in the saturated zone at Yucca Mountain was constructed and linked to particle tracking simulations to produce an estimate of the distribution of groundwater travel times from the potential repository to the boundary of the accessible environment. This effort and associated modeling of groundwater travel times in the unsaturated zone were undertaken to aid in the evaluation of compliance of the site with 10CFR960. These regulations stipulate that pre-waste-emplacement groundwater travel time to the accessible environment shall exceed 1,000 years along any path of likely and significant radionuclide travel

  14. A modeling study of water flow in the vadose zone beneath the Radioactive Waste Management Complex

    International Nuclear Information System (INIS)

    Baca, R.G.; Magnuson, S.O.; Nguyen, H.D.; Martian, P.

    1992-01-01

    A modeling study was conducted for the purpose of gaining insight into the nature of water flow in the vadose zone beneath the Radioactive Waste Management Complex (RWMC). The modeling study focused on three specific hydrologic aspects: (1) relationship between meteorologic conditions and net infiltration, (2) water movement associated with past flooding events, and (3) estimation of water travel-times through the vadose zone. This information is necessary for understanding how contaminants may be transported through the vadose zone. Evaluations of net infiltration at the RWMC were performed by modeling the processes of precipitation, evaporation, infiltration and soil-moisture redistribution. Water flow simulations were performed for two distinct time periods, namely 1955--1964 and 1984--1990. The patterns of infiltration were calculated for both the undisturbed (or natural sediments) and the pit/trench cover materials. Detailed simulations of the 1969 flooding of Pit 10 were performed to estimate the rate and extent of water movement through the vadose zone. Water travel-times through the vadose zone were estimated using a Monte Carlo simulation approach. The simulations accounted for variability of soil and rock hydraulic properties as well as variations in the infiltration rate

  15. Predicting Freeway Work Zone Delays and Costs with a Hybrid Machine-Learning Model

    Directory of Open Access Journals (Sweden)

    Bo Du

    2017-01-01

    Full Text Available A hybrid machine-learning model, integrating an artificial neural network (ANN and a support vector machine (SVM model, is developed to predict spatiotemporal delays, subject to road geometry, number of lane closures, and work zone duration in different periods of a day and in the days of a week. The model is very user friendly, allowing the least inputs from the users. With that the delays caused by a work zone on any location of a New Jersey freeway can be predicted. To this end, tremendous amounts of data from different sources were collected to establish the relationship between the model inputs and outputs. A comparative analysis was conducted, and results indicate that the proposed model outperforms others in terms of the least root mean square error (RMSE. The proposed hybrid model can be used to calculate contractor penalty in terms of cost overruns as well as incentive reward schedule in case of early work competition. Additionally, it can assist work zone planners in determining the best start and end times of a work zone for developing and evaluating traffic mitigation and management plans.

  16. Age of Sulfate Methane Transition Zone Determined by Modelling Barium Sulfate Growth

    Science.gov (United States)

    Lin, S.; Wang, W. C.; Lien, K. L.; Liu, C. C.; Fan, L. F.

    2017-12-01

    Methane seep to the sediment/water interface could initiate anaerobic methane oxidation (AOM) with subsequent build up of chemosynthetic community, carbonate, pyrite and a number of other authigenic mineral formation. Determination the duration, sequence and time of methane seeps are keys to understand how methane seep to the environment and degree of alteration to the vicinity area. However, limited method existed in defining time of methane seep since there are some known problems involving typical dating methods, i.e. old carbon on C14 of fossil test or authigenic carbonate, thorium from surrounding matrix on U/Th authigenic carbonate dating. In this study, we have employed barium determination method (Dickens, 2001) to model timing of methane seep at two locations in the South China Sea. Our objective is to compare timing of the barium accumulation near the sulfate methane transition zone (SMTZ) on these two different locations and to seek if a similar mechanism driving the methane seep at two locations far apart. Dissolved barium, total sediment barium and aluminum were measured as well as pore water sulfate, and sediment pyrite concentrations. Time for the barium sulfate accumulation is calculated by: T = C/F, C= ∫ I x p x (1-Ø) Our results show that SMTZ is stabilized at each site for a duration of about 4000-5000 years. AOM process have been active at both sites at about the same time. In conjunction, pyrite also accumulated at a depth near the SMTZ as a result of methane oxidation. This result show that AOM could stay at the SMTZ for a relatively long period of time, on a scale of thousands of years.

  17. Permafrost Degradation Risk Zone Assessment using Simulation Models

    DEFF Research Database (Denmark)

    Daanen, R.P.; Ingeman-Nielsen, Thomas; Marchenko, S.

    2011-01-01

    as the potential active layer increase due to climate warming and surface alterations. PTP is then used in a simple risk assessment procedure useful for engineering applications. The modelling shows that climate warming will result in continuing wide-spread permafrost warming and degradation in Greenland......In this proof-of-concept study we focus on linking large scale climate and permafrost simulations to small scale engineering projects by bridging the gap between climate and permafrost sciences on the one hand and on the other technical recommendation for adaptation of planned infrastructures...

  18. The 2016 central Italy earthquake sequence: surface effects, fault model and triggering scenarios

    Science.gov (United States)

    Chatzipetros, Alexandros; Pavlides, Spyros; Papathanassiou, George; Sboras, Sotiris; Valkaniotis, Sotiris; Georgiadis, George

    2017-04-01

    The results of fieldwork performed during the 2016 earthquake sequence around the karstic basins of Norcia and La Piana di Castelluccio, at an altitude of 1400 m, on the Monte Vettore (altitude 2476 m) and Vettoretto, as well as the three mapped seismogenic faults, striking NNW-SSW, are presented in this paper. Surface co-seismic ruptures were observed in the Vettore and Vettoretto segment of the fault for several kilometres ( 7 km) in the August earthquakes at high altitudes, and were re-activated and expanded northwards during the October earthquakes. Coseismic ruptures and the neotectonic Mt. Vettore fault zone were modelled in detail using images acquired from specifically planned UAV (drone) flights. Ruptures, typically with displacement of up to 20 cm, were observed after the August event both in the scree and weathered mantle (elluvium), as well as the bedrock, consisting mainly of fragmented carbonate rocks with small tectonic surfaces. These fractures expanded and new ones formed during the October events, typically of displacements of up to 50 cm, although locally higher displacements of up to almost 2 m were observed. Hundreds of rock falls and landslides were mapped through satellite imagery, using pre- and post- earthquake Sentinel 2A images. Several of them were also verified in the field. Based on field mapping results and seismological information, the causative faults were modelled. The model consists of five seismogenic sources, each one associated with a strong event in the sequence. The visualisation of the seismogenic sources follows INGV's DISS standards for the Individual Seismogenic Sources (ISS) layer, while strike, dip and rake of the seismic sources are obtained from selected focal mechanisms. Based on this model, the ground deformation pattern was inferred, using Okada's dislocation solution formulae, which shows that the maximum calculated vertical displacement is 0.53 m. This is in good agreement with the statistical analysis of the

  19. Analytical modelling of stable isotope fractionation of volatile organic compounds in the unsaturated zone

    OpenAIRE

    Bouchard, D.; Cornaton, F.; Höhener, P.; Hunkeler, D.

    2011-01-01

    Analytical models were developed that simulate stable isotope ratios of volatile organic compounds (VOCs) near a point source contamination in the unsaturated zone. The models describe diffusive transport of VOCs, biodegradation and source ageing. The mass transport is governed by Fick's law for diffusion. The equation for reactive transport of VOCs in the soil gas phase was solved for different source geometries and for different boundary conditions. Model results were compared to experiment...

  20. Modeling of Solute transport in a fractured rock zone at KURT

    International Nuclear Information System (INIS)

    Park, Chung Kyun; Lee, Jae Kwang; Baik, Min Hoon; Jeong, Jong Tae

    2010-01-01

    A solute transport model has developed to simulate migration of tracers which has tested in KURT. KAERI built an underground research laboratory so called KURT, which stands for Korea Underground Research Tunnel. Dipole tests has performed with some nonradioactive conservative tracers in a fractured zone which having a single fracture at KURT. The objectives of this study are not only developing a migration model of solutes for in-situ open environments but also validating the model by comparing and estimating experimental results

  1. Creep model of unsaturated sliding zone soils and long-term deformation analysis of landslides

    Science.gov (United States)

    Zou, Liangchao; Wang, Shimei; Zhang, Yeming

    2015-04-01

    Sliding zone soil is a special soil layer formed in the development of a landslide. Its creep behavior plays a significant role in long-term deformation of landslides. Due to rainfall infiltration and reservoir water level fluctuation, the soils in the slide zone are often in unsaturated state. Therefore, the investigation of creep behaviors of the unsaturated sliding zone soils is of great importance for understanding the mechanism of the long-term deformation of a landslide in reservoir areas. In this study, the full-process creep curves of the unsaturated soils in the sliding zone in different net confining pressure, matric suctions and stress levels were obtained from a large number of laboratory triaxial creep tests. A nonlinear creep model for unsaturated soils and its three-dimensional form was then deduced based on the component model theory and unsaturated soil mechanics. This creep model was validated with laboratory creep data. The results show that this creep model can effectively and accurately describe the nonlinear creep behaviors of the unsaturated sliding zone soils. In order to apply this creep model to predict the long-term deformation process of landslides, a numerical model for simulating the coupled seepage and creep deformation of unsaturated sliding zone soils was developed based on this creep model through the finite element method (FEM). By using this numerical model, we simulated the deformation process of the Shuping landslide located in the Three Gorges reservoir area, under the cycling reservoir water level fluctuation during one year. The simulation results of creep displacement were then compared with the field deformation monitoring data, showing a good agreement in trend. The results show that the creeping deformations of landslides have strong connections with the changes of reservoir water level. The creep model of unsaturated sliding zone soils and the findings obtained by numerical simulations in this study are conducive to

  2. Performance assessment model development and analysis of radionuclide transport in the unsaturated zone, Yucca Mountain, Nevada

    Science.gov (United States)

    Robinson, Bruce A.; Li, Chunhong; Ho, Clifford K.

    2003-05-01

    This paper describes the development and use of a particle-tracking model to perform radionuclide-transport simulations in the unsaturated zone at Yucca Mountain, Nevada. The goal of the effort was to produce a computational model that can be coupled to the project's calibrated 3D site-scale flow model so that the results of that effort could be incorporated directly into the Total System Performance Assessment (TSPA) analyses. The transport model simulates multiple species (typically 20 or more) with complex time-varying and spatially varying releases from the potential repository. Water-table rise, climate-change scenarios, and decay chains are additional features of the model. A cell-based particle-tracking method was employed that includes a dual-permeability formulation, advection, longitudinal dispersion, matrix diffusion, and colloid-facilitated transport. This paper examines the transport behavior of several key radionuclides through the unsaturated zone using the calibrated 3D unsaturated flow fields. Computational results illustrate the relative importance of fracture flow, matrix diffusion, and lateral diversion on the distribution of travel times from the simulated repository to the water table for various climatic conditions. Results also indicate rapid transport through fractures for a portion of the released mass. Further refinement of the model will address several issues, including conservatism in the transport model, the assignment of parameters in the flow and transport models, and the underlying assumptions used to support the conceptual models of flow and transport in the unsaturated zone at Yucca Mountain.

  3. Calibrating E-values for hidden Markov models using reverse-sequence null models.

    Science.gov (United States)

    Karplus, Kevin; Karchin, Rachel; Shackelford, George; Hughey, Richard

    2005-11-15

    Hidden Markov models (HMMs) calculate the probability that a sequence was generated by a given model. Log-odds scoring provides a context for evaluating this probability, by considering it in relation to a null hypothesis. We have found that using a reverse-sequence null model effectively removes biases owing to sequence length and composition and reduces the number of false positives in a database search. Any scoring system is an arbitrary measure of the quality of database matches. Significance estimates of scores are essential, because they eliminate model- and method-dependent scaling factors, and because they quantify the importance of each match. Accurate computation of the significance of reverse-sequence null model scores presents a problem, because the scores do not fit the extreme-value (Gumbel) distribution commonly used to estimate HMM scores' significance. To get a better estimate of the significance of reverse-sequence null model scores, we derive a theoretical distribution based on the assumption of a Gumbel distribution for raw HMM scores and compare estimates based on this and other distribution families. We derive estimation methods for the parameters of the distributions based on maximum likelihood and on moment matching (least-squares fit for Student's t-distribution). We evaluate the modeled distributions of scores, based on how well they fit the tail of the observed distribution for data not used in the fitting and on the effects of the improved E-values on our HMM-based fold-recognition methods. The theoretical distribution provides some improvement in fitting the tail and in providing fewer false positives in the fold-recognition test. An ad hoc distribution based on assuming a stretched exponential tail does an even better job. The use of Student's t to model the distribution fits well in the middle of the distribution, but provides too heavy a tail. The moment-matching methods fit the tails better than maximum-likelihood methods

  4. FEM modelling of firing temperature and stress zones

    Energy Technology Data Exchange (ETDEWEB)

    Schulle, W.; Schultz, K. [Bergakademie Freiberg (Germany)

    1999-03-01

    In the introduction, the principal possibilities of using finite element modelling (FEM) for problem solving in the firing processes of ceramics are given. Subsequently, two concrete application examples are described. In the first example, the temperature and stress calculation during biscuit firing of porcelain is discussed. The results are given for the influence of the heating rate for stacked firing and single-layer firing of flat tableware, the influence of the positioning of the individual plates in the plate stack, and changes in shape of the article during the formation of temperature and stress fields could be estimated. In a second example, the heat stresses that arise during the firing of high voltage insulators were calculated. It can be shown how the progression of the stresses is influenced by the body geometry, especially with the insulators ''cup'' design. During the course of the firing process, a regulating influence is possible. The examples should encourage further problem solving by specific use of FEM. (orig.)

  5. A modified version of the SMAR model for estimating root-zone soil ...

    African Journals Online (AJOL)

    Previous studies have proved the effectiveness of SMAR in estimating root-zone soil moisture, yet there is still room for improvement in its application. For example, the soil water loss function (i.e. deep percolation and evapotranspiration), assumed to be a linear function in the SMAR model, may produce approximations in ...

  6. A Groundwater Model to Assess Water Resource Impacts at the Imperial East Solar Energy Zone

    Energy Technology Data Exchange (ETDEWEB)

    Quinn, John [Argonne National Lab. (ANL), Argonne, IL (United States); Greer, Chris [Argonne National Lab. (ANL), Argonne, IL (United States); O' Connor, Ben L. [Argonne National Lab. (ANL), Argonne, IL (United States); Tompson, Andrew F.B. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2013-12-01

    The purpose of this study is to develop a groundwater flow model to examine the influence of potential groundwater withdrawal to support the utility-scale solar energy development at the Imperial East Solar Energy Zone (SEZ) as a part of the Bureau of Land Management’s (BLM) solar energy program.

  7. Solid Waste and Water Quality Management Models for Sagarmatha National Park and Buffer Zone, Nepal.

    NARCIS (Netherlands)

    Manfredi, Emanuela Chiara; Flury, Bastian; Viviano, Gaetano; Thakuri, Sudeep; Khanal, Sanjay Nath; Jha, Pramod Kumar; Maskey, Ramesh Kumar; Kayastha, Rijan Bhakta; Kafle, Kumud Raj; Bhochhibhoya, Silu; Ghimire, Narayan Prasad; Shrestha, Bharat Babu; Chaudhary, Gyanendra; Giannino, Francesco; Carteni, Fabrizio; Mazzoleni, Stefano; Salerno, Franco

    2010-01-01

    The problem of supporting decision- and policy-makers in managing issues related to solid waste and water quality was addressed within the context of a participatory modeling framework in the Sagarmatha National Park and Buffer Zone in Nepal. We present the main findings of management-oriented

  8. Reanalysis of water and carbon cycle models at a critical zone observatory

    Science.gov (United States)

    The Susquehanna Shale Hills Critical Zone Observatory (SSHCZO) is a forested, hill-slope catchment located in the temperate-climate of central Pennsylvania with an extensive network of ground-based instrumentation for model testing and development. In this paper we discuss the use of multi-state fi...

  9. A hybrid model of swash-zone longshore sediment transport on refelctive beaches

    NARCIS (Netherlands)

    Jiang, A.W.; Hughes, M.; Cowell, P.; Gordon, A.; Savioli, J.C.; Ranasinghe, R.W.M.R.J.B.

    2010-01-01

    The hydrodynamics and sediment transport in the swash zone is currently outside the domain of coastal-area models, which is a significant limitation in obtaining littoral sediment-transport estimates, especially on steep reflective beaches where the waves practically break on the beachface. In this

  10. Predictions of mixed mode interface crack growth using a cohesive zone model for ductile fracture

    DEFF Research Database (Denmark)

    Tvergaard, Viggo

    2004-01-01

    with the surrounding material in the tangential direction. Thus, the present interface description incorporates the important effect of stress triaxiality on damage evolution, which is not part of the usual cohesive zone models. The interface elements have been used previously for mode I loading conditions...

  11. A Groundwater Model to Assess Water Resource Impacts at the Brenda Solar Energy Zone

    Energy Technology Data Exchange (ETDEWEB)

    Quinn, John [Argonne National Lab. (ANL), Argonne, IL (United States); Carr, Adrianne E. [Argonne National Lab. (ANL), Argonne, IL (United States); Greer, Chris [Argonne National Lab. (ANL), Argonne, IL (United States); Bowen, Esther E. [Argonne National Lab. (ANL), Argonne, IL (United States)

    2013-12-01

    The purpose of this study is to develop a groundwater flow model to examine the influence of potential groundwater withdrawal to support utility-scale solar energy development at the Brenda Solar Energy Zone (SEZ), as a part of the Bureau of Land Management’s (BLM’s) Solar Energy Program.

  12. Zone-specific logistic regression models improve classification of prostate cancer on multi-parametric MRI.

    Science.gov (United States)

    Dikaios, Nikolaos; Alkalbani, Jokha; Abd-Alazeez, Mohamed; Sidhu, Harbir Singh; Kirkham, Alex; Ahmed, Hashim U; Emberton, Mark; Freeman, Alex; Halligan, Steve; Taylor, Stuart; Atkinson, David; Punwani, Shonit

    2015-09-01

    To assess the interchangeability of zone-specific (peripheral-zone (PZ) and transition-zone (TZ)) multiparametric-MRI (mp-MRI) logistic-regression (LR) models for classification of prostate cancer. Two hundred and thirty-one patients (70 TZ training-cohort; 76 PZ training-cohort; 85 TZ temporal validation-cohort) underwent mp-MRI and transperineal-template-prostate-mapping biopsy. PZ and TZ uni/multi-variate mp-MRI LR-models for classification of significant cancer (any cancer-core-length (CCL) with Gleason > 3 + 3 or any grade with CCL ≥ 4 mm) were derived from the respective cohorts and validated within the same zone by leave-one-out analysis. Inter-zonal performance was tested by applying TZ models to the PZ training-cohort and vice-versa. Classification performance of TZ models for TZ cancer was further assessed in the TZ validation-cohort. ROC area-under-curve (ROC-AUC) analysis was used to compare models. The univariate parameters with the best classification performance were the normalised T2 signal (T2nSI) within the TZ (ROC-AUC = 0.77) and normalized early contrast-enhanced T1 signal (DCE-nSI) within the PZ (ROC-AUC = 0.79). Performance was not significantly improved by bi-variate/tri-variate modelling. PZ models that contained DCE-nSI performed poorly in classification of TZ cancer. The TZ model based solely on maximum-enhancement poorly classified PZ cancer. LR-models dependent on DCE-MRI parameters alone are not interchangable between prostatic zones; however, models based exclusively on T2 and/or ADC are more robust for inter-zonal application. • The ADC and T2-nSI of benign/cancer PZ are higher than benign/cancer TZ. • DCE parameters are significantly different between benign PZ and TZ, but not between cancerous PZ and TZ. • Diagnostic models containing contrast enhancement parameters have reduced performance when applied across zones.

  13. Comparison of static model and dynamic model for the evaluation of station blackout sequences

    International Nuclear Information System (INIS)

    Lee, Kwang-Nam; Kang, Sun-Koo; Hong, Sung-Yull.

    1992-01-01

    Station blackout is one of major contributors to the core damage frequency (CDF) in many PSA studies. Since station blackout sequence exhibits dynamic features, accurate calculation of CDF for the station blackout sequence is not possible with event tree/fault tree (ET/FT) method. Although the integral method can determine accurate CDF, it is time consuming and is difficult to evaluate various alternative AC source configuration and sensitivities. In this study, a comparison is made between static model and dynamic model and a new methodology which combines static model and dynamic model is provided for the accurate quantification of CDF and evaluation of improvement alternatives. Results of several case studies show that accurate calculation of CDF is possible by introducing equivalent mission time. (author)

  14. Viscoelastic shear zone model of a strike-slip earthquake cycle

    Science.gov (United States)

    Pollitz, F.F.

    2001-01-01

    I examine the behavior of a two-dimensional (2-D) strike-slip fault system embedded in a 1-D elastic layer (schizosphere) overlying a uniform viscoelastic half-space (plastosphere) and within the boundaries of a finite width shear zone. The viscoelastic coupling model of Savage and Prescott [1978] considers the viscoelastic response of this system, in the absence of the shear zone boundaries, to an earthquake occurring within the upper elastic layer, steady slip beneath a prescribed depth, and the superposition of the responses of multiple earthquakes with characteristic slip occurring at regular intervals. So formulated, the viscoelastic coupling model predicts that sufficiently long after initiation of the system, (1) average fault-parallel velocity at any point is the average slip rate of that side of the fault and (2) far-field velocities equal the same constant rate. Because of the sensitivity to the mechanical properties of the schizosphere-plastosphere system (i.e., elastic layer thickness, plastosphere viscosity), this model has been used to infer such properties from measurements of interseismic velocity. Such inferences exploit the predicted behavior at a known time within the earthquake cycle. By modifying the viscoelastic coupling model to satisfy the additional constraint that the absolute velocity at prescribed shear zone boundaries is constant, I find that even though the time-averaged behavior remains the same, the spatiotemporal pattern of surface deformation (particularly its temporal variation within an earthquake cycle) is markedly different from that predicted by the conventional viscoelastic coupling model. These differences are magnified as plastosphere viscosity is reduced or as the recurrence interval of periodic earthquakes is lengthened. Application to the interseismic velocity field along the Mojave section of the San Andreas fault suggests that the region behaves mechanically like a ???600-km-wide shear zone accommodating 50 mm/yr fault

  15. Wave-Ice interaction in the Marginal Ice Zone: Toward a Wave-Ocean-Ice Coupled Modeling System

    Science.gov (United States)

    2015-09-30

    1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. Wave-Ice interaction in the Marginal Ice Zone: Toward a...scattering of waves by interaction with ice in the Marginal Ice Zone (MIZ). The wave model physics developed here will later be part of an operational...10.5670/oceanog.2014.73. Liu, A.K., B. Holt, and P.W. Vachon, 1991: Wave propagation in the Marginal Ice Zone: Model predictions and comparisons

  16. A Developmental Sequence Model to University Adjustment of International Undergraduate Students

    OpenAIRE

    Chavoshi, Saeid; Wintre, Maxine Gallander; Dentakos, Stella; Wright, Lorna

    2017-01-01

    The current study proposes a Developmental Sequence Model to University Adjustment and uses a multifaceted measure, including academic, social and psychological adjustment, to examine factors predictive of undergraduate international student adjustment. A hierarchic regression model is carried out on the Student Adaptation to College Questionnaire to examine theoretically pertinent predictors arranged in a developmental sequence in determining adjustment outcomes. This model...

  17. Design of an Artificial Pancreas using Zone Model Predictive Control with a Moving Horizon State Estimator.

    Science.gov (United States)

    Lee, Justin J; Gondhalekar, Ravi; Doyle, Francis J

    2014-12-01

    A zone model predictive control (zone-MPC) algorithm that utilizes the Moving Horizon State Estimator (MHSE) is presented. The control application is an artificial pancreas for treating people with type 1 diabetes mellitus. During the meal challenge, the prediction quality of the zone-MPC algorithm with the MHSE was significantly better than when using the current Luenberger observer to provide the state estimate. Consequently, the controller using the MHSE rejected the meal disturbance faster and without inducing extra hypoglycemia risk (e.g., lower postprandial blood glucose peak by 10 mg/dL and higher postprandial minimum blood glucose by 11 mg/dL). The faster rejection of the meal disturbance led to a longer time in the clinically accepted safe region (70-180 mg/dL) by 13%, and this may reduce the likelihood of the complications related to type 1 diabetes mellitus.

  18. Automated Translation and Thermal Zoning of Digital Building Models for Energy Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Jones, Nathaniel L. [Cornell University; McCrone, Colin J. [Cornell University; Walter, Bruce J. [Cornell University; Pratt, Kevin B. [Cornell University; Greenberg, Donald P. [Cornell University

    2013-08-26

    Building energy simulation is valuable during the early stages of design, when decisions can have the greatest impact on energy performance. However, preparing digital design models for building energy simulation typically requires tedious manual alteration. This paper describes a series of five automated steps to translate geometric data from an unzoned CAD model into a multi-zone building energy model. First, CAD input is interpreted as geometric surfaces with materials. Second, surface pairs defining walls of various thicknesses are identified. Third, normal directions of unpaired surfaces are determined. Fourth, space boundaries are defined. Fifth, optionally, settings from previous simulations are applied, and spaces are aggregated into a smaller number of thermal zones. Building energy models created quickly using this method can offer guidance throughout the design process.

  19. Modeling of heat transfer into a heat pipe for a localized heat input zone

    International Nuclear Information System (INIS)

    Rosenfeld, J.H.

    1987-01-01

    A general model is presented for heat transfer into a heat pipe using a localized heat input. Conduction in the wall of the heat pipe and boiling in the interior structure are treated simultaneously. The model is derived from circumferential heat transfer in a cylindrical heat pipe evaporator and for radial heat transfer in a circular disk with boiling from the interior surface. A comparison is made with data for a localized heat input zone. Agreement between the theory and the model is good. This model can be used for design purposes if a boiling correlation is available. The model can be extended to provide improved predictions of heat pipe performance

  20. Modeling and Experimental Investigation of Pressure Field in the Grinding Zone with Nanoparticle Jet of MQL

    Directory of Open Access Journals (Sweden)

    C. H. Li

    2013-01-01

    Full Text Available Solid nano particles were added in minimum quantity lubrication (MQL fluid medium to make nanofluids, that is, after the mixing and atomization of nanoparticle, lubricants and high pressure gas, to inject solid nano particle in the grinding zone with the form of jet flow. The mathematical model of two-phase flow pressure field of grinding zone with nanoparticle jet flow of MQL was established, and the simulation study was conducted. The results show that pressures in the grinding zone increased with the acceleration of grinding wheel, sharply decreased with the increased minimum clearance, and increased with the acceleration of jet flow. At three spraying angles of nozzles, when the nozzle angle was 15°, the pressure of grinding zone along the speed of grinding wheel was larger than the rest two angles. On the experimental platform built by KP-36 precision grinder and nanoparticle jet flow feed way, CY3018 pressure sensor was used to test the regularities of pressure field variations. The impact of the speed of grinding wheel, the gap between workpiece and grinding wheel, jet flow velocity, and spraying angles of nozzles on the pressure field of grinding zone was explored. The experimental result was generally consistent with the theoretical simulation, which verified the accuracy of the theoretical analysis.

  1. Time-lapse gravity data for monitoring and modeling artificial recharge through a thick unsaturated zone

    Science.gov (United States)

    Kennedy, Jeffrey R.; Ferre, Ty P.A.; Creutzfeldt, Benjamin

    2016-01-01

    Groundwater-level measurements in monitoring wells or piezometers are the most common, and often the only, hydrologic measurements made at artificial recharge facilities. Measurements of gravity change over time provide an additional source of information about changes in groundwater storage, infiltration, and for model calibration. We demonstrate that for an artificial recharge facility with a deep groundwater table, gravity data are more sensitive to movement of water through the unsaturated zone than are groundwater levels. Groundwater levels have a delayed response to infiltration, change in a similar manner at many potential monitoring locations, and are heavily influenced by high-frequency noise induced by pumping; in contrast, gravity changes start immediately at the onset of infiltration and are sensitive to water in the unsaturated zone. Continuous gravity data can determine infiltration rate, and the estimate is only minimally affected by uncertainty in water-content change. Gravity data are also useful for constraining parameters in a coupled groundwater-unsaturated zone model (Modflow-NWT model with the Unsaturated Zone Flow (UZF) package).

  2. MODELING OF THERMOELECTRIC SYSTEM FOR LOCAL THERMAL EFFECTS ON HUMAN FOREARM ZONE

    Directory of Open Access Journals (Sweden)

    T. A. Ismailov

    2013-01-01

    Full Text Available In this paper we consider a model of the thermoelectric system for the thermal effect on the human forearm. The model is implemented on the basis of numerical solution of differentialequations of heat conduction for bodies of complex configuration. Two-dimensional and onedimensional graphs of the temperature change in different zones of the object of exposure aregiven.

  3. The thermochemical, two-phase dynamics of subduction zones: results from new, fully coupled models

    Science.gov (United States)

    Rees Jones, D. W.; Katz, R. F.; May, D.; Tian, M.; Rudge, J. F.

    2017-12-01

    Subduction zones are responsible for most of Earth's subaerial volcanism. However, previous geodynamic modelling of subduction zones has largely neglected magmatism. We previously showed that magmatism has a significant thermal impact, by advecting sensible heat into the lithosphere beneath arc volcanos [1]. Inclusion of this effect helps reconcile subduction zone models with petrological and heat flow observations. Many important questions remain, including how magma-mantle dynamics of subduction zones affects the position of arc volcanos and the character of their lavas. In this presentation, we employ a fully coupled, thermochemical, two-phase flow theory to investigate the dynamics of subduction zones. We present the first results from our new software (SubFUSc), which solves the coupled equations governing conservation of mass, momentum, energy and chemical species. The presence and migration of partial melts affect permeability and mantle viscosity (both directly and through their thermal impact); these, in turn, feed back on the magma-mantle flow. Thus our fully coupled modelling improves upon previous two-phase models that decoupled the governing equations and fixed the thermal structure [2]. To capture phase change, we use a novel, simplified model of the mantle melting in the presence of volatile species. As in the natural system, volatiles are associated with low-degree melting at temperatures beneath the anhydrous solidus; dehydration reactions in the slab supply volatiles into the wedge, triggering silicic melting. We simulate the migration of melts under buoyancy forces and dynamic pressure gradients. We thereby demonstrate the dynamical controls on the pattern of subduction-zone volcanism (particularly its location, magnitude, and chemical composition). We build on our previous study of the thermal consequences of magma genesis and segregation. We address the question of what controls the location of arc volcanoes themselves [3]. [1] Rees Jones, D. W

  4. Zone modelling of the thermal performances of a large-scale bloom reheating furnace

    International Nuclear Information System (INIS)

    Tan, Chee-Keong; Jenkins, Joana; Ward, John; Broughton, Jonathan; Heeley, Andy

    2013-01-01

    This paper describes the development and comparison of a two- (2D) and three-dimensional (3D) mathematical models, based on the zone method of radiation analysis, to simulate the thermal performances of a large bloom reheating furnace. The modelling approach adopted in the current paper differs from previous work since it takes into account the net radiation interchanges between the top and bottom firing sections of the furnace and also allows for enthalpy exchange due to the flows of combustion products between these sections. The models were initially validated at two different furnace throughput rates using experimental and plant's model data supplied by Tata Steel. The results to-date demonstrated that the model predictions are in good agreement with measured heating profiles of the blooms encountered in the actual furnace. It was also found no significant differences between the predictions from the 2D and 3D models. Following the validation, the 2D model was then used to assess the impact of the furnace responses to changing throughput rate. It was found that the potential furnace response to changing throughput rate influences the settling time of the furnace to the next steady state operation. Overall the current work demonstrates the feasibility and practicality of zone modelling and its potential for incorporation into a model based furnace control system. - Highlights: ► 2D and 3D zone models of large-scale bloom reheating furnace. ► The models were validated with experimental and plant model data. ► Examine the transient furnace response to changing the furnace throughput rates. ► No significant differences found between the predictions from the 2D and 3D models.

  5. Simple Elastic Dislocation Models for Interpreting Interseismic Deformation in Subduction Zones

    Science.gov (United States)

    Kanda, R. V.; Simons, M.

    2006-12-01

    Models of interseismic surface deformation in the vicinity of subduction zones frequently rely on the back slip model (BSM). This model employs artificial extensional slip along the locked zone in order to explain the observed sense of interseismic displacements. Here, we introduce the elastic subducting plate model (ESPM) which is more representative of plate subduction. This model has only one additional degree of freedom over the standard BSM the thickness of the subducting elastic plate. In our present formulation, the base of the elastic plate is forced to move continuously at the long term convergence rate, as is the top surface of the subducting plate below the locking depth. The ESPM reduces exactly to the BSM in the limiting case of zero plate thickness - thereby providing a more intuitive rationale for the success of the BSM since details associated with finite plate thickness are hard to resolve with data distant from the trench. If the effective thickness of a subducting plate is large compared to the depth of its locked zone, or when the curvature of the subduction interface is sufficiently high, it may be more appropriate to adopt the ESPM. Practically, our ability to distinguish between the BSM and the ESPM depends on simultaneously modeling vertical and horizontal displacement fields, and on having data from close to the trench. We use geodetic measurements from Japan and Sumatra to compare the observed surface deformation with that predicted by both ESPM & BSM, and invert for the allowable ranges of effective plate thickness.

  6. Numerical simulation of fatigue crack growth rate and crack retardation due to an overload using a cohesive zone model

    NARCIS (Netherlands)

    Silitonga, S.; Maljaars, J.; Soetens, F.; Snijder, H.H.

    2014-01-01

    In this work, a numerical method is pursued based on a cohesive zone model (CZM). The method is aimed at simulating fatigue crack growth as well as crack growth retardation due to an overload. In this cohesive zone model, the degradation of the material strength is represented by a variation of the

  7. Preliminary modeling for solute transport in a fractured zone at the Korea underground research tunnel (KURT)

    International Nuclear Information System (INIS)

    Park, Chung Kyun; Lee, Jaek Wang; Baik, Min Hoon; Jeong, Jong Tae

    2012-01-01

    Migration tests were performed with conservative tracers in a fractured zone that had a single fracture of about 2.5 m distance at the KURT. To interpret the migration of the tracers in the fractured rock, a solute transport model was developed. A two dimensional variable aperture channel model was adopted to describe the fractured path and hydrology, and a particle tracking method was used for solute transport. The simulation tried not only to develop a migration model of solutes for open flow environments but also to produce ideas for a better understanding of solute behaviours in indefinable fracture zones by comparing them to experimental results. The results of our simulations and experiments are described as elution and breakthrough curves, and are quantified by momentum analysis. The main retardation mechanism of nonsorbing tracers, including matrixdiffusion, was investigated.

  8. Validation of a Perceptual Distraction Model in a Complex Personal Sound Zone System

    DEFF Research Database (Denmark)

    Rämö, Jussi; Marsh, Steven; Bech, Søren

    2016-01-01

    This paper evaluates a previously proposed perceptual model predicting user’s perceived distraction caused by interfering audio programmes. The distraction model was originally trained using a simple sound reproduction system for music-on-music interference situations and it has not been formally...... tested using more complex sound systems. A listening experiment was conducted to evaluate the performance of the model, using music target and speech interferer reproduced by a complex personal sound-zone system. The model was found to successfully predict the perceived distraction of a more complex...

  9. Hydrodynamic modelling in the Polish Zone of the Baltic Sea - an overview of Polish achievements

    Directory of Open Access Journals (Sweden)

    Ewa Jasińska

    2003-03-01

    Full Text Available This paper gives a general overview of Polish experience and achievements with regard to hydrodynamic modelling in the Polish zone of the Baltic Sea. The first work started already at the end of the sixties when the first 1D and 2D hydrodynamic models were set up. With the development of numerical methods and increasing computational power a number of 1D, 2D and 3D models were set up and tested. Global, regional and local models cover the most important water bodies,i.e. the Pomeranian Bay - Szczecin Lagoon and Gulf of Gdansk - Vistula Lagoon systems.

  10. Surveillance for sulfadoxine-pyrimethamine resistant malaria parasites in the Lake and Southern Zones, Tanzania, using pooling and next-generation sequencing.

    Science.gov (United States)

    Ngondi, Jeremiah M; Ishengoma, Deus S; Doctor, Stephanie M; Thwai, Kyaw L; Keeler, Corinna; Mkude, Sigsbert; Munishi, Oresto M; Willilo, Ritha A; Lalji, Shabbir; Kaspar, Naomi; Kitojo, Chonge; Paxton, Lynn A; Hathaway, Nicholas J; Bailey, Jeffrey A; Juliano, Jonathan J; Meshnick, Steven R; Gutman, Julie

    2017-06-05

    Malaria in pregnancy (MiP) remains a major public health challenge in areas of high malaria transmission. Intermittent preventive treatment in pregnancy (IPTp) with sulfadoxine-pyrimethamine (SP) is recommended to prevent the adverse consequences of MiP. The effectiveness of SP for IPTp may be reduced in areas where the dhps581 mutation (a key marker of high level SP resistance) is found; this mutation was previously reported to be common in the Tanga Region of northern Tanzania, but there are limited data from other areas. The frequency of molecular markers of SP resistance was investigated in malaria parasites from febrile patients at health centres (HC) in seven regions comprising the Lake and Southern Zones of mainland Tanzania as part of the ongoing efforts to generate national-wide data of SP resistance. A cross-sectional survey was conducted in the outpatient departments of 14 HCs in seven regions from April to June, 2015. 1750 dried blood spot (DBS) samples were collected (117 to 160 per facility) from consenting patients with positive rapid diagnostic tests for malaria, and no recent (within past 2 months) exposure to SP or related drugs. DNA was extracted from the DBS, pooled by HC, and underwent pooled targeted amplicon deep sequencing to yield estimates of mutated parasite allele frequency at each locus of interest. The dhps540 mutation was common across all 14 sites, ranging from 55 to 98.4% of sequences obtained. Frequency of the dhps581 mutation ranged from 0 to 2.4%, except at Kayanga HC (Kagera Region, Lake Zone) where 24.9% of sequences obtained were mutated. The dhfr164 mutation was detected only at Kanyanga HC (0.06%). By pooling DNA extracts, the allele frequency of mutations in 14 sites could be directly determined on a single deep-sequencing run. The dhps540 mutant was very common at all locations. Surprisingly, the dhps581 was common at one health center, but rare in all the others, suggesting that there is geographic micro-heterogeneity in

  11. BUILDING CONCEPTUAL AND MATHEMATICAL MODEL FOR WATER FLOW AND SOLUTE TRANSPORT IN THE UNSATURATED ZONE AT KOSNICA SITE

    Directory of Open Access Journals (Sweden)

    Stanko Ružičić

    2012-12-01

    Full Text Available Conceptual model of flow and solute transport in unsaturated zone at Kosnica site, which is the basis for modeling pollution migration through the unsaturated zone to groundwater, is set up. The main characteristics of the unsaturated zone of the Kosnica site are described. Detailed description of investigated profile of unsaturated zone, with all necessary analytical results performed and used in building of conceptual models, is presented. Experiments that are in progress and processes which are modeled are stated. Monitoring of parameters necessary for calibration of models is presented. The ultimate goal of research is risk assessment of groundwater contamination at Kosnica site that has its source in or on unsaturated zone.

  12. A saturated zone site-scale flow model for Yucca mountain

    Energy Technology Data Exchange (ETDEWEB)

    Eddebbarh, Al Aziz [Los Alamos National Laboratory

    2008-01-01

    A saturated zone site-scale flow model (YMSZFM) was developed for licensing requirements for the Yucca Mountain nuclear waste repository to incorporate recent data and analyses including recent stratigraphic and water-level data from Nye County wells, single-and multiple-well hydraulic testing data, and recent hydrochemistry data. Analyses include use of data from the 2004 transient Death Valley Regional (ground-water) Flow System (DVRFS) model, the 2003 unsaturated zone flow model, and the latest hydrogeologic framework model (HFM). This model includes: (1) the latest understanding of SZ flow, (2) enhanced model validation and uncertainty analyses, (3) improved locations and definitions of fault zones, (4) refined grid resolution (500-to 250-m grid spacing), and (5) use of new data. The flow model was completed using the three-dimensional, Finite-Element Heat and Mass Transfer computer code (FEHM). The SZ site-scale flow model was calibrated with the commercial parameter estimation code, PEST to achieve a minimum difference between observed water levels and predicted water levels, and also between volumetric/mass flow rates along specific boundary segments as supplied by the DVRFS. A total of 161 water level and head measurements with varied weights were used for calibration. A comparison between measured water-level data and the potentiometric surface yielded an RMSE of 20.7 m (weighted RMSE of 8.8 m). The calibrated model was used to generate flow paths and specific discharge predictions. Model confidence was built by comparing: (l) calculated to observed hydraulic heads, and (2) calibrated to measured permeabilities (and therefore specific discharge). In addition, flowpaths emanating from below the repository footprint are consistent with those inferred both from gradients of measured head and from independent water-chemistry data. Uncertainties in the SZ site-scale flow model were quantified because all uncertainty contributes to inaccuracy in system

  13. A model of the statistical power of comparative genome sequence analysis.

    OpenAIRE

    Sean R Eddy

    2005-01-01

    Comparative genome sequence analysis is powerful, but sequencing genomes is expensive. It is desirable to be able to predict how many genomes are needed for comparative genomics, and at what evolutionary distances. Here I describe a simple mathematical model for the common problem of identifying conserved sequences. The model leads to some useful rules of thumb. For a given evolutionary distance, the number of comparative genomes needed for a constant level of statistical stringency in identi...

  14. Elucidating Critical Zone Process Interactions with an Integrated Hydrology Model in a Headwaters Research Catchment

    Science.gov (United States)

    Collins, C.; Maxwell, R. M.

    2017-12-01

    Providence Creek (P300) watershed is an alpine headwaters catchment located at the Southern Sierra Critical Zone Observatory (SSCZO). Evidence of groundwater-dependent vegetation and drought-induced tree mortality at P300 along with the effect of subsurface characterization on mountain ecohydrology motivates this study. A hyper resolution integrated hydrology model of this site, along with extensive instrumentation, provides an opportunity to study the effects of lateral groundwater flow on vegetation's tolerance to drought. ParFlow-CLM is a fully integrated surface-subsurface model that is driven with reconstructed meteorology, such as the North American Land Data Assimilation System project phase 2 (NLDAS-2) dataset. However, large-scale data products mute orographic effects on climate at smaller scales. Climate variables often do not behave uniformly in highly heterogeneous mountain regions. Therefore, forcing physically-based integrated hydrologic models—especially of mountain headwaters catchments—with a large-scale data product is a major challenge. Obtaining reliable observations in complex terrain is challenging and while climate data products introduce uncertainties likewise, documented discrepancies between several data products and P300 observations suggest these data products may suffice. To tackle these issues, a suite of simulations was run to parse out (1) the effects of climate data source (data products versus observations) and (2) the effects of climate data spatial variability. One tool for evaluating the effect of climate data on model outputs is the relationship between latent head flux (LH) and evapotranspiration (ET) partitioning with water table depth (WTD). This zone of LH sensitivity to WTD is referred to as the "critical zone." Preliminary results suggest that these critical zone relationships are preserved despite forcing albeit significant shifts in magnitude. These results demonstrate that integrated hydrology models are sensitive

  15. A model of disordered zone formation in Cu3Au under cascade-producing irradiation

    International Nuclear Information System (INIS)

    Kapinos, V.G.; Bacon, D.J.

    1995-01-01

    A model to describe the disordering of ordered Cu 3 Au under irradiation is proposed. For the thermal spike phase of a displacement cascade, the processes of heat evolution and conduction in the cascade region are modelled by solving the thermal conduction equation by a discretization method for a medium that can melt and solidify under appropriate conditions. The model considers disordering to result from cascade core melting, with the final disordered zone corresponding to the largest molten zone achieved. The initial conditions for this treatment are obtained by simulation of cascades by the MARLOWE code. The contrast of disordered zones imaged in a superlattice dark-field reflection and projected on the plane parallel to the surface of a thin foil was calculated. The average size of images from hundreds of cascades created by incident Cu + ions were calculated for different ion energies and compared with experimental transmission electron microscopy data. The model is in reasonable quantitative agreement with the experimentally observed trends. (author)

  16. Mechanics and modeling of flow, sediment transport and morphologic change in riverine lateral separation zones

    Science.gov (United States)

    Logan, Brandy L.; Nelson, Jonathan M.; McDonald, Richard R.; Wright, Scott A.

