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. Modeling earthquake sequences along the Manila subduction zone: Effects of three-dimensional fault geometry

    Science.gov (United States)

    Yu, Hongyu; Liu, Yajing; Yang, Hongfeng; Ning, Jieyuan

    2018-05-01

    To assess the potential of catastrophic megathrust earthquakes (MW > 8) along the Manila Trench, the eastern boundary of the South China Sea, we incorporate a 3D non-planar fault geometry in the framework of rate-state friction to simulate earthquake rupture sequences along the fault segment between 15°N-19°N of northern Luzon. Our simulation results demonstrate that the first-order fault geometry heterogeneity, the transitional-segment (possibly related to the subducting Scarborough seamount chain) connecting the steeper south segment and the flatter north segment, controls earthquake rupture behaviors. The strong along-strike curvature at the transitional-segment typically leads to partial ruptures of MW 8.3 and MW 7.8 along the southern and northern segments respectively. The entire fault occasionally ruptures in MW 8.8 events when the cumulative stress in the transitional-segment is sufficiently high to overcome the geometrical inhibition. Fault shear stress evolution, represented by the S-ratio, is clearly modulated by the width of seismogenic zone (W). At a constant plate convergence rate, a larger W indicates on average lower interseismic stress loading rate and longer rupture recurrence period, and could slow down or sometimes stop ruptures that initiated from a narrower portion. Moreover, the modeled interseismic slip rate before whole-fault rupture events is comparable with the coupling state that was inferred from the interplate seismicity distribution, suggesting the Manila trench could potentially rupture in a M8+ earthquake.

  3. Seismic sequences in the Sombrero Seismic Zone

    Science.gov (United States)

    Pulliam, J.; Huerfano, V. A.; ten Brink, U.; von Hillebrandt, C.

    2007-05-01

    The northeastern Caribbean, in the vicinity of Puerto Rico and the Virgin Islands, has a long and well-documented history of devastating earthquakes and tsunamis, including major events in 1670, 1787, 1867, 1916, 1918, and 1943. Recently, seismicity has been concentrated to the north and west of the British Virgin Islands, in the region referred to as the Sombrero Seismic Zone by the Puerto Rico Seismic Network (PRSN). In the combined seismicity catalog maintained by the PRSN, several hundred small to moderate magnitude events can be found in this region prior to 2006. However, beginning in 2006 and continuing to the present, the rate of seismicity in the Sombrero suddenly increased, and a new locus of activity developed to the east of the previous location. Accurate estimates of seismic hazard, and the tsunamigenic potential of seismic events, depend on an accurate and comprehensive understanding of how strain is being accommodated in this corner region. Are faults locked and accumulating strain for release in a major event? Or is strain being released via slip over a diffuse system of faults? A careful analysis of seismicity patterns in the Sombrero region has the potential to both identify faults and modes of failure, provided the aggregation scheme is tuned to properly identify related events. To this end, we experimented with a scheme to identify seismic sequences based on physical and temporal proximity, under the assumptions that (a) events occur on related fault systems as stress is refocused by immediately previous events and (b) such 'stress waves' die out with time, so that two events that occur on the same system within a relatively short time window can be said to have a similar 'trigger' in ways that two nearby events that occurred years apart cannot. Patterns that emerge from the identification, temporal sequence, and refined locations of such sequences of events carry information about stress accommodation that is obscured by large clouds of

  4. 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.

  5. HABITABLE ZONES OF POST-MAIN SEQUENCE STARS

    International Nuclear Information System (INIS)

    Ramirez, Ramses M.; Kaltenegger, Lisa

    2016-01-01

    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. 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.

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

    Science.gov (United States)

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

    2007-09-01

    Relocated Engdahl et al. (1998) global seismological data for 10 aftershock sequences were used to analyze the internal tectonic structure of the Central American subduction zone; the main shocks of several of these were the most destructive and often referenced earthquakes in the region (e.g., the 1970 Chiapas, 1983 Osa, 1992 Nicaragua, 1999 Quepos, 2001 El Salvador earthquakes). The spatial analysis of aftershock foci distribution was performed in a rotated Cartesian coordinate system (x, y, z) related to the Wadati-Benioff zone, and not in a standard coordinate system ($\\varphi$, λ, h are latitude, longitude, focal depth, respectively). Available fault plane solutions were also transformed into the plane approximating the Wadati-Benioff zone. The spatial distribution of earthquakes in each aftershock sequence was modeled as either a plane fit using a least squares approximation or a volume fit with a minimum thickness rectangular box. The analysis points to a quasi-planar distribution of earthquake foci in all aftershock sequences, manifesting the appurtenance of aftershocks to fracture zones. Geometrical parameters of fracture zones (strike, dip, and dimensions) hosting individual sequences were calculated and compared with the seafloor morphology of the Cocos Plate. The smooth character of the seafloor correlates with the aftershock fracture zones oriented parallel to the trench and commonly subparallel to the subducting slab, whereas subduction of the Cocos Ridge and seamounts around the Quepos Plateau coincides with steeply dipping fracture zones. Transformed focal mechanisms are almost exclusively (>90%) of normal character.

  8. Foundations of Sequence-to-Sequence Modeling for Time Series

    OpenAIRE

    Kuznetsov, Vitaly; Mariet, Zelda

    2018-01-01

    The availability of large amounts of time series data, paired with the performance of deep-learning algorithms on a broad class of problems, has recently led to significant interest in the use of sequence-to-sequence models for time series forecasting. We provide the first theoretical analysis of this time series forecasting framework. We include a comparison of sequence-to-sequence modeling to classical time series models, and as such our theory can serve as a quantitative guide for practiti...

  9. HABITABLE ZONES AROUND MAIN-SEQUENCE STARS: NEW ESTIMATES

    Energy Technology Data Exchange (ETDEWEB)

    Kopparapu, Ravi Kumar; Ramirez, Ramses; Kasting, James F. [Department of Geosciences, Penn State University, 443 Deike Building, University Park, PA 16802 (United States); Eymet, Vincent [Laboratoire d' Astrophysique de Bordeaux, Universite de Bordeaux 1, UMR 5804, F-33270 Floirac (France); Robinson, Tyler D.; Domagal-Goldman, Shawn; Meadows, Victoria [NASA Astrobiology Institute' s Virtual Planetary Laboratory (United States); Mahadevan, Suvrath; Terrien, Ryan C.; Deshpande, Rohit [Center for Exoplanets and Habitable Worlds, The Pennsylvania State University, University Park, PA 16802 (United States)

    2013-03-10

    Identifying terrestrial planets in the habitable zones (HZs) of other stars is one of the primary goals of ongoing radial velocity (RV) and transit exoplanet surveys and proposed future space missions. Most current estimates of the boundaries of the HZ are based on one-dimensional (1D), cloud-free, climate model calculations by Kasting et al. However, this model used band models that were based on older HITRAN and HITEMP line-by-line databases. The inner edge of the HZ in the Kasting et al. model was determined by loss of water, and the outer edge was determined by the maximum greenhouse provided by a CO{sub 2} atmosphere. A conservative estimate for the width of the HZ from this model in our solar system is 0.95-1.67 AU. Here an updated 1D radiative-convective, cloud-free climate model is used to obtain new estimates for HZ widths around F, G, K, and M stars. New H{sub 2}O and CO{sub 2} absorption coefficients, derived from the HITRAN 2008 and HITEMP 2010 line-by-line databases, are important improvements to the climate model. According to the new model, the water-loss (inner HZ) and maximum greenhouse (outer HZ) limits for our solar system are at 0.99 and 1.70 AU, respectively, suggesting that the present Earth lies near the inner edge. Additional calculations are performed for stars with effective temperatures between 2600 and 7200 K, and the results are presented in parametric form, making them easy to apply to actual stars. The new model indicates that, near the inner edge of the HZ, there is no clear distinction between runaway greenhouse and water-loss limits for stars with T{sub eff} {approx}< 5000 K, which has implications for ongoing planet searches around K and M stars. To assess the potential habitability of extrasolar terrestrial planets, we propose using stellar flux incident on a planet rather than equilibrium temperature. This removes the dependence on planetary (Bond) albedo, which varies depending on the host star's spectral type. We suggest

  10. HABITABLE ZONES AROUND MAIN-SEQUENCE STARS: NEW ESTIMATES

    International Nuclear Information System (INIS)

    Kopparapu, Ravi Kumar; Ramirez, Ramses; Kasting, James F.; Eymet, Vincent; Robinson, Tyler D.; Domagal-Goldman, Shawn; Meadows, Victoria; Mahadevan, Suvrath; Terrien, Ryan C.; Deshpande, Rohit

    2013-01-01

    Identifying terrestrial planets in the habitable zones (HZs) of other stars is one of the primary goals of ongoing radial velocity (RV) and transit exoplanet surveys and proposed future space missions. Most current estimates of the boundaries of the HZ are based on one-dimensional (1D), cloud-free, climate model calculations by Kasting et al. However, this model used band models that were based on older HITRAN and HITEMP line-by-line databases. The inner edge of the HZ in the Kasting et al. model was determined by loss of water, and the outer edge was determined by the maximum greenhouse provided by a CO 2 atmosphere. A conservative estimate for the width of the HZ from this model in our solar system is 0.95-1.67 AU. Here an updated 1D radiative-convective, cloud-free climate model is used to obtain new estimates for HZ widths around F, G, K, and M stars. New H 2 O and CO 2 absorption coefficients, derived from the HITRAN 2008 and HITEMP 2010 line-by-line databases, are important improvements to the climate model. According to the new model, the water-loss (inner HZ) and maximum greenhouse (outer HZ) limits for our solar system are at 0.99 and 1.70 AU, respectively, suggesting that the present Earth lies near the inner edge. Additional calculations are performed for stars with effective temperatures between 2600 and 7200 K, and the results are presented in parametric form, making them easy to apply to actual stars. The new model indicates that, near the inner edge of the HZ, there is no clear distinction between runaway greenhouse and water-loss limits for stars with T eff ∼ ⊕ , so that future flagship missions like TPF-C and Darwin are not undersized. Our model does not include the radiative effects of clouds; thus, the actual HZ boundaries may extend further in both directions than the estimates just given.

  11. Lower bounds on the periodic Hamming correlations of frequency hopping sequences with low hit zone

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    In this paper, several periodic Hamming correlation lower bounds for frequency hopping sequences with low hit zone, with respect to the size p of the frequency slot set, the sequence length L, the family size M, low hit zone LH ( or no hit zone NH ), the maximum periodic Hamming autocorrelation sidelobe Ha and the maximum periodic Hamming crosscorrelation Hc, are established. It is shown that the new bounds include the known Lempel-Greenberger bounds, T.S. Seay bounds and Peng-Fan bounds for the conventional frequency hopping sequences as special cases.