    2010-01-01

    Lateral separation zones or eddies in rivers are critically important features for sediment storage and for a variety of roles they play in riparian and aquatic ecology. As part of a larger effort to predict the morphology of lateral separation zones in the Colorado River in Grand Canyon for a selection of sediment supply and discharge scenarios, we evaluated the performance of two modeling techniques for predicting flow, sediment transport, and morphodynamics in eddies using field data. In order to understand the relative roles of various exchange mechanisms between the main channel and eddies, we applied two-dimensional unsteady and three-dimensional unsteady models in a reach containing a lateral separation zone. Both models were developed, calibrated, and evaluated using detailed field data comprising acoustic-Doppler velocity measurements, water-surface elevations, sediment concentration by size class, and bathymetry measured during a flood event in the Colorado River. Model results and measurements are used to develop a better understanding of the mechanics of water and sediment exchange between the eddy and the mainstem and other factors that control the morphology of the reach.

  17. Prediction and assimilation of surf-zone processes using a Bayesian network: Part I: Forward models

    Science.gov (United States)

    Plant, Nathaniel G.; Holland, K. Todd

    2011-01-01

    Prediction of coastal processes, including waves, currents, and sediment transport, can be obtained from a variety of detailed geophysical-process models with many simulations showing significant skill. This capability supports a wide range of research and applied efforts that can benefit from accurate numerical predictions. However, the predictions are only as accurate as the data used to drive the models and, given the large temporal and spatial variability of the surf zone, inaccuracies in data are unavoidable such that useful predictions require corresponding estimates of uncertainty. We demonstrate how a Bayesian-network model can be used to provide accurate predictions of wave-height evolution in the surf zone given very sparse and/or inaccurate boundary-condition data. The approach is based on a formal treatment of a data-assimilation problem that takes advantage of significant reduction of the dimensionality of the model system. We demonstrate that predictions of a detailed geophysical model of the wave evolution are reproduced accurately using a Bayesian approach. In this surf-zone application, forward prediction skill was 83%, and uncertainties in the model inputs were accurately transferred to uncertainty in output variables. We also demonstrate that if modeling uncertainties were not conveyed to the Bayesian network (i.e., perfect data or model were assumed), then overly optimistic prediction uncertainties were computed. More consistent predictions and uncertainties were obtained by including model-parameter errors as a source of input uncertainty. Improved predictions (skill of 90%) were achieved because the Bayesian network simultaneously estimated optimal parameters while predicting wave heights.

  18. A nonsteady-state firn-densification model for the percolation zone of a glacier

    DEFF Research Database (Denmark)

    Reeh, Niels

    2008-01-01

    A simple steady state firn-densification model is modified to account for short-term time variations of accumulation rate and surface temperature. The temporal surface-elevation- and mass changes at two sites in the percolation zone of an ice sheet in response to various climate histories...... are determined. It is shown that a straight-forward translation of observed short-term ice-sheet surface-elevation variations into mass changes may be completely misleading, particularly for the percolation zone of the ice sheet, where temperature driven variations of melting/re-freezing rates have a strong...... occur even in periods of constant surface climate, and consequently unchanged mass balance, as a delayed response to previous changes of the local surface climate. Forcing the model with cyclic temperature variations mimicking fluctuations of West Greenland instrumental temperature records during...

  19. Effect of upstream fencing on shelter zone behind solid models simulating sand formations and dunes

    Directory of Open Access Journals (Sweden)

    Mahmoud A. Hassan

    2013-04-01

    Moreover, results indicate that some dune/fence combinations may cause shifting of the dune upwind (instead of downwind in the absence of fence. This effect means that, with such combinations, a dune would eventually disappear. The distance between the model downwind base line and the location of reattachment (length of shelter zone was plotted against the distance of fence from upwind base line of model to determine the best possible dune/fence combination. Solid fencing (constructed from masonry bricks or stones to shelter isolated sand humps and dunes is effective in alleviating dangers on nearby structures (dune shifting upwind and to less sand drift and saltation downwind. Also, the results indicated that, it is recommended to start by dune fencing and give enough time for the project zone to widen and be effectively protected before starting the construction.

  20. [Combustion zone investigation and modelling in fuel flexible suspension fired boilers]. Result summary and status

    Energy Technology Data Exchange (ETDEWEB)

    Lovmand Hvid, S.

    2011-12-15

    The project has been designed to obtain data from a power plant boiler with co-combustion, partly to gain greater knowledge of particle turnover in the fuel zone, partly to support the development of modeling tools. Data collection occurred at Studstrup Power Station Unit 4, where the fuel is a combination of coal and biomass. The boiler is equipped with 24 dust burners, four of which have been converted to firing with biomass. Measurements have been carried out in the flame zone with different fuels: coal alone, coal + straw and coal + wood. During the experiments velocity fields, temperature fields and gas concentration fields were measured in the firing zone. Also, particle samples from the flame zone ware collected. Several measurements are performed with well-known techniques, but in addition, the project developed new optical measurement methods based on UV spectroscopy. They allow measuring other gases than the hitherto known methods and allow you to gain insight into the dynamic variations beyond just mean fields. The collection of particle samples from the boiler was, as expected, a very challenging task under the given conditions, but was carried out with a largely satisfactory result. Analysis of the samples has initially failed to lead to an increased recognition of the speed of the conversion process, but the samples will be analyzed in more detail in other projects. (LN)

  1. Evolution of the conceptual model of unsaturated zone hydrology at yucca mountain, nevada

    International Nuclear Information System (INIS)

    Flint, A. L.; Flint, L. E.; Bodvarsson, G. S.; Kwicklis, E. M.; Fabryka-Martin, J.

    2001-01-01

    Yucca Mountain is an arid site proposed for consideration as the United States' first underground high-level radioactive waste repository. Low rainfall (approximately 170 mm/yr) and a thick unsaturated zone (500-1000 m) are important physical attributes of the site because the quantity of water likely to reach the waste and the paths and rates of movement of the water to the saturated zone under future climates would be major factors in controlling the concentrations and times of arrival of radionuclides at the surrounding accessible environment. The framework for understanding the hydrologic processes that occur at this site and that control how quickly water will penetrate through the unsaturated zone to the water table has evolved during the past 15 yr. Early conceptual models assumed that very small volumes of water infiltrated into the bedrock (0.5-4.5 mm/yr, or 2-3 percent of rainfall), that much of the infiltrated water flowed laterally within the upper nonwelded units because o f capillary barrier effects, and that the remaining water flowed down faults with a small amount flowing through the matrix of the lower welded, fractured rocks. It was believed that the matrix had to be saturated for fractures to show. However, accumulating evidence indicated that infiltration rates were higher than initially estimated, such as infiltration modeling based on neutron borehole data, bomb-pulse isotopes deep in the mountain, perched water analyses and thermal analyses. Mechanisms supporting lateral diversion did not apply at these higher fluxes, and the flux calculated in the lower welded unit exceeded the conductivity of the matrix, implying vertical flow of water into the high permeability fractures of the potential repository host rock, and disequilibrium between matrix and fracture water potentials. The development of numerical modeling methods and parameter values evolved concurrently with the conceptual model in order to account for the observed field data

  2. Computer modelling of technogenic thermal pollution zones in large water bodies

    Science.gov (United States)

    Parshakova, Ya N.; Lyubimova, T. P.

    2018-01-01

    In the present work, the thermal pollution zones created due to discharge of heated water from thermal power plants are investigated using the example of the Permskaya Thermal Power Plant (Permskaya TPP or Permskaya GRES), which is one of the largest thermal power plants in Europe. The study is performed for different technological and hydrometeorological conditions. Since the vertical temperature distribution in such wastewater reservoirs is highly inhomogeneous, the computations are performed in the framework of 3D model.

  3. MODELLING AND SIMULATION OF A SINGLE-ZONE HEATING AND VENTILATION SYSTEM

    Directory of Open Access Journals (Sweden)

    Mesut ŞENGİRGİN

    2005-03-01

    Full Text Available In this study, modelling and simulation results of a single-zone heating and ventilation system of a large office room are introduced. Heating system is controlled by an on-off controller. By considering the sinusoidal outdoor air tempareture variation and various outdoor/return air ratios as input parameters, dynamic behaviour of room air tempereture are investigated. For this purpose, MATLAB/Simulink code is used.

  4. A cohesive plastic/damage-zone model for ductile crack analysis

    International Nuclear Information System (INIS)

    Zhang, C.; Gross, D.

    1995-01-01

    A cohesive plastic/damage-zone model of the Dugdale-Barenblatt type (G.I. Barenblatt, Adv. Appl. Mech. 7 (1962) 55-129; D.S. Dugdale, J. Mech. Phys. Solids 8 (1960) 100-104) is presented for analyzing crack growth in ductile materials with damage evolution. A semi-infinite Mode I crack in plane stress or plane stress is considered. The damage is assumed to be present in form of dispersed microvoids which are localized into a narrow strip ahead of the crack-tip. A simple damage model of the Gurson model type (A.L. Gurson, J. Eng. Mater. Technol. 99 (1977) 2-15; V. Tvergaard, Advances in Applied Mechanics, Vol. 27, Academic Press, 1990, pp. 83-151) is developed for uniaxial tension to describe the macroscopic properties of the cohesive plastic/damage-zone. Under small-scale yielding and small-scale damage conditions, a system of nonlinear integral equations for the plastic strain and the length of the cohesive plastic/damage-zone is derived. Numerical results are presented and discussed to reveal the effect of damage evolution on the ductile crack growth. (orig.)

  5. Cohesive Zone Model Based Numerical Analysis of Steel-Concrete Composite Structure Push-Out Tests

    Directory of Open Access Journals (Sweden)

    J. P. Lin

    2014-01-01

    Full Text Available Push-out tests were widely used to determine the shear bearing capacity and shear stiffness of shear connectors in steel-concrete composite structures. The finite element method was one efficient alternative to push-out testing. This paper focused on a simulation analysis of the interface between concrete slabs and steel girder flanges as well as the interface of the shear connectors and the surrounding concrete. A cohesive zone model was used to simulate the tangential sliding and normal separation of the interfaces. Then, a zero-thickness cohesive element was implemented via the user-defined element subroutine UEL in the software ABAQUS, and a multiple broken line mode was used to define the constitutive relations of the cohesive zone. A three-dimensional numerical analysis model was established for push-out testing to analyze the load-displacement curves of the push-out test process, interface relative displacement, and interface stress distribution. This method was found to accurately calculate the shear capacity and shear stiffness of shear connectors. The numerical results showed that the multiple broken lines mode cohesive zone model could describe the nonlinear mechanical behavior of the interface between steel and concrete and that a discontinuous deformation numerical simulation could be implemented.

  6. The Summerville Formation: Evidence for a sub-horizontal stratigraphic sequence below the post-rift unconformity in the Middleton Place Summerville Seismic Zone

    Science.gov (United States)

    Getz, Joseph Edward

    The Middleton Place Summerville Seismic Zone (MPSSZ) near Summerville, South Carolina was the site of renewed extensive investigation, beginning in the 1970's, for the source of the 1886 Charleston earthquake. Reactivation of faults associated with a putative fault-bounded Triassic rift basin through analysis of seismic reflection, seismic refraction, and well data has since become the favored interpretation for the source of MPSSZ seismicity. Critical to this interpretation is the association of continental redbed sedimentary rocks with Triassic basins identified throughout the North American Atlantic margin. Reanalysis of 18 seismic reflection profiles and 25 seismic refraction profiles within the MPSSZ suggests that the red beds found here are a thin, sub-horizontal, regionally extensive, generally unbroken subsurface stratigraphic sequence distinct from the sedimentary architecture observed in analog Triassic rift systems. In addition, this sequence appears to unconformably overly a structural depression (the Jedberg basin) previously interpreted as a Triassic rift basin in the vicinity of the MPSSZ. In addition to the geometries observed on seismic reflection profiles, seismic refraction velocities ranging from 4.2 to 6.1 km/s can be correlated with (1) Jurassic basalt flows, (2) the newly proposed Summerville Formation, and (3) the Basement (B) sequences respectively. The current study maps the Summerville red bed section and its bounding reflectors. In addition to mapping the regional extent of the newly proposed Summerville Formation, refraction velocities and changes in reflection character, the lateral extent of the basalt flows can be changed to a more localized flow rather than a regionally extensive flow of which was previously thought. Reanalysis of data in the MPSSZ suggests that the area may not be part of the Triassic South Georgia Rift system due to the sub-horizontal geometry of the red bed reflections, the apparent lack of faulting, and their

  7. Modeling the Effects of Hydrogeomorphology and Climactic Factors on Nitrogen, Phosphorus, and Greenhouse Gas Dynamics in Riparian Zones.

    Science.gov (United States)

    Hassanzadeh, Y.; Vidon, P.; Gold, A.; Pradhanang, S. M.; Addy, K.

    2017-12-01

    Vegetated riparian zones are often considered for use as best management practices to mitigate the impacts of agriculture on water quality. However, riparian zones can also be a source of greenhouse gases and their influence on water quality varies depending on landscape hydrogeomorphic characteristics and climate. Methods used to evaluate riparian zone functions include conceptual models, and spatially explicit and process based models (REMM), but very few attempts have been made to connect riparian zone characteristics with function using easily accessible landscape scale data. Here, we present comprehensive statistical models that can be used to assess riparian zone functions with easily obtainable landscape-scale hydrogeomorphic attributes and climate data. Models were developed from a database spanning 88 years and 36 sites. Statistical methods including principal component analysis and stepwise regression were used to reduced data dimensionality and identify significant predictors. Models were validated using additional data collected from scientific literature. The 8 models developed connect landscape characteristics to nitrogen and phosphorus concentration and removal (1-4), greenhouse gas emissions (5-7), and water table depth (8). Results show the range of influence that various climate and landscape characteristics have on riparian zone functions, and the tradeoffs that exist with regards to nitrogen, phosphorous, and greenhouse gases. These models will help reduce the need for extensive field measurements and help scientists and land managers make more informed decisions regarding the use of riparian zones for water quality management.

  8. Imaging the Chicxulub central crater zone from large scale seismic acoustic wave propagation and gravity modeling

    Science.gov (United States)

    Fucugauchi, J. U.; Ortiz-Aleman, C.; Martin, R.

    2017-12-01

    Large complex craters are characterized by central uplifts that represent large-scale differential movement of deep basement from the transient cavity. Here we investigate the central sector of the large multiring Chicxulub crater, which has been surveyed by an array of marine, aerial and land-borne geophysical methods. Despite high contrasts in physical properties,contrasting results for the central uplift have been obtained, with seismic reflection surveys showing lack of resolution in the central zone. We develop an integrated seismic and gravity model for the main structural elements, imaging the central basement uplift and melt and breccia units. The 3-D velocity model built from interpolation of seismic data is validated using perfectly matched layer seismic acoustic wave propagation modeling, optimized at grazing incidence using shift in the frequency domain. Modeling shows significant lack of illumination in the central sector, masking presence of the central uplift. Seismic energy remains trapped in an upper low velocity zone corresponding to the sedimentary infill, melt/breccias and surrounding faulted blocks. After conversion of seismic velocities into a volume of density values, we use massive parallel forward gravity modeling to constrain the size and shape of the central uplift that lies at 4.5 km depth, providing a high-resolution image of crater structure.The Bouguer anomaly and gravity response of modeled units show asymmetries, corresponding to the crater structure and distribution of post-impact carbonates, breccias, melt and target sediments

  9. Modeling breathing-zone concentrations of airborne contaminants generated during compressed air spray painting.

    Science.gov (United States)

    Flynn, M R; Gatano, B L; McKernan, J L; Dunn, K H; Blazicko, B A; Carlton, G N

    1999-01-01

    This paper presents a mathematical model to predict breathing-zone concentrations of airborne contaminants generated during compressed air spray painting in cross-flow ventilated booths. The model focuses on characterizing the generation and transport of overspray mist. It extends previous work on conventional spray guns to include exposures generated by HVLP guns. Dimensional analysis and scale model wind-tunnel studies are employed using non-volatile oils, instead of paint, to produce empirical equations for estimating exposure to total mass. Results indicate that a dimensionless breathing zone concentration is a nonlinear function of the ratio of momentum flux of air from the spray gun to the momentum flux of air passing through the projected area of the worker's body. The orientation of the spraying operation within the booth is also very significant. The exposure model requires an estimate of the contaminant generation rate, which is approximated by a simple impactor model. The results represent an initial step in the construction of more realistic models capable of predicting exposure as a mathematical function of the governing parameters.

  10. Two-phase modeling of DDT: Structure of the velocity-relaxation zone

    International Nuclear Information System (INIS)

    Kapila, A.K.; Son, S.F.; Bdzil, J.B.; Menikoff, R.; Stewart, D.S.

    1997-01-01

    The structure of the velocity relaxation zone in a hyperbolic, nonconservative, two-phase model is examined in the limit of large drag, and in the context of the problem of deflagration-to-detonation transition in a granular explosive. The primary motivation for the study is the desire to relate the end states across the relaxation zone, which can then be treated as a discontinuity in a reduced, equivelocity model, that is computationally more efficient than its parent. In contrast to a conservative system, where end states across thin zones of rapid variation are determined principally by algebraic statements of conservation, the nonconservative character of the present system requires an explicit consideration of the structure. Starting with the minimum admissible wave speed, the structure is mapped out as the wave speed increases. Several critical wave speeds corresponding to changes in the structure are identified. The archetypal structure is partly dispersed, monotonic, and involves conventional hydrodynamic shocks in one or both phases. The picture is reminiscent of, but more complex than, what is observed in such (simpler) two-phase media as a dusty gas. copyright 1997 American Institute of Physics

  11. A distributed, mobile-immobile domain transport model based on local mass transfer with recirculation zones

    Science.gov (United States)

    Zhou, J.; Wang, L.; Chen, Y.; Cardenas, M. B.

    2017-12-01

    Eddies or recirculation zones and stagnation zones are common in many environmental, engineering, and geophysical flow phenomena. Near rough boundaries, eddies are persistently and distinctly separate to the bulk flow. This leads to delays and long tails in the chemical transport by fluids since the entities being transported can be trapped and later released from the eddies. Here we provide a process-based insight on the anomalous transport induced by eddies using computational experiments with fully resolved flow and transport fields within rough fractures. A computationally tractable and objective eddy detection technique was developed. This allowed for direct insight into the mass transfer process at the interface between eddies and its neighboring main flow channel. A distributed mobile-immobile model with high fidelity has been proposed that incorporates the full local information of eddies and transport within the eddy. This local information includes eddy geometry and mass transfer coefficients. Taking this into account is critical for prediction of anomalous transport, and further provides a physically-based approach for modifying the classic mobile-immobile domain model into a distributed one. The methods and results in this study can serve as the foundation for the analysis and prediction of flow and transport phenomena in different environmental settings with immobile zones.

  12. Next-generation phylogeography: a targeted approach for multilocus sequencing of non-model organisms.

    Directory of Open Access Journals (Sweden)

    Jonathan B Puritz

    Full Text Available The field of phylogeography has long since realized the need and utility of incorporating nuclear DNA (nDNA sequences into analyses. However, the use of nDNA sequence data, at the population level, has been hindered by technical laboratory difficulty, sequencing costs, and problematic analytical methods dealing with genotypic sequence data, especially in non-model organisms. Here, we present a method utilizing the 454 GS-FLX Titanium pyrosequencing platform with the capacity to simultaneously sequence two species of sea star (Meridiastra calcar and Parvulastra exigua at five different nDNA loci across 16 different populations of 20 individuals each per species. We compare results from 3 populations with traditional Sanger sequencing based methods, and demonstrate that this next-generation sequencing platform is more time and cost effective and more sensitive to rare variants than Sanger based sequencing. A crucial advantage is that the high coverage of clonally amplified sequences simplifies haplotype determination, even in highly polymorphic species. This targeted next-generation approach can greatly increase the use of nDNA sequence loci in phylogeographic and population genetic studies by mitigating many of the time, cost, and analytical issues associated with highly polymorphic, diploid sequence markers.

  13. Construction of avulsion potential zone model for Kulik River of Barind Tract, India and Bangladesh.

    Science.gov (United States)

    Sarkar, Debabrata; Pal, Swades

    2018-04-21

    Avulsion is a natural fluvial process but considered it as a hazard in the populated region due to the chance of immense failure of lives and properties. So, early warning indicates that the zone of avulsion can facilitate the people living there. About 317 numbers of local and regional historical imprints of channel cutoff along river Kulik claim the need of this work. The present study tried to identify avulsion potential zone (APZ) of Kulik river of Indo-Bangladesh using multi-parametric weighted combination approach. Analytic hierarchy approach (AHP) is applied for weighting the used parameters. Avulsion potential model clearly exhibits that 9.51-km stream segment of middle and lower catchment is highly susceptible for avulsion especially during sudden high discharge and earthquake incidents. There is also high chance of channel avulsion following the existing Paleo-avulsion courses and left channels. Hard points can also be erected alongside the main channel for resisting channel avulsion propensity.

  14. De novo structural modeling and computational sequence analysis ...

    African Journals Online (AJOL)

    Different bioinformatics tools and machine learning techniques were used for protein structural classification. De novo protein modeling was performed by using I-TASSER server. The final model obtained was accessed by PROCHECK and DFIRE2, which confirmed that the final model is reliable. Until complete biochemical ...

  15. Unsaturated zone leaching models for assessing risk to groundwater of contaminated sites

    DEFF Research Database (Denmark)

    Troldborg, Mads; Binning, Philip John; Nielsen, Signe

    2009-01-01

    Risk assessments of sites contaminated with organic contaminants are typically conducted using models that ignore gas phase transport in the unsaturated zone. Here a general approach to developing analytical solutions to multiphase transport is presented. The approach is based on a combined gas......, lateral gas diffusion, sorption and degradation; a simple one-dimensional screening model, and two one-dimensional radial gas diffusion models for use in simulating volatile organic contaminant diffusion in unsaturated soils with an impermeable cover. The models show that both degradation and diffusion...... are important mechanisms for attenuation of contaminant concentrations at the water table. Finally, model results are compared with field data to illustrate the applicability of the solutions in risk assessment....

  16. Analytical modelling of stable isotope fractionation of volatile organic compounds in the unsaturated zone

    Science.gov (United States)

    Bouchard, Daniel; Cornaton, Fabien; Höhener, Patrick; Hunkeler, Daniel

    2011-01-01

    Analytical models were developed that simulate stable isotope ratios of volatile organic compounds (VOCs) near a point source contamination in the unsaturated zone. The models describe diffusive transport of VOCs, biodegradation and source ageing. The mass transport is governed by Fick's law for diffusion. The equation for reactive transport of VOCs in the soil gas phase was solved for different source geometries and for different boundary conditions. Model results were compared to experimental data from a one-dimensional laboratory column and a radial-symmetric field experiment. The comparison yielded a satisfying agreement. The model results clearly illustrate the significant isotope fractionation by gas phase diffusion under transient state conditions. This leads to an initial depletion of heavy isotopes with increasing distance from the source. The isotope evolution of the source is governed by the combined effects of isotope fractionation due to vaporisation, diffusion and biodegradation. The net effect can lead to an enrichment or depletion of the heavy isotope in the remaining organic phase, depending on the compound and element considered. Finally, the isotope evolution of molecules migrating away from the source and undergoing degradation is governed by a combined degradation and diffusion isotope effect. This suggests that, in the unsaturated zone, the interpretation of biodegradation of VOC based on isotopic data must always be based on a model combining gas phase diffusion and degradation.

  17. Regional groundwater modeling of the saturated zone in the vicinity of Yucca Mountain, Nevada

    International Nuclear Information System (INIS)

    Ahola, M.; Sagar, B.

    1992-10-01

    Results of groundwater modeling of the saturated zone in the vicinity of Yucca Mountain are presented. Both a regional (200 x 200 km) and subregional (50 x 50 km) model were used in the analyses. Simulations were conducted to determine the impact of various disruptive that might take place over the life span of a proposed Yucca Mountain geologic conditions repository on the groundwater flow field, as well as changes in the water-table elevations. These conditions included increases in precipitation and groundwater recharge within the regional model, changes in permeability of existing hydrogeologic barriers, a:nd the vertical intrusion of volcanic dikes at various orientations through the saturated zone. Based on the regional analysis, the rise in the water-table under Yucca Mountain due to various postulated conditions ranged from only a few meters to 275 meters. Results of the subregional model analysis, which was used to simulate intrusive dikes approximately 4 kilometers in length in the vicinity of Yucca Mountain, showed water-table rises ranging from a few meters to as much as 103 meters. Dikes oriented approximately north-south beneath Yucca Mountain produced the highest water-table rises. The conclusions drawn from this analysis are likely to change as more site-specific data become available and as the assumptions in the model are improved

  18. Stream flow simulation and verification in ungauged zones by coupling hydrological and hydrodynamic models: a case study of the Poyang Lake ungauged zone

    Directory of Open Access Journals (Sweden)

    L. Zhang

    2017-11-01

    Full Text Available To solve the problem of estimating and verifying stream flow without direct observation data, we estimated stream flow in ungauged zones by coupling a hydrological model with a hydrodynamic model, using the Poyang Lake basin as a test case. To simulate the stream flow of the ungauged zone, we built a soil and water assessment tool (SWAT model for the entire catchment area covering the upstream gauged area and ungauged zone, and then calibrated the SWAT model using the data in the gauged area. To verify the results, we built two hydrodynamic scenarios (the original and adjusted scenarios for Poyang Lake using the Delft3D model. In the original scenario, the upstream boundary condition is the observed stream flow from the upstream gauged area, while, in the adjusted scenario, it is the sum of the observed stream flow from the gauged area and the simulated stream flow from the ungauged zone. The experimental results showed that there is a stronger correlation and lower bias (R2 = 0.81, PBIAS  =  10.00 % between the observed and simulated stream flow in the adjusted scenario compared to that (R2 = 0.77, PBIAS  =  20.10 % in the original scenario, suggesting the simulated stream flow of the ungauged zone is reasonable. Using this method, we estimated the stream flow of the Poyang Lake ungauged zone as 16.4 ± 6.2 billion m3 a−1, representing ∼ 11.24 % of the annual total water yield of the entire watershed. Of the annual water yield, 70 % (11.48 billion m3 a−1 is concentrated in the wet season, while 30 % (4.92 billion m3 a−1 comes from the dry season. The ungauged stream flow significantly improves the water balance with the closing error decreased by 13.48 billion m3 a−1 (10.10 % of the total annual water resource from 30.20 ± 9.1 billion m3 a−1 (20.10 % of the total annual water resource to 16.72 ± 8.53 billion m3 a−1 (10.00 % of the total

  19. A Kinetic Ladle Furnace Process Simulation Model: Effective Equilibrium Reaction Zone Model Using FactSage Macro Processing

    Science.gov (United States)

    Van Ende, Marie-Aline; Jung, In-Ho

    2017-02-01

    The ladle furnace (LF) is widely used in the secondary steelmaking process in particular for the de-sulfurization, alloying, and reheating of liquid steel prior to the casting process. The Effective Equilibrium Reaction Zone model using the FactSage macro processing code was applied to develop a kinetic LF process model. The slag/metal interactions, flux additions to slag, various metallic additions to steel, and arcing in the LF process were taken into account to describe the variations of chemistry and temperature of steel and slag. The LF operation data for several steel grades from different plants were accurately described using the present kinetic model.

  20. Modeling sustainable groundwater management: packaging and sequencing of policy interventions.

    Science.gov (United States)

    Esteban, Encarna; Dinar, Ariel

    2013-04-15

    Of the many studies estimating effectiveness of policy reforms most have been considering various types of policy reforms in isolation from each other. Such pattern has also been the case in water resource regulations. In the case of groundwater almost all policy interventions considered in the literature have been implemented individually, without taking into account the possible interactions and impacts among them. In this paper, we focus on two policy instruments: water quota and uniform water tax. The paper demonstrates how packaging and sequencing sets of policy interventions, with possible triggers to initiate their time of implementation, may be more effective in achieving a sustainable groundwater management than single policies when environmental externalities exist. The policy instruments are applied to the Western la Mancha aquifer in Southeast Spain, a major aquifer that is managed by a command and control approach. Copyright © 2013 Elsevier Ltd. All rights reserved.

  1. Rupture Complexity Promoted by Damaged Fault Zones in Earthquake Cycle Models

    Science.gov (United States)

    Idini, B.; Ampuero, J. P.

    2017-12-01

    Pulse-like ruptures tend to be more sensitive to stress heterogeneity than crack-like ones. For instance, a stress-barrier can more easily stop the propagation of a pulse than that of a crack. While crack-like ruptures tend to homogenize the stress field within their rupture area, pulse-like ruptures develop heterogeneous stress fields. This feature of pulse-like ruptures can potentially lead to complex seismicity with a wide range of magnitudes akin to the Gutenberg-Richter law. Previous models required a friction law with severe velocity-weakening to develop pulses and complex seismicity. Recent dynamic rupture simulations show that the presence of a damaged zone around a fault can induce pulse-like rupture, even under a simple slip-weakening friction law, although the mechanism depends strongly on initial stress conditions. Here we aim at testing if fault zone damage is a sufficient ingredient to generate complex seismicity. In particular, we investigate the effects of damaged fault zones on the emergence and sustainability of pulse-like ruptures throughout multiple earthquake cycles, regardless of initial conditions. We consider a fault bisecting a homogeneous low-rigidity layer (the damaged zone) embedded in an intact medium. We conduct a series of earthquake cycle simulations to investigate the effects of two fault zone properties: damage level D and thickness H. The simulations are based on classical rate-and-state friction, the quasi-dynamic approximation and the software QDYN (https://github.com/ydluo/qdyn). Selected fully-dynamic simulations are also performed with a spectral element method. Our numerical results show the development of complex rupture patterns in some damaged fault configurations, including events of different sizes, as well as pulse-like, multi-pulse and hybrid pulse-crack ruptures. We further apply elasto-static theory to assess how D and H affect ruptures with constant stress drop, in particular the flatness of their slip profile

  2. A model of ischemia-induced neuroblast activation in the adult subventricular zone.

    Directory of Open Access Journals (Sweden)

    Davide Vergni

    Full Text Available We have developed a rat brain organotypic culture model, in which tissue slices contain cortex-subventricular zone-striatum regions, to model neuroblast activity in response to in vitro ischemia. Neuroblast activation has been described in terms of two main parameters, proliferation and migration from the subventricular zone into the injured cortex. We observed distinct phases of neuroblast activation as is known to occur after in vivo ischemia. Thus, immediately after oxygen/glucose deprivation (6-24 hours, neuroblasts reduce their proliferative and migratory activity, whereas, at longer time points after the insult (2 to 5 days, they start to proliferate and migrate into the damaged cortex. Antagonism of ionotropic receptors for extracellular ATP during and after the insult unmasks an early activation of neuroblasts in the subventricular zone, which responded with a rapid and intense migration of neuroblasts into the damaged cortex (within 24 hours. The process is further enhanced by elevating the production of the chemoattractant SDf-1alpha and may also be boosted by blocking the activation of microglia. This organotypic model which we have developed is an excellent in vitro system to study neurogenesis after ischemia and other neurodegenerative diseases. Its application has revealed a SOS response to oxygen/glucose deprivation, which is inhibited by unfavorable conditions due to the ischemic environment. Finally, experimental quantifications have allowed us to elaborate a mathematical model to describe neuroblast activation and to develop a computer simulation which should have promising applications for the screening of drug candidates for novel therapies of ischemia-related pathologies.

  3. Quantifying Uncertainty in Inverse Models of Geologic Data from Shear Zones

    Science.gov (United States)

    Davis, J. R.; Titus, S.

    2016-12-01

    We use Bayesian Markov chain Monte Carlo simulation to quantify uncertainty in inverse models of geologic data. Although this approach can be applied to many tectonic settings, field areas, and mathematical models, we focus on transpressional shear zones. The underlying forward model, either kinematic or dynamic, produces a velocity field, which predicts the dikes, foliation-lineations, crystallographic preferred orientation (CPO), shape preferred orientation (SPO), and other geologic data that should arise in the shear zone. These predictions are compared to data using modern methods of geometric statistics, including the Watson (for lines such as dike poles), isotropic matrix Fisher (for orientations such as foliation-lineations and CPO), and multivariate normal (for log-ellipsoids such as SPO) distributions. The result of the comparison is a likelihood, which is a key ingredient in the Bayesian approach. The other key ingredient is a prior distribution, which reflects the geologist's knowledge of the parameters before seeing the data. For some parameters, such as shear zone strike and dip, we identify realistic informative priors. For other parameters, where the geologist has no prior knowledge, we identify useful uninformative priors.We investigate the performance of this approach through numerical experiments on synthetic data sets. A fundamental issue is that many models of deformation exhibit asymptotic behavior (e.g., flow apophyses, fabric attractors) or periodic behavior (e.g., SPO when the clasts are rigid), which causes the likelihood to be too uniform. Based on our experiments, we offer rules of thumb for how many data, of which types, are needed to constrain deformation.

  4. A Model Study on the Role of Wetland Zones in Lake Eutrophication and Restoration

    Directory of Open Access Journals (Sweden)

    J.H. Janse

    2001-01-01

    Full Text Available Shallow lakes respond in different ways to changes in nutrient loading (nitrogen, phosphorus. These lakes may be in two different states: turbid, dominated by phytoplankton, and clear, dominated by submerged macrophytes. Both states are self-stabilizing; a shift from turbid to clear occurs at much lower nutrient loading than a shift in the opposite direction. These critical loading levels vary among lakes and are dependent on morphological, biological, and lake management factors. This paper focuses on the role of wetland zones. Several processes are important: transport and settling of suspended solids, denitrification, nutrient uptake by marsh vegetation (increasing nutrient retention, and improvement of habitat conditions for predatory fish. A conceptual model of a lake with surrounding reed marsh was made, including these relations. The lake-part of this model consists of an existing lake model named PCLake[1]. The relative area of lake and marsh can be varied. Model calculations revealed that nutrient concentrations are lowered by the presence of a marsh area, and that the critical loading level for a shift to clear water is increased. This happens only if the mixing rate of the lake and marsh water is adequate. In general, the relative marsh area should be quite large in order to have a substantial effect. Export of nutrients can be enhanced by harvesting of reed vegetation. Optimal predatory fish stock contributes to water quality improvement, but only if combined with favourable loading and physical conditions. Within limits, the presence of a wetland zone around lakes may thus increase the ability of lakes to cope with nutrients and enhance restoration. Validation of the conclusions in real lakes is recommended, a task hampered by the fact that, in the Netherlands, many wetland zones have disappeared in the past.

  5. Ignition and growth modeling of detonation reaction zone experiments on single crystals of PETN and HMX

    Science.gov (United States)

    White, Bradley W.; Tarver, Craig M.

    2017-01-01

    It has long been known that detonating single crystals of solid explosives have much larger failure diameters than those of heterogeneous charges of the same explosive pressed or cast to 98 - 99% theoretical maximum density (TMD). In 1957, Holland et al. demonstrated that PETN single crystals have failure diameters of about 8 mm, whereas heterogeneous PETN charges have failure diameters of less than 0.5 mm. Recently, Fedorov et al. quantitatively determined nanosecond time resolved detonation reaction zone profiles of single crystals of PETN and HMX by measuring the interface particle velocity histories of the detonating crystals and LiF windows using a PDV system. The measured reaction zone time durations for PETN and HMX single crystal detonations were approximately 100 and 260 nanoseconds, respectively. These experiments provided the necessary data to develop Ignition and Growth (I&G) reactive flow model parameters for the single crystal detonation reaction zones. Using these parameters, the calculated unconfined failure diameter of a PETN single crystal was 7.5 +/- 0.5 mm, close to the 8 mm experimental value. The calculated failure diameter of an unconfined HMX single crystal was 15 +/- 1 mm. The unconfined failure diameter of an HMX single crystal has not yet been determined precisely, but Fedorov et al. detonated 14 mm diameter crystals confined by detonating a HMX-based plastic bonded explosive (PBX) without initially overdriving the HMX crystals.

  6. Numerical modeling of fracking fluid migration through fault zones and fractures in the North German Basin

    Science.gov (United States)

    Pfunt, Helena; Houben, Georg; Himmelsbach, Thomas

    2016-09-01

    Gas production from shale formations by hydraulic fracturing has raised concerns about the effects on the quality of fresh groundwater. The migration of injected fracking fluids towards the surface was investigated in the North German Basin, based on the known standard lithology. This included cases with natural preferential pathways such as permeable fault zones and fracture networks. Conservative assumptions were applied in the simulation of flow and mass transport triggered by a high pressure boundary of up to 50 MPa excess pressure. The results show no significant fluid migration for a case with undisturbed cap rocks and a maximum of 41 m vertical transport within a permeable fault zone during the pressurization. Open fractures, if present, strongly control the flow field and migration; here vertical transport of fracking fluids reaches up to 200 m during hydraulic fracturing simulation. Long-term transport of the injected water was simulated for 300 years. The fracking fluid rises vertically within the fault zone up to 485 m due to buoyancy. Progressively, it is transported horizontally into sandstone layers, following the natural groundwater flow direction. In the long-term, the injected fluids are diluted to minor concentrations. Despite the presence of permeable pathways, the injected fracking fluids in the reported model did not reach near-surface aquifers, either during the hydraulic fracturing or in the long term. Therefore, the probability of impacts on shallow groundwater by the rise of fracking fluids from a deep shale-gas formation through the geological underground to the surface is small.

  7. Assessment of freeway work zone safety with improved cellular automata model

    Directory of Open Access Journals (Sweden)

    Guohua Liang

    2014-08-01

    Full Text Available To accurately assess the safety of freeway work zones, this paper investigates the safety of vehicle lane change maneuvers with improved cellular automata model. Taking the traffic conflict and standard deviation of operating speed as the evaluation indexes, the study evaluates the freeway work zone safety. With improved deceleration probability in car-following raies and the addition of lanechanging rules under critical state, the lane-changing behavior under critical state is defined as a conflict count. Through 72 schemes of simulation runs, the possible states of the traffic flow are carefully studied. The results show that under the condition of constant saturation traffic conflict count and vehicle speed standard deviation reach their maximums when the mixed rate of heave vehicles is 40%. Meanwhile, in the case of constant heavy vehicles mix, traffic conflict count and vehicle speed standard deviation reach maximum values when saturation rate is 0. 75. Integrating ail simulation results, it is known the traffic safety in freeway work zones is classified into four levels : safe, relatively safe, relatively dangerous, and dangerous.

  8. In what root-zone N concentration does nitrate start to leach significantly? A reasonable answer from modeling Mediterranean field data and closed root-zone experiments

    Science.gov (United States)

    Kurtzman, D.; Kanner, B.; Levy, Y.; Shapira, R. H.; Bar-Tal, A.

    2017-12-01

    Closed-root-zone experiments (e.g. pots, lyzimeters) reveal in many cases a mineral-nitrogen (N) concentration from which the root-N-uptake efficiency reduces significantly and nitrate leaching below the root-zone increases dramatically. A les-direct way to reveal this threshold concentration in agricultural fields is to calibrate N-transport models of the unsaturated zone to nitrate data of the deep samples (under the root-zone) by fitting the threshold concentration of the nitrate-uptake function. Independent research efforts of these two types in light soils where nitrate problems in underlying aquifers are common reviled: 1) that the threshold exists for most crops (filed, vegetables and orchards); 2) nice agreement on the threshold value between the two very different research methodologies; and 3) the threshold lies within 20-50 mg-N/L. Focusing on being below the threshold is a relatively simple aim in the way to maintain intensive agriculture with limited effects on the nitrate concentration in the underlying water resource. Our experience show that in some crops this threshold coincides with the end-of-rise of the N-yield curve (e.g. corn); in this case, it is relatively easy to convince farmers to fertilize below threshold. In other crops, although significant N is lost to leaching the crop can still use higher N concentration to increase yield (e.g. potato).

  9. Quasi 3D modeling of water flow in vadose zone and groundwater

    Science.gov (United States)

    Kuznetsov, M.; Yakirevich, A.; Pachepsky, Y. A.; Sorek, S.; Weisbrod, N.

    2012-07-01

    SummaryThe complexity of subsurface flow systems calls for a variety of concepts leading to the multiplicity of simplified flow models. One habitual simplification is based on the assumption that lateral flow and transport in unsaturated zone are not significant unless the capillary fringe is involved. In such cases the flow and transport in the unsaturated zone above groundwater level can be simulated as a 1D phenomenon, whereas the flow and transport through groundwater are viewed as 2D or 3D phenomena. A new approach for a numerical scheme for 3D variably saturated flow using quasi 3D Richards' equation and finite difference scheme is presented. The corresponding numerical algorithm and the QUASI-3D computer code were developed. Results of the groundwater level simulations were compared with transient laboratory experimental data for 2D data constant-flux infiltration, quasi-3D HYDRUS-MODFLOW numerical model and a FULL-3D numerical model using Richards' equation. Hypothetical 3D examples of infiltration, pumping and groundwater mound dissipation for different spatial-time scales are presented. Water flow simulation for the Alto Piura aquifer (Peru) demonstrates the QUASI-3D model application at the regional scale. Computationally the QUASI-3D code was found to be more efficient by an order of 10-300%, while being accurate with respect to the benchmark fully 3D variable saturation code, when the capillary fringe was considered.

  10. De novo structural modeling and computational sequence analysis ...

    African Journals Online (AJOL)

    Jane

    2011-07-25

    Jul 25, 2011 ... Our study was aimed towards computational proteomic analysis and 3D structural modeling of this novel bacteriocin protein encoded by the earlier aforementioned gene. Different bioinformatics tools and machine learning techniques were used for protein structural classification. De novo protein modeling ...

  11. Two-dimensional finite elements model for selenium transport in saturated and unsaturated zones.

    Science.gov (United States)

    Tayfur, Gokmen; Tanji, Kenneth K; Baba, Alper

    2010-10-01

    A two-dimensional finite element model was developed to simulate species of selenium transport in two dimensions in both saturated and unsaturated soil zones. The model considers water, selenate, selenite, and selenomethionine uptake by plants. It also considers adsorption and desorption, oxidation and reduction, volatilization, and chemical and biological transformations of selenate, selenite, and selenomethionine. In addition to simulating water flow, selenate, selenite, and selenomethionine transport, the model also simulates organic and gaseous selenium transport. The developed model was applied to simulate two different observed field data. The simulation of the observed data was satisfactory, with mean absolute error of 48.5 microg/l and mean relative error of 8.9%.

  12. Modeling foam delivery mechanisms in deep vadose-zone remediation using method of characteristics

    International Nuclear Information System (INIS)

    Roostapour, A.; Kam, S.I.

    2012-01-01

    Highlights: ► A new mathematical framework established for vadose-zone foam remediation. ► Graphical solutions presented by Method of Characteristics quantitatively. ► Effects of design parameters in the field applications thoroughly investigated. ► Implication of modeling study for successful field treatment discussed. - Abstract: This study investigates foam delivery mechanisms in vadose-zone remediation by using Method of Characteristics (MoC), a mathematical tool long been used for the analysis of miscible and immiscible flooding in porous media in petroleum industry. MoC converts the governing material-balance partial differential equations into a series of ordinary differential equations, and the resulting solutions are in a form of wave propagation (more specifically, for chemical species and phase saturations) through the system as a function of time and space. Deep vadose-zone remediation has special features compared to other conventional remediation applications. They include, not limited to, a high level of heterogeneity, a very dry initial condition with low water saturation (S w ), pollutants such as metals and radionuclides fully dissolved in groundwater, and a serious concern about downward migration during the remediation treatments. For the vadose-zone remediation processes to be successful, the injected aqueous phase should carry chemicals to react with pollutants and precipitate them for immobilization and stabilization purposes. As a result, foams are believed to be an effective means, and understanding foam flow mechanism in situ is a key to the optimal design of field applications. Results show that foam delivery mechanism is indeed very complicated, making the optimum injection condition field-specific. The five major parameters selected (i.e., initial saturation of the medium, injection foam quality, surfactant adsorption, foam strength, and foam stability) are shown to be all important, interacting with each other. Results also

  13. Design of a three-dimensional site-scale model for the unsaturated zone at Yucca Mountain, Nevada

    International Nuclear Information System (INIS)

    Wittwer, C.S.; Bodvarsson, G.S.; Chornack, M.P.; Flint, A.L.; Lewis, B.D.; Spengler, R.W.; Flint, L.E.; Rautman, C.A.

    1992-01-01

    A three-dimensional model of moisture flow within the unsaturated zone at Yucca Mountain is being developed. This site-scale model covers an area of about 30 km 2 and is bounded by major faults to the east and west. A detailed numerical grid has been developed based on location of boreholes, different infiltration zones, hydrogeological units and their outcrops, major faults, and water level data. Different maps, such as contour maps and isopachs maps, are presented for the different infiltration zones, and for the base of the Tiva Canyon, the Paintbrush, and the Topopah Spring hydrogeological units

  14. Water-Level Data Analysis for the Saturated Zone Site-Scale Flow and Transport Model

    International Nuclear Information System (INIS)

    Tucci, P.

    2001-01-01

    This Analysis/Model Report (AMR) documents an updated analysis of water-level data performed to provide the saturated-zone, site-scale flow and transport model (CRWMS M and O 2000) with the configuration of the potentiometric surface, target water-level data, and hydraulic gradients for model calibration. The previous analysis was presented in ANL-NBS-HS-000034, Rev 00 ICN 01, Water-Level Data Analysis for the Saturated Zone Site-Scale Flow and Transport Model (USGS 2001). This analysis is designed to use updated water-level data as the basis for estimating water-level altitudes and the potentiometric surface in the SZ site-scale flow and transport model domain. The objectives of this revision are to develop computer files containing (1) water-level data within the model area (DTN: GS010908312332.002), (2) a table of known vertical head differences (DTN: GS0109083 12332.003), and (3) a potentiometric-surface map (DTN: GS010608312332.001) using an alternate concept from that presented in ANL-NBS-HS-000034, Rev 00 ICN 01 for the area north of Yucca Mountain. The updated water-level data include data obtained from the Nye County Early Warning Drilling Program (EWDP) and data from borehole USW WT-24. In addition to being utilized by the SZ site-scale flow and transport model, the water-level data and potentiometric-surface map contained within this report will be available to other government agencies and water users for ground-water management purposes. The potentiometric surface defines an upper boundary of the site-scale flow model, as well as provides information useful to estimation of the magnitude and direction of lateral ground-water flow within the flow system. Therefore, the analysis documented in this revision is important to SZ flow and transport calculations in support of total system performance assessment

  15. 3D-modeling for determination of axial forces acting in elements of the end zone of power turbogenerators

    Directory of Open Access Journals (Sweden)

    Y.A.Haydenko

    2013-12-01

    Full Text Available A field mathematical model of the end zone of a powerful generator type TVV-1000-2U3 in the 3D-setting is developed. Modelling of the nominal mode of turbogenerator operation is done. The distribution of the electromagnetic field, eddy currents, and the Ampere force appearing in such elements of the end zone of turbogenerator as the pressure plate, push pins and electrically conductive screen.

  16. Fast and Sequence-Adaptive Whole-Brain Segmentation Using Parametric Bayesian Modeling

    DEFF Research Database (Denmark)

    Puonti, Oula; Iglesias, Juan Eugenio; Van Leemput, Koen

    2016-01-01

    the performance of a segmentation algorithm designed to meet these requirements, building upon generative parametric models previously used in tissue classification. The method is tested on four different datasets acquired with different scanners, field strengths and pulse sequences, demonstrating comparable...

  17. Kinetic Modeling of Mineral Sequences on Early Mars Using Fully Open Systems

    Science.gov (United States)

    Uceda, E. R.; Fairén, A. G.; Gil-Lozano, C.; Losa-Adams, E.; Gago-Duport, L.

    2017-10-01

    We model the formation of mineral sequences known to exist on Mars considering open system conditions both at the atmosphere-water and water-rock interfaces, and implementing a kinetic approach for the dissolution and precipitation of solid phases.

  18. Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes.

    Science.gov (United States)

    Shekhar, Karthik; Ruberman, Claire F; Ferguson, Andrew L; Barton, John P; Kardar, Mehran; Chakraborty, Arup K

    2013-12-01

    Mutational escape from vaccine-induced immune responses has thwarted the development of a successful vaccine against AIDS, whose causative agent is HIV, a highly mutable virus. Knowing the virus' fitness as a function of its proteomic sequence can enable rational design of potent vaccines, as this information can focus vaccine-induced immune responses to target mutational vulnerabilities of the virus. Spin models have been proposed as a means to infer intrinsic fitness landscapes of HIV proteins from patient-derived viral protein sequences. These sequences are the product of nonequilibrium viral evolution driven by patient-specific immune responses and are subject to phylogenetic constraints. How can such sequence data allow inference of intrinsic fitness landscapes? We combined computer simulations and variational theory á la Feynman to show that, in most circumstances, spin models inferred from patient-derived viral sequences reflect the correct rank order of the fitness of mutant viral strains. Our findings are relevant for diverse viruses.

  19. Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes

    Science.gov (United States)

    Shekhar, Karthik; Ruberman, Claire F.; Ferguson, Andrew L.; Barton, John P.; Kardar, Mehran; Chakraborty, Arup K.

    2013-12-01

    Mutational escape from vaccine-induced immune responses has thwarted the development of a successful vaccine against AIDS, whose causative agent is HIV, a highly mutable virus. Knowing the virus' fitness as a function of its proteomic sequence can enable rational design of potent vaccines, as this information can focus vaccine-induced immune responses to target mutational vulnerabilities of the virus. Spin models have been proposed as a means to infer intrinsic fitness landscapes of HIV proteins from patient-derived viral protein sequences. These sequences are the product of nonequilibrium viral evolution driven by patient-specific immune responses and are subject to phylogenetic constraints. How can such sequence data allow inference of intrinsic fitness landscapes? We combined computer simulations and variational theory á la Feynman to show that, in most circumstances, spin models inferred from patient-derived viral sequences reflect the correct rank order of the fitness of mutant viral strains. Our findings are relevant for diverse viruses.

  20. Microscopic Analysis and Modeling of Airport Surface Sequencing, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — Although a number of airportal surface models exist and have been successfully used for analysis of airportal operations, only recently has it become possible to...

  1. A simulation-optimization model for effective water resources management in the coastal zone

    Science.gov (United States)

    Spanoudaki, Katerina; Kampanis, Nikolaos

    2015-04-01

    Coastal areas are the most densely-populated areas in the world. Consequently water demand is high, posing great pressure on fresh water resources. Climatic change and its direct impacts on meteorological variables (e.g. precipitation) and indirect impact on sea level rise, as well as anthropogenic pressures (e.g. groundwater abstraction), are strong drivers causing groundwater salinisation and subsequently affecting coastal wetlands salinity with adverse effects on the corresponding ecosystems. Coastal zones are a difficult hydrologic environment to represent with a mathematical model due to the large number of contributing hydrologic processes and variable-density flow conditions. Simulation of sea level rise and tidal effects on aquifer salinisation and accurate prediction of interactions between coastal waters, groundwater and neighbouring wetlands requires the use of integrated surface water-groundwater mathematical models. In the past few decades several computer codes have been developed to simulate coupled surface and groundwater flow. However, most integrated surface water-groundwater models are based on the assumption of constant fluid density and therefore their applicability to coastal regions is questionable. Thus, most of the existing codes are not well-suited to represent surface water-groundwater interactions in coastal areas. To this end, the 3D integrated surface water-groundwater model IRENE (Spanoudaki et al., 2009; Spanoudaki, 2010) has been modified in order to simulate surface water-groundwater flow and salinity interactions in the coastal zone. IRENE, in its original form, couples the 3D shallow water equations to the equations describing 3D saturated groundwater flow of constant density. A semi-implicit finite difference scheme is used to solve the surface water flow equations, while a fully implicit finite difference scheme is used for the groundwater equations. Pollution interactions are simulated by coupling the advection

  2. Numerical modeling of fracking fluid and methane migration through fault zones in shale gas reservoirs

    Science.gov (United States)

    Taherdangkoo, Reza; Tatomir, Alexandru; Sauter, Martin

    2017-04-01

    Hydraulic fracturing operation in shale gas reservoir has gained growing interest over the last few years. Groundwater contamination is one of the most important environmental concerns that have emerged surrounding shale gas development (Reagan et al., 2015). The potential impacts of hydraulic fracturing could be studied through the possible pathways for subsurface migration of contaminants towards overlying aquifers (Kissinger et al., 2013; Myers, 2012). The intent of this study is to investigate, by means of numerical simulation, two failure scenarios which are based on the presence of a fault zone that penetrates the full thickness of overburden and connect shale gas reservoir to aquifer. Scenario 1 addresses the potential transport of fracturing fluid from the shale into the subsurface. This scenario was modeled with COMSOL Multiphysics software. Scenario 2 deals with the leakage of methane from the reservoir into the overburden. The numerical modeling of this scenario was implemented in DuMux (free and open-source software), discrete fracture model (DFM) simulator (Tatomir, 2012). The modeling results are used to evaluate the influence of several important parameters (reservoir pressure, aquifer-reservoir separation thickness, fault zone inclination, porosity, permeability, etc.) that could affect the fluid transport through the fault zone. Furthermore, we determined the main transport mechanisms and circumstances in which would allow frack fluid or methane migrate through the fault zone into geological layers. The results show that presence of a conductive fault could reduce the contaminant travel time and a significant contaminant leakage, under certain hydraulic conditions, is most likely to occur. Bibliography Kissinger, A., Helmig, R., Ebigbo, A., Class, H., Lange, T., Sauter, M., Heitfeld, M., Klünker, J., Jahnke, W., 2013. Hydraulic fracturing in unconventional gas reservoirs: risks in the geological system, part 2. Environ Earth Sci 70, 3855

  3. Insight into collision zone dynamics from topography: numerical modelling results and observations

    Directory of Open Access Journals (Sweden)

    A. D. Bottrill

    2012-11-01

    Full Text Available Dynamic models of subduction and continental collision are used to predict dynamic topography changes on the overriding plate. The modelling results show a distinct evolution of topography on the overriding plate, during subduction, continental collision and slab break-off. A prominent topographic feature is a temporary (few Myrs basin on the overriding plate after initial collision. This "collisional mantle dynamic basin" (CMDB is caused by slab steepening drawing, material away from the base of the overriding plate. Also, during this initial collision phase, surface uplift is predicted on the overriding plate between the suture zone and the CMDB, due to the subduction of buoyant continental material and its isostatic compensation. After slab detachment, redistribution of stresses and underplating of the overriding plate cause the uplift to spread further into the overriding plate. This topographic evolution fits the stratigraphy found on the overriding plate of the Arabia-Eurasia collision zone in Iran and south east Turkey. The sedimentary record from the overriding plate contains Upper Oligocene-Lower Miocene marine carbonates deposited between terrestrial clastic sedimentary rocks, in units such as the Qom Formation and its lateral equivalents. This stratigraphy shows that during the Late Oligocene–Early Miocene the surface of the overriding plate sank below sea level before rising back above sea level, without major compressional deformation recorded in the same area. Our modelled topography changes fit well with this observed uplift and subsidence.

  4. Simulating Dynamic Fracture in Oxide Fuel Pellets Using Cohesive Zone Models

    Energy Technology Data Exchange (ETDEWEB)

    R. L. Williamson

    2009-08-01

    It is well known that oxide fuels crack during the first rise to power, with continued fracture occurring during steady operation and especially during power ramps or accidental transients. Fractures have a very strong influence on the stress state in the fuel which, in turn, drives critical phenomena such as fission gas release, fuel creep, and eventual fuel/clad mechanical interaction. Recently, interest has been expressed in discrete fracture methods, such as the cohesive zone approach. Such models are attractive from a mechanistic and physical standpoint, since they reflect the localized nature of cracking. The precise locations where fractures initiate, as well as the crack evolution characteristics, are determined as part of the solution. This paper explores the use of finite element cohesive zone concepts to predict dynamic crack behavior in oxide fuel pellets during power-up, steady operation, and power ramping. The aim of this work is first to provide an assessment of cohesive zone models for application to fuel cracking and explore important numerical issues associated with this fracture approach. A further objective is to provide basic insight into where and when cracks form, how they interact, and how cracking effects the stress field in a fuel pellet. The ABAQUS commercial finite element code, which includes powerful cohesive zone capabilities, was used for this study. Fully-coupled thermo-mechanical behavior is employed, including the effects of thermal expansion, swelling due to solid and gaseous fission products, and thermal creep. Crack initiation is determined by a temperature-dependent maximum stress criterion, based on measured fracture strengths for UO2. Damage evolution is governed by a traction-separation relation, calibrated to data from temperature and burn-up dependent fracture toughness measurements. Numerical models are first developed in 2D based on both axisymmetric (to explore axial cracking) and plane strain (to explore radial

  5. A Local Poisson Graphical Model for inferring networks from sequencing data.

    Science.gov (United States)

    Allen, Genevera I; Liu, Zhandong

    2013-09-01

    Gaussian graphical models, a class of undirected graphs or Markov Networks, are often used to infer gene networks based on microarray expression data. Many scientists, however, have begun using high-throughput sequencing technologies such as RNA-sequencing or next generation sequencing to measure gene expression. As the resulting data consists of counts of sequencing reads for each gene, Gaussian graphical models are not optimal for this discrete data. In this paper, we propose a novel method for inferring gene networks from sequencing data: the Local Poisson Graphical Model. Our model assumes a Local Markov property where each variable conditional on all other variables is Poisson distributed. We develop a neighborhood selection algorithm to fit our model locally by performing a series of l1 penalized Poisson, or log-linear, regressions. This yields a fast parallel algorithm for estimating networks from next generation sequencing data. In simulations, we illustrate the effectiveness of our methods for recovering network structure from count data. A case study on breast cancer microRNAs (miRNAs), a novel application of graphical models, finds known regulators of breast cancer genes and discovers novel miRNA clusters and hubs that are targets for future research.

  6. Numerical modelling of wind effects on breaking waves in the surf zone

    Science.gov (United States)

    Xie, Zhihua

    2017-10-01

    Wind effects on periodic breaking waves in the surf zone have been investigated in this study using a two-phase flow model. The model solves the Reynolds-averaged Navier-Stokes equations with the k - 𝜖 turbulence model simultaneously for the flows both in the air and water. Both spilling and plunging breakers over a 1:35 sloping beach have been studied under the influence of wind, with a focus during wave breaking. Detailed information of the distribution of wave amplitudes and mean water level, wave-height-to-water-depth ratio, the water surface profiles, velocity, vorticity, and turbulence fields have been presented and discussed. The inclusion of wind alters the air flow structure above water waves, increases the generation of vorticity, and affects the wave shoaling, breaking, overturning, and splash-up processes. Wind increases the water particle velocities and causes water waves to break earlier and seaward, which agrees with the previous experiment.

  7. Sequence Domain Harmonic Modeling of Type-IV Wind Turbines

    DEFF Research Database (Denmark)

    Guest, Emerson; Jensen, Kim Høj; Rasmussen, Tonny Wederberg

    2017-01-01

    -sampled pulsewidth modulation and an analysis of converter generated voltage harmonics due to compensated dead-time. The decoupling capabilities of the proposed the SD harmonic model are verified through a power quality (PQ) assessment of a 3MW Type-IV wind turbine. The assessment shows that the magnitude and phase...... of low-order odd converter generated voltage harmonics are dependent on the converter operating point and the phase of the fundamental component of converter current respectively. The SD harmonic model can be used to make PQ assessments of Type-IV wind turbines or incorporated into harmonic load flows...... for computation of PQ in wind power plants....

  8. Quasi 3D modeling of water flow and solute transport in vadose zone and groundwater

    Science.gov (United States)

    Yakirevich, A.; Kuznetsov, M.; Weisbrod, N.; Pachepsky, Y. A.

    2013-12-01

    The complexity of subsurface flow systems calls for a variety of concepts leading to the multiplicity of simplified flow models. One commonly used simplification is based on the assumption that lateral flow and transport in unsaturated zone is insignificant unless the capillary fringe is involved. In such cases the flow and transport in the unsaturated zone above groundwater level can be simulated as a 1D phenomenon, whereas through groundwater they are viewed as 2D or 3D phenomena. A new approach for a numerical scheme for 3D variably saturated flow and transport is presented. A Quasi-3D approach allows representing flow in the 'vadose zone - aquifer' system by a series of 1D Richards' equations solved in variably-saturated zone and by 3D-saturated flow equation in groundwater (modified MODFLOW code). The 1D and 3D equations are coupled at the phreatic surface in a way that aquifer replenishment is calculated using the Richards' equation, and solving for the moving water table does not require definition of the specific yield parameter. The 3D advection-dispersion equation is solved in the entire domain by the MT3D code. Using implicit finite differences approximation to couple processes in the vadose zone and groundwater provides mass conservation and increase of computational efficiency. The above model was applied to simulate the impact of irrigation on groundwater salinity in the Alto Piura aquifer (Northern Peru). Studies on changing groundwater quality in arid and semi-arid lands show that irrigation return flow is one of the major factors contributing to aquifer salinization. Existing mathematical models do not account explicitly for the solute recycling during irrigation on a daily scale. Recycling occurs throughout the unsaturated and saturated zones, as function of the solute mass extracted from pumping wells. Salt concentration in irrigation water is calculated at each time step as a function of concentration of both surface water and groundwater

  9. Nonstationary porosity evolution in mixing zone in coastal carbonate aquifer using an alternative modeling approach.

    Science.gov (United States)

    Laabidi, Ezzeddine; Bouhlila, Rachida

    2015-07-01

    In the last few decades, hydrogeochemical problems have benefited from the strong interest in numerical modeling. One of the most recognized hydrogeochemical problems is the dissolution of the calcite in the mixing zone below limestone coastal aquifer. In many works, this problem has been modeled using a coupling algorithm between a density-dependent flow model and a geochemical model. A related difficulty is that, because of the high nonlinearity of the coupled set of equations, high computational effort is needed. During calcite dissolution, an increase in permeability can be identified, which can induce an increase in the penetration of the seawater into the aquifer. The majority of the previous studies used a fully coupled reactive transport model in order to model such problem. Romanov and Dreybrodt (J Hydrol 329:661-673, 2006) have used an alternative approach to quantify the porosity evolution in mixing zone below coastal carbonate aquifer at steady state. This approach is based on the analytic solution presented by Phillips (1991) in his book Flow and Reactions in Permeable Rock, which shows that it is possible to decouple the complex set of equation. This equation is proportional to the square of the salinity gradient, which can be calculated using a density driven flow code and to the reaction rate that can be calculated using a geochemical code. In this work, this equation is used in nonstationary step-by-step regime. At each time step, the quantity of the dissolved calcite is quantified, the change of porosity is calculated, and the permeability is updated. The reaction rate, which is the second derivate of the calcium equilibrium concentration in the equation, is calculated using the PHREEQC code (Parkhurst and Apello 1999). This result is used in GEODENS (Bouhlila 1999; Bouhlila and Laabidi 2008) to calculate change of the porosity after calculating the salinity gradient. For the next time step, the same protocol is used but using the updated porosity

  10. Model comparison for aftershock sequences following the 2005 Kashmir disaster

    NARCIS (Netherlands)

    K. Turkyilmaz (Kerem); M.N.M. van Lieshout (Marie-Colette); A. Stein (Alfred)

    2011-01-01

    htmlabstractIn an earlier study (Van Lieshout and Stein, in press) we postulated the existence of two major earthquakes in Kashmir instead of a single one, based upon the pattern of aftershocks. In this note we explore this pattern further by fitting several spatial point pattern models. In

  11. An efficient binomial model-based measure for sequence comparison and its application.

    Science.gov (United States)

    Liu, Xiaoqing; Dai, Qi; Li, Lihua; He, Zerong

    2011-04-01

    Sequence comparison is one of the major tasks in bioinformatics, which could serve as evidence of structural and functional conservation, as well as of evolutionary relations. There are several similarity/dissimilarity measures for sequence comparison, but challenges remains. This paper presented a binomial model-based measure to analyze biological sequences. With help of a random indicator, the occurrence of a word at any position of sequence can be regarded as a random Bernoulli variable, and the distribution of a sum of the word occurrence is well known to be a binomial one. By using a recursive formula, we computed the binomial probability of the word count and proposed a binomial model-based measure based on the relative entropy. The proposed measure was tested by extensive experiments including classification of HEV genotypes and phylogenetic analysis, and further compared with alignment-based and alignment-free measures. The results demonstrate that the proposed measure based on binomial model is more efficient.

  12. Mathematical Optimal Sequence Model Development to Process Planes and Other Interconnected Surfaces of Complex Body Parts

    Directory of Open Access Journals (Sweden)

    I. I. Kravchenko

    2016-01-01

    Full Text Available Experience in application of multi-operational machines CNC (MOM CNC shows that they are efficient only in case of significantly increasing productivity and dramatically reducing time-to-market cycle of new products. Most full technological MOM capabilities are revealed when processing the complex body parts. The more complex is a part design and the more is its number of machined surfaces, the more tools are necessary for its processing and positioning, the more is an efficiency of their application. At the same time, the case history of using these machines in industry shows that MOM CNC are, virtually, used mostly for technological processes of universal equipment, which is absolutely unacceptable. One way to improve the processing performance on MOM CNC is to reduce nonproductive machine time through reducing the mutual idle movements of the working machine. This problem is solved using dynamic programming methods, one of which is the solution of the traveling salesman problem (Bellman's method. With a known plan for treatment of all elementary surfaces of the body part, i.e. the known number of performed transitions, each transition is represented as a vertex of some graph, while technological links between the vertices are its edges. A mathematical model is developed on the Bellman principle, which is adapted to technological tasks to minimize the idle time of mutual idle movements of the working machine to perform all transitions in the optimal sequence. The initial data to fill matrix of time expenditures are time consumed by the hardware after executing the i-th transition, and necessary to complete the j-transition. The programmer fills in matrix cells according to known routing body part taking into account the time for part and table positioning, tool exchange, spindle and table approach to the working zone, and the time of table rotation, etc. The mathematical model was tested when machining the body part with 36 transitions on the

  13. Review of ground-water flow and transport models in the unsaturated zone

    International Nuclear Information System (INIS)

    Oster, C.A.

    1982-11-01

    Models of partially saturated flow and transport in porous media have application in the analysis of existing as well as future low-level radioactive waste facilities located above the water table. An extensive literature search along with telephone and mail correspondence with recognized leading experts in the field, was conducted to identify computer models suitable for studies of low-level radioactive waste facilities located in the unsaturated zone. Fifty-five existing models were identified as potentially useful. Ten of these models were selected for further examination. This report contains a statement of the ground-water flow-contaminant transport problem, a discussion of those methods used to reduce the physical problem to a computer model, a brief discussion about the data requirements of these models. The procedure used to select the ten codes for further discussion is given, along with a list of these models. Finally, the Appendices contain the data about the fifty-five codes examined. Specifically Appendix D contains the detailed discussion of each of the ten selected codes. Included in each discussion are such items which a potential user requires in determining whether the code is suitable for his applications. Appendix E contains brief summary information about each of the fifty-five codes. Included in the summaries are identification data, authors, pertinent references, and model type

  14. Facial pressure zones of an oronasal interface for noninvasive ventilation: a computer model analysis

    Directory of Open Access Journals (Sweden)

    Luana Souto Barros

    2014-12-01

    Full Text Available OBJECTIVE: To study the effects of an oronasal interface (OI for noninvasive ventilation, using a three-dimensional (3D computational model with the ability to simulate and evaluate the main pressure zones (PZs of the OI on the human face. METHODS: We used a 3D digital model of the human face, based on a pre-established geometric model. The model simulated soft tissues, skull, and nasal cartilage. The geometric model was obtained by 3D laser scanning and post-processed for use in the model created, with the objective of separating the cushion from the frame. A computer simulation was performed to determine the pressure required in order to create the facial PZs. We obtained descriptive graphical images of the PZs and their intensity. RESULTS: For the graphical analyses of each face-OI model pair and their respective evaluations, we ran 21 simulations. The computer model identified several high-impact PZs in the nasal bridge and paranasal regions. The variation in soft tissue depth had a direct impact on the amount of pressure applied (438-724 cmH2O. CONCLUSIONS: The computer simulation results indicate that, in patients submitted to noninvasive ventilation with an OI, the probability of skin lesion is higher in the nasal bridge and paranasal regions. This methodology could increase the applicability of biomechanical research on noninvasive ventilation interfaces, providing the information needed in order to choose the interface that best minimizes the risk of skin lesion.

  15. Evaluation of unsaturated-zone solute-transport models for studies of agricultural chemicals

    Science.gov (United States)

    Nolan, Bernard T.; Bayless, E. Randall; Green, Christopher T.; Garg, Sheena; Voss, Frank D.; Lampe, David C.; Barbash, Jack E.; Capel, Paul D.; Bekins, Barbara A.

    2005-01-01

    Seven unsaturated-zone solute-transport models were tested with two data sets to select models for use by the Agricultural Chemical Team of the U.S. Geological Survey's National Water-Quality Assessment Program. The data sets were from a bromide tracer test near Merced, California, and an atrazine study in the White River Basin, Indiana. In this study the models are designated either as complex or simple based on the water flux algorithm. The complex models, HYDRUS2D, LEACHP, RZWQM, and VS2DT, use Richards' equation to simulate water flux and are well suited to process understanding. The simple models, CALF, GLEAMS, and PRZM, use a tipping-bucket algorithm and are more amenable to extrapolation because they require fewer input parameters. The purpose of this report is not to endorse a particular model, but to describe useful features, potential capabilities, and possible limitations that emerged from working with the model input data sets. More rigorous assessment of model applicability involves proper calibration, which was beyond the scope of this study.

  16. Sequence2Vec: a novel embedding approach for modeling transcription factor binding affinity landscape.

    Science.gov (United States)

    Dai, Hanjun; Umarov, Ramzan; Kuwahara, Hiroyuki; Li, Yu; Song, Le; Gao, Xin

    2017-11-15

    An accurate characterization of transcription factor (TF)-DNA affinity landscape is crucial to a quantitative understanding of the molecular mechanisms underpinning endogenous gene regulation. While recent advances in biotechnology have brought the opportunity for building binding affinity prediction methods, the accurate characterization of TF-DNA binding affinity landscape still remains a challenging problem. Here we propose a novel sequence embedding approach for modeling the transcription factor binding affinity landscape. Our method represents DNA binding sequences as a hidden Markov model which captures both position specific information and long-range dependency in the sequence. A cornerstone of our method is a novel message passing-like embedding algorithm, called Sequence2Vec, which maps these hidden Markov models into a common nonlinear feature space and uses these embedded features to build a predictive model. Our method is a novel combination of the strength of probabilistic graphical models, feature space embedding and deep learning. We conducted comprehensive experiments on over 90 large-scale TF-DNA datasets which were measured by different high-throughput experimental technologies. Sequence2Vec outperforms alternative machine learning methods as well as the state-of-the-art binding affinity prediction methods. Our program is freely available at https://github.com/ramzan1990/sequence2vec. xin.gao@kaust.edu.sa or lsong@cc.gatech.edu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  17. Exploiting Non-sequence Data in Dynamic Model Learning

    Science.gov (United States)

    2013-10-01

    observed data, due to internal variation of the dynamic process of interest or measurement error. This problem arises in many time series modeling...estimated A was always nearly diagonal and exhibited dynamics as depicted in Figure 3.9. This is a concrete example of the identifiability issue...estimators of covariances. Most of these results originate from the idea of shrinkage estimators, which shrink the covariance matrix towards some target

  18. Intellectual Capital in Enterprises and a Model Study in an Industrial Zone

    Directory of Open Access Journals (Sweden)

    Selcuk Kendirli

    2014-09-01

    Full Text Available Intellectual Capital in Enterprises and a Model Study in an Industrial Zone   Abstract The study mainly consists of two parts. The first part includes theoretical knowledge, the second part includes application-oriented information. In the theoretical part of the study, intellectual capital and SMEs are emphasized in general. In the application-oriented part of the study, a field research will be done for Corum SME. In this study, the demographic structure of Corum SMEs, intellectual capital structure and financial performance of this structure will be evaluated. The resulting data will be analyzed in this context. The businesses operating in the Organized Industrial Zone of Corum and those matching the definition of SME will be considered within the research scope. Surveys will be applied by interviewers face to face and each survey will be evaluated individually. After the evaluation, a model will be proposed. The aim of our study is to investigate the relationship between components of intellectual capital in SMEs and business performance. For this reason, a survey will be conducted for SMEs. Since the results of the study will be shared with scientific circles and the public, they will prove to be guiding for Çorum SMEs.

  19. The three-zone composite productivity model for a multi-fractured horizontal shale gas well

    Science.gov (United States)

    Qi, Qian; Zhu, Weiyao

    2018-02-01

    Due to the nano-micro pore structures and the massive multi-stage multi-cluster hydraulic fracturing in shale gas reservoirs, the multi-scale seepage flows are much more complicated than in most other conventional reservoirs, and are crucial for the economic development of shale gas. In this study, a new multi-scale non-linear flow model was established and simplified, based on different diffusion and slip correction coefficients. Due to the fact that different flow laws existed between the fracture network and matrix zone, a three-zone composite model was proposed. Then, according to the conformal transformation combined with the law of equivalent percolation resistance, the productivity equation of a horizontal fractured well, with consideration given to diffusion, slip, desorption, and absorption, was built. Also, an analytic solution was derived, and the interference of the multi-cluster fractures was analyzed. The results indicated that the diffusion of the shale gas was mainly in the transition and Fick diffusion regions. The matrix permeability was found to be influenced by slippage and diffusion, which was determined by the pore pressure and diameter according to the Knudsen number. It was determined that, with the increased half-lengths of the fracture clusters, flow conductivity of the fractures, and permeability of the fracture network, the productivity of the fractured well also increased. Meanwhile, with the increased number of fractures, the distance between the fractures decreased, and the productivity slowly increased due to the mutual interfere of the fractures.

  20. Identification of mineralized zones in the Zardu area, Kushk SEDEX deposit (Central Iran, based on geological and multifractal modeling

    Directory of Open Access Journals (Sweden)

    Dahooei Ahmad Heidari

    2016-02-01

    Full Text Available The aim of this paper is to delineate the different lead–zinc mineralized zones in the Zardu area of the Kushk zinc–lead stratabound SEDEX deposit, Central Iran, through concentration–volume (C–V modeling of geological and lithogeochemical drillcore data. The geological model demonstrated that the massive sulfide and pyrite+dolomite ore types as main rock types hosting mineralization. The C–V fractal modeling used lead, zinc and iron geochemical data to outline four types of mineralized zones, which were then compared to the mineralized rock types identified in the geological model. ‘Enriched’ mineralized zones contain lead and zinc values higher than 6.93% and 19.95%, respectively, with iron values lower than 12.02%. Areas where lead and zinc values were higher than 1.58% and 5.88%, respectively, and iron grades lower than 22% are labelled “high-grade” mineralized zones, and these zones are linked to massive sulfide and pyrite+dolomite lithologies of the geological model. Weakly mineralized zones, labelled ‘low-grade’ in the C– V model have 0–0.63% lead, 0–3.16% zinc and > 30.19% iron, and are correlated to those lithological units labeled as gangue in the geological model, including shales and dolomites, pyritized dolomites. Finally, a log-ratio matrix was employed to validate the results obtained and check correlations between the geological and fractal modeling. Using this method, a high overall accuracy (OA was confirmed for the correlation between the enriched and high-grade mineralized zones and two lithological units — the massive sulfide and pyrite+dolomite ore types.

  1. Identification of mineralized zones in the Zardu area, Kushk SEDEX deposit (Central Iran), based on geological and multifractal modeling

    Science.gov (United States)

    Dahooei, Ahmad Heidari; Afzal, Peyman; Lotfi, Mohammad; Jafarirad, Alireza

    2016-02-01

    The aim of this paper is to delineate the different lead-zinc mineralized zones in the Zardu area of the Kushk zinc-lead stratabound SEDEX deposit, Central Iran, through concentration-volume (C-V) modeling of geological and lithogeochemical drillcore data. The geological model demonstrated that the massive sulfide and pyrite+dolomite ore types as main rock types hosting mineralization. The C-V fractal modeling used lead, zinc and iron geochemical data to outline four types of mineralized zones, which were then compared to the mineralized rock types identified in the geological model. `Enriched' mineralized zones contain lead and zinc values higher than 6.93% and 19.95%, respectively, with iron values lower than 12.02%. Areas where lead and zinc values were higher than 1.58% and 5.88%, respectively, and iron grades lower than 22% are labelled "high-grade" mineralized zones, and these zones are linked to massive sulfide and pyrite+dolomite lithologies of the geological model. Weakly mineralized zones, labelled `low-grade' in the C- V model have 0-0.63% lead, 0-3.16% zinc and > 30.19% iron, and are correlated to those lithological units labeled as gangue in the geological model, including shales and dolomites, pyritized dolomites. Finally, a log-ratio matrix was employed to validate the results obtained and check correlations between the geological and fractal modeling. Using this method, a high overall accuracy (OA) was confirmed for the correlation between the enriched and high-grade mineralized zones and two lithological units — the massive sulfide and pyrite+dolomite ore types.

  2. Combining next-generation sequencing and online databases for microsatellite development in non-model organisms.

    Science.gov (United States)

    Rico, Ciro; Normandeau, Eric; Dion-Côté, Anne-Marie; Rico, María Inés; Côté, Guillaume; Bernatchez, Louis

    2013-12-03

    Next-generation sequencing (NGS) is revolutionising marker development and the rapidly increasing amount of transcriptomes published across a wide variety of taxa is providing valuable sequence databases for the identification of genetic markers without the need to generate new sequences. Microsatellites are still the most important source of polymorphic markers in ecology and evolution. Motivated by our long-term interest in the adaptive radiation of a non-model species complex of whitefishes (Coregonus spp.), in this study, we focus on microsatellite characterisation and multiplex optimisation using transcriptome sequences generated by Illumina® and Roche-454, as well as online databases of Expressed Sequence Tags (EST) for the study of whitefish evolution and demographic history. We identified and optimised 40 polymorphic loci in multiplex PCR reactions and validated the robustness of our analyses by testing several population genetics and phylogeographic predictions using 494 fish from five lakes and 2 distinct ecotypes.

  3. Combining next-generation sequencing and online databases for microsatellite development in non-model organisms

    Science.gov (United States)

    Rico, Ciro; Normandeau, Eric; Dion-Côté, Anne-Marie; Rico, María Inés; Côté, Guillaume; Bernatchez, Louis

    2013-01-01

    Next-generation sequencing (NGS) is revolutionising marker development and the rapidly increasing amount of transcriptomes published across a wide variety of taxa is providing valuable sequence databases for the identification of genetic markers without the need to generate new sequences. Microsatellites are still the most important source of polymorphic markers in ecology and evolution. Motivated by our long-term interest in the adaptive radiation of a non-model species complex of whitefishes (Coregonus spp.), in this study, we focus on microsatellite characterisation and multiplex optimisation using transcriptome sequences generated by Illumina® and Roche-454, as well as online databases of Expressed Sequence Tags (EST) for the study of whitefish evolution and demographic history. We identified and optimised 40 polymorphic loci in multiplex PCR reactions and validated the robustness of our analyses by testing several population genetics and phylogeographic predictions using 494 fish from five lakes and 2 distinct ecotypes. PMID:24296905

  4. Dynamic fracture of adhesively bonded composite structures using cohesive zone models

    Science.gov (United States)

    Makhecha, Dhaval P.

    Using experimental data obtained from standard fracture test configurations, theoretical and numerical tools are developed to mathematically describe non-self-similar progression of cracks without specifying an initial crack. A cohesive-decohesive zone model, similar to the cohesive zone model known in the fracture mechanics literature as the Dugdale-Barenblatt model, is adopted to represent the degradation of the material ahead of the crack tip. This model unifies strength-based crack initiation and fracture-mechanics-based crack progression. The cohesive-decohesive zone model is implemented with an interfacial surface material that consists of an upper and a lower surface that are connected by a continuous distribution of normal and tangential nonlinear elastic springs that act to resist either Mode I opening, Mode II sliding, Mode III sliding, or a mixed anode. The initiation of fracture is determined by the interfacial strength and the progression of the crack is determined by the critical energy release rate. The adhesive is idealized with an interfacial surface material to predict interfacial fracture. The interfacial surface material is positioned within the bulk material to predict discrete cohesive cracks. The interfacial surface material is implemented through an interface element, which is incorporated in ABAQUS using the user defined element (UEL) option. A procedure is established to formulate a rate dependent model based on experiments carried out on compact tension test specimens. The rate dependent model is incorporated into the interface element approach to capture the unstable crack growth observed in experiments under quasi-static loading conditions. The compact tension test gives the variation of the fracture toughness with the rate of loading, this information is processed and a relationship between the fracture toughness and the rate of the opening displacement is established. The cohesive-decohesive zone model is implemented through a

  5. Analysis of vadose zone tritium transport from an underground storage tank release using numerical modeling and geostatistics

    Energy Technology Data Exchange (ETDEWEB)

    Lee, K.H.

    1997-09-01

    Numerical and geostatistical analyses show that the artificial smoothing effect of kriging removes high permeability flow paths from hydrogeologic data sets, reducing simulated contaminant transport rates in heterogeneous vadose zone systems. therefore, kriging alone is not recommended for estimating the spatial distribution of soil hydraulic properties for contaminant transport analysis at vadose zone sites. Vadose zone transport if modeled more effectively by combining kriging with stochastic simulation to better represent the high degree of spatial variability usually found in the hydraulic properties of field soils. However, kriging is a viable technique for estimating the initial mass distribution of contaminants in the subsurface.

  6. Modeling the Ductile Brittle Fracture Transition in Reactor Pressure Vessel Steels using a Cohesive Zone Model based approach

    Energy Technology Data Exchange (ETDEWEB)

    Pritam Chakraborty; S. Bulent Biner

    2013-10-01

    Fracture properties of Reactor Pressure Vessel (RPV) steels show large variations with changes in temperature and irradiation levels. Brittle behavior is observed at lower temperatures and/or higher irradiation levels whereas ductile mode of failure is predominant at higher temperatures and/or lower irradiation levels. In addition to such temperature and radiation dependent fracture behavior, significant scatter in fracture toughness has also been observed. As a consequence of such variability in fracture behavior, accurate estimates of fracture properties of RPV steels are of utmost importance for safe and reliable operation of reactor pressure vessels. A cohesive zone based approach is being pursued in the present study where an attempt is made to obtain a unified law capturing both stable crack growth (ductile fracture) and unstable failure (cleavage fracture). The parameters of the constitutive model are dependent on both temperature and failure probability. The effect of irradiation has not been considered in the present study. The use of such a cohesive zone based approach would allow the modeling of explicit crack growth at both stable and unstable regimes of fracture. Also it would provide the possibility to incorporate more physical lower length scale models to predict DBT. Such a multi-scale approach would significantly improve the predictive capabilities of the model, which is still largely empirical.

  7. Modelling the ductile brittle fracture transition in reactor pressure vessel steels using a cohesive zone model based approach

    International Nuclear Information System (INIS)

    Chakraborty, Pritam; Bulent Biner, S.

    2015-01-01

    Fracture properties of Reactor Pressure Vessel (RPV) steels show large variations with changes in temperature and irradiation levels. Brittle behaviour is observed at lower temperatures and/or higher irradiation levels whereas ductile mode of failure is predominant at higher temperatures and/or lower irradiation levels. In addition to such temperature and radiation dependent fracture behaviour, significant scatter in fracture toughness has also been observed. As a consequence of such variability in fracture behaviour, accurate estimates of fracture properties of RPV steels are of utmost importance for safe and reliable operation of reactor pressure vessels. A cohesive zone based approach is being pursued in the present study where an attempt is made to obtain a unified law capturing both stable crack growth (ductile fracture) and unstable failure (cleavage fracture). The parameters of the constitutive model are dependent on both temperature and failure probability. The effect of irradiation has not been considered in the present study. The use of such a cohesive zone based approach would allow the modelling of explicit crack growth at both stable and unstable regimes of fracture. Also it would provide the possibility to incorporate more physical lower length scale models to predict DBT. Such a multi-scale approach would significantly improve the predictive capabilities of the model, which is still largely empirical. (authors)

  8. Anatomy of the Andean subduction zone: three-dimensional density model upgraded and compared against global-scale models

    Science.gov (United States)

    Tassara, Andrés.; Echaurren, Andrés.

    2012-04-01

    We present an upgraded version of a previously published 3-D density model of the Andean subduction zone between 18°S and 45°S. This model consists of 3-D bodies of constant density, which geometry is constrained by independent seismic data and is triangulated from vertical cross-sections. These bodies define the first-order morphology and internal structure of the subducted Nazca slab and South American Plate. The new version of the density model results after forward modelling the Bouguer anomaly as computed from the most recent version of the Earth Gravitational Model (EGM2008). The 3-D density model incorporates new seismic information to better constrain the geometry of the subducted slab and continental Moho (CMH) and has a trench-parallel resolution doubling the resolution of the previous model. As an example of the potential utility of our model, we compare the geometry of the subducted slab and CMH against the corresponding global models Slab1.0 and Crust2.0, respectively. This exercise demonstrates that, although global models provide a good first-order representation of the slab and upper-plate crustal geometries, they show large discrepancies (up to ±40 km) with our upgraded model for some well-constrained areas. The geometries of the slab, lithosphere-asthenosphere boundary below the continent, CMH and intracrustal density discontinuity that we present here as Supporting Information can be used to study Andean geodynamic processes from a wide range of quantitative approaches.

  9. Modeling compositional dynamics based on GC and purine contents of protein-coding sequences

    KAUST Repository

    Zhang, Zhang

    2010-11-08

    Background: Understanding the compositional dynamics of genomes and their coding sequences is of great significance in gaining clues into molecular evolution and a large number of publically-available genome sequences have allowed us to quantitatively predict deviations of empirical data from their theoretical counterparts. However, the quantification of theoretical compositional variations for a wide diversity of genomes remains a major challenge.Results: To model the compositional dynamics of protein-coding sequences, we propose two simple models that take into account both mutation and selection effects, which act differently at the three codon positions, and use both GC and purine contents as compositional parameters. The two models concern the theoretical composition of nucleotides, codons, and amino acids, with no prerequisite of homologous sequences or their alignments. We evaluated the two models by quantifying theoretical compositions of a large collection of protein-coding sequences (including 46 of Archaea, 686 of Bacteria, and 826 of Eukarya), yielding consistent theoretical compositions across all the collected sequences.Conclusions: We show that the compositions of nucleotides, codons, and amino acids are largely determined by both GC and purine contents and suggest that deviations of the observed from the expected compositions may reflect compositional signatures that arise from a complex interplay between mutation and selection via DNA replication and repair mechanisms.Reviewers: This article was reviewed by Zhaolei Zhang (nominated by Mark Gerstein), Guruprasad Ananda (nominated by Kateryna Makova), and Daniel Haft. 2010 Zhang and Yu; licensee BioMed Central Ltd.

  10. Cohesive zone model of carbon nanotube-coated carbon fiber/polyester composites

    International Nuclear Information System (INIS)

    Agnihotri, Prabhat Kamal; Kar, Kamal K; Basu, Sumit

    2012-01-01

    It has been previously reported that the average properties of carbon nanotube-coated carbon fiber/polyester multiscale composites critically depend on the length and density of nanotubes on the fiber surface. In this paper the effect of nanotube length and density on the interfacial properties of the carbon nanotube-coated carbon fiber–polymer interface has been studied using shear lag and a cohesive zone model. The latter model incorporates frictional sliding after complete debonding between the fiber and matrix and has been developed to quantify the effect of nanotube coating on various interfacial characterizing parameters. Our numerical results indicate that fibers with an optimal coverage and length of nanotubes significantly increase the interfacial strength and friction between the fiber and polymer. However, they also embrittle the interface compared with bare fibers. (paper)

  11. Modeling solute transport through saturated zone ground water at 10 km scale: Example from the Yucca Mountain license application

    Science.gov (United States)

    Kelkar, Sharad; Ding, Mei; Chu, Shaoping; Robinson, Bruce A.; Arnold, Bill; Meijer, Arend; Eddebbarh, Al-Aziz

    2010-09-01

    This paper presents a study of solute transport through ground water in the saturated zone and the resulting breakthrough curves (BTCs), using a field-scale numerical model that incorporates the processes of advection, dispersion, matrix diffusion in fractured volcanic formations, sorption, and colloid-facilitated transport. Such BTCs at compliance boundaries are often used as performance measures for a site. The example considered here is that of the saturated zone study prepared for the Yucca Mountain license application. The saturated zone at this site occurs partly in volcanic, fractured rock formations and partly in alluvial formations. This paper presents a description of the site and the ground water flow model, the development of the conceptual model of transport, model uncertainties, model validation, and the influence of uncertainty in input parameters on the downstream BTCs at the Yucca Mountain site.