  12. 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.)

  13. 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

  14. DNA sequence modeling based on context trees

    NARCIS (Netherlands)

    Kusters, C.J.; Ignatenko, T.; Roland, J.; Horlin, F.

    2015-01-01

    Genomic sequences contain instructions for protein and cell production. Therefore understanding and identification of biologically and functionally meaningful patterns in DNA sequences is of paramount importance. Modeling of DNA sequences in its turn can help to better understand and identify such

  15. 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.

  16. 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.

  17. 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

  18. 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)

  19. 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

  20. 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

  1. Modeling of Prepregs during Automated Draping Sequences

    DEFF Research Database (Denmark)

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

    2017-01-01

    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...

  2. 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.

  3. 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.

  4. Near-field/altered-zone models report

    International Nuclear Information System (INIS)

    Hardin, E. L.

    1998-01-01

    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 nonlithophysal and lower

  5. 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

  6. 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...

  7. A Simple Model of Service Trade with Time Zone Differences

    OpenAIRE

    Kikuchi, Toru; Iwasa, Kazumichi

    2008-01-01

    This note proposes a two-country monopolistic competition model of service trade that captures the role of time zone differences as a determinant of trade patterns. It is shown that the utilization of time zone differences induces drastic change in trade patterns: Due to taking advantage of time zone differences, service firms learve larger countries for smaller countries.

  8. 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.

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

    International Nuclear Information System (INIS)

    Kopparapu, Ravi Kumar; Ramirez, Ramses M.; Kasting, James F.; SchottelKotte, James; Domagal-Goldman, Shawn; Eymet, Vincent

    2014-01-01

    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 ⊕ and 5 M ⊕ . Assuming H 2 O-(inner HZ) and CO 2 -(outer HZ) dominated atmospheres, and scaling the background N 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 2 O column depth. For larger planets, the H 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

  10. Habitable Zones Around Main-Sequence Stars: Dependence on Planetary Mass

    Science.gov (United States)

    Kopparapu, Ravi Kumar; Ramirez, Ramses M.; Kotte, James Schottel; Kasting, James F.; Domagal-Goldman, Shawn; Eymet, Vincent

    2014-01-01

    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 0.1M and 5M. Assuming H2O-(inner HZ) and CO2-(outer HZ) dominated atmospheres, and scaling the background N2 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 (approx.10% lower than Earth flux) for low mass planets due to larger greenhouse effect arising from the increased H2O column depth. For larger planets, the H2O column depth is smaller, and higher temperatures are needed before water vapor completely dominates the outgoing long-wave radiation. Hence the inner edge moves inward (approx.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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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

  17. Investigating Some Technical Issues on Cohesive Zone Modeling of Fracture

    Science.gov (United States)

    Wang, John T.

    2011-01-01

    This study investigates some technical issues related to the use of cohesive zone models (CZMs) in modeling fracture processes. These issues include: why cohesive laws of different shapes can produce similar fracture predictions; under what conditions CZM predictions have a high degree of agreement with linear elastic fracture mechanics (LEFM) analysis results; when the shape of cohesive laws becomes important in the fracture predictions; and why the opening profile along the cohesive zone length needs to be accurately predicted. Two cohesive models were used in this study to address these technical issues. They are the linear softening cohesive model and the Dugdale perfectly plastic cohesive model. Each cohesive model constitutes five cohesive laws of different maximum tractions. All cohesive laws have the same cohesive work rate (CWR) which is defined by the area under the traction-separation curve. The effects of the maximum traction on the cohesive zone length and the critical remote applied stress are investigated for both models. For a CZM to predict a fracture load similar to that obtained by an LEFM analysis, the cohesive zone length needs to be much smaller than the crack length, which reflects the small scale yielding condition requirement for LEFM analysis to be valid. For large-scale cohesive zone cases, the predicted critical remote applied stresses depend on the shape of cohesive models used and can significantly deviate from LEFM results. Furthermore, this study also reveals the importance of accurately predicting the cohesive zone profile in determining the critical remote applied load.

  18. 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

  19. Time Variability of the Dust Sublimation Zones in Pre-Main Sequence Disk Systems

    Science.gov (United States)

    Sitko, Michael L.; Carpenter, W. J.; Grady, C. A.; Russel, R. W.; Lynch, D. K.; Rudy, R. J.; Mazuk, S. M.; Venturini, C. C.; Kimes, R. L.; Beerman, L. C.; hide

    2007-01-01

    The dust sublimation zone (DSZ) is the region of pre-main sequence (PMS) disks where dust grains most easily anneal, sublime, and condense out of the gas. Because of this, it is a location where crystalline material may be enhanced and redistributed throughout the rest of the disk. A decade-long program to monitor the thermal emission of the grains located in this region demonstrates that large changes in emitted flux occur in many systems. Changes in the thermal emission between 3 and 13.5 microns were observed in HD 31648 (MWC 480), HD 163296 (MWC 275), and DG Tau. This emission is consistent with it being produced at the DSZ, where the transition from a disk of gas to one of gas+dust occurs. In the case of DG Tau, the outbursts were accompanied by increased emission on the 10 micron silicate band on one occasion, while on another occasion it went into absorption. This requires lofting of the material above the disk into the line of sight. Such changes will affect the determination of the inner disk structure obtained through interferometry measurements, and this has been confirmed in the case of HD 163296. Cyclic variations in the heating of the DSZ will lead to the annealing of large grains, the sublimation of smaller grains, possibly followed by re-condensation as the zone enters a cooling phase. Lofting of dust above the disk plane, and outward acceleration by stellar winds and radiation pressure, can re-distribute the processed material to cooler regions of the disk, where cometesimals form. This processing is consistent with the detection of the preferential concentration of large crystalline grains in the inner few AU of PMS disks using interferometric spectroscopy with the VLTI.