  12. Spatiotemporal evolution of slow slip events in a nonplanar fault model for northern Cascadia subduction zone

    Science.gov (United States)

    Li, Duo; Liu, Yajing

    2016-09-01

    Slow slip events (SSEs) are identified as the quasi-stable fault deformation in the deep transition zone from locked to continuous sliding in many subduction zones. In the well-instrumented Cascadia margin, a class of Mw6.0 slow slip events arise beneath Port Angeles every ˜14 months, as inferred from two decades of continuous geodetic monitoring. The along-strike bending of the incoming oceanic plate beneath north Washington is a unique geometric feature whose influence on slow slip processes is still unknown. Here we incorporate a realistic fault geometry of northern Cascadia in the framework of rate- and state-dependent friction law, to simulate the spatiotemporal evolution of slow slip events on a nonplanar subduction fault. The modeled SSEs capture the major characteristics revealed by GPS observations. The central 150 km long fault segment beneath Port Angeles acts as a repetitive slip patch, where SSEs appear every ˜1.5 years with a maximum slip of ˜2.5 cm. Two minor slip patches with smaller areas and cumulative slips straddle this central slip patch. The along-strike segmentation of slow slip is inversely related to the local fault dip and strike angles of the slow slip zone, suggesting strong geometrical control on the slow slip process. This correlation holds even after removing the effect of W/h∗, ratio between velocity-weakening SSE fault width and characteristic nucleation size. Besides the GPS-detectable fast-spreading phase, we find that each SSE cycle consists of deep pre-SSE preparation and post-SSE relaxation phases, which may be the driving mechanism for the deep tremor activity between major SSE episodes discovered in Cascadia.

  13. Assessment of risk factors in radionuclides pollution of coastal zone and river basins by numerical modelling

    International Nuclear Information System (INIS)

    Tsitskishvili, M.; Tsitskishvili, L.; Kordzakhia, G.; Diasamidze, R.; Shaptoshvili, A.; Valiaev, A.

    2006-01-01

    Full text: All types of industrial activities require the norms of protection, assessment of corresponding risks to preserve the pollution and degradation of corresponding areas. To make available the sustainable development of the country the risk assessment of possible accidents on the big enterprises is foreseen that provides preparedness of the country and possibility of the prevention measures and mitigation of the accidents. While big anthropogenic accidents in mountainous countries - the main paths for transportation of the pollution are the rivers and sea basins. Due to overpopulation of these areas assessment of the pollution risks are very important. For this aim the special deterministic models on the basis of passive admixture's turbulence diffusion equation is used. For numerical calculations Mc Kormack's predictor-corrector two steps scheme is used. The scheme is disintegrated, second order in space and time. Such scheme is established because the turbulent velocities very differ in horizontal and vertical directions and model allows implementing singular independent steps in different directions. Grid step for the model is 26.88 km in horizontal direction and 20 m m in vertical until 200 m. Time step is equal to 4 hours and computational time period - 4 months. Number of grid points is equal to 4983 for all calculation areas. Computations are carried out separately for big rivers basins as well as for Black and Caspian Seas water areas. The model calculations are made for cases with various locations of pollutant sources including accidental throws. For different realistic scenarios are calculated the concentrations of admixtures. The directions of their propagation are also determined. The risks are calculated in comparison with the Maximum Permissible Concentrations (MPC) of the pollutants according to achieved results. That gives possibility to define the most vulnerable areas in coastal zones. Realized methodology is verified by means of various

  14. The 2015 Gorkha (Nepal) earthquake sequence: I. Source modeling and deterministic 3D ground shaking

    Science.gov (United States)

    Wei, Shengji; Chen, Meng; Wang, Xin; Graves, Robert; Lindsey, Eric; Wang, Teng; Karakaş, Çağıl; Helmberger, Don

    2018-01-01

    To better quantify the relatively long period (earthquake sequence, we study the finite rupture processes and the associated 3D ground motion of the Mw7.8 mainshock and the Mw7.2 aftershock. The 3D synthetics are then used in the broadband ground shaking in Kathmandu with a hybrid approach, summarized in a companion paper (Chen and Wei, 2017, submitted together). We determined the coseismic rupture process of the mainshock by joint inversion of InSAR/SAR, GPS (static and high-rate), strong motion and teleseismic waveforms. Our inversion for the mainshock indicates unilateral rupture towards the ESE, with an average rupture speed of 3.0 km/s and a total duration of 60 s. Additionally, we find that the beginning part of the rupture (5-18 s) has about 40% longer rise time than the rest of the rupture, as well as slower rupture velocity. Our model shows two strong asperities occurring 24 s and 36 s after the origin and located 30 km to the northwest and northeast of the Kathmandu valley, respectively. In contrast, the Mw7.2 aftershock is more compact both in time and space, as revealed by joint inversion of teleseismic body waves and InSAR data. The different rupture features between the mainshock and the aftershock could be related to difference in fault zone structure. The mainshock and aftershock ground motions in the Kathmandu valley, recorded by both strong motion and high-rate GPS stations, exhibited strong amplification around 0.2 Hz. A simplified 3D basin model, calibrated by an Mw5.2 aftershock, can match the observed waveforms reasonably well at 0.3 Hz and lower frequency. The 3D simulations indicate that the basin structure trapped the wavefield and produced an extensive ground vibration. Our study suggests that the combination of rupture characteristics and propagational complexity are required to understand the ground shaking produced by hazardous earthquakes such as the Gorkha event.

  15. Conserved intergenic sequences revealed by CTAG-profiling in Salmonella: thermodynamic modeling for function prediction

    Science.gov (United States)

    Tang, Le; Zhu, Songling; Mastriani, Emilio; Fang, Xin; Zhou, Yu-Jie; Li, Yong-Guo; Johnston, Randal N.; Guo, Zheng; Liu, Gui-Rong; Liu, Shu-Lin

    2017-03-01

    Highly conserved short sequences help identify functional genomic regions and facilitate genomic annotation. We used Salmonella as the model to search the genome for evolutionarily conserved regions and focused on the tetranucleotide sequence CTAG for its potentially important functions. In Salmonella, CTAG is highly conserved across the lineages and large numbers of CTAG-containing short sequences fall in intergenic regions, strongly indicating their biological importance. Computer modeling demonstrated stable stem-loop structures in some of the CTAG-containing intergenic regions, and substitution of a nucleotide of the CTAG sequence would radically rearrange the free energy and disrupt the structure. The postulated degeneration of CTAG takes distinct patterns among Salmonella lineages and provides novel information about genomic divergence and evolution of these bacterial pathogens. Comparison of the vertically and horizontally transmitted genomic segments showed different CTAG distribution landscapes, with the genome amelioration process to remove CTAG taking place inward from both terminals of the horizontally acquired segment.

  16. Modelling The Transport Of Solutes And Colloids In The Grimsel Migration Shear Zone

    Energy Technology Data Exchange (ETDEWEB)

    Kosakowski, G.; Smith, P

    2005-02-01

    This report describes modelling of the transport of solutes and colloids in an experimental system comprising an artificial dipole flow field in a water-conducting shear zone at Nagra's Grimsel Test Site (GTS) in the central Swiss Alps. The modelling work forms part of the Colloid and Radionuclide Retardation Project (CRR), which includes a series of field transport experiments and a supporting laboratory programme, as well as modelling studies. Four independent groups representing different organisations or research institutes have conducted the modelling, with each group employing its own modelling approach or approaches. Only the work conducted at the Paul Scherrer Institute (PSI) is described in the present report. The modelling approaches used in the present study may not be directly applicable to safety assessment problems and the direct implications of the results of this study for safety assessment are limited. It can, however, be said that the study has demonstrated the high degree of mobility of bentonite and other colloids in a system that is at least in some ways comparable to those of interest in safety assessment, and has shown that bentonite colloids can at least potentially affect the transport of some safety relevant radionuclides over longer temporal and spatial scales than those addressed here. (author)

  17. Calibration of Yucca Mountain unsaturated zone flow and transport model using porewater chloride data

    International Nuclear Information System (INIS)

    Liu, Jianchun; Sonnenthal, Eric L.; Bodvarsson, Gudmundur S.

    2002-01-01

    In this study, porewater chloride data from Yucca Mountain, Nevada, are analyzed and modeled by 3-D chemical transport simulations and analytical methods. The simulation modeling approach is based on a continuum formulation of coupled multiphase fluid flow and tracer transport processes through fractured porous rock, using a dual-continuum concept. Infiltration-rate calibrations were using the pore water chloride data. Model results of chloride distributions were improved in matching the observed data with the calibrated infiltration rates. Statistical analyses of the frequency distribution for overall percolation fluxes and chloride concentration in the unsaturated zone system demonstrate that the use of the calibrated infiltration rates had insignificant effect on the distribution of simulated percolation fluxes but significantly changed the predicated distribution of simulated chloride concentrations. An analytical method was also applied to model transient chloride transport. The method was verified by 3-D simulation results as able to capture major chemical transient behavior and trends. Effects of lateral flow in the Paintbrush nonwelded unit on percolation fluxes and chloride distribution were studied by 3-D simulations with increased horizontal permeability. The combined results from these model calibrations furnish important information for the UZ model studies, contributing to performance assessment of the potential repository

  18. Predicting self-pollution inside school buses using a CFD and multi-zone coupled model

    Science.gov (United States)

    Li, Fei; Lee, Eon S.; Liu, Junjie; Zhu, Yifang

    2015-04-01

    The in-cabin environment of a school bus is important for children's health. The pollutants from a bus's own exhaust contribute to children's overall exposure to air pollutants inside the school bus cabin. In this study, we adapted a coupled model originally developed for indoor environment to determine the relative contribution of the bus own exhaust to the in-cabin pollutant concentrations. The coupled model uses CFD (computational fluent dynamics) model to simulate outside concentration and CONTAM (a multi-zone model) for inside the school bus. The model was validated with experimental data in the literature. Using the validated model, we analyzed the effects of vehicle speed and tailpipe location on self-pollution inside the bus cabin. We confirmed that the pollution released from the tailpipe can penetrate into the bus cabin through gaps in the back emergency door. We found the pollution concentration inside school buses was the highest when buses were driven at a medium speed. In addition, locating the tailpipe on the side, behind the rear axle resulted in less self-pollution since there is less time for the suction effect to take place. The developed theoretical framework can be generalized to study other types of buses. These findings can be used in developing policy recommendations for reducing human exposure to air pollution inside buses.

  19. Water-Level Data Analysis for the Saturated Zone Site-Scale Flow and Transport Model

    International Nuclear Information System (INIS)

    K. Rehfeldt

    2004-01-01

    This report is an updated analysis of water-level data performed to provide the ''Saturated Zone Site-Scale Flow Model'' (BSC 2004 [DIRS 170037]) (referred to as the saturated zone (SZ) site-scale flow model or site-scale SZ flow model in this report) with the configuration of the potentiometric surface, target water-level data, and hydraulic gradients for calibration of groundwater flow models. This report also contains an expanded discussion of uncertainty in the potentiometric-surface map. The analysis of the potentiometric data presented in Revision 00 of this report (USGS 2001 [DIRS 154625]) provides the configuration of the potentiometric surface, target heads, and hydraulic gradients for the calibration of the SZ site-scale flow model (BSC 2004 [DIRS 170037]). Revision 01 of this report (USGS 2004 [DIRS 168473]) used updated water-level data for selected wells through the year 2000 as the basis for estimating water-level altitudes and the potentiometric surface in the SZ site-scale flow and transport model domain based on an alternative interpretation of perched water conditions. That revision developed computer files containing: Water-level data within the model area (DTN: GS010908312332.002); A table of known vertical head differences (DTN: GS010908312332.003); and A potentiometric-surface map (DTN: GS010608312332.001) using an alternative concept from that presented by USGS (2001 [DIRS 154625]) for the area north of Yucca Mountain. The updated water-level data presented in USGS (2004 [DIRS 168473]) include data obtained from the Nye County Early Warning Drilling Program (EWDP) Phases I and II and data from Borehole USW WT-24. This document is based on Revision 01 (USGS 2004 [DIRS 168473]) and expands the discussion of uncertainty in the potentiometric-surface map. This uncertainty assessment includes an analysis of the impact of more recent water-level data and the impact of adding data from the EWDP Phases III and IV wells. In addition to being utilized

  20. Multiple-Use Zoning Model for Private Forest Owners in Agricultural Landscapes: A Case Study

    Directory of Open Access Journals (Sweden)

    Benoit Truax

    2015-10-01

    Full Text Available Many small-scale private forest owners increasingly focus their management on amenity functions rather than on wood production functions. This paradigm shift is an opportunity to implement novel forestry management approaches, such as forested land zoning. Forest zoning consists in separating the land base in three zones that have different management objectives: (1 conservation zones; (2 ecosystem management zones; and (3 intensive production zones, which locally increase productivity, as a trade off to increase the land area dedicated to conservation and ecosystem management. We evaluate the ecological feasibility of implementing forest zoning on a private property (216 ha at St-Benoît-du-Lac, Québec (Canada characterised by agricultural and forest land uses. As a basis for delineating conservation and ecosystem management zones, historical and contemporary data and facts on forest composition and dynamics were reviewed, followed by a detailed forest vegetation analysis of forest communities. Delineating intensive production zones was straightforward, as fertile agricultural field margins located downslope were used to establish multifunctional hybrid poplar buffers. At St-Benoît-du-Lac, a realistic zoning scenario would consist of (1 conservation zones covering 25% of the forestland (37 ha; (2 ecosystem management zones covering 75% of the forestland (113 ha, including restoration zones on 24 ha; and (3 intensive production zones on 2.8 ha. Based on a yield projection of 13 t/ha/year for hybrid poplars, only 5.6% of agricultural field areas would need to be converted into agroforestry systems to allow for the loss of wood production in a conservation zone of 37 ha of forest. Ecosystem services provision following the implementation of zoning would include increased habitat quality, biodiversity protection and enhancement (by restoration of some tree species, carbon storage, non-point source aquatic pollution control, local biomass

  1. Protein secondary structure prediction for a single-sequence using hidden semi-Markov models

    Directory of Open Access Journals (Sweden)

    Borodovsky Mark

    2006-03-01

    Full Text Available Abstract Background The accuracy of protein secondary structure prediction has been improving steadily towards the 88% estimated theoretical limit. There are two types of prediction algorithms: Single-sequence prediction algorithms imply that information about other (homologous proteins is not available, while algorithms of the second type imply that information about homologous proteins is available, and use it intensively. The single-sequence algorithms could make an important contribution to studies of proteins with no detected homologs, however the accuracy of protein secondary structure prediction from a single-sequence is not as high as when the additional evolutionary information is present. Results In this paper, we further refine and extend the hidden semi-Markov model (HSMM initially considered in the BSPSS algorithm. We introduce an improved residue dependency model by considering the patterns of statistically significant amino acid correlation at structural segment borders. We also derive models that specialize on different sections of the dependency structure and incorporate them into HSMM. In addition, we implement an iterative training method to refine estimates of HSMM parameters. The three-state-per-residue accuracy and other accuracy measures of the new method, IPSSP, are shown to be comparable or better than ones for BSPSS as well as for PSIPRED, tested under the single-sequence condition. Conclusions We have shown that new dependency models and training methods bring further improvements to single-sequence protein secondary structure prediction. The results are obtained under cross-validation conditions using a dataset with no pair of sequences having significant sequence similarity. As new sequences are added to the database it is possible to augment the dependency structure and obtain even higher accuracy. Current and future advances should contribute to the improvement of function prediction for orphan proteins inscrutable

  2. Existing and potential infection risk zones of yellow fever worldwide: a modelling analysis

    Directory of Open Access Journals (Sweden)

    Freya M Shearer, BSc

    2018-03-01

    Full Text Available Summary: Background: Yellow fever cases are under-reported and the exact distribution of the disease is unknown. An effective vaccine is available but more information is needed about which populations within risk zones should be targeted to implement interventions. Substantial outbreaks of yellow fever in Angola, Democratic Republic of the Congo, and Brazil, coupled with the global expansion of the range of its main urban vector, Aedes aegypti, suggest that yellow fever has the propensity to spread further internationally. The aim of this study was to estimate the disease's contemporary distribution and potential for spread into new areas to help inform optimal control and prevention strategies. Methods: We assembled 1155 geographical records of yellow fever virus infection in people from 1970 to 2016. We used a Poisson point process boosted regression tree model that explicitly incorporated environmental and biological explanatory covariates, vaccination coverage, and spatial variability in disease reporting rates to predict the relative risk of apparent yellow fever virus infection at a 5 × 5 km resolution across all risk zones (47 countries across the Americas and Africa. We also used the fitted model to predict the receptivity of areas outside at-risk zones to the introduction or reintroduction of yellow fever transmission. By use of previously published estimates of annual national case numbers, we used the model to map subnational variation in incidence of yellow fever across at-risk countries and to estimate the number of cases averted by vaccination worldwide. Findings: Substantial international and subnational spatial variation exists in relative risk and incidence of yellow fever as well as varied success of vaccination in reducing incidence in several high-risk regions, including Brazil, Cameroon, and Togo. Areas with the highest predicted average annual case numbers include large parts of Nigeria, the Democratic Republic of the

  3. Existing and potential infection risk zones of yellow fever worldwide: a modelling analysis.

    Science.gov (United States)

    Shearer, Freya M; Longbottom, Joshua; Browne, Annie J; Pigott, David M; Brady, Oliver J; Kraemer, Moritz U G; Marinho, Fatima; Yactayo, Sergio; de Araújo, Valdelaine E M; da Nóbrega, Aglaêr A; Fullman, Nancy; Ray, Sarah E; Mosser, Jonathan F; Stanaway, Jeffrey D; Lim, Stephen S; Reiner, Robert C; Moyes, Catherine L; Hay, Simon I; Golding, Nick

    2018-03-01

    Yellow fever cases are under-reported and the exact distribution of the disease is unknown. An effective vaccine is available but more information is needed about which populations within risk zones should be targeted to implement interventions. Substantial outbreaks of yellow fever in Angola, Democratic Republic of the Congo, and Brazil, coupled with the global expansion of the range of its main urban vector, Aedes aegypti, suggest that yellow fever has the propensity to spread further internationally. The aim of this study was to estimate the disease's contemporary distribution and potential for spread into new areas to help inform optimal control and prevention strategies. We assembled 1155 geographical records of yellow fever virus infection in people from 1970 to 2016. We used a Poisson point process boosted regression tree model that explicitly incorporated environmental and biological explanatory covariates, vaccination coverage, and spatial variability in disease reporting rates to predict the relative risk of apparent yellow fever virus infection at a 5 × 5 km resolution across all risk zones (47 countries across the Americas and Africa). We also used the fitted model to predict the receptivity of areas outside at-risk zones to the introduction or reintroduction of yellow fever transmission. By use of previously published estimates of annual national case numbers, we used the model to map subnational variation in incidence of yellow fever across at-risk countries and to estimate the number of cases averted by vaccination worldwide. Substantial international and subnational spatial variation exists in relative risk and incidence of yellow fever as well as varied success of vaccination in reducing incidence in several high-risk regions, including Brazil, Cameroon, and Togo. Areas with the highest predicted average annual case numbers include large parts of Nigeria, the Democratic Republic of the Congo, and South Sudan, where vaccination coverage in 2016

  4. Strain localisation in mechanically layered rocks beneath detachment zones: insights from numerical modelling

    Directory of Open Access Journals (Sweden)

    L. Le Pourhiet

    2013-04-01

    Full Text Available We have designed a series of fully dynamic numerical simulations aimed at assessing how the orientation of mechanical layering in rocks controls the orientation of shear bands and the depth of penetration of strain in the footwall of detachment zones. Two parametric studies are presented. In the first one, the influence of stratification orientation on the occurrence and mode of strain localisation is tested by varying initial dip of inherited layering in the footwall with regard to the orientation of simple shear applied at the rigid boundary simulating a rigid hanging wall, all scaling and rheological parameter kept constant. It appears that when Mohr–Coulomb plasticity is being used, shear bands are found to localise only when the layering is being stretched. This corresponds to early deformational stages for inital layering dipping in the same direction as the shear is applied, and to later stages for intial layering dipping towards the opposite direction of shear. In all the cases, localisation of the strain after only γ=1 requires plastic yielding to be activated in the strong layer. The second parametric study shows that results are length-scale independent and that orientation of shear bands is not sensitive to the viscosity contrast or the strain rate. However, decreasing or increasing strain rate is shown to reduce the capacity of the shear zone to localise strain. In the later case, the strain pattern resembles a mylonitic band but the rheology is shown to be effectively linear. Based on the results, a conceptual model for strain localisation under detachment faults is presented. In the early stages, strain localisation occurs at slow rates by viscous shear instabilities but as the layered media is exhumed, the temperature drops and the strong layers start yielding plastically, forming shear bands and localising strain at the top of the shear zone. Once strain localisation has occured, the deformation in the shear band becomes

  5. Modeling and zoning of land subsidence in the southwest of Tehran using artificial neural networks

    Directory of Open Access Journals (Sweden)

    M. Pishro

    2016-07-01

    Full Text Available The earth's surface, due to its natural conditions and its structure is always changing and reshaping. One of the created deformations is the land subsidence. This is the most dangerous events which can be seen in most urban areas especially in the agricultural plains today. This study aims at zoning land subsidence and recognition of geometrical factors in southwest of Tehran. To estimate and predict land subsidence, all the effective subsidence factors were identified. Among the factors, nine most important factors including, downfall of groundwater, thickness of clay, depth of groundwater, annual discharge of water from wells, the distance of well to each other, slop, elevation, land use and geology were evaluated. Ultimately, three variables were selected as the most important variables. For modeling and zoning these factors, artificial neural network using Matlab software and Arc-GIS software for creating primary layers were used. The results indicate that the main cause of subsidence is excessive removal of underground water resources. Since the use of water resources in agriculture is accounted for the highest percentage of consumption and also because a large part of the study area have an agriculture land use, therefore the underground water drop and agricultural land uses are the most susceptible areas of land subsidence occurrence.

  6. A standardised graphic method for describing data privacy frameworks in primary care research using a flexible zone model.

    Science.gov (United States)

    Kuchinke, Wolfgang; Ohmann, Christian; Verheij, Robert A; van Veen, Evert-Ben; Arvanitis, Theodoros N; Taweel, Adel; Delaney, Brendan C

    2014-12-01

    To develop a model describing core concepts and principles of data flow, data privacy and confidentiality, in a simple and flexible way, using concise process descriptions and a diagrammatic notation applied to research workflow processes. The model should help to generate robust data privacy frameworks for research done with patient data. Based on an exploration of EU legal requirements for data protection and privacy, data access policies, and existing privacy frameworks of research projects, basic concepts and common processes were extracted, described and incorporated into a model with a formal graphical representation and a standardised notation. The Unified Modelling Language (UML) notation was enriched by workflow and own symbols to enable the representation of extended data flow requirements, data privacy and data security requirements, privacy enhancing techniques (PET) and to allow privacy threat analysis for research scenarios. Our model is built upon the concept of three privacy zones (Care Zone, Non-care Zone and Research Zone) containing databases, data transformation operators, such as data linkers and privacy filters. Using these model components, a risk gradient for moving data from a zone of high risk for patient identification to a zone of low risk can be described. The model was applied to the analysis of data flows in several general clinical research use cases and two research scenarios from the TRANSFoRm project (e.g., finding patients for clinical research and linkage of databases). The model was validated by representing research done with the NIVEL Primary Care Database in the Netherlands. The model allows analysis of data privacy and confidentiality issues for research with patient data in a structured way and provides a framework to specify a privacy compliant data flow, to communicate privacy requirements and to identify weak points for an adequate implementation of data privacy. Copyright © 2014 Elsevier Ireland Ltd. All rights

  7. A Developmental Sequence Model to University Adjustment of International Undergraduate Students

    Science.gov (United States)

    Chavoshi, Saeid; Wintre, Maxine Gallander; Dentakos, Stella; Wright, Lorna

    2017-01-01

    The current study proposes a Developmental Sequence Model to University Adjustment and uses a multifaceted measure, including academic, social and psychological adjustment, to examine factors predictive of undergraduate international student adjustment. A hierarchic regression model is carried out on the Student Adaptation to College Questionnaire…

  8. Modeling and optimization of a sequence of chemical cleaning cycles in dead-end ultrafiltration

    NARCIS (Netherlands)

    Zondervan, Edwin; Betlem, Ben H.L.; Blankert, Bastiaan; Roffel, Brian

    2008-01-01

    In this paper a chemical cleaning sequence model is proposed that can be used to predict the fouling status of a membrane during multiple chemical cleaning cycles. The proposed model is used to minimize the overall operating costs – based on chemicals consumption, energy consumption and investment

  9. Modeling Soft Institutional Change and the Improvement of Freshwater Governance in the Coastal Zone

    Directory of Open Access Journals (Sweden)

    Rémi Mongruel

    2011-12-01

    Full Text Available The contribution of soft institutional change to improve freshwater governance in the coastal zone will be examined. Freshwater management seeks to reduce losses due to overexploitation of the common-pool resources provided by river catchments and their associated ecosystems. Due to the complexity of the governance system, improving the performance of one coastal social-ecological system means searching for the appropriate "soft" institutional change. In the Pertuis Charentais region, increasing scarcity of freshwater in summer threatens the health of the coastal ecosystem and the sustainability of human activities, which depend on the use of natural resources. The allocation of freshwater among competing uses or concerns is a core issue for integrated coastal zone management. To address this issue, we have constructed an analytical framework that combines the ecosystem services approach with the institutional analysis of common-pool resources, and have developed an integrated simulation tool based on the system dynamic modeling approach. Freshwater scarcity generates three kinds of user conflict: (1 conflict between two extractive uses of freshwater (irrigation and drinking water, (2 conflicts between extractive uses (provisioning services and other services (support, regulatory, and cultural provided by freshwater, and (3 competition within a given activity sector (agriculture or shellfish farming. Participation by local managers led to the identification of realistic soft institutional changes that might mitigate conflicts and improve the governance system. These possible institutional changes were then integrated as fixed exogenous parameters in the simulation model. The simulated scenarios suggest that innovative collective arrangements involving farmers could be an alternative to other more restrictive top-down measures. This participatory experiment also illustrates the potential of social-ecological modeling for exploring acceptable new

  10. Probabilistic Modeling and Evaluation of Surf Zone Injury Occurrence along the Delaware Coast

    Science.gov (United States)

    Doelp, M.; Puleo, J. A.

    2017-12-01

    Beebe Healthcare in Lewes, DE collected along the DE coast surf zone injury (SZI) data for seven summer seasons from 2010 through 2016. Data include, but are not limited to, time of injury, gender, age, and activity. Over 2000 injuries were recorded over the seven year period, including 116 spinal injuries and three fatalities. These injuries are predominantly wave related incidents including wading (41%), bodysurfing (26%), and body-boarding (20%). Despite the large number of injuries, beach associated hazards do not receive the same level of awareness that rip currents receive. Injury population statistics revealed those between the ages of 11 and 15 years old suffered the greatest proportion of injuries (18.8%). Male water users were twice as likely to sustain injury as their female counterparts. Also, non-locals were roughly six times more likely to sustain injury than locals. In 2016, five or more injuries occurred for 18.5% of the days sampled, and no injuries occurred for 31.4% of the sample days. The episodic nature of injury occurrence and population statistics indicate the importance of environmental conditions and human behavior on surf zone injuries. Higher order statistics are necessary to effectively assess SZI cause and likelihood of occurrence on a particular day. A Bayesian network using Netica software (Norsys) was constructed to model SZI and predict changes in injury likelihood on an hourly basis. The network incorporates environmental data collected by weather stations, NDBC buoy #44009, USACE buoy at Bethany Beach, and by researcher personnel on the beach. The Bayesian model includes prior (e.g., historic) information to infer relationships between provided parameters. Sensitivity analysis determined the most influential variables to injury likelihood are population, water temperature, nearshore wave height, beach slope, and the day of the week. Forecasting during the 2017 summer season will test model ability to predict injury likelihood.

  11. Non-invasive monitoring and modelling of the root active zones: progresses, caveats and outlook.

    Science.gov (United States)

    Cassiani, G.; Putti, M.; Boaga, J.; Busato, L.; Vanella, D.; Consoli, S.

    2016-12-01

    Roots play a fundamental role in soil-plant-atmosphere interactions as they not only control water and nutrient exchanges necessary for plant sustenance, but also largely contribute, through the plant system, to the mass and energy exchanges between soil and atmosphere. Therefore understanding root zone processes is of major importance not only for crop management but also for wider scale catchment and global issues. Geophysical methods can greatly contribute to imaging the root zone geometry and processes, provided that high-resolution, time-lapse measurements are set up, and provided that the survey design takes into due considerations the expected processes to be imaged. In this respect, modelling and monitoring go hand in hand not only a-posteriori to try and interpret the data, but also a-priori in the attempt to optimise monitoring strategies. In this work we present a few case studies concerning root monitoring using ERT with the support of ancillary data of hydrological and physiological nature. Different degrees of integration with modelling will be presented, with the aim of showing how a full Data Assimilation scheme can be built. In addition, the results will help address fundamental questions such as: (a) is root growth controlled by optimality principles under the constraints posed by soil hydraulic and mechanical properties, by water and nutrient availability and by plant competition? (b) is the optimality above also controlling the dynamic processing of root adaptation to changing constraints? (c) to what extent can these processes of soil-plant interaction be monitored in controlled conditions as well as in true-life environments? These questions, and the availability of ever advancing modelling and monitoring capabilities, are likely to develop into a growing and exciting field of research.

  12. Model-free aftershock forecasts constructed from similar sequences in the past

    Science.gov (United States)

    van der Elst, N.; Page, M. T.

    2017-12-01

    The basic premise behind aftershock forecasting is that sequences in the future will be similar to those in the past. Forecast models typically use empirically tuned parametric distributions to approximate past sequences, and project those distributions into the future to make a forecast. While parametric models do a good job of describing average outcomes, they are not explicitly designed to capture the full range of variability between sequences, and can suffer from over-tuning of the parameters. In particular, parametric forecasts may produce a high rate of "surprises" - sequences that land outside the forecast range. Here we present a non-parametric forecast method that cuts out the parametric "middleman" between training data and forecast. The method is based on finding past sequences that are similar to the target sequence, and evaluating their outcomes. We quantify similarity as the Poisson probability that the observed event count in a past sequence reflects the same underlying intensity as the observed event count in the target sequence. Event counts are defined in terms of differential magnitude relative to the mainshock. The forecast is then constructed from the distribution of past sequences outcomes, weighted by their similarity. We compare the similarity forecast with the Reasenberg and Jones (RJ95) method, for a set of 2807 global aftershock sequences of M≥6 mainshocks. We implement a sequence-specific RJ95 forecast using a global average prior and Bayesian updating, but do not propagate epistemic uncertainty. The RJ95 forecast is somewhat more precise than the similarity forecast: 90% of observed sequences fall within a factor of two of the median RJ95 forecast value, whereas the fraction is 85% for the similarity forecast. However, the surprise rate is much higher for the RJ95 forecast; 10% of observed sequences fall in the upper 2.5% of the (Poissonian) forecast range. The surprise rate is less than 3% for the similarity forecast. The similarity

  13. Analysis of the 2012 Ahar-Varzeghan (Iran) seismic sequence: Insights from statistical and stress transfer modeling

    Science.gov (United States)

    Yazdi, Pouye; Santoyo, Miguel Angel; Gaspar-Escribano, Jorge M.

    2018-02-01

    The 2012 Ahar-Varzeghan (Northwestern Iran) earthquake doublet and its following seismic sequence are analyzed in this paper. First, it is examined the time-varying statistical characteristics of seismic activity since the occurrence of the doublet (two large events with Mw = 6.4 and 6.2) that initiated the sequence on 11 August 2012. A power law magnitude-frequency distribution (1.9 ≤ M ≤ 6.4) is obtained, with relatively low b-values for the complete series indicating the existence of relatively large magnitudes and high-stress level in the area. The Omori-Utsu model of the aftershock population decay with time shows a moderate decrease in activity rate. An epidemic-type aftershock sequence model that separates background seismicity from triggered aftershocks is then used to describe the temporal evolution of the seismicity during the period following the occurrence of the doublet. Results for the entire series (above cutoff magnitude Mc = 1.9) indicate a relatively low productivity related to the earthquake-earthquake triggering. Indeed, the majority of these events seems to be generated by underlying transient or aseismic processes, which might be added to the tectonic loading stress. The proportion of aftershock events significantly increases when the analysis is limited to larger events (M ≥ 3.0) suggesting that the triggered large aftershocks entail a substantial portion of the energy released. In order to analyze the spatial distribution of the sequence, new source models are proposed for the two main shocks. For the first shock, the coseismic slip distribution is constrained by the available data on surface ruptures. A Coulomb failure stress transfer model produced by the first event along optimally-oriented planes allows identifying the areas with positive stress loads where the rupture of the subsequent aftershocks may have occurred. The positive Δ CFS areas are compared for two depth intervals: 3-10 km and 15-22 km overlapping over 350 relocated

  14. Precision Measurements of the Cluster Red Sequence using an Error Corrected Gaussian Mixture Model

    Energy Technology Data Exchange (ETDEWEB)

    Hao, Jiangang; /Fermilab /Michigan U.; Koester, Benjamin P.; /Chicago U.; Mckay, Timothy A.; /Michigan U.; Rykoff, Eli S.; /UC, Santa Barbara; Rozo, Eduardo; /Ohio State U.; Evrard, August; /Michigan U.; Annis, James; /Fermilab; Becker, Matthew; /Chicago U.; Busha, Michael; /KIPAC, Menlo Park /SLAC; Gerdes, David; /Michigan U.; Johnston, David E.; /Northwestern U. /Brookhaven

    2009-07-01

    The red sequence is an important feature of galaxy clusters and plays a crucial role in optical cluster detection. Measurement of the slope and scatter of the red sequence are affected both by selection of red sequence galaxies and measurement errors. In this paper, we describe a new error corrected Gaussian Mixture Model for red sequence galaxy identification. Using this technique, we can remove the effects of measurement error and extract unbiased information about the intrinsic properties of the red sequence. We use this method to select red sequence galaxies in each of the 13,823 clusters in the maxBCG catalog, and measure the red sequence ridgeline location and scatter of each. These measurements provide precise constraints on the variation of the average red galaxy populations in the observed frame with redshift. We find that the scatter of the red sequence ridgeline increases mildly with redshift, and that the slope decreases with redshift. We also observe that the slope does not strongly depend on cluster richness. Using similar methods, we show that this behavior is mirrored in a spectroscopic sample of field galaxies, further emphasizing that ridgeline properties are independent of environment. These precise measurements serve as an important observational check on simulations and mock galaxy catalogs. The observed trends in the slope and scatter of the red sequence ridgeline with redshift are clues to possible intrinsic evolution of the cluster red-sequence itself. Most importantly, the methods presented in this work lay the groundwork for further improvements in optically-based cluster cosmology.

  15. Prediction and assimilation of surf-zone processes using a Bayesian network: Part II: Inverse models

    Science.gov (United States)

    Plant, Nathaniel G.; Holland, K. Todd

    2011-01-01

    A Bayesian network model has been developed to simulate a relatively simple problem of wave propagation in the surf zone (detailed in Part I). Here, we demonstrate that this Bayesian model can provide both inverse modeling and data-assimilation solutions for predicting offshore wave heights and depth estimates given limited wave-height and depth information from an onshore location. The inverse method is extended to allow data assimilation using observational inputs that are not compatible with deterministic solutions of the problem. These inputs include sand bar positions (instead of bathymetry) and estimates of the intensity of wave breaking (instead of wave-height observations). Our results indicate that wave breaking information is essential to reduce prediction errors. In many practical situations, this information could be provided from a shore-based observer or from remote-sensing systems. We show that various combinations of the assimilated inputs significantly reduce the uncertainty in the estimates of water depths and wave heights in the model domain. Application of the Bayesian network model to new field data demonstrated significant predictive skill (R2 = 0.7) for the inverse estimate of a month-long time series of offshore wave heights. The Bayesian inverse results include uncertainty estimates that were shown to be most accurate when given uncertainty in the inputs (e.g., depth and tuning parameters). Furthermore, the inverse modeling was extended to directly estimate tuning parameters associated with the underlying wave-process model. The inverse estimates of the model parameters not only showed an offshore wave height dependence consistent with results of previous studies but the uncertainty estimates of the tuning parameters also explain previously reported variations in the model parameters.

  16. Dynamic rupture models of subduction zone earthquakes with off-fault plasticity

    Science.gov (United States)

    Wollherr, S.; van Zelst, I.; Gabriel, A. A.; van Dinther, Y.; Madden, E. H.; Ulrich, T.

    2017-12-01

    Modeling tsunami-genesis based on purely elastic seafloor displacement typically underpredicts tsunami sizes. Dynamic rupture simulations allow to analyse whether plastic energy dissipation is a missing rheological component by capturing the complex interplay of the rupture front, emitted seismic waves and the free surface in the accretionary prism. Strike-slip models with off-fault plasticity suggest decreasing rupture speed and extensive plastic yielding mainly at shallow depths. For simplified subduction geometries inelastic deformation on the verge of Coulomb failure may enhance vertical displacement, which in turn favors the generation of large tsunamis (Ma, 2012). However, constraining appropriate initial conditions in terms of fault geometry, initial fault stress and strength remains challenging. Here, we present dynamic rupture models of subduction zones constrained by long-term seismo-thermo-mechanical modeling (STM) without any a priori assumption of regions of failure. The STM model provides self-consistent slab geometries, as well as stress and strength initial conditions which evolve in response to tectonic stresses, temperature, gravity, plasticity and pressure (van Dinther et al. 2013). Coseismic slip and coupled seismic wave propagation is modelled using the software package SeisSol (www.seissol.org), suited for complex fault zone structures and topography/bathymetry. SeisSol allows for local time-stepping, which drastically reduces the time-to-solution (Uphoff et al., 2017). This is particularly important in large-scale scenarios resolving small-scale features, such as the shallow angle between the megathrust fault and the free surface. Our dynamic rupture model uses a Drucker-Prager plastic yield criterion and accounts for thermal pressurization around the fault mimicking the effect of pore pressure changes due to frictional heating. We first analyze the influence of this rheology on rupture dynamics and tsunamigenic properties, i.e. seafloor

  17. An Updated Site Scale Saturated Zone Ground Water Transport Model for Yucca Mountain

    Science.gov (United States)

    Kelkar, S.; Ding, M.; Chu, S.; Robinson, B.; Arnold, B.; Meijer, A.

    2007-12-01

    The Yucca Mountain site scale saturated zone transport model has been revised to incorporate the updated flow model based on a hydrogeologic framework model using the latest lithology data, increased grid resolution that better resolves the geology within the model domain, updated sorption coefficient (Kd ) distributions for radionuclides of interest, and updated retardation factor distributions. The resulting numerical transport model is used for performance assessment predictions of radionuclide transport and to guide future data collection and modeling activities. The transport model results are validated by comparing the model transport pathways with those derived from geochemical data, and by comparing the transit times from the repository footprint to the compliance boundary at the accessible environment with those derived from 14C-based age estimates. The transport model includes the processes of advection, dispersion, fracture flow, matrix diffusion in fractured volcanic formations, sorption, and colloid-facilitated transport. The transport of sorbing radionuclides in the aqueous phase is modeled as a linear, equilibrium process using the Kd model. The colloid-facilitated transport of radionuclides is modeled using two approaches: the colloids with irreversibly embedded radionuclides undergo reversible filtration only, while the migration of radionuclides that reversibly sorb to colloids is modeled with modified values for sorption coefficients and matrix diffusion coefficients. The base case results predict a transport time of 810 years for the breakthrough of half of the mass of a nonreactive radionuclide originating at a point within the footprint of the repository to the compliance boundary of the accessible environment at a distance of ~18 km downstream. The transport time is quite sensitive to the specific discharge through the model, varying between 31 to 52840 years for a range of specific discharge multiplier values between 0.1 to 8.9. Other

  18. Using single cell sequencing data to model the evolutionary history of a tumor.

    Science.gov (United States)

    Kim, Kyung In; Simon, Richard

    2014-01-24

    The introduction of next-generation sequencing (NGS) technology has made it possible to detect genomic alterations within tumor cells on a large scale. However, most applications of NGS show the genetic content of mixtures of cells. Recently developed single cell sequencing technology can identify variation within a single cell. Characterization of multiple samples from a tumor using single cell sequencing can potentially provide information on the evolutionary history of that tumor. This may facilitate understanding how key mutations accumulate and evolve in lineages to form a heterogeneous tumor. We provide a computational method to infer an evolutionary mutation tree based on single cell sequencing data. Our approach differs from traditional phylogenetic tree approaches in that our mutation tree directly describes temporal order relationships among mutation sites. Our method also accommodates sequencing errors. Furthermore, we provide a method for estimating the proportion of time from the earliest mutation event of the sample to the most recent common ancestor of the sample of cells. Finally, we discuss current limitations on modeling with single cell sequencing data and possible improvements under those limitations. Inferring the temporal ordering of mutational sites using current single cell sequencing data is a challenge. Our proposed method may help elucidate relationships among key mutations and their role in tumor progression.

  19. Global patterns of dissolved silica export to the coastal zone: Results from a spatially explicit global model

    NARCIS (Netherlands)

    Beusen, A.H.W.; Bouwman, A.F.; Dürr, H.H.; Dekkers, A.L.M.; Hartmann, J.

    2009-01-01

    We present a multiple linear regression model developed for describing global river export of dissolved SiO2 (DSi) to coastal zones. The model, with river basin spatial scale and an annual temporal scale, is based on four variables with a significant influence on DSi yields (soil bulk density,

  20. The softened heat-affected zone in resistance spot welded tailor hardened boron steel: a material model for crash simulation

    NARCIS (Netherlands)

    Eller, Tom; Greve, L; Andres, M.T.; Medricky, M; Geijselaers, Hubertus J.M.; Meinders, Vincent T.; van den Boogaard, Antonius H.

    2016-01-01

    A hardness-based model for tailor hardened boron steel is presented that takes into account the softened heat-affected zone of resistance spot welds. The computational model is designed for crashworthiness simulation of fully and partially hardened components obtained by tailored tooling. Five

  1. Sequence2Vec: A novel embedding approach for modeling transcription factor binding affinity landscape

    KAUST Repository

    Dai, Hanjun

    2017-07-26

    Motivation: An accurate characterization of transcription factor (TF)-DNA affinity landscape is crucial to a quantitative understanding of the molecular mechanisms underpinning endogenous gene regulation. While recent advances in biotechnology have brought the opportunity for building binding affinity prediction methods, the accurate characterization of TF-DNA binding affinity landscape still remains a challenging problem. Results: Here we propose a novel sequence embedding approach for modeling the transcription factor binding affinity landscape. Our method represents DNA binding sequences as a hidden Markov model (HMM) which captures both position specific information and long-range dependency in the sequence. A cornerstone of our method is a novel message passing-like embedding algorithm, called Sequence2Vec, which maps these HMMs into a common nonlinear feature space and uses these embedded features to build a predictive model. Our method is a novel combination of the strength of probabilistic graphical models, feature space embedding and deep learning. We conducted comprehensive experiments on over 90 large-scale TF-DNA data sets which were measured by different high-throughput experimental technologies. Sequence2Vec outperforms alternative machine learning methods as well as the state-of-the-art binding affinity prediction methods.

  2. Geophysical and geochemical models of the Earth's shields and rift zones

    International Nuclear Information System (INIS)

    Chung, D.H.

    1977-01-01

    This report summarizes a collection of, synthesis of, and speculation on the geophysical and geochemical models of the earth's stable shields and rift zones. Two basic crustal types, continental and oceanic, and two basic mantle types, stable and unstable, are described. It is pointed out that both the crust and upper mantle play a strongly interactive role with surface geological phenomena ranging from the occurrence of mountains, ocean trenches, oceanic and continental rifts to geographic distributions of earthquakes, faults, and volcanoes. On the composition of the mantle, there is little doubt regarding the view that olivine constitutes a major fraction of the mineralogy of the earth's upper mantle. Studies are suggested to simulate the elasticity and composition of the earth's lower crust and upper mantle

  3. An overview of the recent approaches to terroir functional modelling, footprinting and zoning

    Science.gov (United States)

    Vaudour, E.; Costantini, E.; Jones, G. V.; Mocali, S.

    2015-03-01

    Notions of terroir and their conceptualization through agro-environmental sciences have become popular in many parts of world. Originally developed for wine, terroir now encompasses many other crops including fruits, vegetables, cheese, olive oil, coffee, cacao and other crops, linking the uniqueness and quality of both beverages and foods to the environment where they are produced, giving the consumer a sense of place. Climate, geology, geomorphology and soil are the main environmental factors which make up the terroir effect on different scales. Often considered immutable culturally, the natural components of terroir are actually a set of processes, which together create a delicate equilibrium and regulation of its effect on products in both space and time. Due to both a greater need to better understand regional-to-site variations in crop production and the growth in spatial analytic technologies, the study of terroir has shifted from a largely descriptive regional science to a more applied, technical research field. Furthermore, the explosion of spatial data availability and sensing technologies has made the within-field scale of study more valuable to the individual grower. The result has been greater adoption of these technologies but also issues associated with both the spatial and temporal scales required for practical applications, as well as the relevant approaches for data synthesis. Moreover, as soil microbial communities are known to be of vital importance for terrestrial processes by driving the major soil geochemical cycles and supporting healthy plant growth, an intensive investigation of the microbial organization and their function is also required. Our objective is to present an overview of existing data and modelling approaches for terroir functional modelling, footprinting and zoning on local and regional scales. This review will focus on two main areas of recent terroir research: (1) using new tools to unravel the biogeochemical cycles of both

  4. CONSTRUCTIVE MODELLING FOR ZONE OF RECOVERY ENERGY DISTRIBUTION OF DC TRACTION

    Directory of Open Access Journals (Sweden)

    V. I. Shynkarenko

    2016-10-01

    Full Text Available Purpose.The article is aimed to develop the means and methods of forming a plurality of real and potential structural diagrams for zones of energy recovery and different locations of trains for further training neuro-fuzzy networks on the basis of expert solutions and also for the formation of good control. Methodology. Methodology of mathematical and algorithmic constructivism for modeling the structural diagrams of the electric supply system and modes of traction power consumption and the train’s locations in zones of energy recovery was applied. This approach involves the development of constructive-synthesizing structures (CSS with transformation by specialization, interpretation, specification and implementation. Development CSS provides an extensible definition media, relations and the signature of operations and constructive axiomatic. The most complex and essential part of the axioms is the set formed by the substitution rules defining the process of withdrawal of the corresponding structures. Findings. A specialized and specified CSS, which allows considering all the possibilities and features, that supply power traction systems with modern equipment, stations and trains location was designed. Its feature: the semantic content of the terminal alphabet images of electrical traction network and power consumers with relevant attributes. A special case of the formation of the structural diagram shows the possibilities CSS in relation to this problem. Originality. A new approach to solving the problem of rational use of energy recovery, which consists in application of the methods and means of artificial neural networks, expert systems, fuzzy logic and mathematical and algorithmic constructivism. This paper presents the methods of constructive simulation of a production-distribution of energy recovery zone structure in the system of the DC traction. Practical value. The tasks decision of the rational use of energy recovery can

  5. A nested pre-operational model for the Egyptian shelf zone: Model configuration and validation/calibration

    Science.gov (United States)

    Nagy, H.; Elgindy, A.; Pinardi, N.; Zavatarelli, M.; Oddo, P.

    2017-12-01

    We explored the variability of the Egyptian shelf zone circulation connected to atmospheric forcing by means of a numerical simulation of the general circulation. A high resolution model grid was used at 1/60° horizontal resolution and 25 sigma layers. The simulation was carried out using the most recent version of the Princeton Ocean Model (POM). The initialised model was run the whole year of 2006 using the analysis forcing data for the same year obtained from ECMWF and MFS (Mediterranean Forecasting System, Pinardi et al., 2003). The model skills were evaluated by means of the root mean square error (RMSE) and correlations. The Egyptian Shelf Model (EGYSHM) simulation suggests the presence of an Egyptian Shelf Slope Current (ESSC), which is flowing eastward at different depths in the domain. We found that the maximum velocity of the ESSC [0.25 m/s] is located near the continental slope during the summer time, while in winter the velocity of ESSC is weaker [0.12 m/s] in the same location. The ESSC appears to be directly affected by Mersa-Matruh gyre system. EGYSHM reproduced the main region circulation patterns, especially after adding the Nile River outflow. We found that wind stress is crucial to force the circulation of the Egyptian shelf zone. EGYSHM SST was significantly correlated to satellite SST in all months at a 95% confidence limit, with a maximum of 0.9743 which was obtained in May 2006. The RMSE between EGYSHM and Argo floats salinity data was about 0.09. We compared our results with satellite altimetry to verify the positions and shapes of mesoscale features.

  6. Modeling tritium transport through a deep unsaturated zone in an arid environment

    Science.gov (United States)

    Mayers, C.J.; Andraski, Brian J.; Cooper, C.A.; Wheatcraft, S.W.; Stonestrom, David A.; Michel, R.L.

    2005-01-01

    Understanding transport of tritium (3H) in unsaturated zones is critical to evaluating options for waste isolation. Tritium typically is a large component of low-level radioactive waste (LLRW). Studies at the U.S. Geological Survey's Amargosa Desert Research Site (ADRS) in Nevada investigate 3H transport from a closed LLRW facility. Two boreholes are 100 and 160 m from the nearest waste trench and extend to the water table at 110 m. Soil-water vapor samples from the deep boreholes show elevated levels of 3H at all depths. The objectives of this study were to (i) test source thermal and gas-advection mechanisms driving 3H transport and (ii) evaluate model sensitivity to these mechanisms and to selected physical and hydraulic properties including porosity, tortuosity, and anisotropy. A two-dimensional numerical model incorporated a non-isothermal, heterogeneous domain of the unsaturated zone and instantaneous isotopic equilibrium. The TOUGH2 code was used; however, it required modification to account for temperature dependence of both the Henry's law equilibrium constant and isotopic fractionation with respect to tritiated water. Increases in source temperature, pressure, and porosity enhanced 3H migration, but failed to match measured 3H distributions. All anisotropic simulations with a source pressure component resembled, in shape, the upper portion of the 3H distribution of the nearest borehole. Isotopic equilibrium limited migration of 3H, while effects of radioactive decay were negligible. A 500 Pa pressure increase above ambient pressure in conjunction with a high degree of anisotropy (1:100) was necessary for simulated 3H transport to reach the nearest borehole.

  7. Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method

    Directory of Open Access Journals (Sweden)

    Sette Alessandro

    2005-05-01

    Full Text Available Abstract Background Many processes in molecular biology involve the recognition of short sequences of nucleic-or amino acids, such as the binding of immunogenic peptides to major histocompatibility complex (MHC molecules. From experimental data, a model of the sequence specificity of these processes can be constructed, such as a sequence motif, a scoring matrix or an artificial neural network. The purpose of these models is two-fold. First, they can provide a summary of experimental results, allowing for a deeper understanding of the mechanisms involved in sequence recognition. Second, such models can be used to predict the experimental outcome for yet untested sequences. In the past we reported the development of a method to generate such models called the Stabilized Matrix Method (SMM. This method has been successfully applied to predicting peptide binding to MHC molecules, peptide transport by the transporter associated with antigen presentation (TAP and proteasomal cleavage of protein sequences. Results Herein we report the implementation of the SMM algorithm as a publicly available software package. Specific features determining the type of problems the method is most appropriate for are discussed. Advantageous features of the package are: (1 the output generated is easy to interpret, (2 input and output are both quantitative, (3 specific computational strategies to handle experimental noise are built in, (4 the algorithm is designed to effectively handle bounded experimental data, (5 experimental data from randomized peptide libraries and conventional peptides can easily be combined, and (6 it is possible to incorporate pair interactions between positions of a sequence. Conclusion Making the SMM method publicly available enables bioinformaticians and experimental biologists to easily access it, to compare its performance to other prediction methods, and to extend it to other applications.

  8. Technical Report on Modeling for Quasispecies Abundance Inference with Confidence Intervals from Metagenomic Sequence Data

    Energy Technology Data Exchange (ETDEWEB)

    McLoughlin, K. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2016-01-11

    The overall aim of this project is to develop a software package, called MetaQuant, that can determine the constituents of a complex microbial sample and estimate their relative abundances by analysis of metagenomic sequencing data. The goal for Task 1 is to create a generative model describing the stochastic process underlying the creation of sequence read pairs in the data set. The stages in this generative process include the selection of a source genome sequence for each read pair, with probability dependent on its abundance in the sample. The other stages describe the evolution of the source genome from its nearest common ancestor with a reference genome, breakage of the source DNA into short fragments, and the errors in sequencing the ends of the fragments to produce read pairs.

  9. Genome sequence analysis of the model grass Brachypodium distachyon: insights into grass genome evolution

    Energy Technology Data Exchange (ETDEWEB)

    Schulman, Al

    2009-08-09

    Three subfamilies of grasses, the Erhardtoideae (rice), the Panicoideae (maize, sorghum, sugar cane and millet), and the Pooideae (wheat, barley and cool season forage grasses) provide the basis of human nutrition and are poised to become major sources of renewable energy. Here we describe the complete genome sequence of the wild grass Brachypodium distachyon (Brachypodium), the first member of the Pooideae subfamily to be completely sequenced. Comparison of the Brachypodium, rice and sorghum genomes reveals a precise sequence- based history of genome evolution across a broad diversity of the grass family and identifies nested insertions of whole chromosomes into centromeric regions as a predominant mechanism driving chromosome evolution in the grasses. The relatively compact genome of Brachypodium is maintained by a balance of retroelement replication and loss. The complete genome sequence of Brachypodium, coupled to its exceptional promise as a model system for grass research, will support the development of new energy and food crops

  10. Logistic regression model for diagnosis of transition zone prostate cancer on multi-parametric MRI

    Energy Technology Data Exchange (ETDEWEB)

    Dikaios, Nikolaos; Halligan, Steve; Taylor, Stuart; Atkinson, David; Punwani, Shonit [University College London, Centre for Medical Imaging, London (United Kingdom); University College London Hospital, Departments of Radiology, London (United Kingdom); Alkalbani, Jokha; Sidhu, Harbir Singh; Fujiwara, Taiki [University College London, Centre for Medical Imaging, London (United Kingdom); Abd-Alazeez, Mohamed; Ahmed, Hashim; Emberton, Mark [University College London, Research Department of Urology, London (United Kingdom); Kirkham, Alex; Allen, Clare [University College London Hospital, Departments of Radiology, London (United Kingdom); Freeman, Alex [University College London Hospital, Department of Histopathology, London (United Kingdom)

    2014-09-17

    We aimed to develop logistic regression (LR) models for classifying prostate cancer within the transition zone on multi-parametric magnetic resonance imaging (mp-MRI). One hundred and fifty-five patients (training cohort, 70 patients; temporal validation cohort, 85 patients) underwent mp-MRI and transperineal-template-prostate-mapping (TPM) biopsy. Positive cores were classified by cancer definitions: (1) any-cancer; (2) definition-1 [≥Gleason 4 + 3 or ≥ 6 mm cancer core length (CCL)] [high risk significant]; and (3) definition-2 (≥Gleason 3 + 4 or ≥ 4 mm CCL) cancer [intermediate-high risk significant]. For each, logistic-regression mp-MRI models were derived from the training cohort and validated internally and with the temporal cohort. Sensitivity/specificity and the area under the receiver operating characteristic (ROC-AUC) curve were calculated. LR model performance was compared to radiologists' performance. Twenty-eight of 70 patients from the training cohort, and 25/85 patients from the temporal validation cohort had significant cancer on TPM. The ROC-AUC of the LR model for classification of cancer was 0.73/0.67 at internal/temporal validation. The radiologist A/B ROC-AUC was 0.65/0.74 (temporal cohort). For patients scored by radiologists as Prostate Imaging Reporting and Data System (Pi-RADS) score 3, sensitivity/specificity of radiologist A 'best guess' and LR model was 0.14/0.54 and 0.71/0.61, respectively; and radiologist B 'best guess' and LR model was 0.40/0.34 and 0.50/0.76, respectively. LR models can improve classification of Pi-RADS score 3 lesions similar to experienced radiologists. (orig.)

  11. E-Area LLWF Vadose Zone Model: Probabilistic Model for Estimating Subsided-Area Infiltration Rates

    Energy Technology Data Exchange (ETDEWEB)

    Dyer, J. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Flach, G. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2017-12-12

    A probabilistic model employing a Monte Carlo sampling technique was developed in Python to generate statistical distributions of the upslope-intact-area to subsided-area ratio (AreaUAi/AreaSAi) for closure cap subsidence scenarios that differ in assumed percent subsidence and the total number of intact plus subsided compartments. The plan is to use this model as a component in the probabilistic system model for the E-Area Performance Assessment (PA), contributing uncertainty in infiltration estimates.

  12. ToPS: a framework to manipulate probabilistic models of sequence data.

    Directory of Open Access Journals (Sweden)

    André Yoshiaki Kashiwabara

    Full Text Available Discrete Markovian models can be used to characterize patterns in sequences of values and have many applications in biological sequence analysis, including gene prediction, CpG island detection, alignment, and protein profiling. We present ToPS, a computational framework that can be used to implement different applications in bioinformatics analysis by combining eight kinds of models: (i independent and identically distributed process; (ii variable-length Markov chain; (iii inhomogeneous Markov chain; (iv hidden Markov model; (v profile hidden Markov model; (vi pair hidden Markov model; (vii generalized hidden Markov model; and (viii similarity based sequence weighting. The framework includes functionality for training, simulation and decoding of the models. Additionally, it provides two methods to help parameter setting: Akaike and Bayesian information criteria (AIC and BIC. The models can be used stand-alone, combined in Bayesian classifiers, or included in more complex, multi-model, probabilistic architectures using GHMMs. In particular the framework provides a novel, flexible, implementation of decoding in GHMMs that detects when the architecture can be traversed efficiently.

  13. Monitoring well utility in a heterogeneous DNAPL source zone area: Insights from proximal multilevel sampler wells and sampling capture-zone modelling

    Science.gov (United States)

    McMillan, Lindsay A.; Rivett, Michael O.; Wealthall, Gary P.; Zeeb, Peter; Dumble, Peter

    2018-03-01

    Groundwater-quality assessment at contaminated sites often involves the use of short-screen (1.5 to 3 m) monitoring wells. However, even over these intervals considerable variation may occur in contaminant concentrations in groundwater adjacent to the well screen. This is especially true in heterogeneous dense non-aqueous phase liquid (DNAPL) source zones, where cm-scale contamination variability may call into question the effectiveness of monitoring wells to deliver representative data. The utility of monitoring wells in such settings is evaluated by reference to high-resolution multilevel sampler (MLS) wells located proximally to short-screen wells, together with sampling capture-zone modelling to explore controls upon well sample provenance and sensitivity to monitoring protocols. Field data are analysed from the highly instrumented SABRE research site that contained an old trichloroethene source zone within a shallow alluvial aquifer at a UK industrial facility. With increased purging, monitoring-well samples tend to a flow-weighted average concentration but may exhibit sensitivity to the implemented protocol and degree of purging. Formation heterogeneity adjacent to the well-screen particularly, alongside pump-intake position and water level, influence this sensitivity. Purging of low volumes is vulnerable to poor reproducibility arising from concentration variability predicted over the initial 1 to 2 screen volumes purged. Marked heterogeneity may also result in limited long-term sample concentration stabilization. Development of bespoke monitoring protocols, that consider screen volumes purged, alongside water-quality indicator parameter stabilization, is recommended to validate and reduce uncertainty when interpreting monitoring-well data within source zone areas. Generalised recommendations on monitoring well based protocols are also developed. A key monitoring well utility is their proportionately greater sample draw from permeable horizons constituting a

  14. Modeling bias and variation in the stochastic processes of small RNA sequencing.

    Science.gov (United States)

    Argyropoulos, Christos; Etheridge, Alton; Sakhanenko, Nikita; Galas, David

    2017-06-20

    The use of RNA-seq as the preferred method for the discovery and validation of small RNA biomarkers has been hindered by high quantitative variability and biased sequence counts. In this paper we develop a statistical model for sequence counts that accounts for ligase bias and stochastic variation in sequence counts. This model implies a linear quadratic relation between the mean and variance of sequence counts. Using a large number of sequencing datasets, we demonstrate how one can use the generalized additive models for location, scale and shape (GAMLSS) distributional regression framework to calculate and apply empirical correction factors for ligase bias. Bias correction could remove more than 40% of the bias for miRNAs. Empirical bias correction factors appear to be nearly constant over at least one and up to four orders of magnitude of total RNA input and independent of sample composition. Using synthetic mixes of known composition, we show that the GAMLSS approach can analyze differential expression with greater accuracy, higher sensitivity and specificity than six existing algorithms (DESeq2, edgeR, EBSeq, limma, DSS, voom) for the analysis of small RNA-seq data. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Computer modelling of RF ablation in cortical osteoid osteoma: Assessment of the insulating effect of the reactive zone.

    Science.gov (United States)

    Irastorza, Ramiro M; Trujillo, Macarena; Martel Villagrán, Jose; Berjano, Enrique

    2016-05-01

    The aim was to study by computer simulations the insulating role of the reactive zone surrounding a cortical osteoid osteoma (OO) in terms of electrical and thermal performance during radiofrequency ablation (RFA). We modelled a cortical OO consisting of a nidus (10 mm diameter) enclosed by a reactive zone. The OO was near a layer of cortical bone 1.5 mm thick. Trabecular bone partially surrounds the OO and there was muscle around the cortical bone layer. We modelled RF ablations with a non-cooled-tip 17-gauge needle electrode (300 s duration and 90 °C target temperature). Sensitivity analyses were conducted assuming a reactive zone electrical conductivity value (σrz) within the limits of the cortical and trabecular bone, i.e. 0.02 S/m and 0.087 S/m, respectively. In this way we were really modelling the different degrees of osteosclerosis associated with the reactive zone. The presence of the reactive zone drastically reduced the maximum temperature reached outside it. The temperature drop was proportional to the thickness of the reactive zone: from 68 °C when it was absent to 44 °C when it is 7.5 mm thick. Higher nidus conductivity values (σn) implied higher temperatures, while lower temperatures meant higher σrz values. Changing σrz from 0.02 S/m to 0.087 S/m reduced lesion diameters from 2.4 cm to 1.8 cm. The computer results suggest that the reactive zone plays the role of insulator in terms of reducing the temperature in the surrounding area.

  16. Numerical modeling of fluid flow in a fault zone: a case of study from Majella Mountain (Italy).

    Science.gov (United States)

    Romano, Valentina; Battaglia, Maurizio; Bigi, Sabina; De'Haven Hyman, Jeffrey; Valocchi, Albert J.

    2017-04-01

    The study of fluid flow in fractured rocks plays a key role in reservoir management, including CO2 sequestration and waste isolation. We present a numerical model of fluid flow in a fault zone, based on field data acquired in Majella Mountain, in the Central Apennines (Italy). This fault zone is considered a good analogue for the massive presence of fluid migration in the form of tar. Faults are mechanical features and cause permeability heterogeneities in the upper crust, so they strongly influence fluid flow. The distribution of the main components (core, damage zone) can lead the fault zone to act as a conduit, a barrier, or a combined conduit-barrier system. We integrated existing information and our own structural surveys of the area to better identify the major fault features (e.g., type of fractures, statistical properties, geometrical and petro-physical characteristics). In our model the damage zones of the fault are described as discretely fractured medium, while the core of the fault as a porous one. Our model utilizes the dfnWorks code, a parallelized computational suite, developed at Los Alamos National Laboratory (LANL), that generates three dimensional Discrete Fracture Network (DFN) of the damage zones of the fault and characterizes its hydraulic parameters. The challenge of the study is the coupling between the discrete domain of the damage zones and the continuum one of the core. The field investigations and the basic computational workflow will be described, along with preliminary results of fluid flow simulation at the scale of the fault.

  17. A conceptual dynamic vegetation-soil model for arid and semiarid zones

    Directory of Open Access Journals (Sweden)

    D. I. Quevedo

    2008-09-01

    Full Text Available Plant ecosystems in arid and semiarid climates show high complexity, since they depend on water availability to carry out their vital processes. In these climates, water stress is the main factor controlling vegetation development and its dynamic evolution. The available water-soil content results from the water balance in the system, where the key issues are the soil, the vegetation and the atmosphere. However, it is the vegetation, which modulates, to a great extent, the water fluxes and the feedback mechanisms between soil and atmosphere. Thus, soil moisture content is most relevant for plant growth maintenance and final water balance assessment. A conceptual dynamic vegetation-soil model (called HORAS for arid and semi-arid zones has been developed. This conceptual model, based on a series of connected tanks, represents in a way suitable for a Mediterranean climate, the vegetation response to soil moisture fluctuations and the actual leaf biomass influence on soil water availability and evapotranspiration. Two tanks were considered using at each of them the water balance and the appropriate dynamic equation for all considered fluxes. The first one corresponds to the interception process, whereas the second one models the evolution of moisture by the upper soil. The model parameters were based on soil and vegetation properties, but reduced their numbers. Simulations for dominant species, Quercus coccifera L., were carried out to calibrate and validate the model. Our results show that HORAS succeeded in representing the vegetation dynamics and, on the one hand, reflects how following a fire this monoculture stabilizes after 9 years. On the other hand, the model shows the adaptation of the vegetation to the variability of climatic and soil conditions, demonstrating that in the presence or shortage of water, the vegetation regulates its leaf biomass as well as its rate of transpiration in an attempt to minimize total water stress.

  18. A cohesive zone model to simulate the hydrogen embrittlement effect on a high-strength steel

    Directory of Open Access Journals (Sweden)

    G. Gobbi

    2016-01-01

    Full Text Available The present work aims to model the fracture mechanical behavior of a high-strength low carbon steel, AISI 4130 operating in hydrogen contaminated environment. The study deals with the development of 2D finite element cohesive zone model (CZM reproducing a toughness test. Along the symmetry plane over the crack path of a C(T specimen a zero thickness layer of cohesive elements are implemented in order to simulate the crack propagation. The main feature of this kind of model is the definition of a traction-separation law (TSL that reproduces the constitutive response of the material inside to the cohesive elements. Starting from a TSL calibrated on hydrogen non-contaminated material, the embrittlement effect is simulated by reducing the cohesive energy according to the total hydrogen content including the lattice sites (NILS and the trapped amount. In this perspective, the proposed model consists of three steps of simulations. First step evaluates the hydrostatic pressure. It drives the initial hydrogen concentration assigned in the second step, a mass diffusion analysis, defining in this way the contribution of hydrogen moving across the interstitial lattice sites. The final stress analysis, allows getting the total hydrogen content, including the trapped amount, and evaluating the new crack initiation and propagation due to the hydrogen presence. The model is implemented in both plane strain and plane stress configurations; results are compared in the discussion. From the analyses, it resulted that hydrogen is located only into lattice sites and not in traps, and that the considered steel experiences a high hydrogen susceptibility. By the proposed procedure, the developed numerical model seems a reliable and quick tool able to estimate the mechanical behavior of steels in presence of hydrogen.

  19. Expanding the role of reactive transport models in critical zone processes

    Science.gov (United States)

    Li, Li; Maher, Kate; Navarre-Sitchler, Alexis; Druhan, Jennifer; Meile, Christof; Lawrence, Corey; Moore, Joel; Perdrial, Julia; Sullivan, Pamela; Thompson, Aaron; Jin, Lixin; Bolton, Edward W.; Brantley, Susan L.; Dietrich, William E.; Mayer, K. Ulrich; Steefel, Carl; Valocchi, Albert J.; Zachara, John M.; Kocar, Benjamin D.; McIntosh, Jennifer; Tutolo, Benjamin M.; Kumar, Mukesh; Sonnenthal, Eric; Bao, Chen; Beisman, Joe

    2017-01-01

    Models test our understanding of processes and can reach beyond the spatial and temporal scales of measurements. Multi-component Reactive Transport Models (RTMs), initially developed more than three decades ago, have been used extensively to explore the interactions of geothermal, hydrologic, geochemical, and geobiological processes in subsurface systems. Driven by extensive data sets now available from intensive measurement efforts, there is a pressing need to couple RTMs with other community models to explore non-linear interactions among the atmosphere, hydrosphere, biosphere, and geosphere. Here we briefly review the history of RTM development, summarize the current state of RTM approaches, and identify new research directions, opportunities, and infrastructure needs to broaden the use of RTMs. In particular, we envision the expanded use of RTMs in advancing process understanding in the Critical Zone, the veneer of the Earth that extends from the top of vegetation to the bottom of groundwater. We argue that, although parsimonious models are essential at larger scales, process-based models offer tools to explore the highly nonlinear coupling that characterizes natural systems. We present seven testable hypotheses that emphasize the unique capabilities of process-based RTMs for (1) elucidating chemical weathering and its physical and biogeochemical drivers; (2) understanding the interactions among roots, micro-organisms, carbon, water, and minerals in the rhizosphere; (3) assessing the effects of heterogeneity across spatial and temporal scales; and (4) integrating the vast quantity of novel data, including “omics” data (genomics, transcriptomics, proteomics, metabolomics), elemental concentration and speciation data, and isotope data into our understanding of complex earth surface systems. With strong support from data-driven sciences, we are now in an exciting era where integration of RTM framework into other community models will facilitate process

  20. Simulations of a stretching bar using a plasticity model from the shear transformation zone theory

    Energy Technology Data Exchange (ETDEWEB)

    Rycroft, Chris H.; Gibou, Frederic

    2010-06-05

    An Eulerian simulation is developed to study an elastoplastic model of amorphous materials that is based upon the shear transformation zone theory developed by Langer and coworkers. In this theory, plastic deformation is controlled by an effective temperature that measures the amount of configurational disorder in the material. The simulation is used to model ductile fracture in a stretching bar that initially contains a small notch, and the effects of many of the model parameters are examined. The simulation tracks the shape of the bar using the level set method. Within the bar, a finite difference discretization is employed that makes use of the essentially non-oscillatory (ENO) scheme. The system of equations is moderately stiff due to the presence of large elastic constants, and one of the key numerical challenges is to accurately track the level set and construct extrapolated field values for use in boundary conditions. A new approach to field extrapolation is discussed that is second order accurate and requires a constant amount of work per gridpoint.

  1. Contact models of repaired articular surfaces: influence of loading conditions and the superficial tangential zone.

    Science.gov (United States)

    Owen, John R; Wayne, Jennifer S

    2011-07-01

    The superficial tangential zone (STZ) plays a significant role in normal articular cartilage's ability to support loads and retain fluids. To date, tissue engineering efforts have not replicated normal STZ function in cartilage repairs. This finite element study examined the STZ's role in normal and repaired articular surfaces under different contact conditions. Contact area and pressure distributions were allowed to change with time, tension-compression nonlinearity modeled collagen behavior in the STZ, and nonlinear geometry was incorporated to accommodate finite deformation. Responses to loading via impermeable and permeable rigid surfaces were compared to loading via normal cartilage, a more physiologic condition, anticipating the two rigid loading surfaces would bracket that of normal. For models loaded by normal cartilage, an STZ placed over the inferior repair region reduced the short-term axial compression of the articular surface by 15%, when compared to a repair without an STZ. Covering the repair with a normal STZ shifted the flow patterns and strain levels back toward that of normal cartilage. Additionally, reductions in von Mises stress (21%) and an increase in fluid pressure (13%) occurred in repair tissue under the STZ. This continues to show that STZ properties of sufficient quality are likely critical for the survival of transplanted constructs in vivo. However, response to loading via normal cartilage did not always fall within ranges predicted by the rigid surfaces. Use of more physiologic contact models is recommended for more accurate investigations into properties critical to the success of repair tissues.

  2. Rock Physics Modeling and Seismic Interpretation to Estimate Shally Cemented Zone in Carbonate Reservoir Rock

    Directory of Open Access Journals (Sweden)

    Handoyo Handoyo

    2016-12-01

    Full Text Available Carbonate rock are important hydrocarbon reservoir rocks with complex texture and petrophysical properties (porosity and permeability. These complexities make the prediction reservoir characteristics (e.g. porosity and permeability from their seismic properties more difficult. The goal of this paper are to understanding the relationship of physical properties and to see the signature carbonate initial rock and shally-carbonate rock from the reservoir. To understand the relationship between the seismic, petrophysical and geological properties, we used rock physics modeling from ultrasonic P- and S- wave velocity that measured from log data. The measurements obtained from carbonate reservoir field (gas production. X-ray diffraction and scanning electron microscope studies shown the reservoir rock are contain wackestone-packstone content. Effective medium theory to rock physics modeling are using Voigt, Reuss, and Hill.  It is shown the elastic moduly proposionally decrease with increasing porosity. Elastic properties and wave velocity are decreasing proporsionally with increasing porosity and shally cemented on the carbonate rock give higher elastic properties than initial carbonate non-cemented. Rock physics modeling can separated zones which rich of shale and less of shale.

  3. Modelling wave-induced sea ice break-up in the marginal ice zone.

    Science.gov (United States)

    Montiel, F; Squire, V A

    2017-10-01

    A model of ice floe break-up under ocean wave forcing in the marginal ice zone (MIZ) is proposed to investigate how floe size distribution (FSD) evolves under repeated wave break-up events. A three-dimensional linear model of ocean wave scattering by a finite array of compliant circular ice floes is coupled to a flexural failure model, which breaks a floe into two floes provided the two-dimensional stress field satisfies a break-up criterion. A closed-feedback loop algorithm is devised, which (i) solves the wave-scattering problem for a given FSD under time-harmonic plane wave forcing, (ii) computes the stress field in all the floes, (iii) fractures the floes satisfying the break-up criterion, and (iv) generates an updated FSD, initializing the geometry for the next iteration of the loop. The FSD after 50 break-up events is unimodal and near normal, or bimodal, suggesting waves alone do not govern the power law observed in some field studies. Multiple scattering is found to enhance break-up for long waves and thin ice, but to reduce break-up for short waves and thick ice. A break-up front marches forward in the latter regime, as wave-induced fracture weakens the ice cover, allowing waves to travel deeper into the MIZ.

  4. Impact of global warming on the geobotanic zones: an experiment with a statistical-dynamical climate model

    Energy Technology Data Exchange (ETDEWEB)

    Franchito, Sergio H.; Brahmananda Rao, V. [Instituto Nacional de Pesquisas Espaciais, Centro de Ciencia do Sistema Terrestre, CCST, Sau Paulo, SP (Brazil); Moraes, E.C. [Instituto Nacional de Pesquisas Espaciais, Divisao de Sensoriamento Remoto, DSR, Sau Paulo, SP (Brazil)

    2011-11-15

    In this study, a zonally-averaged statistical climate model (SDM) is used to investigate the impact of global warming on the distribution of the geobotanic zones over the globe. The model includes a parameterization of the biogeophysical feedback mechanism that links the state of surface to the atmosphere (a bidirectional interaction between vegetation and climate). In the control experiment (simulation of the present-day climate) the geobotanic state is well simulated by the model, so that the distribution of the geobotanic zones over the globe shows a very good agreement with the observed ones. The impact of global warming on the distribution of the geobotanic zones is investigated considering the increase of CO{sub 2} concentration for the B1, A2 and A1FI scenarios. The results showed that the geobotanic zones over the entire earth can be modified in future due to global warming. Expansion of subtropical desert and semi-desert zones in the Northern and Southern Hemispheres, retreat of glaciers and sea-ice, with the Arctic region being particularly affected and a reduction of the tropical rainforest and boreal forest can occur due to the increase of the greenhouse gases concentration. The effects were more pronounced in the A1FI and A2 scenarios compared with the B1 scenario. The SDM results confirm IPCC AR4 projections of future climate and are consistent with simulations of more complex GCMs, reinforcing the necessity of the mitigation of climate change associated to global warming. (orig.)

  5. Modeling Transient Root-zone Soil Moisture Dichotomies in Landscapes with Intermixed Land Covers

    Science.gov (United States)

    Patrignani, A.; Ochsner, T. E.

    2015-12-01

    Although large-scale in situ soil moisture monitoring networks are becoming increasingly valuable research tools, deficiencies of many existing networks include the small spatial support of each station, the low spatial density of stations, and the almost exclusive deployment of stations in grassland vegetation. These grassland soil moisture observations may not adequately represent the real soil moisture patterns in landscapes with intermixed land cover types. The objectives of this study were i) to compare root-zone soil moisture dynamics of two dominant vegetation types across Oklahoma, grassland (observed) and winter wheat cropland (simulated); ii) to relate the soil moisture dynamics of grassland and cropland vegetation using an artificial neural network (ANN) as a transfer function; and iii) to use the resulting ANN to estimate the soil moisture spatial patterns for a landscape of intermixed grassland and wheat cropland. Root-zone soil moisture was represented by plant available water (PAW) in the top 0.8 m of the soil profile. PAW under grassland was calculated from 18 years of soil moisture observations at 78 stations of the Oklahoma Mesonet, whereas PAW under winter wheat was simulated for the same 78 locations using a soil water balance model. Then, we trained an ANN to reproduce the simulated PAW under winter wheat using only seven inputs: day of the year, latitude and longitude, measured PAW under grassland, and percent sand, silt, and clay. The resulting ANN was used, along with grassland soil moisture observations, to estimate the detailed soil moisture pattern for a 9x9 km2 Soil Moisture Active Passive (SMAP) grid cell. The seasonal dynamics of root-zone PAW for grassland and winter wheat were strongly asynchronous, so grassland soil moisture observations rarely reflect cropland soil moisture conditions in the region. The simple ANN approach facilitated efficient and accurate prediction of the simulated PAW under winter wheat, RMSE = 24 mm, using

  6. Modeling the influence of coupled mass transfer processes on mass flux downgradient of heterogeneous DNAPL source zones.

    Science.gov (United States)

    Yang, Lurong; Wang, Xinyu; Mendoza-Sanchez, Itza; Abriola, Linda M

    2018-04-01

    Sequestered mass in low permeability zones has been increasingly recognized as an important source of organic chemical contamination that acts to sustain downgradient plume concentrations above regulated levels. However, few modeling studies have investigated the influence of this sequestered mass and associated (coupled) mass transfer processes on plume persistence in complex dense nonaqueous phase liquid (DNAPL) source zones. This paper employs a multiphase flow and transport simulator (a modified version of the modular transport simulator MT3DMS) to explore the two- and three-dimensional evolution of source zone mass distribution and near-source plume persistence for two ensembles of highly heterogeneous DNAPL source zone realizations. Simulations reveal the strong influence of subsurface heterogeneity on the complexity of DNAPL and sequestered (immobile/sorbed) mass distribution. Small zones of entrapped DNAPL are shown to serve as a persistent source of low concentration plumes, difficult to distinguish from other (sorbed and immobile dissolved) sequestered mass sources. Results suggest that the presence of DNAPL tends to control plume longevity in the near-source area; for the examined scenarios, a substantial fraction (43.3-99.2%) of plume life was sustained by DNAPL dissolution processes. The presence of sorptive media and the extent of sorption non-ideality are shown to greatly affect predictions of near-source plume persistence following DNAPL depletion, with plume persistence varying one to two orders of magnitude with the selected sorption model. Results demonstrate the importance of sorption-controlled back diffusion from low permeability zones and reveal the importance of selecting the appropriate sorption model for accurate prediction of plume longevity. Large discrepancies for both DNAPL depletion time and plume longevity were observed between 2-D and 3-D model simulations. Differences between 2- and 3-D predictions increased in the presence of

  7. Monte Carlo simulation of a statistical mechanical model of multiple protein sequence alignment.

    Science.gov (United States)

    Kinjo, Akira R

    2017-01-01

    A grand canonical Monte Carlo (MC) algorithm is presented for studying the lattice gas model (LGM) of multiple protein sequence alignment, which coherently combines long-range interactions and variable-length insertions. MC simulations are used for both parameter optimization of the model and production runs to explore the sequence subspace around a given protein family. In this Note, I describe the details of the MC algorithm as well as some preliminary results of MC simulations with various temperatures and chemical potentials, and compare them with the mean-field approximation. The existence of a two-state transition in the sequence space is suggested for the SH3 domain family, and inappropriateness of the mean-field approximation for the LGM is demonstrated.

  8. Blackout sequence modeling for Atucha-I with MARCH3 code

    International Nuclear Information System (INIS)

    Baron, J.; Bastianelli, B.

    1997-01-01

    The modeling of a blackout sequence in Atucha I nuclear power plant is presented in this paper, as a preliminary phase for a level II probabilistic safety assessment. Such sequence is analyzed with the code MARCH3 from STCP (Source Term Code Package), based on a specific model developed for Atucha, that takes into accounts it peculiarities. The analysis includes all the severe accident phases, from the initial transient (loss of heat sink), loss of coolant through the safety valves, core uncovered, heatup, metal-water reaction, melting and relocation, heatup and failure of the pressure vessel, core-concrete interaction in the reactor cavity, heatup and failure of the containment building (multi-compartmented) due to quasi-static overpressurization. The results obtained permit to visualize the time sequence of these events, as well as provide the basis for source term studies. (author) [es

  9. On Statistical Modeling of Sequencing Noise in High Depth Data to Assess Tumor Evolution

    Science.gov (United States)

    Rabadan, Raul; Bhanot, Gyan; Marsilio, Sonia; Chiorazzi, Nicholas; Pasqualucci, Laura; Khiabanian, Hossein

    2017-12-01

    One cause of cancer mortality is tumor evolution to therapy-resistant disease. First line therapy often targets the dominant clone, and drug resistance can emerge from preexisting clones that gain fitness through therapy-induced natural selection. Such mutations may be identified using targeted sequencing assays by analysis of noise in high-depth data. Here, we develop a comprehensive, unbiased model for sequencing error background. We find that noise in sufficiently deep DNA sequencing data can be approximated by aggregating negative binomial distributions. Mutations with frequencies above noise may have prognostic value. We evaluate our model with simulated exponentially expanded populations as well as data from cell line and patient sample dilution experiments, demonstrating its utility in prognosticating tumor progression. Our results may have the potential to identify significant mutations that can cause recurrence. These results are relevant in the pretreatment clinical setting to determine appropriate therapy and prepare for potential recurrence pretreatment.

  10. Mapping of groundwater potential zones across Ghana using remote sensing, geographic information systems, and spatial modeling.

    Science.gov (United States)

    Gumma, Murali Krishna; Pavelic, Paul

    2013-04-01

    Groundwater development across much of sub-Saharan Africa is constrained by a lack of knowledge on the suitability of aquifers for borehole construction. The main objective of this study was to map groundwater potential at the country-scale for Ghana to identify locations for developing new supplies that could be used for a range of purposes. Groundwater potential zones were delineated using remote sensing and geographical information system (GIS) techniques drawing from a database that includes climate, geology, and satellite data. Subjective scores and weights were assigned to each of seven key spatial data layers and integrated to identify groundwater potential according to five categories ranging from very good to very poor derived from the total percentage score. From this analysis, areas of very good groundwater potential are estimated to cover 689,680 ha (2.9 % of the country), good potential 5,158,955 ha (21.6 %), moderate potential 10,898,140 ha (45.6 %), and poor/very poor potential 7,167,713 ha (30 %). The results were independently tested against borehole yield data (2,650 measurements) which conformed to the anticipated trend between groundwater potential and borehole yield. The satisfactory delineation of groundwater potential zones through spatial modeling suggests that groundwater development should first focus on areas of the highest potential. This study demonstrates the importance of remote sensing and GIS techniques in mapping groundwater potential at the country-scale and suggests that similar methods could be applied across other African countries and regions.

  11. Species distribution models contribute to determine the effect of climate and interspecific interactions in moving hybrid zones.

    Science.gov (United States)

    Engler, J O; Rödder, D; Elle, O; Hochkirch, A; Secondi, J

    2013-11-01

    Climate is a major factor delimiting species' distributions. However, biotic interactions may also be prominent in shaping geographical ranges, especially for parapatric species forming hybrid zones. Determining the relative effect of each factor and their interaction of the contact zone location has been difficult due to the lack of broad scale environmental data. Recent developments in species distribution modelling (SDM) now allow disentangling the relative contributions of climate and species' interactions in hybrid zones and their responses to future climate change. We investigated the moving hybrid zone between the breeding ranges of two parapatric passerines in Europe. We conducted SDMs representing the climatic conditions during the breeding season. Our results show a large mismatch between the realized and potential distributions of the two species, suggesting that interspecific interactions, not climate, account for the present location of the contact zone. The SDM scenarios show that the southerly distributed species, Hippolais polyglotta, might lose large parts of its southern distribution under climate change, but a similar gain of novel habitat along the hybrid zone seems unlikely, because interactions with the other species (H. icterina) constrain its range expansion. Thus, whenever biotic interactions limit range expansion, species may become 'trapped' if range loss due to climate change is faster than the movement of the contact zone. An increasing number of moving hybrid zones are being reported, but the proximate causes of movement often remain unclear. In a global context of climate change, we call for more interest in their interactions with climate change. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

  12. A Flexible, Efficient Binomial Mixed Model for Identifying Differential DNA Methylation in Bisulfite Sequencing Data

    Science.gov (United States)

    Lea, Amanda J.

    2015-01-01

    Identifying sources of variation in DNA methylation levels is important for understanding gene regulation. Recently, bisulfite sequencing has become a popular tool for investigating DNA methylation levels. However, modeling bisulfite sequencing data is complicated by dramatic variation in coverage across sites and individual samples, and because of the computational challenges of controlling for genetic covariance in count data. To address these challenges, we present a binomial mixed model and an efficient, sampling-based algorithm (MACAU: Mixed model association for count data via data augmentation) for approximate parameter estimation and p-value computation. This framework allows us to simultaneously account for both the over-dispersed, count-based nature of bisulfite sequencing data, as well as genetic relatedness among individuals. Using simulations and two real data sets (whole genome bisulfite sequencing (WGBS) data from Arabidopsis thaliana and reduced representation bisulfite sequencing (RRBS) data from baboons), we show that our method provides well-calibrated test statistics in the presence of population structure. Further, it improves power to detect differentially methylated sites: in the RRBS data set, MACAU detected 1.6-fold more age-associated CpG sites than a beta-binomial model (the next best approach). Changes in these sites are consistent with known age-related shifts in DNA methylation levels, and are enriched near genes that are differentially expressed with age in the same population. Taken together, our results indicate that MACAU is an efficient, effective tool for analyzing bisulfite sequencing data, with particular salience to analyses of structured populations. MACAU is freely available at www.xzlab.org/software.html. PMID:26599596

  13. Experimental Investigation of Land Mobile Prediction Methods and Modeling of Radio Planning Tool Parameters along Indian Rail Road Rural Zones

    Directory of Open Access Journals (Sweden)

    M. V. S. N. Prasad

    2008-01-01

    Full Text Available Mobile communication networks in rural zones were not given enough importance and emphasis unlike their urban counter parts due to the unattractive revenues and economic considerations for the cellular operators. In order to identify the suitable prediction methods for Indian rail road rural zones, train-based measurements were conducted in the northern and western rural zones along rail roads. These were carried out by recording the carriers emitted by the trackside base stations inside the moving train. The observed signal levels converted into path losses were compared initially with various conventional prediction methods. The observed results were also compared with the predicted results of radio planning tool utilizing digital terrain data. The constants of the model incorporated in the radio planning tool were tuned separately for north Indian and west Indian base stations based on the observed results. The suitability of the models has been evaluated in terms of standard statistical parameters.

  14. Extended Finite Element Method XFEM for ductile tearing: Large crack growth modelization based on the transition from a continuous medium to the crack via a cohesive zone model

    International Nuclear Information System (INIS)

    Simatos, A.