  20. 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.

  1. 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

  2. Comparison of lesion conspicuity of radiofrequency ablation zones among MR sequences according to time in the normal rabbit liver

    International Nuclear Information System (INIS)

    Ku, Myong Seo; Kim, Seung Kwon; Hong, Hyun Pyo; Kwag, Hyon Joo

    2007-01-01

    To compare the lesion conspicuity of radiofrequency ablation (RFA) zones among MR sequences according to time in the normal rabbit liver. RFA zones were created in 12 rabbit livers with a 17-gauge internally cooled electrode (1-cm active tip, 30 Watts, 3 minutes). Three rabbits were sacrificed immediately, three days, two weeks, and six weeks after the RFA procedure, respectively. Before sacrifice, T1-, T2-weighted images (WI), and gadolinium-enhanced (GE)-T1WI images were obtained. The lesion conspicuity of the RAF zone and the contrast-to-noise ratio (CNR) of the RFA zone to the liver parenchyma were analyzed and compared among the MR sequences according to time. On T1WI, the RFA zones were only clearly seen on acute phase. On T2WI, the RFA zones were clearly seen on all phases except the hyperacute phase. On GE T1WI, the RFA zones were clearly seen on all phases. The CNRs of the RFA zone to the liver parenchyma of GE-T1WI (8.1-12.4) were significantly higher than the CNRs of TIWI (1.6-2.7) and T2WI (1.7-6.3) on all phases (ρ < 0.05), but the visual lesion conspicuity between GE T1WI and T2WI were similar. On hyperacute phase, GE T1WI showed better lesion conspicuity of the RFA zone than T1WI and T2WI. On other phases, GE T1WI and T2WI showed similar lesion conspicuity

  3. Calibrating Vadose Zone Models with Time-Lapse Gravity Data

    DEFF Research Database (Denmark)

    Christiansen, Lars; Hansen, A. B.; Looms, M. C.

    2009-01-01

    A change in soil water content is a change in mass stored in the subsurface. Given that the mass change is big enough, the change can be measured with a gravity meter. Attempts have been made with varying success over the last decades to use ground-based time-lapse gravity measurements to infer...... hydrogeological parameters. These studies focused on the saturated zone with specific yield as the most prominent target parameter. Any change in storage in the vadose zone has been considered as noise. Our modeling results show a measureable change in gravity from the vadose zone during a forced infiltration...... experiment on 10m by 10m grass land. Simulation studies show a potential for vadose zone model calibration using gravity data in conjunction with other geophysical data, e.g. cross-borehole georadar. We present early field data and calibration results from a forced infiltration experiment conducted over 30...

  4. 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.

  5. Strain Anomalies during an Earthquake Sequence in the South Iceland Seismic Zone

    Science.gov (United States)

    Arnadottir, T.; Haines, A. J.; Geirsson, H.; Hreinsdottir, S.

    2017-12-01

    The South Iceland Seismic Zone (SISZ) accommodates E-W translation due to oblique spreading between the North American/Hreppar microplate and Eurasian plate, in South Iceland. Strain is released in the SISZ during earthquake sequences that last days to years, at average intervals of 80-100 years. The SISZ is currently in the midst of an earthquake sequence that started with two M6.5 earthquakes in June 2000, and continued with two M6 earthquakes in May 2008. Estimates of geometric strain accumulation, and seismic strain release in these events indicate that they released at most only half of the strain accumulated since the last earthquake cycle in 1896-1912. Annual GPS campaigns and continuous measurements during 2001-2015 were used to calculate station velocities and strain rates from a new method using the vertical derivatives of horizontal stress (VDoHS). This new method allows higher resolution of strain rates than other (older) approaches, as the strain rates are estimated by integrating VDoHS rates obtained by inversion rather than differentiating interpolated GPS velocities. Estimating the strain rates for eight 1-2 year intervals indicates temporal and spatial variation of strain rates in the SISZ. In addition to earthquake faulting, the strain rates in the SISZ are influenced by anthropogenic signals due to geothermal exploitation, and magma movements in neighboring volcanoes - Hekla and Eyjafjallajökull. Subtle signals of post-seismic strain rate changes are seen following the June 2000 M6.5 main shocks, but interestingly, much larger strain rate variations are observed after the two May 2008 M6 main shocks. A prominent strain anomaly is evident in the epicentral area prior to the May 2008 earthquake sequence. The strain signal persists over at least 4 years in the epicentral area, leading up to the M6 main shocks. The strain is primarily extension in ESE-WNW direction (sub-parallel to the direction of plate spreading), but overall shear across the N

  6. GAMMA RAYS FROM THE TYCHO SUPERNOVA REMNANT: MULTI-ZONE VERSUS SINGLE-ZONE MODELING

    Energy Technology Data Exchange (ETDEWEB)