    2010-01-01

    This work extends the applicability of local models for ductile fracture to large crack growth modelization for ductile tearing. This is done inserting a cohesive zone model whose constitutive law is identified in order to be consistent with the local model. The consistency is obtained through the cohesive law incremental construction which ensures the equivalence of the energy and of the mechanical response of the models. The extension of the applicability domain of the local modelization is enabled via the XFEM framework which allows for maintaining the mechanical energy during the crack extension step. This method permits also to introduce the cohesive zone model during the calculation without regards to the mesh of the structure for its maximal tensile stress. To apply the XFEM to ductile tearing, this method is extended to non linear problems (Updated Lagrangian Formulation, large scale yield plasticity). The cohesive zone model grows when the criterion defined in term of porosity, tested at the front of the cohesive crack front, is verified. The cohesive zone growth criterion is determined in order to model most of the damaging phase with the local model to ensure that the modelization takes into account the triaxiality ratio history accurately. The proposed method is applied to the Rousselier local model for ductile fracture in the XFEM framework of Cast3M, the FE software of the CEA. (author) [fr

  15. Currency target-zone modeling: An interplay between physics and economics

    Science.gov (United States)

    Lera, Sandro Claudio; Sornette, Didier

    2015-12-01

    We study the performance of the euro-Swiss franc exchange rate in the extraordinary period from September 6, 2011 to January 15, 2015 when the Swiss National Bank enforced a minimum exchange rate of 1.20 Swiss francs per euro. Within the general framework built on geometric Brownian motions and based on the analogy between Brownian motion in finance and physics, the first-order effect of such a steric constraint would enter a priori in the form of a repulsive entropic force associated with the paths crossing the barrier that are forbidden. Nonparametric empirical estimates of drift and volatility show that the predicted first-order analogy between economics and physics is incorrect. The clue is to realize that the random-walk nature of financial prices results from the continuous anticipation of traders about future opportunities, whose aggregate actions translate into an approximate efficient market with almost no arbitrage opportunities. With the Swiss National Bank's stated commitment to enforce the barrier, traders' anticipation of this action leads to a vanishing drift together with a volatility of the exchange rate that depends on the distance to the barrier. This effect is described by Krugman's model [P. R. Krugman, Target zones and exchange rate dynamics, Q. J. Econ. 106, 669 (1991), 10.2307/2937922]. We present direct quantitative empirical evidence that Krugman's theoretical model provides an accurate description of the euro-Swiss franc target zone. Motivated by the insights from the economic model, we revise the initial economics-physics analogy and show that, within the context of hindered diffusion, the two systems can be described with the same mathematics after all. Using a recently proposed extended analogy in terms of a colloidal Brownian particle embedded in a fluid of molecules associated with the underlying order book, we derive that, close to the restricting boundary, the dynamics of both systems is described by a stochastic differential

  16. Currency target-zone modeling: An interplay between physics and economics.

    Science.gov (United States)

    Lera, Sandro Claudio; Sornette, Didier

    2015-12-01

    We study the performance of the euro-Swiss franc exchange rate in the extraordinary period from September 6, 2011 to January 15, 2015 when the Swiss National Bank enforced a minimum exchange rate of 1.20 Swiss francs per euro. Within the general framework built on geometric Brownian motions and based on the analogy between Brownian motion in finance and physics, the first-order effect of such a steric constraint would enter a priori in the form of a repulsive entropic force associated with the paths crossing the barrier that are forbidden. Nonparametric empirical estimates of drift and volatility show that the predicted first-order analogy between economics and physics is incorrect. The clue is to realize that the random-walk nature of financial prices results from the continuous anticipation of traders about future opportunities, whose aggregate actions translate into an approximate efficient market with almost no arbitrage opportunities. With the Swiss National Bank's stated commitment to enforce the barrier, traders' anticipation of this action leads to a vanishing drift together with a volatility of the exchange rate that depends on the distance to the barrier. This effect is described by Krugman's model [P. R. Krugman, Target zones and exchange rate dynamics, Q. J. Econ. 106, 669 (1991)]. We present direct quantitative empirical evidence that Krugman's theoretical model provides an accurate description of the euro-Swiss franc target zone. Motivated by the insights from the economic model, we revise the initial economics-physics analogy and show that, within the context of hindered diffusion, the two systems can be described with the same mathematics after all. Using a recently proposed extended analogy in terms of a colloidal Brownian particle embedded in a fluid of molecules associated with the underlying order book, we derive that, close to the restricting boundary, the dynamics of both systems is described by a stochastic differential equation with a very

  17. Modeling genetic imprinting effects of DNA sequences with multilocus polymorphism data

    Directory of Open Access Journals (Sweden)

    Staud Roland

    2009-08-01

    Full Text Available Abstract Single nucleotide polymorphisms (SNPs represent the most widespread type of DNA sequence variation in the human genome and they have recently emerged as valuable genetic markers for revealing the genetic architecture of complex traits in terms of nucleotide combination and sequence. Here, we extend an algorithmic model for the haplotype analysis of SNPs to estimate the effects of genetic imprinting expressed at the DNA sequence level. The model provides a general procedure for identifying the number and types of optimal DNA sequence variants that are expressed differently due to their parental origin. The model is used to analyze a genetic data set collected from a pain genetics project. We find that DNA haplotype GAC from three SNPs, OPRKG36T (with two alleles G and T, OPRKA843G (with alleles A and G, and OPRKC846T (with alleles C and T, at the kappa-opioid receptor, triggers a significant effect on pain sensitivity, but with expression significantly depending on the parent from which it is inherited (p = 0.008. With a tremendous advance in SNP identification and automated screening, the model founded on haplotype discovery and statistical inference may provide a useful tool for genetic analysis of any quantitative trait with complex inheritance.

  18. Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques

    DEFF Research Database (Denmark)

    Yan, Guangmei; Zhang, Guojie; Fang, Xiaodong

    2011-01-01

    The nonhuman primates most commonly used in medical research are from the genus Macaca. To better understand the genetic differences between these animal models, we present high-quality draft genome sequences from two macaque species, the cynomolgus/crab-eating macaque and the Chinese rhesus...

  19. Draft Genome Sequence of the Phyllosphere Model Bacterium Pantoea agglomerans 299R

    NARCIS (Netherlands)

    Remus-Emsermann, M.N.P.; Kim, E.B.; Marco, M.L.; Tecon, R.; Leveau, J.H.J.

    2013-01-01

    Bacteria belonging to the genus Pantoea are common colonizers of plant leaf surfaces. Here, we present the draft genome sequence of Pantoea agglomerans 299R, a phyllosphere isolate that has become a model strain for studying the ecology of plant leaf-associated bacterial commensals.

  20. Draft Genome Sequence of the Model Naphthalene-Utilizing Organism Pseudomonas putida OUS82

    DEFF Research Database (Denmark)

    Tay, Martin; Roizman, Dan; Cohen, Yehuda

    2014-01-01

    Pseudomonas putida OUS82 was isolated from petrol- and oil-contaminated soil in 1992, and ever since, it has been used as a model organism to study the microbial assimilation of naphthalene and phenanthrene. Here, we report the 6.7-Mb draft genome sequence of P. putida OUS82 and analyze its...

  1. A Reaction Zone Enthalpy Balance Model to Simulate Shock-to-Detonation Transition and Unsteady Detonation Wave Propagation

    Science.gov (United States)

    Froger, A.

    2004-07-01

    The standard models in use to simulate the reactive detonation wave propagation are not accurate in computing the transient evolutions because they focus on the shock front, not on the reaction zone where the coupling of thermodynamic and mechanic effects occurs. The model we propose is based on a new thermodynamic description of the constituents in the reaction zone, and on the use of the enthalpy balance of the chemical reaction as the energetic parameter instead of the heat of reaction. The enthalpy balance of the reaction results from the enthalpies of formation of all the chemical species involved in the reaction and is, therefore, a physical constant. The model is based on four basic assumptions: -1) the reaction zone is anevolving intimate mixture of non-reacted material and detonation products, -2) the energy released by thereaction is inherent to the detonation products alone, -3) the two constituents have the same pressure but different temperatures, -4) the specific energy released is not a constant but is related to the enthalpy balance and depends on the thermodynamic state. The model only needs the physical properties of the materials (equations of state of the constituents, chemical reaction and initiation delay), not the CJ state nor any other sub-model. When coupled with the Euler equations this thermodynamic description of the reaction zone permits us to simulate the transient evolution of an emerging detonation for any geometry (2D or 3D) or confinement structure.

  2. E-Area Low-Level Waste Facility Vadose Zone Model: Confirmation of Water Mass Balance for Subsidence Scenarios

    Energy Technology Data Exchange (ETDEWEB)

    Dyer, J. A. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2017-11-30

    In preparation for the next revision of the E-Area Low-Level Waste Facility (LLWF) Performance Assessment (PA), a mass balance model was developed in Microsoft Excel to confirm correct implementation of intact- and subsided-area infiltration profiles for the proposed closure cap in the PORFLOW vadose-zone model. The infiltration profiles are based on the results of Hydrologic Evaluation of Landfill Performance (HELP) model simulations for both intact and subsided cases.

  3. 3D geodynamic models for the development of opposing continental subduction zones: The Hindu Kush-Pamir example

    Science.gov (United States)

    Liao, Jie; Gerya, Taras; Thielmann, Marcel; Webb, A. Alexander G.; Kufner, Sofia-Katerina; Yin, An

    2017-12-01

    The development of opposing continental subduction zones remains scantly explored in three dimensions. The Hindu Kush-Pamir orogenic system at the western end of the Himalayan orogen provides a rare example of continental collision linked to two opposing intra-continental subduction zones. The subducted plates feature a peculiar 3D geometry consisting of two distinct lithospheric fragments with different polarities, subduction angles and slab-curvatures beneath the Hindu Kush and Pamir, respectively. Using 3D geodynamic modeling, we simulate possible development of two opposing continental subduction zones to understand the dynamic evolution of the Hindu Kush-Pamir orogenic system. Our geodynamic model reproduces the major tectonic elements observed: (1) the deeper subduction depth, the steeper dip angle and the southward offset of the Hindu Kush subduction zone relative to the Pamir naturally occur if convergence direction of the subducting Indian plate and dip-direction of the Hindu Kush subduction zone match. (2) The formation of the highly asymmetrically curved Pamir region and the south-dipping subduction is promoted by the initial geometry of the indenting Indian lithosphere together with the existence of a major strike-slip fault on the eastern margin of the Pamir region. (3) Subduction of only the lower continental crust during continental collision can occur if the coupling between upper and lower crusts is weak enough to allow a separation of these two components, and that (4) the subduction of mainly lower crust then facilitates that conditions for intermediate-depth seismicity can be reached. (5) The secondary tectonic features modeled here such as strike-slip-fault growth, north-northwest striking extension zone, and lateral flow of the thickened ductile upper crust are comparable to the current tectonics of the region. (6) Model results are further compared to the potentially similar orogenic system, i.e., the Alpine orogen, in terms of the curved

  4. The metallogenic model of sandstone-type uranium deposits in interlayer oxidation zone in Yili basin

    International Nuclear Information System (INIS)

    Chen Daisheng; Wang Ruiying; Li Shengxiang; Zhang Kefang

    1997-08-01

    On the basis of comprehensive analysis on various sedimentary environmental criteria, the authors establish a depositional facies model of wet fan formed by alluvial fan's fast pouring into lake for the ore-bearing rocks, and point out favourable horizons and facies for the formation of uranium mineralizations. Deep researches are also done to uranium mineralization characteristics in interlayer oxidation zone, zonation features of ore bodies and spatial distribution regularities of uranium mineralizations. Three sets of data on ore-formation ages (19 Ma, 12 Ma, 1.0 Ma) are obtained with U-Pb isotope method. Various ore-controlling factors of the sandstone-type uranium mineralizations are expounded in detail. Ore-formation mechanism and metallogenic model of sandstone-type uranium deposit in the basin are summarized. Finally, the authors propose some detailed suggestions for the delimitation of prospective areas and future work in the basin, and emphasize that the southwest margin of the basin, especially the area between deposit No.511 and deposit No.512 should be a key prospecting area in the future. (4 refs., 6 figs., 3 tabs.)

  5. Developing hydrological model for water quality in Iraq marshes zone using Landsat-TM

    Science.gov (United States)

    Marghany, Maged; Hasab, Hashim Ali; Mansor, Shattri; Shariff, Abdul Rashid Bin Mohamed

    2016-06-01

    The Mesopotamia marshlands constitute the largest wetland ecosystem in the Middle East and Western Eurasia. These wetlands are located at the confluence of the Tigris and Euphrates Rivers in southern Iraq. However, there are series reductions in the wetland zones because of neighbor countries, i.e. Turkey, Syria built dams upstream of Tigris and Euphrates Rivers. In addition, the first Gulf war of the 1980s had damaged majority of the marches resources. In fact,the marshes had been reduced in size to less than 7% since 1973 and had deteriorated in water quality parameters. The study integrates Hydrological Model of RMA-2 with Geographic Information System, and remote sensing techniques to map the water quality in the marshlands south of Iraq. This study shows that RMA-2 shows the two dimensional water flow pattern and water quality quantities in the marshlands. It can be said that the integration between Hydrological Model of RMA-2, Geographic Information System, and remote sensing techniques can be used to monitor water quality in the marshlands south of Iraq.

  6. Modeling Broadband Variability of Blazars with Time-Dependent Multi-Zone Radiative Transfer Simulations

    Science.gov (United States)

    Fossati, Giovanni

    This proposal aims at fully exploiting the large body of X-ray and multiwavelength observational data on TeV gamma-ray bright blazars for a detailed comparison with state- of-the art blazar radiation transfer simulations. The aim of this investigation is to develop diagnostics on critical jet parameters and shock physics, such as the magnetic field, the kinetic energy content in the jets, the characteristics of the shock acceleration mechanisms, and the detailed influence on geometry on the observed spectral variability features. Our project will comprises a systematic, uniform re-analysis of the relevant (in particular, X-ray) data sets. We will extract time-dependent spectral energy distributions, light curves, and intra-band as well as inter-band time lags from the available data. The modeling tasks will start with a quick sweep through parameter space using a semi- analytical internal-shock model. This will help to narrow down parameters such as the Lorentz factors of interacting emission regions, the overall energy requirements, the characteristics of the electron distributions accelerated at internal shocks, and the magnetic field. The parameters of this semi-analytical internal-shock model that allow for a representation of time-dependent SEDs, light curves and inter-band time lags, will form the starting point for our detailed modeling using our state-of-the-art time-dependent multi-zone Monte-Carlo simulation code. Using that code, we will explore in more detail the characteristics of the particle acceleration in active regions and the influence of various geometries on the observable features. By capitalizing on archival data of several NASA space astrophysics missions our proposal is in agreement with the NASA ADAP research objective, "the analysis io NASA space astrophysics data that are archived in the public domain at the time of submission", as stated in the NASA Research announcement.

  7. Modelling of blackout sequence at Atucha-1 using the MARCH3 code

    International Nuclear Information System (INIS)

    Baron, J.; Bastianelli, B.

    1997-01-01

    This paper presents the modelling of a complete blackout at the Atucha-1 NPP as preliminary phase for a Level II safety probabilistic analysis. The MARCH3 code of the STCP (Source Term Code Package) is used, based on a plant model made in accordance with particularities of the plant design. The analysis covers all the severe accident phases. The results allow to view the time sequence of the events, and provide the basis for source term studies. (author). 6 refs., 2 figs

  8. Constructing an everywhere and locally relevant predictive model of the West-African critical zone

    Science.gov (United States)

    Hector, B.; Cohard, J. M.; Pellarin, T.; Maxwell, R. M.; Cappelaere, B.; Demarty, J.; Grippa, M.; Kergoat, L.; Lebel, T.; Mamadou, O.; Mougin, E.; Panthou, G.; Peugeot, C.; Vandervaere, J. P.; Vischel, T.; Vouillamoz, J. M.

    2017-12-01

    Considering water resources and hydrologic hazards, West Africa is among the most vulnerable regions to face both climatic (e.g. with the observed intensification of precipitation) and anthropogenic changes. With +3% of demographic rate, the region experiences rapid land use changes and increased pressure on surface and groundwater resources with observed consequences on the hydrological cycle (water table rise result of the sahelian paradox, increase in flood occurrence, etc.) Managing large hydrosystems (such as transboundary aquifers or rivers basins as the Niger river) requires anticipation of such changes. However, the region significantly lacks observations, for constructing and validating critical zone (CZ) models able to predict future hydrologic regime, but also comprises hydrosystems which encompass strong environmental gradients (e.g. geological, climatic, ecological) with highly different dominating hydrological processes. We address these issues by constructing a high resolution (1 km²) regional scale physically-based model using ParFlow-CLM which allows modeling a wide range of processes without prior knowledge on their relative dominance. Our approach combines multiple scale modeling from local to meso and regional scales within the same theoretical framework. Local and meso-scale models are evaluated thanks to the rich AMMA-CATCH CZ observation database which covers 3 supersites with contrasted environments in Benin (Lat.: 9.8°N), Niger (Lat.: 13.3°N) and Mali (Lat.: 15.3°N). At the regional scale the lack of relevant map of soil hydrodynamic parameters is addressed using remote sensing data assimilation. Our first results show the model's ability to reproduce the known dominant hydrological processes (runoff generation, ET, groundwater recharge…) across the major West-African regions and allow us to conduct virtual experiments to explore the impact of global changes on the hydrosystems. This approach is a first step toward the construction of

  9. Detection of mesoscale zones of atmospheric instabilities using remote sensing and weather forecasting model data

    Science.gov (United States)

    Winnicki, I.; Jasinski, J.; Kroszczynski, K.; Pietrek, S.

    2009-04-01

    The paper presents elements of research conducted in the Faculty of Civil Engineering and Geodesy of the Military University of Technology, Warsaw, Poland, concerning application of mesoscale models and remote sensing data to determining meteorological conditions of aircraft flight directly related with atmospheric instabilities. The quality of meteorological support of aviation depends on prompt and effective forecasting of weather conditions changes. The paper presents a computer module for detecting and monitoring zones of cloud cover, precipitation and turbulence along the aircraft flight route. It consists of programs and scripts for managing, processing and visualizing meteorological and remote sensing databases. The application was developed in Matlab® for Windows®. The module uses products of COAMPS (Coupled Ocean/Atmosphere Mesoscale Prediction System) mesoscale non-hydrostatic model of the atmosphere developed by the US Naval Research Laboratory, satellite images acquisition system from the MSG-2 (Meteosat Second Generation) of the European Organization for the Exploitation of Meteorological Satellites (EUMETSAT) and meteorological radars data acquired from the Institute of Meteorology and Water Management (IMGW), Warsaw, Poland. The satellite images acquisition system and the COAMPS model are run operationally in the Faculty of Civil Engineering and Geodesy. The mesoscale model is run on an IA64 Feniks multiprocessor 64-bit computer cluster. The basic task of the module is to enable a complex analysis of data sets of miscellaneous information structure and to verify COAMPS results using satellite and radar data. The research is conducted using uniform cartographic projection of all elements of the database. Satellite and radar images are transformed into the Lambert Conformal projection of COAMPS. This facilitates simultaneous interpretation and supports decision making process for safe execution of flights. Forecasts are based on horizontal

  10. Models and observations of foam coverage and bubble content in the surf zone

    Science.gov (United States)

    Kirby, J. T.; Shi, F.; Holman, R. A.

    2010-12-01

    column motion. Preliminary steps to calibrate and verify the resulting models will be taken based on results to be collected during the Surf Zone Optics experiment at Duck, NC in September 2010. Initial efforts will focus on an examination of breaking wave patterns and persistent foam distributions, using ARGUS imagery.

  11. Deriving Rich Coastal Morphology and Shore Zone Classification from LIDAR Terrain Models

    NARCIS (Netherlands)

    Nijland, Wiebe|info:eu-repo/dai/nl/304823643; Reshitnyk, Luba Y.; Starzomski, Brian M.; Reynolds, John D.; Darimont, Chris T.; Nelson, Trisalyn A.

    2017-01-01

    Comprehensive mapping of shore-zone morphology supports evaluation of shore habitat, monitoring of environmental hazards, and characterization of the transfer of nutrients between marine and terrestrial environments. This article shows how rich shore-zone morphological metrics can be derived from

  12. Process-based and Surrogate Modelling of Fine Sediment Transport in the Dutch Coastal Zone

    NARCIS (Netherlands)

    Kai, C.

    2009-01-01

    Coastal zones which are known as the interface between continents and oceans are vital and important to human beings because a majority of the world's population live in such zones (Nelson, 2007). Coastal systems are among the most dynamic and energetic environments on earth and they are

  13. VT Data - Zoning 20081203, Norwich

    Data.gov (United States)

    Vermont Center for Geographic Information — BASE DISTRICTS. Models a municipality’s zoning zones and related information. Final boundary determinations must be obtained from the town Zoning Administrator. All...

  14. VT Data - Zoning 20170710, Woodstock

    Data.gov (United States)

    Vermont Center for Geographic Information — BASE DISTRICTS. Models a municipality’s zoning zones and related information. Final boundary determinations must be obtained from the town Zoning Administrator. All...

  15. VT Data - Zoning 20170227, Fairlee

    Data.gov (United States)

    Vermont Center for Geographic Information — BASE DISTRICTS. Models a municipality’s zoning zones and related information. Final boundary determinations must be obtained from the town Zoning Administrator. All...

  16. Modeling of tropospheric NO2 column over different climatic zones and land use/land cover types in South Asia

    Science.gov (United States)

    ul-Haq, Zia; Rana, Asim Daud; Tariq, Salman; Mahmood, Khalid; Ali, Muhammad; Bashir, Iqra

    2018-03-01

    We have applied regression analyses for the modeling of tropospheric NO2 (tropo-NO2) as the function of anthropogenic nitrogen oxides (NOx) emissions, aerosol optical depth (AOD), and some important meteorological parameters such as temperature (Temp), precipitation (Preci), relative humidity (RH), wind speed (WS), cloud fraction (CLF) and outgoing long-wave radiation (OLR) over different climatic zones and land use/land cover types in South Asia during October 2004-December 2015. Simple linear regression shows that, over South Asia, tropo-NO2 variability is significantly linked to AOD, WS, NOx, Preci and CLF. Also zone-5, consisting of tropical monsoon areas of eastern India and Myanmar, is the only study zone over which all the selected parameters show their influence on tropo-NO2 at statistical significance levels. In stepwise multiple linear modeling, tropo-NO2 column over landmass of South Asia, is significantly predicted by the combination of RH (standardized regression coefficient, β = - 49), AOD (β = 0.42) and NOx (β = 0.25). The leading predictors of tropo-NO2 columns over zones 1-5 are OLR, AOD, Temp, OLR, and RH respectively. Overall, as revealed by the higher correlation coefficients (r), the multiple regressions provide reasonable models for tropo-NO2 over South Asia (r = 0.82), zone-4 (r = 0.90) and zone-5 (r = 0.93). The lowest r (of 0.66) has been found for hot semi-arid region in northwestern Indus-Ganges Basin (zone-2). The highest value of β for urban area AOD (of 0.42) is observed for megacity Lahore, located in warm semi-arid zone-2 with large scale crop-residue burning, indicating strong influence of aerosols on the modeled tropo-NO2 column. A statistical significant correlation (r = 0.22) at the 0.05 level is found between tropo-NO2 and AOD over Lahore. Also NOx emissions appear as the highest contributor (β = 0.59) for modeled tropo-NO2 column over megacity Dhaka.

  17. Prediction of groundwater flowing well zone at An-Najif Province, central Iraq using evidential belief functions model and GIS.

    Science.gov (United States)

    Al-Abadi, Alaa M; Pradhan, Biswajeet; Shahid, Shamsuddin

    2015-10-01

    The objective of this study is to delineate groundwater flowing well zone potential in An-Najif Province of Iraq in a data-driven evidential belief function model developed in a geographical information system (GIS) environment. An inventory map of 68 groundwater flowing wells was prepared through field survey. Seventy percent or 43 wells were used for training the evidential belief functions model and the reset 30 % or 19 wells were used for validation of the model. Seven groundwater conditioning factors mostly derived from RS were used, namely elevation, slope angle, curvature, topographic wetness index, stream power index, lithological units, and distance to the Euphrates River in this study. The relationship between training flowing well locations and the conditioning factors were investigated using evidential belief functions technique in a GIS environment. The integrated belief values were classified into five categories using natural break classification scheme to predict spatial zoning of groundwater flowing well, namely very low (0.17-0.34), low (0.34-0.46), moderate (0.46-0.58), high (0.58-0.80), and very high (0.80-0.99). The results show that very low and low zones cover 72 % (19,282 km(2)) of the study area mostly clustered in the central part, the moderate zone concentrated in the west part covers 13 % (3481 km(2)), and the high and very high zones extended over the northern part cover 15 % (3977 km(2)) of the study area. The vast spatial extension of very low and low zones indicates that groundwater flowing wells potential in the study area is low. The performance of the evidential belief functions spatial model was validated using the receiver operating characteristic curve. A success rate of 0.95 and a prediction rate of 0.94 were estimated from the area under relative operating characteristics curves, which indicate that the developed model has excellent capability to predict groundwater flowing well zones. The produced map of groundwater

  18. Automated side-chain model building and sequence assignment by template matching

    International Nuclear Information System (INIS)

    Terwilliger, Thomas C.

    2002-01-01

    A method for automated macromolecular side-chain model building and for aligning the sequence to the map is described. An algorithm is described for automated building of side chains in an electron-density map once a main-chain model is built and for alignment of the protein sequence to the map. The procedure is based on a comparison of electron density at the expected side-chain positions with electron-density templates. The templates are constructed from average amino-acid side-chain densities in 574 refined protein structures. For each contiguous segment of main chain, a matrix with entries corresponding to an estimate of the probability that each of the 20 amino acids is located at each position of the main-chain model is obtained. The probability that this segment corresponds to each possible alignment with the sequence of the protein is estimated using a Bayesian approach and high-confidence matches are kept. Once side-chain identities are determined, the most probable rotamer for each side chain is built into the model. The automated procedure has been implemented in the RESOLVE software. Combined with automated main-chain model building, the procedure produces a preliminary model suitable for refinement and extension by an experienced crystallographer

  19. Markovian and non-Markovian protein sequence evolution: aggregated Markov process models.

    Science.gov (United States)

    Kosiol, Carolin; Goldman, Nick

    2011-08-26

    Over the years, there have been claims that evolution proceeds according to systematically different processes over different timescales and that protein evolution behaves in a non-Markovian manner. On the other hand, Markov models are fundamental to many applications in evolutionary studies. Apparent non-Markovian or time-dependent behavior has been attributed to influence of the genetic code at short timescales and dominance of physicochemical properties of the amino acids at long timescales. However, any long time period is simply the accumulation of many short time periods, and it remains unclear why evolution should appear to act systematically differently across the range of timescales studied. We show that the observed time-dependent behavior can be explained qualitatively by modeling protein sequence evolution as an aggregated Markov process (AMP): a time-homogeneous Markovian substitution model observed only at the level of the amino acids encoded by the protein-coding DNA sequence. The study of AMPs sheds new light on the relationship between amino acid-level and codon-level models of sequence evolution, and our results suggest that protein evolution should be modeled at the codon level rather than using amino acid substitution models. Copyright © 2011 Elsevier Ltd. All rights reserved.

  20. Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences.

    Directory of Open Access Journals (Sweden)

    Zhang Zhang

    2009-06-01

    Full Text Available A major analytical challenge in computational biology is the detection and description of clusters of specified site types, such as polymorphic or substituted sites within DNA or protein sequences. Progress has been stymied by a lack of suitable methods to detect clusters and to estimate the extent of clustering in discrete linear sequences, particularly when there is no a priori specification of cluster size or cluster count. Here we derive and demonstrate a maximum likelihood method of hierarchical clustering. Our method incorporates a tripartite divide-and-conquer strategy that models sequence heterogeneity, delineates clusters, and yields a profile of the level of clustering associated with each site. The clustering model may be evaluated via model selection using the Akaike Information Criterion, the corrected Akaike Information Criterion, and the Bayesian Information Criterion. Furthermore, model averaging using weighted model likelihoods may be applied to incorporate model uncertainty into the profile of heterogeneity across sites. We evaluated our method by examining its performance on a number of simulated datasets as well as on empirical polymorphism data from diverse natural alleles of the Drosophila alcohol dehydrogenase gene. Our method yielded greater power for the detection of clustered sites across a breadth of parameter ranges, and achieved better accuracy and precision of estimation of clusters, than did the existing empirical cumulative distribution function statistics.

  1. Mesoscopic modeling of DNA denaturation rates: Sequence dependence and experimental comparison

    Energy Technology Data Exchange (ETDEWEB)

    Dahlen, Oda, E-mail: oda.dahlen@ntnu.no; Erp, Titus S. van, E-mail: titus.van.erp@ntnu.no [Department of Chemistry, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, Realfagbygget D3-117 7491 Trondheim (Norway)

    2015-06-21

    Using rare event simulation techniques, we calculated DNA denaturation rate constants for a range of sequences and temperatures for the Peyrard-Bishop-Dauxois (PBD) model with two different parameter sets. We studied a larger variety of sequences compared to previous studies that only consider DNA homopolymers and DNA sequences containing an equal amount of weak AT- and strong GC-base pairs. Our results show that, contrary to previous findings, an even distribution of the strong GC-base pairs does not always result in the fastest possible denaturation. In addition, we applied an adaptation of the PBD model to study hairpin denaturation for which experimental data are available. This is the first quantitative study in which dynamical results from the mesoscopic PBD model have been compared with experiments. Our results show that present parameterized models, although giving good results regarding thermodynamic properties, overestimate denaturation rates by orders of magnitude. We believe that our dynamical approach is, therefore, an important tool for verifying DNA models and for developing next generation models that have higher predictive power than present ones.

  2. An overview of the recent approaches for terroir functional modelling, footprinting and zoning

    Science.gov (United States)

    Vaudour, E.; Costantini, E.; Jones, G. V.; Mocali, S.

    2014-11-01

    Notions of terroir and their conceptualization through agri-environmental sciences have become popular in many parts of world. Originally developed for wine, terroir now encompasses many other crops including fruits, vegetables, cheese, olive oil, coffee, cacao and other crops, linking the uniqueness and quality of both beverages and foods to the environment where they are produced, giving the consumer a sense of place. Climate, geology, geomorphology, and soil are the main environmental factors which compose the terroir effect at different scales. Often considered immutable at the cultural scale, the natural components of terroir are actually a set of processes, which together create a delicate equilibrium and regulation of its effect on products in both space and time. Due to both a greater need to better understand regional to site variations in crop production and the growth in spatial analytic technologies, the study of terroir has shifted from a largely descriptive regional science to a more applied, technical research field. Furthermore, the explosion of spatial data availability and sensing technologies has made the within-field scale of study more valuable to the individual grower. The result has been greater adoption but also issues associated with both the spatial and temporal scales required for practical applications, as well as the relevant approaches for data synthesis. Moreover, as soil microbial communities are known to be of vital importance for terrestrial processes by driving the major soil geochemical cycles and supporting healthy plant growth, an intensive investigation of the microbial organization and their function is also required. Our objective is to present an overview of existing data and modelling approaches for terroir functional modelling, footprinting and zoning at local and regional scales. This review will focus on three main areas of recent terroir research: (1) quantifying the influences of terroir components on plant growth

  3. Protection zone in a diffusive predator-prey model with Beddington-DeAngelis functional response.

    Science.gov (United States)

    He, Xiao; Zheng, Sining

    2017-07-01

    In any reaction-diffusion system of predator-prey models, the population densities of species are determined by the interactions between them, together with the influences from the spatial environments surrounding them. Generally, the prey species would die out when their birth rate is too low, the habitat size is too small, the predator grows too fast, or the predation pressure is too high. To save the endangered prey species, some human interference is useful, such as creating a protection zone where the prey could cross the boundary freely but the predator is prohibited from entering. This paper studies the existence of positive steady states to a predator-prey model with reaction-diffusion terms, Beddington-DeAngelis type functional response and non-flux boundary conditions. It is shown that there is a threshold value [Formula: see text] which characterizes the refuge ability of prey such that the positivity of prey population can be ensured if either the prey's birth rate satisfies [Formula: see text] (no matter how large the predator's growth rate is) or the predator's growth rate satisfies [Formula: see text], while a protection zone [Formula: see text] is necessary for such positive solutions if [Formula: see text] with [Formula: see text] properly large. The more interesting finding is that there is another threshold value [Formula: see text], such that the positive solutions do exist for all [Formula: see text]. Letting [Formula: see text], we get the third threshold value [Formula: see text] such that if [Formula: see text], prey species could survive no matter how large the predator's growth rate is. In addition, we get the fourth threshold value [Formula: see text] for negative [Formula: see text] such that the system admits positive steady states if and only if [Formula: see text]. All these results match well with the mechanistic derivation for the B-D type functional response recently given by Geritz and Gyllenberg (J Theoret Biol 314:106-108, 2012

  4. Comparison of Enzymes / Non-Enzymes Proteins Classification Models Based on 3D, Composition, Sequences and Topological Indices

    OpenAIRE

    Munteanu, Cristian Robert

    2014-01-01

    Comparison of Enzymes / Non-Enzymes Proteins Classification Models Based on 3D, Composition, Sequences and Topological Indices, German Conference on Bioinformatics (GCB), Potsdam, Germany (September, 2007)

  5. Mathematical modelling of surface water-groundwater flow and salinity interactions in the coastal zone

    Science.gov (United States)

    Spanoudaki, Katerina; Kampanis, Nikolaos A.

    2014-05-01

    Coastal areas are the most densely-populated areas in the world. Consequently water demand is high, posing great pressure on fresh water resources. Climatic change and its direct impacts on meteorological variables (e.g. precipitation) and indirect impact on sea level rise, as well as anthropogenic pressures (e.g. groundwater abstraction), are strong drivers causing groundwater salinisation and subsequently affecting coastal wetlands salinity with adverse effects on the corresponding ecosystems. Coastal zones are a difficult hydrologic environment to represent with a mathematical model due to the large number of contributing hydrologic processes and variable-density flow conditions. Simulation of sea level rise and tidal effects on aquifer salinisation and accurate prediction of interactions between coastal waters, groundwater and neighbouring wetlands requires the use of integrated surface water-groundwater models. In the past few decades several computer codes have been developed to simulate coupled surface and groundwater flow. In these numerical models surface water flow is usually described by the 1-D Saint Venant equations (e.g. Swain and Wexler, 1996) or the 2D shallow water equations (e.g. Liang et al., 2007). Further simplified equations, such as the diffusion and kinematic wave approximations to the Saint Venant equations, are also employed for the description of 2D overland flow and 1D stream flow (e.g. Gunduz and Aral, 2005). However, for coastal bays, estuaries and wetlands it is often desirable to solve the 3D shallow water equations to simulate surface water flow. This is the case e.g. for wind-driven flows or density-stratified flows. Furthermore, most integrated models are based on the assumption of constant fluid density and therefore their applicability to coastal regions is questionable. Thus, most of the existing codes are not well-suited to represent surface water-groundwater interactions in coastal areas. To this end, the 3D integrated

  6. Simulation Methods for High-Cycle Fatigue-Driven Delamination using Cohesive Zone Models - Fundamental Behavior and Benchmark Studies

    DEFF Research Database (Denmark)

    Bak, Brian Lau Verndal; Lindgaard, Esben; Turon, A.

    2015-01-01

    A novel computational method for simulating fatigue-driven delamination cracks in composite laminated structures under cyclic loading based on a cohesive zone model [2] and new benchmark studies with four other comparable methods [3-6] are presented. The benchmark studies describe and compare the...

  7. Generation of 3-D hydrostratigraphic zones from dense airborne electromagnetic data to assess groundwater model prediction error

    Science.gov (United States)

    Christensen, Nikolaj K; Minsley, Burke J.; Christensen, Steen

    2017-01-01

    We present a new methodology to combine spatially dense high-resolution airborne electromagnetic (AEM) data and sparse borehole information to construct multiple plausible geological structures using a stochastic approach. The method developed allows for quantification of the performance of groundwater models built from different geological realizations of structure. Multiple structural realizations are generated using geostatistical Monte Carlo simulations that treat sparse borehole lithological observations as hard data and dense geophysically derived structural probabilities as soft data. Each structural model is used to define 3-D hydrostratigraphical zones of a groundwater model, and the hydraulic parameter values of the zones are estimated by using nonlinear regression to fit hydrological data (hydraulic head and river discharge measurements). Use of the methodology is demonstrated for a synthetic domain having structures of categorical deposits consisting of sand, silt, or clay. It is shown that using dense AEM data with the methodology can significantly improve the estimated accuracy of the sediment distribution as compared to when borehole data are used alone. It is also shown that this use of AEM data can improve the predictive capability of a calibrated groundwater model that uses the geological structures as zones. However, such structural models will always contain errors because even with dense AEM data it is not possible to perfectly resolve the structures of a groundwater system. It is shown that when using such erroneous structures in a groundwater model, they can lead to biased parameter estimates and biased model predictions, therefore impairing the model's predictive capability.

  8. Modeling Raw Sewage Leakage and Transport in the Unsaturated Zone of Carbonate Aquifer Using Carbamazepine as an Indicator

    Science.gov (United States)

    Yakirevich, A.; Kuznetsov, M.; Livshitz, Y.; Gasser, G.; Pankratov, I.; Lev, O.; Adar, E.; Dvory, N. Z.

    2016-12-01

    Fast contamination of groundwater in karstic aquifers can be caused due to leaky sewers, for example, or overflow from sewer networks. When flowing through a karst system, wastewater has the potential to reach the aquifer in a relatively short time. The Western Mountain Aquifer (Yarkon-Taninim) of Israel is one of the country's major water resources. During late winter 2013, maintenance actions were performed on a central sewage pipe that caused raw sewage to leak into the creek located in the study area. The subsequent infiltration of sewage through the thick ( 100 m) fractured/karst unsaturated zone led to a sharp increase in contaminant concentrations in the groundwater, which was monitored in a well located 29 meters from the center of the creek. Carbamazepine (CBZ) was used as an indicator for the presence of untreated raw sewage and its quantification in groundwater. The ultimate research goal was to develop a mathematical model for quantifying flow and contaminant transport processes in the fractured-porous unsaturated zone and karstified groundwater system. A quasi-3D dual permeability numerical model, representing the 'vadose zone - aquifer' system, was developed by a series of 1D equations solved in variably-saturated zone and by 3D-saturated flow and transport equation in groundwater. The 1D and 3D equations were coupled at the moving phreatic surface. The model was calibrated and applied to a simulated water flow scenario and CBZ transport during and after the observed sewage leakage event. The results of simulation showed that after the leakage stopped, significant amounts of CBZ were retained in the porous matrix of the unsaturated zone below the creek. Water redistribution and slow recharge during the dry summer season contributed to elevated CBZ concentrations in the groundwater in the vicinity of the creek and tens of meters downstream. The resumption of autumn rains enhanced flushing of CBZ from the unsaturated zone and led to an increase in

  9. Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity.

    Directory of Open Access Journals (Sweden)

    Lorenzo Asti

    2016-04-01

    Full Text Available The immune system has developed a number of distinct complex mechanisms to shape and control the antibody repertoire. One of these mechanisms, the affinity maturation process, works in an evolutionary-like fashion: after binding to a foreign molecule, the antibody-producing B-cells exhibit a high-frequency mutation rate in the genome region that codes for the antibody active site. Eventually, cells that produce antibodies with higher affinity for their cognate antigen are selected and clonally expanded. Here, we propose a new statistical approach based on maximum entropy modeling in which a scoring function related to the binding affinity of antibodies against a specific antigen is inferred from a sample of sequences of the immune repertoire of an individual. We use our inference strategy to infer a statistical model on a data set obtained by sequencing a fairly large portion of the immune repertoire of an HIV-1 infected patient. The Pearson correlation coefficient between our scoring function and the IC50 neutralization titer measured on 30 different antibodies of known sequence is as high as 0.77 (p-value 10-6, outperforming other sequence- and structure-based models.

  10. Modeling the Process of Event Sequence Data Generated for Working Condition Diagnosis

    Directory of Open Access Journals (Sweden)

    Jianwei Ding

    2015-01-01

    Full Text Available Condition monitoring systems are widely used to monitor the working condition of equipment, generating a vast amount and variety of telemetry data in the process. The main task of surveillance focuses on analyzing these routinely collected telemetry data to help analyze the working condition in the equipment. However, with the rapid increase in the volume of telemetry data, it is a nontrivial task to analyze all the telemetry data to understand the working condition of the equipment without any a priori knowledge. In this paper, we proposed a probabilistic generative model called working condition model (WCM, which is capable of simulating the process of event sequence data generated and depicting the working condition of equipment at runtime. With the help of WCM, we are able to analyze how the event sequence data behave in different working modes and meanwhile to detect the working mode of an event sequence (working condition diagnosis. Furthermore, we have applied WCM to illustrative applications like automated detection of an anomalous event sequence for the runtime of equipment. Our experimental results on the real data sets demonstrate the effectiveness of the model.

  11. Hydrological modelling over different scales on the edge of the permafrost zone: approaching model realism based on experimentalists' knowledge

    Science.gov (United States)

    Nesterova, Natalia; Makarieva, Olga; Lebedeva, Lyudmila

    2017-04-01

    Quantitative and qualitative experimentalists' data helps to advance both understanding of the runoff generation and modelling strategies. There is significant lack of such information for the dynamic and vulnerable cold regions. The aim of the study is to make use of historically collected experimental hydrological data for modelling poorly-gauged river basins on larger scales near the southern margin of the permafrost zone in Eastern Siberia. Experimental study site "Mogot" includes the Nelka river (30.8 km2) and its three tributaries with watersheds area from 2 to 5.8 km2. It is located in the upper elevated (500 - 1500 m a.s.l.) part of the Amur River basin. Mean annual temperature and precipitation are -7.5°C and 555 mm respectively. Top of the mountains with weak vegetation has well drained soil that prevents any water accumulation. Larch forest on the northern slopes has thick organic layer. It causes shallow active layer and relatively small subsurface water storage. Soil in the southern slopes has thinner organic layer and thaws up to 1.6 m depth. Flood plains are the wettest landscape with highest water storage capacity. Measured monthly evaporation varies from 9 to 100 mm through the year. Experimental data shows importance of air temperature and precipitation changes with the elevation. Their gradient was taken into account for hydrological simulations. Model parameterization was developed according to available quantitative and qualitative data in the Mogot station. The process-based hydrological Hydrograph model was used in the study. It explicitly describes hydrological processes in different permafrost environments. Flexibility of the Hydrograph model allows take advantage from the experimental data for model set-up. The model uses basic meteorological data as input. The level of model complexity is suitable for a remote, sparsely gauged region such as Southern Siberia as it allows for a priori assessment of the model parameters. Model simulation

  12. Dynamic Linkages Between the Transition Zone & Surface Plate Motions in 2D Models of Subduction

    Science.gov (United States)

    Arredondo, K.; Billen, M. I.

    2013-12-01

    While slab pull is considered the dominant force controlling plate motion and speed, its magnitude is controlled by slab behavior in the mantle, where tomographic studies show a wide range of possibilities from direct penetration to folding, or stagnation directly above the lower mantle (e.g. Fukao et al., 2009). Geodynamic studies have investigated various parameters, such as plate age and two phase transitions, to recreate observed behavior (e.g. Běhounková and Cízková, 2008). However, past geodynamic models have left out known slab characteristics that may have a large impact on slab behavior and our understanding of subduction processes. Mineral experiments and seismic observations have indicated the existence of additional phase transitions in the mantle transition zone that may produce buoyancy forces large enough to affect the descent of a subducting slab (e.g. Ricard et al., 2005). The current study systematically tests different common assumptions used in geodynamic models: kinematic versus free-slip boundary conditions, the effects of adiabatic heating, viscous dissipation and latent heat, compositional layering and a more complete suite of phase transitions. Final models have a complete energy equation, with eclogite, harzburgite and pyrolite lithosphere compositional layers, and seven composition-dependent phase transitions within the olivine, pyroxene and garnet polymorph minerals. Results show important feedback loops between different assumptions and new behavior from the most complete models. Kinematic models show slab weakening or breaking above the 660 km boundary and between compositional layers. The behavior in dynamic models with a free-moving trench and overriding plate is compared to the more commonly found kinematic models. The new behavior may have important implications for the depth distribution of deep earthquakes within the slab. Though the thermodynamic parameters of certain phase transitions may be uncertain, their presence and

  13. Method for predicting homology modeling accuracy from amino acid sequence alignment: the power function.

    Science.gov (United States)

    Iwadate, Mitsuo; Kanou, Kazuhiko; Terashi, Genki; Umeyama, Hideaki; Takeda-Shitaka, Mayuko

    2010-01-01

    We have devised a power function (PF) that can predict the accuracy of a three-dimensional (3D) structure model of a protein using only amino acid sequence alignments. This Power Function (PF) consists of three parts; (1) the length of a model, (2) a homology identity percent value and (3) the agreement rate between PSI-PRED secondary structure prediction and the secondary structure judgment of a reference protein. The PF value is mathematically computed from the execution process of homology search tools, such as FASTA or various BLAST programs, to obtain the amino acid sequence alignments. There is a high correlation between the global distance test-total score (GDT_TS) value of the protein model based upon the PF score and the GDT_TS(MAX) value used as an index of protein modeling accuracy in the international contest Critical Assessment of Techniques for Protein Structure Prediction (CASP). Accordingly, the PF method is valuable for constructing a highly accurate model without wasteful calculations of homology modeling that is normally performed by an iterative method to move the main chain and side chains in the modeling process. Moreover, a model with higher accuracy can be obtained by combining the models ordered by the PF score with models sorted by the size of the CIRCLE score. The CIRCLE software is a 3D-1D program, in which energetic stabilization is estimated based upon the experimental environment of each amino acid residue in the protein solution or protein crystals.

  14. Technetium, Iodine, and Chromium Adsorption/Desorption Kd Values for Vadose Zone Pore Water, ILAW Glass, and Cast Stone Leachates Contacting an IDF Sand Sequence

    Energy Technology Data Exchange (ETDEWEB)

    Last, George V. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Snyder, Michelle M.V. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Um, Wooyong [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Stephenson, John R. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Leavy, Ian I. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Strickland, Christopher E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Bacon, Diana H. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Qafoku, Nikolla [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Serne, R. Jeffrey [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2015-11-01

    Performance and risk assessments of immobilized low-activity waste (ILAW) at the Integrated Disposal Facility (IDF) have shown that risks to groundwater are quite sensitive to adsorption-desorption interactions occurring in the near- and far-field environment. These interactions between the underlying sediments and the contaminants present in the leachates that descend from the buried glass, secondary waste grouts, and potentially Cast Stone low-activity waste packages have been represented in these assessments using the contaminant distribution coefficient (Kd) construct. Some contaminants (99Tc, 129I, and Cr) present in significant quantities in these wastes have low Kd values and tend to drive risk to public health and the environment. Relatively small changes in the Kd value can cause relatively large changes in the retardation factor. Thus, even relatively small uncertainty in the Kd value can result in a relatively large uncertainty in the risk determined through performance assessment modeling. The purpose of this study is to further reduce the uncertainty in Kd values for 99Tc, iodine (iodide and iodate), and Cr (chromate; CrO42-) by conducting systematic adsorption-desorption experiments using actual sand-dominated Hanford formation sediments from beneath the IDF and solutions that closely mimic Hanford vadose zone pore water and leachates from Cast Stone and ILAW glass waste forms. Twenty-four batch and 21 flow-through column experiments were conducted, yielding 261 Kd measurements for these key contaminants, and contributing to our understanding for predicting transport from wastes disposed to the IDF. While the batch Kd methodology is not well-suited for measuring Kd values for non-sorbing species (as noted by the U.S. Environmental Protection Agency), the batch Kd results presented here are not wholly inconsistent with the column Kd results, and could be used for sensitivity purposes. Results from the column experiments are consistent with the best

  15. Profile hidden Markov models for the detection of viruses within metagenomic sequence data.

    Directory of Open Access Journals (Sweden)

    Peter Skewes-Cox

    Full Text Available Rapid, sensitive, and specific virus detection is an important component of clinical diagnostics. Massively parallel sequencing enables new diagnostic opportunities that complement traditional serological and PCR based techniques. While massively parallel sequencing promises the benefits of being more comprehensive and less biased than traditional approaches, it presents new analytical challenges, especially with respect to detection of pathogen sequences in metagenomic contexts. To a first approximation, the initial detection of viruses can be achieved simply through alignment of sequence reads or assembled contigs to a reference database of pathogen genomes with tools such as BLAST. However, recognition of highly divergent viral sequences is problematic, and may be further complicated by the inherently high mutation rates of some viral types, especially RNA viruses. In these cases, increased sensitivity may be achieved by leveraging position-specific information during the alignment process. Here, we constructed HMMER3-compatible profile hidden Markov models (profile HMMs from all the virally annotated proteins in RefSeq in an automated fashion using a custom-built bioinformatic pipeline. We then tested the ability of these viral profile HMMs ("vFams" to accurately classify sequences as viral or non-viral. Cross-validation experiments with full-length gene sequences showed that the vFams were able to recall 91% of left-out viral test sequences without erroneously classifying any non-viral sequences into viral protein clusters. Thorough reanalysis of previously published metagenomic datasets with a set of the best-performing vFams showed that they were more sensitive than BLAST for detecting sequences originating from more distant relatives of known viruses. To facilitate the use of the vFams for rapid detection of remote viral homologs in metagenomic data, we provide two sets of vFams, comprising more than 4,000 vFams each, in the HMMER3

  16. Extending Galactic Habitable Zone Modeling to Include the Emergence of Intelligent Life.

    Science.gov (United States)

    Morrison, Ian S; Gowanlock, Michael G

    2015-08-01

    Previous studies of the galactic habitable zone have been concerned with identifying those regions of the Galaxy that may favor the emergence of complex life. A planet is deemed habitable if it meets a set of assumed criteria for supporting the emergence of such complex life. In this work, we extend the assessment of habitability to consider the potential for life to further evolve to the point of intelligence--termed the propensity for the emergence of intelligent life, φI. We assume φI is strongly influenced by the time durations available for evolutionary processes to proceed undisturbed by the sterilizing effects of nearby supernovae. The times between supernova events provide windows of opportunity for the evolution of intelligence. We developed a model that allows us to analyze these window times to generate a metric for φI, and we examine here the spatial and temporal variation of this metric. Even under the assumption that long time durations are required between sterilizations to allow for the emergence of intelligence, our model suggests that the inner Galaxy provides the greatest number of opportunities for intelligence to arise. This is due to the substantially higher number density of habitable planets in this region, which outweighs the effects of a higher supernova rate in the region. Our model also shows that φI is increasing with time. Intelligent life emerged at approximately the present time at Earth's galactocentric radius, but a similar level of evolutionary opportunity was available in the inner Galaxy more than 2 Gyr ago. Our findings suggest that the inner Galaxy should logically be a prime target region for searches for extraterrestrial intelligence and that any civilizations that may have emerged there are potentially much older than our own.

  17. Next-Generation Sequencing Analysis and Algorithms for PDX and CDX Models.

    Science.gov (United States)

    Khandelwal, Garima; Girotti, María Romina; Smowton, Christopher; Taylor, Sam; Wirth, Christopher; Dynowski, Marek; Frese, Kristopher K; Brady, Ged; Dive, Caroline; Marais, Richard; Miller, Crispin

    2017-08-01

    Patient-derived xenograft (PDX) and circulating tumor cell-derived explant (CDX) models are powerful methods for the study of human disease. In cancer research, these methods have been applied to multiple questions, including the study of metastatic progression, genetic evolution, and therapeutic drug responses. As PDX and CDX models can recapitulate the highly heterogeneous characteristics of a patient tumor, as well as their response to chemotherapy, there is considerable interest in combining them with next-generation sequencing to monitor the genomic, transcriptional, and epigenetic changes that accompany oncogenesis. When used for this purpose, their reliability is highly dependent on being able to accurately distinguish between sequencing reads that originate from the host, and those that arise from the xenograft itself. Here, we demonstrate that failure to correctly identify contaminating host reads when analyzing DNA- and RNA-sequencing (DNA-Seq and RNA-Seq) data from PDX and CDX models is a major confounding factor that can lead to incorrect mutation calls and a failure to identify canonical mutation signatures associated with tumorigenicity. In addition, a highly sensitive algorithm and open source software tool for identifying and removing contaminating host sequences is described. Importantly, when applied to PDX and CDX models of melanoma, these data demonstrate its utility as a sensitive and selective tool for the correction of PDX- and CDX-derived whole-exome and RNA-Seq data. Implications: This study describes a sensitive method to identify contaminating host reads in xenograft and explant DNA- and RNA-Seq data and is applicable to other forms of deep sequencing. Mol Cancer Res; 15(8); 1012-6. ©2017 AACR . ©2017 American Association for Cancer Research.

  18. Two-Stage orders sequencing system for mixed-model assembly

    Science.gov (United States)

    Zemczak, M.; Skolud, B.; Krenczyk, D.

    2015-11-01

    In the paper, the authors focus on the NP-hard problem of orders sequencing, formulated similarly to Car Sequencing Problem (CSP). The object of the research is the assembly line in an automotive industry company, on which few different models of products, each in a certain number of versions, are assembled on the shared resources, set in a line. Such production type is usually determined as a mixed-model production, and arose from the necessity of manufacturing customized products on the basis of very specific orders from single clients. The producers are nowadays obliged to provide each client the possibility to determine a huge amount of the features of the product they are willing to buy, as the competition in the automotive market is large. Due to the previously mentioned nature of the problem (NP-hard), in the given time period only satisfactory solutions are sought, as the optimal solution method has not yet been found. Most of the researchers that implemented inaccurate methods (e.g. evolutionary algorithms) to solving sequencing problems dropped the research after testing phase, as they were not able to obtain reproducible results, and met problems while determining the quality of the received solutions. Therefore a new approach to solving the problem, presented in this paper as a sequencing system is being developed. The sequencing system consists of a set of determined rules, implemented into computer environment. The system itself works in two stages. First of them is connected with the determination of a place in the storage buffer to which certain production orders should be sent. In the second stage of functioning, precise sets of sequences are determined and evaluated for certain parts of the storage buffer under certain criteria.

  19. Modelling Ecosystem Dynamics of the Oxygen Minimum Zones in the Angola Gyre and the Northern Benguela Upwelling System.

    Science.gov (United States)

    Schmidt, M.; Eggert, A.

    2016-02-01

    The Angola Gyre and the Northern Benguela Upwelling System are two major oxygen minimum zones (OMZ) of different kind connected by the system of African Eastern Boundary Currents. We discuss results from a 3-dimensional coupled biogeochemical model covering both oxygen-deficient systems. The biogeochemical model component comprises trophic levels up to zooplankton. Physiological properties of organisms are parameterized from field data gained mainly in the course of the project "Geochemistry and Ecology of the Namibian Upwelling System" (GENUS). The challenge of the modelling effort is the different nature of both systems. The Angola Gyre, located in a "shadow zone" of the tropical Atlantic, has a low productivity and little ventilation, hence a long residence time of water masses. In the northern Benguela Upwelling System, trade winds drive an intermittent, but permanent nutrient supply into the euphotic zone which fuels a high coastal productivity, large particle export and high oxygen consumption from dissimilatory processes. In addition to the local processes, oxygen-deficient water formed in the Angola Gyre is one of the source water masses of the poleward undercurrent, which feeds oxygen depleted water into the Benguela system. In order to simulate the oxygen distribution in the Benguela system, both physical transport as well as local biological processes need to be carefully adjusted in the model. The focus of the analysis is on the time scale and the relative contribution of the different oxygen related processes to the oxygen budgets in both the oxygen minimum zones. Although these are very different in both the OMZ, the model is found as suitable to produce oxygen minimum zones comparable with observations in the Benguela and the Angola Gyre as well. Variability of the oxygen concentration in the Angola Gyre depends strongly on organismic oxygen consumption, whereas the variability of the oxygen concentration on the Namibian shelf is governed mostly by

  20. Spiking neural network model for memorizing sequences with forward and backward recall.

    Science.gov (United States)

    Borisyuk, Roman; Chik, David; Kazanovich, Yakov; da Silva Gomes, João

    2013-06-01

    We present an oscillatory network of conductance based spiking neurons of Hodgkin-Huxley type as a model of memory storage and retrieval of sequences of events (or objects). The model is inspired by psychological and neurobiological evidence on sequential memories. The building block of the model is an oscillatory module which contains excitatory and inhibitory neurons with all-to-all connections. The connection architecture comprises two layers. A lower layer represents consecutive events during their storage and recall. This layer is composed of oscillatory modules. Plastic excitatory connections between the modules are implemented using an STDP type learning rule for sequential storage. Excitatory neurons in the upper layer project star-like modifiable connections toward the excitatory lower layer neurons. These neurons in the upper layer are used to tag sequences of events represented in the lower layer. Computer simulations demonstrate good performance of the model including difficult cases when different sequences contain overlapping events. We show that the model with STDP type or anti-STDP type learning rules can be applied for the simulation of forward and backward replay of neural spikes respectively. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  1. Impacts of Quaternary History on Critical Zone Structure and Processes: Examples and a Conceptual Model From the Intensively Managed Landscapes Critical Zone Observatory

    Directory of Open Access Journals (Sweden)

    Alison M. Anders

    2018-03-01

    Full Text Available The concept of a critical zone (CZ supporting terrestrial life has fostered groundbreaking interdisciplinary science addressing complex interactions among water, soil, rock, air, and life near Earth's surface. Pioneering work has focused on the CZ in areas with residual soils and steady-state or erosional topography. CZ evolution in these areas is conceptualized as progressive weathering of local bedrock (e.g., in the flow-through reactor model. However, this model is not applicable to areas in which weathering profiles form in transported materials including the formerly glaciated portion of the Central Lowland of North America. We present a new conceptual model of CZ evolution in landscapes impacted by continental glaciation based on investigations at three study sites in the Intensively Managed Landscapes Critical Zone Observatory (IML-CZO The IML-CZO is devoted to the study of CZ processes in a region characterized by thick surficial deposits resulting from multiple continental glaciations, with bedrock at depths of up to 150 m. Here the physical (glacial ice, loess, developing soil profiles and biological (microbes, tundra, forest, prairie components of the CZ vary significantly in time. Moreover, the spatial relationships between mineral components of the CZ record a history of glacial-interglacial cycles and landscape evolution. We present cross-sections from IML-CZO sites to provide specific examples of how environmental change is recorded by the structure of the mineral components of the CZ. We build on these examples to create an idealized model of CZ evolution through a glacial cycle that represents the IML-CZO sites and other areas of low relief that have experienced continental glaciation. In addition, we identify two main characteristics of CZ structure which should be included in a conceptual model of CZ development in the IML-CZO and similar settings: (1 mineral components have diverse origins and transport trajectories including

  2. European Regional Climate Zone Modeling of a Commercial Absorption Heat Pump Hot Water Heater

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, Vishaldeep [ORNL; Shen, Bo [ORNL; Keinath, Chris [Stone Mountain Technologies, Inc., Johnson City; Garrabrant, Michael A. [Stone Mountain Technologies, Inc., Johnson City; Geoghegan, Patrick J [ORNL

    2017-01-01

    High efficiency gas-burning hot water heating takes advantage of a condensing heat exchanger to deliver improved combustion efficiency over a standard non-condensing configuration. The water heating is always lower than the gas heating value. In contrast, Gas Absorption Heat Pump (GAHP) hot water heating combines the efficiency of gas burning with the performance increase from a heat pump to offer significant gas energy savings. An ammonia-water system also has the advantage of zero Ozone Depletion Potential and low Global Warming Potential. In comparison with air source electric heat pumps, the absorption system can maintain higher coefficients of performance in colder climates. In this work, a GAHP commercial water heating system was compared to a condensing gas storage system for a range of locations and climate zones across Europe. The thermodynamic performance map of a single effect ammonia-water absorption system was used in a building energy modeling software that could also incorporate the changing ambient air temperature and water mains temperature for a specific location, as well as a full-service restaurant water draw pattern.

  3. Developing an Agro-Ecological Zoning Model for Tumbleweed (Salsola kali, as Energy Crop in Drylands of Argentina

    Directory of Open Access Journals (Sweden)

    Falasca Silvia

    2016-12-01

    Full Text Available Salsola kali is considered extremely valuable as an energy crop worldwide because it adapts easily to environments with strong abiotic stresses (hydric, saline and alkaline and produces large amounts of biomass in drylands. This species is categorized as an important weed in Argentina. The aim of this work was to design an agro-ecological zoning model for tumbleweed in Argentina, employing a Geography Information System. Based on the bioclimatic requirements for the species and the climatic data for Argentina (1981–2010 period, an agro-climatic suitability map was drawn. This map was superimposed on the saline and alkaline soil maps delineated by the Food and Agriculture Organization for dry climates, generating the agro-ecological zoning on a scale of 1 : 500 000. This zoning revealed very suitable and suitable cultivation areas on halomorphic soils. The potential growing areas extend from N of the Salta province (approximately 22° S to the Santa Cruz province (50° S. The use of tumbleweed on halomorphic soils under semi-arid to arid conditions, for the dual purpose of forage use and source of lignocellulosic material for bioenergy, could improve agricultural productivity in these lands. Furthermore, it could also contribute to their environmental sustainability, since the species can be used to reclaim saline soils over the years. Based on international bibliography, the authors outlined an agro-ecological zoning model. This model may be applied to any part of the world, using the agro-ecological limits presented here.

  4. Modeling Venus-like Worlds Through Time and Implications for the Habitable Zone

    Science.gov (United States)

    Way, M.; Del Genio, A. D.; Amundsen, D. S.; Sohl, L. E.; Kiang, N. Y.; Aleinov, I. D.; Kelley, M.

    2017-12-01

    In recent work [1] we demonstrated that the climatic history of Venus may have allowed for surface liquid water to exist for several billion years using a 3D GCM [2]. Model resolution was 4x5 latitude x longitude, 20 atmospheric layers and a 13 layer fully coupled ocean. Several assumptions were made based on what data we have for early Venus: a.) Used a solar spectrum from 2.9 billion years ago, and 715 million years ago for the incident radiation. b.) Assumed Venus had the same slow modern retrograde rotation throughout the 2.9 to 0.715 Gya history explored, although one simulation at faster rotation rate was shown not to be in the HZ. c.) Used atmospheric constituents similar to modern Earth: 1 bar N2, 400ppmv CO2, 1ppmv CH4. d.) Gave the planet a shallow 310m deep ocean constrained by published D/H ratio observations. e.) Used present day Venus topography and one run with Earth topography.In all cases except the faster rotating one the planet was able to maintain surface liquid water. We have now inserted the SOCRATES [3] radiation scheme into our 3D GCM to more accurately calculate heating fluxes for different atmospheric constituents. Using SOCRATES we have explored a number of other possible early histories for Venus including: f.) An aquaplanet configuration at 2.9Gya with present day rotation period.g.) A Land planet configuration at 2.9Gya with the equivalent of 10m of water in soil and lakes. h.) A synchronously rotating version of a, f, and g (supported by recent work of [4] and older work of [5]) i.) A Venus topography with a 310m ocean, but using present day insolation (1.9 x Earth). j.) Versions of most of the worlds above but with solar insolations >1.9 to explore more Venus-like exoplanetary worlds around G-type stars. In these additional cases the planet still resides in the liquid water habitable zone. Studies such as these should help Astronomers better understand whether exoplanets found in the Venus zone [6] are capable of hosting liquid water

  5. Three dimensional numerical modeling for investigation of fracture zone filled with water by borehole radar; Borehole radar ni yoru gansui hasaitai kenshutsu no sanjigen suchi modeling

    Energy Technology Data Exchange (ETDEWEB)

    Sanada, Y.; Watanabe, T.; Ashida, Y. [Kyoto University, Kyoto (Japan); Hasegawa, K.; Yabuuchi, S. [Power Reactor and Nuclear Fuel Development Corp., Tokyo (Japan)

    1997-05-27

    Water bearing fracture zones existing in rock mass largely influence the underground water flow and dynamic property of rock mass. The detailed survey of the location and size of water bearing fracture zones is an important task in the fields such as civil engineering, environment and disaster prevention. Electromagnetic waves of high frequency zones can be grasped as a wave phenomenon, and the record obtained in the actual measurement is wave forms of time series. In the exploration using borehole radar, this water bearing fracture zone becomes the reflection surface, and also becomes a factor of damping in the transmitted wave. By examining changes which these give to the observed wave forms, therefore, water bearing fracture zones can be detected. This study made three dimensional numerical modeling using the time domain finite difference method, and obtained the same output as the observed wave form obtained using borehole radar. By using this program and changing each of the parameters such as frequency and resistivity in the homogeneous medium, changes of the wave forms were observed. Further, examples were shown of modeling of detection of water bearing fracture zones. 5 refs., 16 figs., 1 tab.

  6. Multi-Zone Modeling of the Pulsar Win Nebula HESS J1825-137

    Energy Technology Data Exchange (ETDEWEB)

    Van Etten, Adam; Romani, Roger W.; /Stanford U., Phys. Dept.

    2011-11-08

    The pulsar wind nebula associated with PSR J1826-1334, HESS J1825-137, is a bright very high energy source with an angular extent of {approx} 1{sup o} and spatially-resolved spectroscopic TeV measurements. The gamma-ray spectral index is observed to soften with increasing distance from the pulsar, likely the result of cooling losses as electrons traverse the nebula. We describe analysis of X-ray data of the extended nebula, as well as 3-D time-dependent spectral energy distribution modeling, with emphasis on the spatial variations within HESS J1825-137. The multi-wavelength data places significant constraints on electron injection, transport, and cooling within the nebula. The large size and high nebular energy budget imply a relatively rapid initial pulsar spin period of 13 {+-} 7 ms and an age of 40 {+-} 9 kyr. The relative fluxes of each VHE zone can be explained by advective particle transport with a radially decreasing velocity profile with v(r) {proportional_to} r{sup -0.5}. The evolution of the cooling break requires an evolving magnetic field which also decreases radially from the pulsar, B(r, t) {proportional_to} r{sup -0.7} E(t){sup 1/2}. Detection of 10 TeV flux {approx} 80 pc from the pulsar requires rapid diffusion of high energy particles with {tau}{sub esc} {approx} 90 (R/10 pc){sup 2}(E{sub e}/100TeV){sup -1} year, contrary to the common assumption of toroidal magnetic fields with strong magnetic confinement. The model predicts a rather uniform Fermi LAT surface brightness out to {approx} 1{sup o} from the pulsar, in good agreement with the recently discovered LAT source centered 0.5{sup o} southwest of PSR J1826-1334 with extension 0.6 {+-} 0.1{sup o}.

  7. 3D geostatistical modelling for identifying sinkhole disaster potential zones around the Verkhnekamskoye potash deposit (Russia)

    Science.gov (United States)

    Royer, J. J.; Litaudon, J.; Filippov, L. O.; Lyubimova, T.; Maximovich, N.

    2017-07-01

    This work results from a cooperative scientific program between the Perm State University (Russia) and the University of Lorraine (France). Its objectives are to integrate modern 3D geomodeling in order to improve sustainable mining extraction, especially for predicting and avoiding the formation of sinkholes disaster potential zones. Systematic exploration drill holes performed in the Verkhnekamskoye potash deposit (Perm region, Russia) have been used to build a comprehensive 3D model for better understanding the spatial repartition of the ore quality (geometallurgy). A precise modelling of the mineralized layers allows an estimation of the in-situ ore reserves after interpolating by kriging the potassium (K) and magnesium (Mg) contents at the node of a regular centred grid (over a million cells). Total resources in potassium vary according to the cut-off between 4.7Gt @ 16.1 % K2O; 0.32 % MgCl2 for a cut-off grade at 13.1% K2O and 2.06 Gt @ 18.2 % K2O; 0.32 % MgCl2 at a cut-off of 16.5% K2O. Most of reserves are located in the KPI, KPII and KPIII layers, the KPI being the richest, and KPIII the largest in terms of tonnage. A systematic study of the curvature calculated along the roof of the mineralized layers points out the location of potential main faults which play a major role in the formation of sinkhole during exploitation. A risk map is then derived from this attribute.

  8. Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks.

    Science.gov (United States)

    Avsec, Žiga; Barekatain, Mohammadamin; Cheng, Jun; Gagneur, Julien

    2017-11-16

    Regulatory sequences are not solely defined by their nucleic acid sequence but also by their relative distances to genomic landmarks such as transcription start site, exon boundaries, or polyadenylation site. Deep learning has become the approach of choice for modeling regulatory sequences because of its strength to learn complex sequence features. However, modeling relative distances to genomic landmarks in deep neural networks has not been addressed. Here we developed spline transformation, a neural network module based on splines to flexibly and robustly model distances. Modeling distances to various genomic landmarks with spline transformations significantly increased state-of-the-art prediction accuracy of in vivo RNA-binding protein binding sites for 120 out of 123 proteins. We also developed a deep neural network for human splice branchpoint based on spline transformations that outperformed the current best, already distance-based, machine learning model. Compared to piecewise linear transformation, as obtained by composition of rectified linear units, spline transformation yields higher prediction accuracy as well as faster and more robust training. As spline transformation can be applied to further quantities beyond distances, such as methylation or conservation, we foresee it as a versatile component in the genomics deep learning toolbox. Spline transformation is implemented as a Keras layer in the CONCISE python package: https://github.com/gagneurlab/concise. Analysis code is available at goo.gl/3yMY5w. avsec@in.tum.de; gagneur@in.tum.de. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  9. Enzymes/non-enzymes classification model complexity based on composition, sequence, 3D and topological indices.

    Science.gov (United States)

    Munteanu, Cristian Robert; González-Díaz, Humberto; Magalhães, Alexandre L

    2008-09-21

    The huge amount of new proteins that need a fast enzymatic activity characterization creates demands of protein QSAR theoretical models. The protein parameters that can be used for an enzyme/non-enzyme classification includes the simpler indices such as composition, sequence and connectivity, also called topological indices (TIs) and the computationally expensive 3D descriptors. A comparison of the 3D versus lower dimension indices has not been reported with respect to the power of discrimination of proteins according to enzyme action. A set of 966 proteins (enzymes and non-enzymes) whose structural characteristics are provided by PDB/DSSP files was analyzed with Python/Biopython scripts, STATISTICA and Weka. The list of indices includes, but it is not restricted to pure composition indices (residue fractions), DSSP secondary structure protein composition and 3D indices (surface and access). We also used mixed indices such as composition-sequence indices (Chou's pseudo-amino acid compositions or coupling numbers), 3D-composition (surface fractions) and DSSP secondary structure amino acid composition/propensities (obtained with our Prot-2S Web tool). In addition, we extend and test for the first time several classic TIs for the Randic's protein sequence Star graphs using our Sequence to Star Graph (S2SG) Python application. All the indices were processed with general discriminant analysis models (GDA), neural networks (NN) and machine learning (ML) methods and the results are presented versus complexity, average of Shannon's information entropy (Sh) and data/method type. This study compares for the first time all these classes of indices to assess the ratios between model accuracy and indices/model complexity in enzyme/non-enzyme discrimination. The use of different methods and complexity of data shows that one cannot establish a direct relation between the complexity and the accuracy of the model.

  10. Modelling of the effect of discontinuities on the extent of the fracture zone surrounding deep tunnels

    CSIR Research Space (South Africa)

    Sellers, EJ

    2000-10-01

    Full Text Available stress state (Martin 1997). Similarly the zone of breakout in deep gold mine ore-passes is extended by the passage of the flow of the rock down the pass (Rech et al. 1992) The breakout zone in boreholes for oil... depth. 8 2001 South African Institute of Mining and Metallurgy. Published by Elsevier Science Ltd. All rights reserved. 1 Introduction M ore 500 km oftunnels are excavated annually at depths to 3500 m in South African gold mines...

  11. An optimized chemical kinetic mechanism for HCCI combustion of PRFs using multi-zone model and genetic algorithm

    International Nuclear Information System (INIS)

    Neshat, Elaheh; Saray, Rahim Khoshbakhti

    2015-01-01

    Highlights: • A new chemical kinetic mechanism for PRFs HCCI combustion is developed. • New mechanism optimization is performed using genetic algorithm and multi-zone model. • Engine-related combustion and performance parameters are predicted accurately. • Engine unburned HC and CO emissions are predicted by the model properly. - Abstract: Development of comprehensive chemical kinetic mechanisms is required for HCCI combustion and emissions prediction to be used in engine development. The main purpose of this study is development of a new chemical kinetic mechanism for primary reference fuels (PRFs) HCCI combustion, which can be applied to combustion models to predict in-cylinder pressure and exhaust CO and UHC emissions, accurately. Hence, a multi-zone model is developed for HCCI engine simulation. Two semi-detailed chemical kinetic mechanisms those are suitable for premixed combustion are used for n-heptane and iso-octane HCCI combustion simulation. The iso-octane mechanism contains 84 species and 484 reactions and the n-heptane mechanism contains 57 species and 296 reactions. A simple interaction between iso-octane and n-heptane is considered in new mechanism. The multi-zone model is validated using experimental data for pure n-heptane and iso-octane. A new mechanism is prepared by combination of these two mechanisms for n-heptane and iso-octane blended fuel, which includes 101 species and 594 reactions. New mechanism optimization is performed using genetic algorithm and multi-zone model. Mechanism contains low temperature heat release region, which decreases with increasing octane number. The results showed that the optimized chemical kinetic mechanism is capable of predicting engine-related combustion and performance parameters. Also after implementing the optimized mechanism, engine unburned HC and CO emissions predicted by the model are in good agreement with the corresponding experimental data

  12. Complete genome sequence of the highly Mn(II) tolerant Staphylococcus sp. AntiMn-1 isolated from deep-sea sediment in the Clarion-Clipperton Zone.

    Science.gov (United States)

    Wang, Xing; Lin, Danqiu; Jing, Xiaohuan; Zhu, Sidong; Yang, Jifang; Chen, Jigang

    2018-01-20

    Staphylococcus sp. AntiMn-1 is a deep-sea bacterium inhabiting seafloor sediment in the Clarion-Clipperton Zone (CCZ) that is highly tolerant to Mn(II) and displays efficient Mn(II) oxidation. Herein, we present the assembly and annotation of its genome. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Comparison of pause predictions of two sequence-dependent transcription models

    International Nuclear Information System (INIS)

    Bai, Lu; Wang, Michelle D

    2010-01-01

    Two recent theoretical models, Bai et al (2004, 2007) and Tadigotla et al (2006), formulated thermodynamic explanations of sequence-dependent transcription pausing by RNA polymerase (RNAP). The two models differ in some basic assumptions and therefore make different yet overlapping predictions for pause locations, and different predictions on pause kinetics and mechanisms. Here we present a comprehensive comparison of the two models. We show that while they have comparable predictive power of pause locations at low NTP concentrations, the Bai et al model is more accurate than Tadigotla et al at higher NTP concentrations. The pausing kinetics predicted by Bai et al is also consistent with time-course transcription reactions, while Tadigotla et al is unsuited for this type of kinetic prediction. More importantly, the two models in general predict different pausing mechanisms even for the same pausing sites, and the Bai et al model provides an explanation more consistent with recent single molecule observations

  14. CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles

    DEFF Research Database (Denmark)

    Nielsen, Morten; Lundegaard, Claus; Lund, Ole

    2010-01-01

    CPHmodels-3.0 is a web server predicting protein 3D structure by use of single template homology modeling. The server employs a hybrid of the scoring functions of CPHmodels-2.0 and a novel remote homology-modeling algorithm. A query sequence is first attempted modeled using the fast CPHmodels-2.......0 profile-profile scoring function suitable for close homology modeling. The new computational costly remote homology-modeling algorithm is only engaged provided that no suitable PDB template is identified in the initial search. CPHmodels-3.0 was benchmarked in the CASP8 competition and produced models.......3 A. These performance values place the CPHmodels-3.0 method in the group of high performing 3D prediction tools. Beside its accuracy, one of the important features of the method is its speed. For most queries, the response time of the server is...

  15. A site-scale model for fluid and heat flow in the unsaturated zone of Yucca Mountain, Nevada

    Science.gov (United States)

    Wu, Yu-Shu; Haukwa, Charles; Bodvarsson, G. S.

    1999-05-01

    A three-dimensional unsaturated-zone numerical model has been developed to simulate flow and distribution of moisture, gas and heat at Yucca Mountain, Nevada, a potential repository site for high-level radioactive waste. The model takes into account the simultaneous flow dynamics of liquid water, vapor, air and heat in the highly heterogeneous, fractured porous rock in the unsaturated zone (UZ). This model is intended for use in the prediction of the current and future conditions in the UZ so as to aid in the assessment of the system performance of the proposed repository. The modeling approach is based on a mathematical formulation of coupled multiphase, multicomponent fluid and heat flow through porous and fractured rock. Fracture and matrix flow is treated using both dual-permeability and effective-continuum modeling approaches. The model domain covers a total area of approximately 43 km 2, and uses the land surface and the water table as its top and bottom boundaries. In addition, site-specific data, representative surface infiltration, and geothermal conditions are incorporated into the model. The reliability and accuracy of the model have been the subject of a comprehensive model calibration study, in which the model was calibrated against measured data, including liquid saturation, water potential and temperature. It has been found that the model is generally able to reproduce the overall system behavior at Yucca Mountain with respect to moisture profiles, pneumatic pressure variations in different geological units, and ambient geothermal conditions.

  16. Validation of risk stratification models in acute myeloid leukemia using sequencing-based molecular profiling.

    Science.gov (United States)

    Wang, M; Lindberg, J; Klevebring, D; Nilsson, C; Mer, A S; Rantalainen, M; Lehmann, S; Grönberg, H

    2017-10-01

    Risk stratification of acute myeloid leukemia (AML) patients needs improvement. Several AML risk classification models based on somatic mutations or gene-expression profiling have been proposed. However, systematic and independent validation of these models is required for future clinical implementation. We performed whole-transcriptome RNA-sequencing and panel-based deep DNA sequencing of 23 genes in 274 intensively treated AML patients (Clinseq-AML). We also utilized the The Cancer Genome Atlas (TCGA)-AML study (N=142) as a second validation cohort. We evaluated six previously proposed molecular-based models for AML risk stratification and two revised risk classification systems combining molecular- and clinical data. Risk groups stratified by five out of six models showed different overall survival in cytogenetic normal-AML patients in the Clinseq-AML cohort (P-value0.5). Risk classification systems integrating mutational or gene-expression data were found to add prognostic value to the current European Leukemia Net (ELN) risk classification. The prognostic value varied between models and across cohorts, highlighting the importance of independent validation to establish evidence of efficacy and general applicability. All but one model replicated in the Clinseq-AML cohort, indicating the potential for molecular-based AML risk models. Risk classification based on a combination of molecular and clinical data holds promise for improved AML patient stratification in the future.

  17. Modeling self-potential data in the Abraham and Meadow-Hatton geothermal systems: The search for upflow zones

    Energy Technology Data Exchange (ETDEWEB)

    Schima, S.; Wilt, M. [Lawrence Livermore National Lab., CA (United States); Ross, H. [Utah Univ. Research Inst., Salt Lake City, UT (United States)

    1995-07-01

    Computer code SPXCL is a finite difference modeling algorithm that calculates the response of embedded point sources within a rectangular, two-dimensional medium. The code calculates the electrical potential anywhere in the medium from thermal or pressure sources. This code is useful in calculating self-potential measurements that may be used to locate upflow zones in geothermal systems. Beginning in 1991 data on self-potential was collected at Abraham and Meadow-Hatton Hot Springs, two of the largest thermal spring systems in Utah. In this paper, these data were modeled to determine upflow zones and source characteristics using the SPXCL code. The forward solution for fluid and heat flow models and the resulting self-potential anomalies were calculated.

  18. Conceptual Model of Uranium in the Vadose Zone for Acidic and Alkaline Wastes Discharged at the Hanford Site Central Plateau

    Energy Technology Data Exchange (ETDEWEB)

    Truex, Michael J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Szecsody, James E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Qafoku, Nikolla [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Serne, R. Jeffrey [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2014-09-01

    Historically, uranium was disposed in waste solutions of varying waste chemistry at the Hanford Site Central Plateau. The character of how uranium was distributed in the vadose zone during disposal, how it has continued to migrate through the vadose zone, and the magnitude of potential impacts on groundwater are strongly influenced by geochemical reactions in the vadose zone. These geochemical reactions can be significantly influenced by the disposed-waste chemistry near the disposal location. This report provides conceptual models and supporting information to describe uranium fate and transport in the vadose zone for both acidic and alkaline wastes discharged at a substantial number of waste sites in the Hanford Site Central Plateau. The conceptual models include consideration of how co-disposed acidic or alkaline fluids influence uranium mobility in terms of induced dissolution/precipitation reactions and changes in uranium sorption with a focus on the conditions near the disposal site. This information, when combined with the extensive information describing uranium fate and transport at near background pH conditions, enables focused characterization to support effective fate and transport estimates for uranium in the subsurface.

  19. Development of a model to compute the extension of life supporting zones for Earth-like exoplanets.

    Science.gov (United States)

    Neubauer, David; Vrtala, Aron; Leitner, Johannes J; Firneis, Maria G; Hitzenberger, Regina

    2011-12-01

    A radiative convective model to calculate the width and the location of the life supporting zone (LSZ) for different, alternative solvents (i.e. other than water) is presented. This model can be applied to the atmospheres of the terrestrial planets in the solar system as well as (hypothetical, Earth-like) terrestrial exoplanets. Cloud droplet formation and growth are investigated using a cloud parcel model. Clouds can be incorporated into the radiative transfer calculations. Test runs for Earth, Mars and Titan show a good agreement of model results with observations.

  20. A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data

    KAUST Repository

    Sepúlveda, Nuno

    2013-02-26

    Background: The advent of next generation sequencing technology has accelerated efforts to map and catalogue copy number variation (CNV) in genomes of important micro-organisms for public health. A typical analysis of the sequence data involves mapping reads onto a reference genome, calculating the respective coverage, and detecting regions with too-low or too-high coverage (deletions and amplifications, respectively). Current CNV detection methods rely on statistical assumptions (e.g., a Poisson model) that may not hold in general, or require fine-tuning the underlying algorithms to detect known hits. We propose a new CNV detection methodology based on two Poisson hierarchical models, the Poisson-Gamma and Poisson-Lognormal, with the advantage of being sufficiently flexible to describe different data patterns, whilst robust against deviations from the often assumed Poisson model.Results: Using sequence coverage data of 7 Plasmodium falciparum malaria genomes (3D7 reference strain, HB3, DD2, 7G8, GB4, OX005, and OX006), we showed that empirical coverage distributions are intrinsically asymmetric and overdispersed in relation to the Poisson model. We also demonstrated a low baseline false positive rate for the proposed methodology using 3D7 resequencing data and simulation. When applied to the non-reference isolate data, our approach detected known CNV hits, including an amplification of the PfMDR1 locus in DD2 and a large deletion in the CLAG3.2 gene in GB4, and putative novel CNV regions. When compared to the recently available FREEC and cn.MOPS approaches, our findings were more concordant with putative hits from the highest quality array data for the 7G8 and GB4 isolates.Conclusions: In summary, the proposed methodology brings an increase in flexibility, robustness, accuracy and statistical rigour to CNV detection using sequence coverage data. 2013 Seplveda et al.; licensee BioMed Central Ltd.

  1. Fuzzy Mixed Assembly Line Sequencing and Scheduling Optimization Model Using Multiobjective Dynamic Fuzzy GA

    OpenAIRE

    Tahriri, Farzad; Dawal, Siti Zawiah Md; Taha, Zahari

    2014-01-01

    A new multiobjective dynamic fuzzy genetic algorithm is applied to solve a fuzzy mixed-model assembly line sequencing problem in which the primary goals are to minimize the total make-span and minimize the setup number simultaneously. Trapezoidal fuzzy numbers are implemented for variables such as operation and travelling time in order to generate results with higher accuracy and representative of real-case data. An improved genetic algorithm called fuzzy adaptive genetic algorithm (FAGA) is ...

  2. Whole genome sequencing and assembly of Eukaryotic microbes isolated from ISS environmental surface Kirovograd region soil Chernobyl Nuclear Power Plant and Chernobyl Exclusion Zone

    Data.gov (United States)

    National Aeronautics and Space Administration — The whole-genome sequences of eight fungal strains that were selected for exposure to microgravity at the International Space Station are presented here. These...

  3. Multi-zone modeling of Diesel engine fuel spray development with vegetable oil, bio-diesel or Diesel fuels

    International Nuclear Information System (INIS)

    Rakopoulos, C.D.; Antonopoulos, K.A.; Rakopoulos, D.C.

    2006-01-01

    This work presents a model of fuel sprays development in the cylinders of Diesel engines that is two-dimensional, multi-zone, with the issuing jet (from the nozzle) divided into several discrete volumes, called 'zones', formed along the direction of the fuel injection as well as across it. The model follows each zone, with its own time history, as the spray penetrates into the swirling air environment of the combustion chamber before and after wall impingement. After the jet break up time, a group of droplets is generated in each zone, with the model following their motion during heating, evaporation and mixing with the in-cylinder air. The model is applied for the interesting case of using vegetable oils or their derived bio-diesels as fuels, which recently are considered as promising alternatives to petroleum distillates since they are derived from biological sources. Although there are numerous experimental studies that show curtailment of the emitted smoke with possible increase of the emitted NO x against the use of Diesel fuel, there is an apparent scarcity of theoretical models scrutinizing the formation mechanisms of combustion generated emissions when using these biologically derived fuels. Thus, in the present work, a theoretical detailed model of spray formation is developed that is limited to the related investigation of the physical processes by decoupling it from the chemical effects after combustion initiation. The analysis results show how the widely differing physical properties of these fuels, against the normal Diesel fuel, affect greatly the spray formation and consequently the combustion mechanism and the related emissions

  4. A detached eddy simulation model for the study of lateral separation zones along a large canyon-bound river

    Science.gov (United States)

    Alvarez, Laura V.; Schmeeckle, Mark W.; Grams, Paul E.

    2017-01-01

    Lateral flow separation occurs in rivers where banks exhibit strong curvature. In canyon-boundrivers, lateral recirculation zones are the principal storage of fine-sediment deposits. A parallelized,three-dimensional, turbulence-resolving model was developed to study the flow structures along lateralseparation zones located in two pools along the Colorado River in Marble Canyon. The model employs thedetached eddy simulation (DES) technique, which resolves turbulence structures larger than the grid spacingin the interior of the flow. The DES-3D model is validated using Acoustic Doppler Current Profiler flowmeasurements taken during the 2008 controlled flood release from Glen Canyon Dam. A point-to-pointvalidation using a number of skill metrics, often employed in hydrological research, is proposed here forfluvial modeling. The validation results show predictive capabilities of the DES model. The model reproducesthe pattern and magnitude of the velocity in the lateral recirculation zone, including the size and position ofthe primary and secondary eddy cells, and return current. The lateral recirculation zone is open, havingcontinuous import of fluid upstream of the point of reattachment and export by the recirculation returncurrent downstream of the point of separation. Differences in magnitude and direction of near-bed andnear-surface velocity vectors are found, resulting in an inward vertical spiral. Interaction between therecirculation return current and the main flow is dynamic, with large temporal changes in flow direction andmagnitude. Turbulence structures with a predominately vertical axis of vorticity are observed in the shearlayer becoming three-dimensional without preferred orientation downstream.

  5. Multi-zone modeling of combustion and emissions formation in DI diesel engine operating on ethanol-diesel fuel blends

    International Nuclear Information System (INIS)

    Rakopoulos, C.D.; Antonopoulos, K.A.; Rakopoulos, D.C.; Hountalas, D.T.