    Atoyan, Armen [Department of Mathematics, Concordia University, 1455 de Maisonneuve Blvd. West, Montreal, Quebec H3G 1M8 (Canada); Dermer, Charles D., E-mail: atoyan@mathstat.concordia.ca, E-mail: charles.dermer@nrl.navy.mil [Code 7653, Naval Research Laboratory, Washington, DC 20375-5352 (United States)

    2012-04-20

    Recent Fermi and VERITAS observations of the prototypical Type Ia supernova remnant (SNR) Tycho have discovered {gamma}-rays with energies E in the range 0.4 GeV {approx}< E {approx}< 10 TeV. Crucial for the theory of Galactic cosmic-ray origin is whether the {gamma}-rays from SNRs are produced by accelerated hadrons (protons and ions) or by relativistic electrons. Here we show that strong constraints on the leptonic model imposed in the framework of the commonly used single-zone model are essentially removed if the analysis of the broadband radiation spectrum of Tycho is done in the two-zone (or, in general, multi-zone) approach, which is likely to apply to every SNR. Importantly, we show that the single-zone approach may underpredict the {gamma}-ray fluxes by an order of magnitude. A hadronic model can, however, also fit the detected {gamma}-ray spectrum. The difference between {gamma}-ray fluxes of hadronic and leptonic origins becomes significant only at {approx}<300 MeV, which could be revealed by spectral measurements of Tycho and other SNRs at these energies.

  7. 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

  8. Postseismic deformation following the June 2000 earthquake sequence in the south Iceland seismic zone

    Science.gov (United States)

    Arnadottir, T.; Jonsson, Sigurjon; Pollitz, F.F.; Jiang, W.; Feigl, K.L.

    2005-01-01

    We observe postseismic deformation on two spatiotemporal scales following Mw = 6.5 earthquakes in the south Iceland seismic zone on 17 and 21 June 2000. We see a rapidly decaying deformation transient lasting no more than 2 months and extending about 5 km away from the two main shock ruptures. This local, month-scale transient is captured by several radar interferograms and is also observed at a few campaign GPS sites located near the faults. A slower transient with a characteristic timescale of about a year is detected only by GPS measurements. The month-scale deformation pattern has been explained by poroelastic rebound due to postearthquake pore pressure changes. In contrast, the year-scale deformation can be explained by either afterslip at 8-14 km depth or viscoelastic relaxation of the lower crust and upper mantle in response to the coseismic stress changes. The optimal viscoelastic models have lower crustal viscosities of 0.5-1 ?? 1019 Pa s and upper mantle viscosity of ???3 ?? 1018 Pa s. Because of the limitations of our GPS campaign data, we consider both afterslip and viscoelastic relaxation as plausible mechanisms explaining the deformation field. Both types of postseismic deformation models suggest that the areas of large coseismic stress increase east of the 17 June and west of the 21 June ruptures continue to be loaded by the postseismic deformation. Copyright 2005 by the American Geophysical Union.

  9. Modelling of hydrodynamic mechanisms of pollutant propagation in coastal zones

    International Nuclear Information System (INIS)

    Benque, J.P.

    1982-11-01

    The results of this document have to be distinguished in mathematical models applicable to small-area problems (horizontal scale comparable to depth) and models applicable to large-area phenomena (horizontal scales much greater than depth, quasi-hydrostatic approximation). In the case of the former, progress remains to be made in the simulation of turbulence and in the development of algorithms applicable under often very complex geometrical conditions. Excellent results are obtained by combining mathematical models with reduced-scale models, the former (on larger scales) providing the boundary conditions for the tank of the physical models. Large-area problems can be tackled only by means of mathematical models. These models are extremely efficient for the calculation of mesoscale circulation and transport of pollutants, but they all run into the same difficulty of simulating long-term problems and of determining drift currents. The principal difficulty faced by mesoscale or macroscale models is the determination of atmospheric conditions and of boundary conditions in the open sea. Mathematical models make it possible to determine the situation at every point of a given coastal zone and require only the conditions at the boundaries of the zone for this purpose. However, although these conditions at the boundary correspond to an experimental effort small in relation to total surveillance of the zone, they are essential to the predictions of the mathematical model, and efforts must be made to obtain the best possible boundary conditions. In addition to these experimental surveys at the boundaries, a certain number of observations within the zone are needed for the calibration of the model, i.e. for the determination of certain numerical coefficients appearing in the parametrization

  10. An enriched cohesive zone model for delamination in brittle interfaces

    NARCIS (Netherlands)

    Samimi, M.; Dommelen, van J.A.W.; Geers, M.G.D.

    2009-01-01

    Application of standard cohesive zone models in a finite element framework to simulate delamination in brittle interfaces may trigger non-smooth load-displacement responses that lead to the failure of iterative solution procedures. This non-smoothness is an artifact of the discretization; and hence

  11. 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

  12. 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

  13. Enhanced phytoremediation in the vadose zone: Modeling and column studies

    Science.gov (United States)

    Sung, K.; Chang, Y.; Corapcioglu, M.; Cho, C.

    2002-05-01

    Phytoremediation is a plant-based technique with potential for enhancing the remediation of vadoese zone soils contaminated by pollutants. The use of deep-rooted plants is an alternative to conventional methodologies. However, when the phytoremediation is applied to the vadose zone, it might have some restrictions since it uses solely naturally driven energy and mechanisms in addition to the complesxity of the vadose zone. As a more innovative technique than conventional phytoremediation methods, air injected phytoremediation technique is introduced to enhance the remediation efficiency or to apply at the former soil vapor extraction or bio venting sites. Effects of air injection, vegetation treatment, and air injection with vegetation treatments on the removal of hydrocarbon were investigated by column studies to simulate the field situation. Both the removal efficiency and the microbial activity were highest in air-injected and vegetated column soils. It was suggested that increased microorganisms activity stimulated by plant root exudates enhanced biodegradation of hydrocarbon compounds. Air injection provided sufficient opportunity for promoting the microbial activity at depths where the conditions are anaerobic. Air injection can enhance the physicochemical properties of the medium and contaminant and increase the bioavailability i.e., the plant and microbial accessibility to the contaminant. A mathematical model that can be applied to phytoremediation, especially to air injected phytoremediation, for simulating the fate and the transport of a diesel contaminant in the vadose zone is developed. The approach includes a two-phase model of water flow in vegetated and unplanted vadose zone soil. A time-specific root distribution model and a microbial growth model in the rhizosphere of vegetated soil were combined with an unsaturated soil water flow equation as well as with a contaminant transport equation. The proposed model showed a satisfactory representation of

  14. 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.

  15. 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)

  16. Unified Deep Learning Architecture for Modeling Biology Sequence.

    Science.gov (United States)

    Wu, Hongjie; Cao, Chengyuan; Xia, Xiaoyan; Lu, Qiang

    2017-10-09

    Prediction of the spatial structure or function of biological macromolecules based on their sequence remains an important challenge in bioinformatics. When modeling biological sequences using traditional sequencing models, characteristics, such as long-range interactions between basic units, the complicated and variable output of labeled structures, and the variable length of biological sequences, usually lead to different solutions on a case-by-case basis. This study proposed the use of bidirectional recurrent neural networks based on long short-term memory or a gated recurrent unit to capture long-range interactions by designing the optional reshape operator to adapt to the diversity of the output labels and implementing a training algorithm to support the training of sequence models capable of processing variable-length sequences. Additionally, the merge and pooling operators enhanced the ability to capture short-range interactions between basic units of biological sequences. The proposed deep-learning model and its training algorithm might be capable of solving currently known biological sequence-modeling problems through the use of a unified framework. We validated our model on one of the most difficult biological sequence-modeling problems currently known, with our results indicating the ability of the model to obtain predictions of protein residue interactions that exceeded the accuracy of current popular approaches by 10% based on multiple benchmarks.

  17. Continuous Online Sequence Learning with an Unsupervised Neural Network Model.

    Science.gov (United States)

    Cui, Yuwei; Ahmad, Subutar; Hawkins, Jeff

    2016-09-14

    The ability to recognize and predict temporal sequences of sensory inputs is vital for survival in natural environments. Based on many known properties of cortical neurons, hierarchical temporal memory (HTM) sequence memory recently has been proposed as a theoretical framework for sequence learning in the cortex. In this letter, we analyze properties of HTM sequence memory and apply it to sequence learning and prediction problems with streaming data. We show the model is able to continuously learn a large number of variableorder temporal sequences using an unsupervised Hebbian-like learning rule. The sparse temporal codes formed by the model can robustly handle branching temporal sequences by maintaining multiple predictions until there is sufficient disambiguating evidence. We compare the HTM sequence memory with other sequence learning algorithms, including statistical methods: autoregressive integrated moving average; feedforward neural networks-time delay neural network and online sequential extreme learning machine; and recurrent neural networks-long short-term memory and echo-state networks on sequence prediction problems with both artificial and real-world data. The HTM model achieves comparable accuracy to other state-of-the-art algorithms. The model also exhibits properties that are critical for sequence learning, including continuous online learning, the ability to handle multiple predictions and branching sequences with high-order statistics, robustness to sensor noise and fault tolerance, and good performance without task-specific hyperparameter tuning. Therefore, the HTM sequence memory not only advances our understanding of how the brain may solve the sequence learning problem but is also applicable to real-world sequence learning problems from continuous data streams.

  18. Anatomy of extremely thin marine sequences landward of a passive-margin hinge zone: Neogene Calvert Cliffs succession, Maryland, U.S.A.

    Energy Technology Data Exchange (ETDEWEB)

    Kidwell, S.M. [Univ. of Chicago, IL (United States). Dept. of Geophysical Sciences

    1997-03-01

    Detailed examination of Neogene strata in cliffs 25--35 m high along the western shore of Chesapeake Bay, Maryland, reveals the complexity of the surviving record of siliciclastic sequences {approximately}150 km inland of the structural hinge zone of the Atlantic passive margin. Previous study of the lower to middle Miocene Calvert (Plum Point Member) and Choptank Formations documented a series of third-order sequences 7--10 m thick in which lowstand deposits are entirely lacking, transgressive tracts comprise a mosaic of condensed bioclastic facies, and regressive (highstand) tracts are present but partially truncated by the next sequence boundary; smaller-scale (fourth-order) cyclic units could not be resolved. Together, these sequences constitute the transgressive and early highstand tracts of a larger (second-order Miocene) composite sequence. The present paper documents stratigraphic relations higher in the Calvert Cliffs succession, including the upper Miocene St. Marys Formation, which represents late highstand marine deposits of the Miocene second-order sequence, and younger Neogene fluvial and tidal-inlet deposits representing incised-valley deposits of the succeeding second-order cycle. The St. Marys Formation consists of a series of tabular units 2--5 m thick, each with an exclusively transgressive array of facies and bounded by stranding surfaces of abrupt shallowing. These units, which are opposite to the flooding-surface-bounded regressive facies arrays of model parasequences, are best characterized as shaved sequences in which only the transgressive tract survives, and are stacked into larger transgressive, highstand, and forced-regression sets.