    2008-01-01

    A multi-zone model for calculation of the closed cycle of a direct injection (DI) diesel engine is applied for the interesting case of its operation with ethanol-diesel fuel blends, the ethanol (bio-fuel) being considered recently as a promising extender to petroleum distillates. Although there are many experimental studies, there is an apparent scarcity of theoretical models scrutinizing the formation mechanisms of combustion generated emissions when using bio-fuels. This is a two dimensional, multi-zone model with the issuing fuel jets divided into several discrete volumes, called 'zones', formed along and across the direction of the fuel injection. The model follows each zone, with its own time history, as the spray penetrates into the swirling air environment of the combustion chamber. Droplet evaporation and jet mixing models are used to determine the amount of fuel and entrained air in each zone available for combustion. The mass, energy and state equations are applied in each zone to provide local temperatures and cylinder pressure histories. The concentrations of the various constituents are calculated by adopting a chemical equilibrium scheme for the C-H-O-N system of eleven species considered, together with chemical rate equations for calculation of nitric oxide (NO) and a model for net soot formation. The results from the computer program, implementing the analysis, for the in cylinder pressure, exhaust NO concentration and soot density compare well with the corresponding measurements from an experimental investigation conducted on a fully automated test bed, standard 'Hydra', DI diesel engine located at the authors' laboratory, which is operated with ethanol-diesel fuel blends containing 5%, 10% and 15% (by vol.) ethanol. Iso-contour plots of equivalence ratio, temperature, NO and soot inside the cylinder at various instants of time, when using these ethanol-diesel fuel blends against the diesel fuel (baseline fuel), shed light on the mechanisms

  6. Redox zone II. Coupled modeling of groundwater flow, solute transport, chemical reactions and microbial processes in the Aespoe island

    International Nuclear Information System (INIS)

    Samper, Javier; Molinero, Jorge; Changbing Yang; Guoxiang Zhang

    2003-12-01

    The Redox Zone Experiment was carried out at the Aespoe HRL in order to study the redox behaviour and the hydrochemistry of an isolated vertical fracture zone disturbed by the excavation of an access tunnel. Overall results and interpretation of the Redox Zone Project were reported by Banwart et al. Later, Banwart presented a summary of the hydrochemistry of the Redox Zone Experiment. Coupled groundwater flow and reactive transport models of this experiment were carried out by Molinero who proposed a revised conceptual model for the hydrogeology of the Redox Zone Experiment which could explain simultaneously measured drawdown and salinity data. The numerical model was found useful to understand the natural system. Several conclusions were drawn about the redox conditions of recharge waters, cation exchange capacity of the fracture zone and the role of mineral phases such as pyrite, calcite, hematite and goethite. This model could reproduce the measured trends of dissolved species, except for bicarbonate and sulphate which are affected by microbially-mediated processes. In order to explore the role of microbial processes, a coupled numerical model has been constructed which accounts for water flow, reactive transport and microbial processes. The results of this model is presented in this report. This model accounts for groundwater flow and reactive transport in a manner similar to that of Molinero and extends the preliminary microbial model of Zhang by accounting for microbially-driven organic matter fermentation and organic matter oxidation. This updated microbial model considers simultaneously the fermentation of particulate organic matter by yeast and the oxidation of dissolved organic matter, a product of fermentation. Dissolved organic matter is produced by yeast and serves also as a substrate for iron-reducing bacteria. Model results reproduce the observed increase in bicarbonate and sulfaphe concentration, thus adding additional evidence for the possibility

  7. Redox zone II. Coupled modeling of groundwater flow, solute transport, chemical reactions and microbial processes in the Aespoe island

    Energy Technology Data Exchange (ETDEWEB)

    Samper, Javier; Molinero, Jorge; Changbing Yang; Guoxiang Zhang [Univ. Da Coruna (Spain)

    2003-12-01

    The Redox Zone Experiment was carried out at the Aespoe HRL in order to study the redox behaviour and the hydrochemistry of an isolated vertical fracture zone disturbed by the excavation of an access tunnel. Overall results and interpretation of the Redox Zone Project were reported by Banwart et al. Later, Banwart presented a summary of the hydrochemistry of the Redox Zone Experiment. Coupled groundwater flow and reactive transport models of this experiment were carried out by Molinero who proposed a revised conceptual model for the hydrogeology of the Redox Zone Experiment which could explain simultaneously measured drawdown and salinity data. The numerical model was found useful to understand the natural system. Several conclusions were drawn about the redox conditions of recharge waters, cation exchange capacity of the fracture zone and the role of mineral phases such as pyrite, calcite, hematite and goethite. This model could reproduce the measured trends of dissolved species, except for bicarbonate and sulphate which are affected by microbially-mediated processes. In order to explore the role of microbial processes, a coupled numerical model has been constructed which accounts for water flow, reactive transport and microbial processes. The results of this model is presented in this report. This model accounts for groundwater flow and reactive transport in a manner similar to that of Molinero and extends the preliminary microbial model of Zhang by accounting for microbially-driven organic matter fermentation and organic matter oxidation. This updated microbial model considers simultaneously the fermentation of particulate organic matter by yeast and the oxidation of dissolved organic matter, a product of fermentation. Dissolved organic matter is produced by yeast and serves also as a substrate for iron-reducing bacteria. Model results reproduce the observed increase in bicarbonate and sulfaphe concentration, thus adding additional evidence for the possibility

  8. Fuzzy mixed assembly line sequencing and scheduling optimization model using multiobjective dynamic fuzzy GA.

    Science.gov (United States)

    Tahriri, Farzad; Dawal, Siti Zawiah Md; Taha, Zahari

    2014-01-01

    A new multiobjective dynamic fuzzy genetic algorithm is applied to solve a fuzzy mixed-model assembly line sequencing problem in which the primary goals are to minimize the total make-span and minimize the setup number simultaneously. Trapezoidal fuzzy numbers are implemented for variables such as operation and travelling time in order to generate results with higher accuracy and representative of real-case data. An improved genetic algorithm called fuzzy adaptive genetic algorithm (FAGA) is proposed in order to solve this optimization model. In establishing the FAGA, five dynamic fuzzy parameter controllers are devised in which fuzzy expert experience controller (FEEC) is integrated with automatic learning dynamic fuzzy controller (ALDFC) technique. The enhanced algorithm dynamically adjusts the population size, number of generations, tournament candidate, crossover rate, and mutation rate compared with using fixed control parameters. The main idea is to improve the performance and effectiveness of existing GAs by dynamic adjustment and control of the five parameters. Verification and validation of the dynamic fuzzy GA are carried out by developing test-beds and testing using a multiobjective fuzzy mixed production assembly line sequencing optimization problem. The simulation results highlight that the performance and efficacy of the proposed novel optimization algorithm are more efficient than the performance of the standard genetic algorithm in mixed assembly line sequencing model.

  9. Fuzzy Mixed Assembly Line Sequencing and Scheduling Optimization Model Using Multiobjective Dynamic Fuzzy GA

    Directory of Open Access Journals (Sweden)

    Farzad Tahriri

    2014-01-01

    Full Text Available A new multiobjective dynamic fuzzy genetic algorithm is applied to solve a fuzzy mixed-model assembly line sequencing problem in which the primary goals are to minimize the total make-span and minimize the setup number simultaneously. Trapezoidal fuzzy numbers are implemented for variables such as operation and travelling time in order to generate results with higher accuracy and representative of real-case data. An improved genetic algorithm called fuzzy adaptive genetic algorithm (FAGA is proposed in order to solve this optimization model. In establishing the FAGA, five dynamic fuzzy parameter controllers are devised in which fuzzy expert experience controller (FEEC is integrated with automatic learning dynamic fuzzy controller (ALDFC technique. The enhanced algorithm dynamically adjusts the population size, number of generations, tournament candidate, crossover rate, and mutation rate compared with using fixed control parameters. The main idea is to improve the performance and effectiveness of existing GAs by dynamic adjustment and control of the five parameters. Verification and validation of the dynamic fuzzy GA are carried out by developing test-beds and testing using a multiobjective fuzzy mixed production assembly line sequencing optimization problem. The simulation results highlight that the performance and efficacy of the proposed novel optimization algorithm are more efficient than the performance of the standard genetic algorithm in mixed assembly line sequencing model.

  10. Genomic Sequence and Experimental Tractability of a New Decapod Shrimp Model, Neocaridina denticulata

    Directory of Open Access Journals (Sweden)

    Nathan J. Kenny

    2014-03-01

    Full Text Available The speciose Crustacea is the largest subphylum of arthropods on the planet after the Insecta. To date, however, the only publically available sequenced crustacean genome is that of the water flea, Daphnia pulex, a member of the Branchiopoda. While Daphnia is a well-established ecotoxicological model, previous study showed that one-third of genes contained in its genome are lineage-specific and could not be identified in any other metazoan genomes. To better understand the genomic evolution of crustaceans and arthropods, we have sequenced the genome of a novel shrimp model, Neocaridina denticulata, and tested its experimental malleability. A library of 170-bp nominal fragment size was constructed from DNA of a starved single adult and sequenced using the Illumina HiSeq2000 platform. Core eukaryotic genes, the mitochondrial genome, developmental patterning genes (such as Hox and microRNA processing pathway genes are all present in this animal, suggesting it has not undergone massive genomic loss. Comparison with the published genome of Daphnia pulex has allowed us to reveal 3750 genes that are indeed specific to the lineage containing malacostracans and branchiopods, rather than Daphnia-specific (E-value: 10−6. We also show the experimental tractability of N. denticulata, which, together with the genomic resources presented here, make it an ideal model for a wide range of further aquacultural, developmental, ecotoxicological, food safety, genetic, hormonal, physiological and reproductive research, allowing better understanding of the evolution of crustaceans and other arthropods.

  11. Fuzzy Mixed Assembly Line Sequencing and Scheduling Optimization Model Using Multiobjective Dynamic Fuzzy GA

    Science.gov (United States)

    Tahriri, Farzad; Dawal, Siti Zawiah Md; Taha, Zahari

    2014-01-01

    A new multiobjective dynamic fuzzy genetic algorithm is applied to solve a fuzzy mixed-model assembly line sequencing problem in which the primary goals are to minimize the total make-span and minimize the setup number simultaneously. Trapezoidal fuzzy numbers are implemented for variables such as operation and travelling time in order to generate results with higher accuracy and representative of real-case data. An improved genetic algorithm called fuzzy adaptive genetic algorithm (FAGA) is proposed in order to solve this optimization model. In establishing the FAGA, five dynamic fuzzy parameter controllers are devised in which fuzzy expert experience controller (FEEC) is integrated with automatic learning dynamic fuzzy controller (ALDFC) technique. The enhanced algorithm dynamically adjusts the population size, number of generations, tournament candidate, crossover rate, and mutation rate compared with using fixed control parameters. The main idea is to improve the performance and effectiveness of existing GAs by dynamic adjustment and control of the five parameters. Verification and validation of the dynamic fuzzy GA are carried out by developing test-beds and testing using a multiobjective fuzzy mixed production assembly line sequencing optimization problem. The simulation results highlight that the performance and efficacy of the proposed novel optimization algorithm are more efficient than the performance of the standard genetic algorithm in mixed assembly line sequencing model. PMID:24982962

  12. Modelling the interaction between volcanic sources and fault zones at the Etna Mount

    Science.gov (United States)

    Aloisi, Marco; Mattia, Mario; Monaco, Carmelo; Pulvirenti, Fabio

    2010-05-01

    Analytical and numerical modeling techniques are jointly applied to simulate geophysical processes in the Earth's crust. The methods are of a complementary nature. Analytical models have been used traditionally due to the lightness of the request computational resources but they are strongly limited in the ability to quantify observables, to describe multiphysics processes and to use more complicated material rheologies and Earth's topography. All these properties can be achieved by using numerical models even though it requires long time of calculation and the deep knowledge of the studied geophysical system. The 2002-2003 Etna eruptive event involved two different sectors of the volcano providing a big amount of geophysical data. The eruption produced severe fires in the woods, destroyed many tourist infrastructures and interrupted one of the principal roads. It was heralded, accompanied and followed by an intense seismic activity that was culminated with the earthquake (M ~ 4.4) on October 29 that produced severe damages in the S. Venerina village. The eruption was deeply analyzed by analytical (e.g., Aloisi et al., 2003; Aloisi et al., 2006; Bonforte et al., 2007; Currenti et al., 2008a) and numerical modeling (Walter et al., 2005; Currenti et al., 2008b). The numerical models have proved that the medium heterogeneities and the area topography strongly affect the volcano deformation field. The Etna Mount, jointly with a motley lithological setting, is characterized by a complex tectonic scenery that influences the structural evolution of the volcanic edifice. Important fault zones intersect the volcano edifice, perturbing the deformation pattern produced by the volcanic sources. The displacement and stress of blocks are affected by the deformation of discontinuities to a degree (Liu and Zhongkui, 2007), therefore the fault zones can not be neglected in an overall study. In this work, we present a numerical model for the 2002-2003 Etna eruption that kept in

  13. Outpatient Closed-Loop Control with Unannounced Moderate Exercise in Adolescents Using Zone Model Predictive Control.

    Science.gov (United States)

    Huyett, Lauren M; Ly, Trang T; Forlenza, Gregory P; Reuschel-DiVirgilio, Suzette; Messer, Laurel H; Wadwa, R Paul; Gondhalekar, Ravi; Doyle, Francis J; Pinsker, Jordan E; Maahs, David M; Buckingham, Bruce A; Dassau, Eyal

    2017-06-01

    The artificial pancreas (AP) has the potential to improve glycemic control in adolescents. This article presents the first evaluation in adolescents of the Zone Model Predictive Control and Health Monitoring System (ZMPC+HMS) AP algorithms, and their first evaluation in a supervised outpatient setting with frequent exercise. Adolescents with type 1 diabetes underwent 3 days of closed-loop control (CLC) in a hotel setting with the ZMPC+HMS algorithms on the Diabetes Assistant platform. Subjects engaged in twice-daily exercise, including soccer, tennis, and bicycling. Meal size (unrestricted) was estimated and entered into the system by subjects to trigger a bolus, but exercise was not announced. Ten adolescents (11.9-17.7 years) completed 72 h of CLC, with data on 95 ± 14 h of sensor-augmented pump (SAP) therapy before CLC as a comparison to usual therapy. The percentage of time with continuous glucose monitor (CGM) 70-180 mg/dL was 71% ± 10% during CLC, compared to 57% ± 16% during SAP (P = 0.012). Nocturnal control during CLC was safe, with 0% (0%, 0.6%) of time with CGM 250 mg/dL (16% ± 14% during SAP). The system remained connected in CLC for 97% ± 2% of the total study time. No adverse events or severe hypoglycemia occurred. The use of the ZMPC+HMS algorithms is feasible in the adolescent outpatient environment and achieved significantly more time in the desired glycemic range than SAP in the face of unannounced exercise and large announced meal challenges.

  14. Sequence analysis in multilevel models. A study on different sources of patient cues in medical consultations.

    Science.gov (United States)

    Del Piccolo, Lidia; Mazzi, Maria Angela; Dunn, Graham; Sandri, Marco; Zimmermann, Christa

    2007-12-01

    The aims of the study were to explore the importance of macro (patient, physician, consultation) and micro (doctor-patient speech sequences) variables in promoting patient cues (unsolicited new information or expressions of feelings), and to describe the methodological implications related to the study of speech sequences. Patient characteristics, a consultation index of partnership and doctor-patient speech sequences were recorded for 246 primary care consultations in six primary care surgeries in Verona, Italy. Homogeneity and stationarity conditions of speech sequences allowed the creation of a hierarchy of multilevel logit models including micro and macro level variables, with the presence/absence of cues as the dependent variable. We found that emotional distress of the patient increased cues and that cues appeared among other patient expressions and were preceded by physicians' facilitations and handling of emotion. Partnership, in terms of open-ended inquiry, active listening skills and handling of emotion by the physician and active participation by the patient throughout the consultation, reduced cue frequency.

  15. Rapid and enhanced remote homology detection by cascading hidden Markov model searches in sequence space.

    Science.gov (United States)

    Kaushik, Swati; Nair, Anu G; Mutt, Eshita; Subramanian, Hari Prasanna; Sowdhamini, Ramanathan

    2016-02-01

    In the post-genomic era, automatic annotation of protein sequences using computational homology-based methods is highly desirable. However, often protein sequences diverge to an extent where detection of homology and automatic annotation transfer is not straightforward. Sophisticated approaches to detect such distant relationships are needed. We propose a new approach to identify deep evolutionary relationships of proteins to overcome shortcomings of the available methods. We have developed a method to identify remote homologues more effectively from any protein sequence database by using several cascading events with Hidden Markov Models (C-HMM). We have implemented clustering of hits and profile generation of hit clusters to effectively reduce the computational timings of the cascaded sequence searches. Our C-HMM approach could cover 94, 83 and 40% coverage at family, superfamily and fold levels, respectively, when applied on diverse protein folds. We have compared C-HMM with various remote homology detection methods and discuss the trade-offs between coverage and false positives. A standalone package implemented in Java along with a detailed documentation can be downloaded from https://github.com/RSLabNCBS/C-HMM SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. mini@ncbs.res.in. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  16. Formation of calcareous nodules in loess-paleosol sequences: Reviews of existing models with a proposed new "per evapotranspiration model"

    Science.gov (United States)

    Li, Yanrong; Zhang, Weiwei; Aydin, Adnan; Deng, Xiaohong

    2018-04-01

    Loess is a product of aeolian deposition during Quaternary glaciation cycles. Loess-paleosol sequences are rich in calcareous nodules (CNs). In the literature, two models are widely cited for the formation of CNs, namely "per descendum" and "per ascendum". However, there has been no direct testing or monitoring to support either of these contradictory models. This paper reviews a large number of multidisciplinary literature to evaluate the consistency, reliability and rationality of these two models. Three main conclusions are drawn: (1) the causative factors (variation of pH value along loess-paleosol sequence, decrease of CO2 partial pressure, and reduction of solvent water) that are used to support the per descendum model do not completely explain the supersaturation of infiltration solution with CaCO3, thereby making this model questionable; (2) the per ascendum model explains the formation of CNs along narrow horizons through upward evaporation; however, it fails to produce sporadic distributions and irregular shapes of nodules on loess slope faces and the frequent appearance of nodules around plant roots. In order to reconcile these deficiencies, we conducted an extensive field survey in various parts of Shanxi province. Based on this new set of observations, it was concluded that the "per ascendum" model can be extended to explain all occurrences of CNs. This extended model is called "per evapotranspiration".

  17. An investigation of difficulties experienced by students developing unified modelling language (UML) class and sequence diagrams

    Science.gov (United States)

    Sien, Ven Yu

    2011-12-01

    Object-oriented analysis and design (OOAD) is not an easy subject to learn. There are many challenges confronting students when studying OOAD. Students have particular difficulty abstracting real-world problems within the context of OOAD. They are unable to effectively build object-oriented (OO) models from the problem domain because they essentially do not know "what" to model. This article investigates the difficulties and misconceptions undergraduate students have with analysing systems using unified modelling language analysis class and sequence diagrams. These models were chosen because they represent important static and dynamic aspects of the software system under development. The results of this study will help students produce effective OO models, and facilitate software engineering lecturers design learning materials and approaches for introductory OOAD courses.

  18. Modeling Water Flux at the Base of the Rooting Zone for Soils with Varying Glacial Parent Materials

    Science.gov (United States)

    Naylor, S.; Ellett, K. M.; Ficklin, D. L.; Olyphant, G. A.

    2013-12-01

    Soils of varying glacial parent materials in the Great Lakes Region (USA) are characterized by thin unsaturated zones and widespread use of agricultural pesticides and nutrients that affect shallow groundwater. To better our understanding of the fate and transport of contaminants, improved models of water fluxes through the vadose zones of various hydrogeologic settings are warranted. Furthermore, calibrated unsaturated zone models can be coupled with watershed models, providing a means for predicting the impact of varying climate scenarios on agriculture in the region. To address these issues, a network of monitoring sites was developed in Indiana that provides continuous measurements of precipitation, potential evapotranspiration (PET), soil volumetric water content (VWC), and soil matric potential to parameterize and calibrate models. Flux at the base of the root zone is simulated using two models of varying complexity: 1) the HYDRUS model, which numerically solves the Richards equation, and 2) the soil-water-balance (SWB) model, which assumes vertical flow under a unit gradient with infiltration and evapotranspiration treated as separate, sequential processes. Soil hydraulic parameters are determined based on laboratory data, a pedo-transfer function (ROSETTA), field measurements (Guelph permeameter), and parameter optimization. Groundwater elevation data are available at three of six sites to establish the base of the unsaturated zone model domain. Initial modeling focused on the groundwater recharge season (Nov-Feb) when PET is limited and much of the annual vertical flux occurs. HYDRUS results indicate that base of root zone fluxes at a site underlain by glacial ice-contact parent materials are 48% of recharge season precipitation (VWC RMSE=8.2%), while SWB results indicate that fluxes are 43% (VWC RMSE=3.7%). Due in part to variations in surface boundary conditions, more variable fluxes were obtained for a site underlain by alluvium with the SWB model (68

  19. New modelling of transient well test and rate decline analysis for a horizontal well in a multiple-zone reservoir

    International Nuclear Information System (INIS)

    Nie, Ren-Shi; Guo, Jian-Chun; Jia, Yong-Lu; Zhu, Shui-Qiao; Rao, Zheng; Zhang, Chun-Guang

    2011-01-01

    The no-type curve with negative skin of a horizontal well has been found in the current research. Negative skin is very significant to transient well test and rate decline analysis. This paper first presents the negative skin problem where the type curves with negative skin of a horizontal well are oscillatory. In order to solve the problem, we propose a new model of transient well test and rate decline analysis for a horizontal well in a multiple-zone composite reservoir. A new dimensionless definition of r D is introduced in the dimensionless mathematical modelling under different boundaries. The model is solved using the Laplace transform and separation of variables techniques. In Laplace space, the solutions for both constant rate production and constant wellbore pressure production are expressed in a unified formula. We provide graphs and thorough analysis of the new standard type curves for both well test and rate decline analysis; the characteristics of type curves are the reflections of horizontal well production in a multiple-zone reservoir. An important contribution of our paper is that our model removed the oscillation in type curves and thus solved the negative skin problem. We also show that the characteristics of type curves depend heavily on the properties of different zones, skin factor, well length, formation thickness, etc. Our research can be applied to a real case study

  20. Modeling a thick unsaturated zone at San Gorgonio Pass, California: lessons learned after five years of artificial recharge

    Science.gov (United States)

    Flint, Alan L.; Ellett, Kevin M.; Christensen, Allen H.; Martin, Peter

    2012-01-01

    The information flow among the tasks of framework assessment, numerical modeling, model forecasting and hind casting, and system-performance monitoring is illustrated. Results provide an understanding of artificial recharge in high-altitude desert settings where large vertical distances may separate application ponds from their target aquifers.Approximately 3.8 million cubic meters of surface water was applied to spreading ponds from 2003–2007 to artificially recharge the underlying aquifer through a 200-meter thick unsaturated zone in the San Gorgonio Pass area in southern California. A study was conducted between 1997 and 2003, and a numerical model was developed to help determine the suitability of the site for artificial recharge. Ongoing monitoring results indicated that the existing model needed to be modified and recalibrated to more accurately predict artificial recharge at the site. The objective of this work was to recalibrate the model by using observation of the application rates, the rise and fall of the water level above a perching layer, and the approximate arrival time to the water table during the 5-yr monitoring period following initiation of long-term artificial recharge. Continuous monitoring of soil-matric potential, temperature, and water levels beneath the site indicated that artificial recharge reached the underlying water table between 3.75 and 4.5 yr after the initial application of the recharge water. The model was modified to allow the simulation to more adequately match the perching layer dynamics and the time of arrival at the water table. The instrumentation also showed that the lag time between changes in application of water at the surface and the response at the perching layer decreased from about 4 mo to less than 1 mo due to the wet-up of the unsaturated zone and the increase in relative permeability. The results of this study demonstrate the importance of iteratively monitoring and modeling the unsaturated zone in layered

  1. The Impact of Surface Bending, A Complete Mineralogical Model and Movement of the Overriding Plate on Subduction Zones

    Science.gov (United States)

    Arredondo, Katrina Marie

    Modern observations of subduction zones provide only snapshots of a complex geologic system that can last tens of millions of years. Surface velocity measurements and seismic tomography images provide information on the possible forces acting on the plate and influencing slab shape and behavior. Modern subduction zones exhibit a wide range of behavior, from the rapidly rolling back Tonga subduction zone (where the trench is moving toward the subducting plate) to stationary trenches to trench advance (where the trench is moving toward the overriding plate). Slabs may also stagnate at 660 km while others directly penetrate into the lower mantle. Numerical models can combine observations and laboratory data to test and study possible forces that may explain the wide variety of behavior observed in modern subduction zones. Past numerical model studies have not studied the impact on subduction zone behavior from: composition-dependent phase transitions, a complete mineralogical model and movement of the overriding plate. Here we show that: 1) weakening of the subducting plate can be observed from the forebulge to the trench using highly detailed bathymetry and gravity measurement tracks parallel to the trench, 2) using a complete mineralogy model is important for accurate numerical models because incomplete approximations may overestimate slab stagnation and slab rollback, 3) in free subduction models, the complete mineralogy model creates a strong feedback loop between broad slab folds and trench velocities, and 4) the movement of the overriding plate is very important for slab rollback. Results presented in Chapter 1 indicate that the rheology in the numerical models should produce weakening in the slab as it bends into the trench, which is observed in the models of Chapter 2 and 3. Past published models can be analyzed in relation to Chapter 2 and 3 to determine if their conclusions are skewed by an overestimation of slab stagnation or trench rollback. The presented

  2. Multi-zone modelling of partially premixed low-temperature combustion in pilot-ignited natural-gas engines

    Energy Technology Data Exchange (ETDEWEB)

    Krishnan, S. R.; inivasan, K. K.

    2010-09-14

    Detailed results from a multi-zone phenomenological simulation of partially premixed advanced-injection low-pilot-ignited natural-gas low-temperature combustion are presented with a focus on early injection timings (the beginning of (pilot) injection (BOI)) and very small diesel quantities (2-3 per cent of total fuel energy). Combining several aspects of diesel and spark ignition engine combustion models, the closed-cycle simulation accounted for diesel autoignition, diesel spray combustion, and natural-gas combustion by premixed turbulent flame propagation. The cylinder contents were divided into an unburned zone, several pilot fuel zones (or 'packets') that modelled diesel evaporation and ignition, a flame zone for natural-gas combustion, and a burned zone. The simulation predicted the onset of ignition, cylinder pressures, and heat release rate profiles satisfactorily over a wide range of BOIs (20-60° before top dead centre (before TDC)) but especially well at early BOIs. Strong coupling was observed between pilot spray combustion in the packets and premixed turbulent combustion in the flame zone and, therefore, the number of ignition centres (packets) profoundly affected flame combustion. The highest local peak temperatures (greater than 2000 K) were observed in the packets, while the flame zone was much cooler (about 1650 K), indicating that pilot diesel spray combustion is probably the dominant source of engine-out emissions of nitrogen oxide (NOx). Further, the 60° before TDC BOI yielded the lowest average peak packet temperatures (about 1720 K) compared with the 20° before TDC BOI (about 2480 K) and 40° before TDC BOI (about 2700 K). These trends support experimental NOx trends, which showed the lowest NOx emissions for the 60°, 20°, and 40° before TDC BOIs in that order. Parametric studies showed that increasing the intake charge temperature, pilot quantity, and natural-gas equivalence ratio all led to

  3. Modeling unsaturated-zone flow at Rainier Mesa as a possible analog for a future Yucca Mountain

    International Nuclear Information System (INIS)

    Gauthier, J.H.

    1998-01-01

    Rainier Mesa is structurally similar to Yucca Mountain, and receives precipitation similar to the estimated long-term average for Yucca Mountain. Tunnels through the unsaturated zone at Rainier Mesa have encountered perched water and, after the perched water was drained, flow in fractures and faults. Although flow observations have been primarily qualitative, Rainier Mesa hydrology is a potential analog for Yucca Mountain hydrology in a wetter climate. In this paper, a groundwater flow model that has been used in the performance assessment of Yucca Mountain--the weeps model--is applied to Rainier Mesa. The intent is to gain insight in both Rainier Mesa and the weeps flow model

  4. Analytical Hierarchy Process modeling for malaria risk zones in Vadodara district, Gujarat

    Science.gov (United States)

    Bhatt, B.; Joshi, J. P.

    2014-11-01

    Malaria epidemic is one of the complex spatial problems around the world. According to WHO, an estimated 6, 27, 000 deaths occurred due to malaria in 2012. In many developing nations with diverse ecological regions, it is still a large cause of human mortality. Owing to the incompleteness of epidemiological data and their spatial origin, the quantification of disease incidence burdening basic public health planning is a major constrain especially in developing countries. The present study focuses on the integrated Geospatial and Multi-Criteria Evaluation (AHP) technique to determine malaria risk zones. The study is conducted in Vadodara district, including 12 Taluka among which 4 Taluka are predominantly tribal. The influence of climatic and physical environmental factors viz., rainfall, hydro geomorphology; drainage, elevation, and land cover are used to score their share in the evaluation of malariogenic condition. This was synthesized on the basis of preference over each factor and the total weights of each data and data layer were computed and visualized. The district was divided into three viz., high, moderate and low risk zones .It was observed that a geographical area of 1885.2sq.km comprising 30.3% fall in high risk zone. The risk zones identified on the basis of these parameters and assigned weights shows a close resemblance with ground condition. As the API distribution for 2011overlaid corresponds to the risk zones identified. The study demonstrates the significance and prospect of integrating Geospatial tools and Analytical Hierarchy Process for malaria risk zones and dynamics of malaria transmission.

  5. A new multi-zone model for porosity distribution in Al–Si alloy castings

    DEFF Research Database (Denmark)

    Tiedje, Niels Skat; Taylor, John A.; Easton, Mark A.

    2013-01-01

    and distribution of porosity in Al–Si alloys cast as plates in moulds made with silica, ilmenite or zirconia sand cores or steel chills facing the major plate faces. The alloys cast were Al–7wt.% Si and Al–12.5wt.% Si in unmodified and modified forms, the latter with either Na or Sr addition. It is found that......, regardless of cooling condition, Si content and modification treatment, the microstructure can be divided into three zones of varying size (across the casting thickness) that are determined by the local cooling conditions and the nucleation and growth mode of the Al–Si eutectic. The zones are: (1) an outer...

  6. The approximate thermal-model-testing method for non-stationary temperature fields in central zones of fast reactor assemblies

    International Nuclear Information System (INIS)

    Mikhin, V.I.; Matukhin, N.M.

    2000-01-01

    The approach to generalization of the non-stationary heat exchange data for the central zones of the nuclear reactor fuel assemblies and the approximate thermal-model-testing criteria are proposed. The fuel assemblies of fast and water-cooled reactors with different fuel compositions have been investigated. The reason of the non-stationary heat exchange is the fuel-energy-release time dependence. (author)

  7. Analyzing Dyadic Sequence Data-Research Questions and Implied Statistical Models.

    Science.gov (United States)

    Fuchs, Peter; Nussbeck, Fridtjof W; Meuwly, Nathalie; Bodenmann, Guy

    2017-01-01

    The analysis of observational data is often seen as a key approach to understanding dynamics in romantic relationships but also in dyadic systems in general. Statistical models for the analysis of dyadic observational data are not commonly known or applied. In this contribution, selected approaches to dyadic sequence data will be presented with a focus on models that can be applied when sample sizes are of medium size ( N = 100 couples or less). Each of the statistical models is motivated by an underlying potential research question, the most important model results are presented and linked to the research question. The following research questions and models are compared with respect to their applicability using a hands on approach: (I) Is there an association between a particular behavior by one and the reaction by the other partner? (Pearson Correlation); (II) Does the behavior of one member trigger an immediate reaction by the other? (aggregated logit models; multi-level approach; basic Markov model); (III) Is there an underlying dyadic process, which might account for the observed behavior? (hidden Markov model); and (IV) Are there latent groups of dyads, which might account for observing different reaction patterns? (mixture Markov; optimal matching). Finally, recommendations for researchers to choose among the different models, issues of data handling, and advises to apply the statistical models in empirical research properly are given (e.g., in a new r-package "DySeq").

  8. Depositional sequence analysis and sedimentologic modeling for improved prediction of Pennsylvanian reservoirs (Annex 1)

    Energy Technology Data Exchange (ETDEWEB)

    Watney, W.L.

    1992-01-01

    Interdisciplinary studies of the Upper Pennsylvanian Lansing and Kansas City groups have been undertaken in order to improve the geologic characterization of petroleum reservoirs and to develop a quantitative understanding of the processes responsible for formation of associated depositional sequences. To this end, concepts and methods of sequence stratigraphy are being used to define and interpret the three-dimensional depositional framework of the Kansas City Group. The investigation includes characterization of reservoir rocks in oil fields in western Kansas, description of analog equivalents in near-surface and surface sites in southeastern Kansas, and construction of regional structural and stratigraphic framework to link the site specific studies. Geologic inverse and simulation models are being developed to integrate quantitative estimates of controls on sedimentation to produce reconstructions of reservoir-bearing strata in an attempt to enhance our ability to predict reservoir characteristics.

  9. A multi-task learning approach for compartmental model parameter estimation in DCE-CT sequences.

    Science.gov (United States)

    Romain, Blandine; Letort, Véronique; Lucidarme, Olivier; Rouet, Laurence; Dalché-Buc, Florence

    2013-01-01

    Today's follow-up of patients presenting abdominal tumors is generally performed through acquisition of dynamic sequences of contrast-enhanced CT. Estimating parameters of appropriate models of contrast intake diffusion through tissues should help characterizing the tumor physiology, but is impeded by the high level of noise inherent to the acquisition conditions. To improve the quality of estimation, we consider parameter estimation in voxels as a multi-task learning problem (one task per voxel) that takes advantage from the similarity between two tasks. We introduce a temporal similarity between tasks based on a robust distance between observed contrast-intake profiles of intensity. Using synthetic images, we compare multi-task learning using this temporal similarity, a spatial similarity and a single-task learning. The similarities based on temporal profiles are shown to bring significant improvements compared to the spatial one. Results on real CT sequences also confirm the relevance of the approach.

  10. The complete genome sequence of Haloferax volcanii DS2, a model archaeon.

    Directory of Open Access Journals (Sweden)

    Amber L Hartman

    2010-03-01

    Full Text Available Haloferax volcanii is an easily culturable moderate halophile that grows on simple defined media, is readily transformable, and has a relatively stable genome. This, in combination with its biochemical and genetic tractability, has made Hfx. volcanii a key model organism, not only for the study of halophilicity, but also for archaeal biology in general.We report here the sequencing and analysis of the genome of Hfx. volcanii DS2, the type strain of this species. The genome contains a main 2.848 Mb chromosome, three smaller chromosomes pHV1, 3, 4 (85, 438, 636 kb, respectively and the pHV2 plasmid (6.4 kb.The completed genome sequence, presented here, provides an invaluable tool for further in vivo and in vitro studies of Hfx. volcanii.

  11. Hidden Markov Models in Bioinformatics: SNV Inference from Next Generation Sequence.

    Science.gov (United States)

    Bian, Jiawen; Zhou, Xiaobo

    2017-01-01

    The rapid development of next generation sequencing (NGS) technology provides a novel avenue for genomic exploration and research. Hidden Markov models (HMMs) have wide applications in pattern recognition as well as Bioinformatics such as transcription factor binding sites and cis-regulatory modules detection. An application of HMM is introduced in this chapter with the in-deep developing of NGS. Single nucleotide variants (SNVs) inferred from NGS are expected to reveal gene mutations in cancer. However, NGS has lower sequence coverage and poor SNV detection capability in the regulatory regions of the genome. A specific HMM is developed for this purpose to infer the genotype for each position on the genome by incorporating the mapping quality of each read and the corresponding base quality on the reads into the emission probability of HMM. The procedure and the implementation of the algorithm is presented in detail for understanding and programming.

  12. Correlation peak analysis applied to a sequence of images using two different filters for eye tracking model

    Science.gov (United States)

    Patrón, Verónica A.; Álvarez Borrego, Josué; Coronel Beltrán, Ángel

    2015-09-01

    Eye tracking has many useful applications that range from biometrics to face recognition and human-computer interaction. The analysis of the characteristics of the eyes has become one of the methods to accomplish the location of the eyes and the tracking of the point of gaze. Characteristics such as the contrast between the iris and the sclera, the shape, and distribution of colors and dark/light zones in the area are the starting point for these analyses. In this work, the focus will be on the contrast between the iris and the sclera, performing a correlation in the frequency domain. The images are acquired with an ordinary camera, which with were taken images of thirty-one volunteers. The reference image is an image of the subjects looking to a point in front of them at 0° angle. Then sequences of images are taken with the subject looking at different angles. These images are processed in MATLAB, obtaining the maximum correlation peak for each image, using two different filters. Each filter were analyzed and then one was selected, which is the filter that gives the best performance in terms of the utility of the data, which is displayed in graphs that shows the decay of the correlation peak as the eye moves progressively at different angle. This data will be used to obtain a mathematical model or function that establishes a relationship between the angle of vision (AOV) and the maximum correlation peak (MCP). This model will be tested using different input images from other subject not contained in the initial database, being able to predict angle of vision using the maximum correlation peak data.

  13. Building a model: developing genomic resources for common milkweed (Asclepias syriaca with low coverage genome sequencing

    Directory of Open Access Journals (Sweden)

    Weitemier Kevin

    2011-05-01

    Full Text Available Abstract Background Milkweeds (Asclepias L. have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate and compliment these studies. This study explored how low coverage genome sequencing of the common milkweed (Asclepias syriaca L. could be useful in characterizing the genome of a plant without prior genomic information and for development of genomic resources as a step toward further developing A. syriaca as a model in ecology and evolution. Results A 0.5× genome of A. syriaca was produced using Illumina sequencing. A virtually complete chloroplast genome of 158,598 bp was assembled, revealing few repeats and loss of three genes: accD, clpP, and ycf1. A nearly complete rDNA cistron (18S-5.8S-26S; 7,541 bp and 5S rDNA (120 bp sequence were obtained. Assessment of polymorphism revealed that the rDNA cistron and 5S rDNA had 0.3% and 26.7% polymorphic sites, respectively. A partial mitochondrial genome sequence (130,764 bp, with identical gene content to tobacco, was also assembled. An initial characterization of repeat content indicated that Ty1/copia-like retroelements are the most common repeat type in the milkweed genome. At least one A. syriaca microread hit 88% of Catharanthus roseus (Apocynaceae unigenes (median coverage of 0.29× and 66% of single copy orthologs (COSII in asterids (median coverage of 0.14×. From this partial characterization of the A. syriaca genome, markers for population genetics (microsatellites and phylogenetics (low-copy nuclear genes studies were developed. Conclusions The results highlight the promise of next generation sequencing for development of genomic resources for any organism. Low coverage genome sequencing allows characterization of the high copy fraction of the genome and exploration of the low copy fraction of the genome, which facilitate the development of molecular tools for further study of a target species

  14. Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing.

    Science.gov (United States)

    Straub, Shannon C K; Fishbein, Mark; Livshultz, Tatyana; Foster, Zachary; Parks, Matthew; Weitemier, Kevin; Cronn, Richard C; Liston, Aaron

    2011-05-04

    Milkweeds (Asclepias L.) have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate and compliment these studies. This study explored how low coverage genome sequencing of the common milkweed (Asclepias syriaca L.) could be useful in characterizing the genome of a plant without prior genomic information and for development of genomic resources as a step toward further developing A. syriaca as a model in ecology and evolution. A 0.5× genome of A. syriaca was produced using Illumina sequencing. A virtually complete chloroplast genome of 158,598 bp was assembled, revealing few repeats and loss of three genes: accD, clpP, and ycf1. A nearly complete rDNA cistron (18S-5.8S-26S; 7,541 bp) and 5S rDNA (120 bp) sequence were obtained. Assessment of polymorphism revealed that the rDNA cistron and 5S rDNA had 0.3% and 26.7% polymorphic sites, respectively. A partial mitochondrial genome sequence (130,764 bp), with identical gene content to tobacco, was also assembled. An initial characterization of repeat content indicated that Ty1/copia-like retroelements are the most common repeat type in the milkweed genome. At least one A. syriaca microread hit 88% of Catharanthus roseus (Apocynaceae) unigenes (median coverage of 0.29×) and 66% of single copy orthologs (COSII) in asterids (median coverage of 0.14×). From this partial characterization of the A. syriaca genome, markers for population genetics (microsatellites) and phylogenetics (low-copy nuclear genes) studies were developed. The results highlight the promise of next generation sequencing for development of genomic resources for any organism. Low coverage genome sequencing allows characterization of the high copy fraction of the genome and exploration of the low copy fraction of the genome, which facilitate the development of molecular tools for further study of a target species and its relatives. This study represents a first

  15. Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing

    Science.gov (United States)

    2011-01-01

    Background Milkweeds (Asclepias L.) have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate and compliment these studies. This study explored how low coverage genome sequencing of the common milkweed (Asclepias syriaca L.) could be useful in characterizing the genome of a plant without prior genomic information and for development of genomic resources as a step toward further developing A. syriaca as a model in ecology and evolution. Results A 0.5× genome of A. syriaca was produced using Illumina sequencing. A virtually complete chloroplast genome of 158,598 bp was assembled, revealing few repeats and loss of three genes: accD, clpP, and ycf1. A nearly complete rDNA cistron (18S-5.8S-26S; 7,541 bp) and 5S rDNA (120 bp) sequence were obtained. Assessment of polymorphism revealed that the rDNA cistron and 5S rDNA had 0.3% and 26.7% polymorphic sites, respectively. A partial mitochondrial genome sequence (130,764 bp), with identical gene content to tobacco, was also assembled. An initial characterization of repeat content indicated that Ty1/copia-like retroelements are the most common repeat type in the milkweed genome. At least one A. syriaca microread hit 88% of Catharanthus roseus (Apocynaceae) unigenes (median coverage of 0.29×) and 66% of single copy orthologs (COSII) in asterids (median coverage of 0.14×). From this partial characterization of the A. syriaca genome, markers for population genetics (microsatellites) and phylogenetics (low-copy nuclear genes) studies were developed. Conclusions The results highlight the promise of next generation sequencing for development of genomic resources for any organism. Low coverage genome sequencing allows characterization of the high copy fraction of the genome and exploration of the low copy fraction of the genome, which facilitate the development of molecular tools for further study of a target species and its relatives

  16. Correction for Measurement Error from Genotyping-by-Sequencing in Genomic Variance and Genomic Prediction Models

    DEFF Research Database (Denmark)

    Ashraf, Bilal; Janss, Luc; Jensen, Just

    sample). The GBSeq data can be used directly in genomic models in the form of individual SNP allele-frequency estimates (e.g., reference reads/total reads per polymorphic site per individual), but is subject to measurement error due to the low sequencing depth per individual. Due to technical reasons....... In the current work we show how the correction for measurement error in GBSeq can also be applied in whole genome genomic variance and genomic prediction models. Bayesian whole-genome random regression models are proposed to allow implementation of large-scale SNP-based models with a per-SNP correction...... for measurement error. We show correct retrieval of genomic explained variance, and improved genomic prediction when accounting for the measurement error in GBSeq data...

  17. Developing semi-analytical solution for multiple-zone transient storage model with spatially non-uniform storage

    Science.gov (United States)

    Deng, Baoqing; Si, Yinbing; Wang, Jia

    2017-12-01

    Transient storages may vary along the stream due to stream hydraulic conditions and the characteristics of storage. Analytical solutions of transient storage models in literature didn't cover the spatially non-uniform storage. A novel integral transform strategy is presented that simultaneously performs integral transforms to the concentrations in the stream and in storage zones by using the single set of eigenfunctions derived from the advection-diffusion equation of the stream. The semi-analytical solution of the multiple-zone transient storage model with the spatially non-uniform storage is obtained by applying the generalized integral transform technique to all partial differential equations in the multiple-zone transient storage model. The derived semi-analytical solution is validated against the field data in literature. Good agreement between the computed data and the field data is obtained. Some illustrative examples are formulated to demonstrate the applications of the present solution. It is shown that solute transport can be greatly affected by the variation of mass exchange coefficient and the ratio of cross-sectional areas. When the ratio of cross-sectional areas is big or the mass exchange coefficient is small, more reaches are recommended to calibrate the parameter.

  18. Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence.

    Directory of Open Access Journals (Sweden)

    Shuhei Isami

    Full Text Available Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of temperature factors for several crystal structures of DNA. Second, we propose a coarse-grained elastic network model of DNA, where each nucleotide is described only by one node. This model could effectively reproduce the detailed dynamics obtained with the all-atom elastic network model according to the sequence-dependent geometry. Through normal-mode analysis for the coarse-grained elastic network model, we exhaustively analyzed the dynamic features of a large number of long DNA sequences, approximately ∼150 bp in length. These analyses revealed positive correlations between the nucleosome-forming abilities and the inter-strand fluctuation strength of double-stranded DNA for several DNA sequences.

  19. Hidden Markov event sequence models: toward unsupervised functional MRI brain mapping.

    Science.gov (United States)

    Faisan, Sylvain; Thoraval, Laurent; Armspach, Jean-Paul; Foucher, Jack R; Metz-Lutz, Marie-Noëlle; Heitz, Fabrice

    2005-01-01

    Most methods used in functional MRI (fMRI) brain mapping require restrictive assumptions about the shape and timing of the fMRI signal in activated voxels. Consequently, fMRI data may be partially and misleadingly characterized, leading to suboptimal or invalid inference. To limit these assumptions and to capture the broad range of possible activation patterns, a novel statistical fMRI brain mapping method is proposed. It relies on hidden semi-Markov event sequence models (HSMESMs), a special class of hidden Markov models (HMMs) dedicated to the modeling and analysis of event-based random processes. Activation detection is formulated in terms of time coupling between (1) the observed sequence of hemodynamic response onset (HRO) events detected in the voxel's fMRI signal and (2) the "hidden" sequence of task-induced neural activation onset (NAO) events underlying the HROs. Both event sequences are modeled within a single HSMESM. The resulting brain activation model is trained to automatically detect neural activity embedded in the input fMRI data set under analysis. The data sets considered in this article are threefold: synthetic epoch-related, real epoch-related (auditory lexical processing task), and real event-related (oddball detection task) fMRI data sets. Synthetic data: Activation detection results demonstrate the superiority of the HSMESM mapping method with respect to a standard implementation of the statistical parametric mapping (SPM) approach. They are also very close, sometimes equivalent, to those obtained with an "ideal" implementation of SPM in which the activation patterns synthesized are reused for analysis. The HSMESM method appears clearly insensitive to timing variations of the hemodynamic response and exhibits low sensitivity to fluctuations of its shape (unsustained activation during task). Real epoch-related data: HSMESM activation detection results compete with those obtained with SPM, without requiring any prior definition of the expected

  20. Binary classifiers and latent sequence models for emotion detection in suicide notes.

    Science.gov (United States)

    Cherry, Colin; Mohammad, Saif M; de Bruijn, Berry

    2012-01-01

    This paper describes the National Research Council of Canada's submission to the 2011 i2b2 NLP challenge on the detection of emotions in suicide notes. In this task, each sentence of a suicide note is annotated with zero or more emotions, making it a multi-label sentence classification task. We employ two distinct large-margin models capable of handling multiple labels. The first uses one classifier per emotion, and is built to simplify label balance issues and to allow extremely fast development. This approach is very effective, scoring an F-measure of 55.22 and placing fourth in the competition, making it the best system that does not use web-derived statistics or re-