  19. Mechanical modelling of the Singoe deformation zone. Site descriptive modelling Forsmark stage 2.1

    Energy Technology Data Exchange (ETDEWEB)

    Glamheden, Rune; Maersk Hansen, Lars; Fredriksson, Anders; Bergkvist, Lars; Markstroem, Ingemar; Elfstroem, Mats [Golder Associates AB (Sweden)

    2007-02-15

    This project aims at demonstrating the theoretical approach developed by SKB for determination of mechanical properties of large deformation zones, in particular the Singoe deformation zone. Up to now, only bedrock and minor deformation zones have been characterized by means of this methodology, which has been modified for this project. The Singoe deformation zone is taken as a reference object to get a more comprehensive picture of the structure, which could be incorporated in a future version of the SDM of Forsmark. Furthermore, the Singoe Zone has been chosen because of available data from four tunnels. Scope of work has included compilation and analysis of geological information from site investigations and documentation of existing tunnels. Results have been analyzed and demonstrated by means of RVS-visualization. Numerical modelling has been used to obtain mechanical properties. Numerical modelling has also been carried out in order to verify the results by comparison of calculated and measured deformations. Compilation of various structures in the four tunnels coincides largely with a magnetic anomaly and also with the estimated width. Based on the study it is clear that the Singoe deformation zone has a heterogeneous nature. The number of fracture zones associated with the deformation zone varies on either side of the zone, as does the transition zone between host rock and the Singoe zone. The overall impression from the study is that the results demonstrate that the methodology used for simulating of equivalent mechanical properties is an applicable and adequate method, also in case of large deformation zones. Typical rock mechanical parameters of the Singoe deformations that can be used in the regional stress model considering the zone to be a single fracture are: 200 MPa/m in normal stiffness, 10-15 MPa/m in shear stiffness, 0.4 MPa in cohesion and 31.5 degrees in friction angle.

  20. Mechanical modelling of the Singoe deformation zone. Site descriptive modelling Forsmark stage 2.1

    International Nuclear Information System (INIS)

    Glamheden, Rune; Maersk Hansen, Lars; Fredriksson, Anders; Bergkvist, Lars; Markstroem, Ingemar; Elfstroem, Mats

    2007-02-01

    This project aims at demonstrating the theoretical approach developed by SKB for determination of mechanical properties of large deformation zones, in particular the Singoe deformation zone. Up to now, only bedrock and minor deformation zones have been characterized by means of this methodology, which has been modified for this project. The Singoe deformation zone is taken as a reference object to get a more comprehensive picture of the structure, which could be incorporated in a future version of the SDM of Forsmark. Furthermore, the Singoe Zone has been chosen because of available data from four tunnels. Scope of work has included compilation and analysis of geological information from site investigations and documentation of existing tunnels. Results have been analyzed and demonstrated by means of RVS-visualization. Numerical modelling has been used to obtain mechanical properties. Numerical modelling has also been carried out in order to verify the results by comparison of calculated and measured deformations. Compilation of various structures in the four tunnels coincides largely with a magnetic anomaly and also with the estimated width. Based on the study it is clear that the Singoe deformation zone has a heterogeneous nature. The number of fracture zones associated with the deformation zone varies on either side of the zone, as does the transition zone between host rock and the Singoe zone. The overall impression from the study is that the results demonstrate that the methodology used for simulating of equivalent mechanical properties is an applicable and adequate method, also in case of large deformation zones. Typical rock mechanical parameters of the Singoe deformations that can be used in the regional stress model considering the zone to be a single fracture are: 200 MPa/m in normal stiffness, 10-15 MPa/m in shear stiffness, 0.4 MPa in cohesion and 31.5 degrees in friction angle

  1. Modelling Subduction Zone Magmatism Due to Hydraulic Fracture

    Science.gov (United States)

    Lawton, R.; Davies, J. H.

    2014-12-01

    The aim of this project is to test the hypothesis that subduction zone magmatism involves hydraulic fractures propagating from the oceanic crust to the mantle wedge source region (Davies, 1999). We aim to test this hypothesis by developing a numerical model of the process, and then comparing model outputs with observations. The hypothesis proposes that the water interconnects in the slab following an earthquake. If sufficient pressure develops a hydrofracture occurs. The hydrofracture will expand in the direction of the least compressive stress and propagate in the direction of the most compressive stress, which is out into the wedge. Therefore we can calculate the hydrofracture path and end-point, given the start location on the slab and the propagation distance. We can therefore predict where water is added to the mantle wedge. To take this further we have developed a thermal model of a subduction zone. The model uses a finite difference, marker-in-cell method to solve the heat equation (Gerya, 2010). The velocity field was prescribed using the analytical expression of cornerflow (Batchelor, 1967). The markers contained within the fixed grid are used to track the different compositions and their properties. The subduction zone thermal model was benchmarked (Van Keken, 2008). We used the hydrous melting parameterization of Katz et.al., (2003) to calculate the degree of melting caused by the addition of water to the wedge. We investigate models where the hydrofractures, with properties constrained by estimated water fluxes, have random end points. The model predicts degree of melting, magma productivity, temperature of the melt and water content in the melt for different initial water fluxes. Future models will also include the buoyancy effect of the melt and residue. Batchelor, Cambridge UP, 1967. Davies, Nature, 398: 142-145, 1999. Gerya, Cambridge UP, 2010. Katz, Geochem. Geophys. Geosy, 4(9), 2003 Van Keken et.al. Phys. Earth. Planet. In., 171:187-197, 2008.

  2. Sedimentation across the central California oxygen minimum zone: an alternative coastal upwelling sequence.

    Science.gov (United States)

    Vercoutere, T.L.; Mullins, H.T.; McDougall, K.; Thompson, J.B.

    1987-01-01

    Distribution, abundance, and diversity of terrigenous, authigenous, and biogenous material provide evidence of the effect of bottom currents and oxygen minimum zone (OMZ) on continental slope sedimentation offshore central California. Three major OMZ facies are identified, along the upper and lower edges of OMZ and one at its core.-from Authors

  3. 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...

  4. 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.

  5. Shear heating and metamorphism in subduction zones, 1. Thermal models

    Science.gov (United States)

    Kohn, M. J.; Castro, A. E.; Spear, F. S.

    2017-12-01

    Popular thermal-mechanical models of modern subduction systems are 100-500 °C colder at c. 50 km depth than pressure-temperature (P-T) conditions determined from exhumed metamorphic rocks. This discrepancy has been ascribed by some to profound bias in the rock record, i.e. metamorphic rocks reflect only anomalously warm subduction, not normal subduction. Accurately inferring subduction zone thermal structure, whether from models or rocks, is crucial for predicting depths of seismicity, fluid release, and sub-arc melting conditions. Here, we show that adding realistic shear stresses to thermal models implies P-T conditions quantitatively consistent with those recorded by exhumed metamorphic rocks, suggesting that metamorphic rock P-T conditions are not anomalously warm. Heat flow measurements from subduction zone fore-arcs typically indicate effective coefficients of friction (µ) ranging from 0.025 to 0.1. We included these coefficients of friction in analytical models of subduction zone interface temperatures. Using global averages of subducting plate age (50 Ma), subduction velocity (6 cm/yr), and subducting plate geometry (central Chile), temperatures at 50 km depth (1.5 GPa) increase by c. 200 °C for µ=0.025 to 700 °C for µ=0.1. However, at high temperatures, thermal softening will reduce frictional heating, and temperatures will not increase as much with depth. Including initial weakening of materials ranging from wet quartz (c. 300 °C) to diabase (c. 600 °C) in the analytical models produces concave-upward P-T distributions on P-T diagrams, with temperatures c. 100 to 500 °C higher than models with no shear heating. The absolute P-T conditions and concave-upward shape of the shear-heating + thermal softening models almost perfectly matches the distribution of P-T conditions derived from a compilation of exhumed metamorphic rocks. Numerical models of modern subduction zones that include shear heating also overlap metamorphic data. Thus, excepting the

  6. Mesoscale modeling of amorphous metals by shear transformation zone dynamics

    International Nuclear Information System (INIS)

    Homer, Eric R.; Schuh, Christopher A.

    2009-01-01

    A new mesoscale modeling technique for the thermo-mechanical behavior of metallic glasses is proposed. The modeling framework considers the shear transformation zone (STZ) as the fundamental unit of deformation, and coarse-grains an amorphous collection of atoms into an ensemble of STZs on a mesh. By employing finite element analysis and a kinetic Monte Carlo algorithm, the modeling technique is capable of simulating glass processing and deformation on time and length scales greater than those usually attainable by atomistic modeling. A thorough explanation of the framework is presented, along with a specific two-dimensional implementation for a model metallic glass. The model is shown to capture the basic behaviors of metallic glasses, including high-temperature homogeneous flow following the expected constitutive law, and low-temperature strain localization into shear bands. Details of the effects of processing and thermal history on the glass structure and properties are also discussed.

  7. Modelling of hydro-zones for layout planning and numerical flow model in 2006

    International Nuclear Information System (INIS)

    Ahokas, H.; Vaittinen, T.; Tammisto, E.; Nummela, J.

    2007-11-01

    As part of the programme for the final disposal of spent nuclear fuel, a model was compiled of hydrogeologically significant zones on the Olkiluoto site. These deterministic zones dominate the groundwater flow especially deep in the bedrock, and because of their nature intersections by disposal tunnels will be avoided, if possible. For layout planning purposes, a brief description was made of the deformation zones of the geological model that intersect the planned repository area and are of hydraulic significance from the point of view of long-term safety. In addition, the hydraulic properties of the zones and the bedrock outside the zones needed for the numerical flow simulations were described. Modelling was mainly based on hydrological observations including an extensive number of single-hole hydraulic tests as well as some long-term pumping test results. Some geophysical mise-a-la-masse results were also used in the compilation of the zones. A comparison between the modelled hydrogeological zones and the deformation zones identified in the geological model of the Olkiluoto site is also presented. (orig.)

  8. 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.

  9. Modeling Degradation Product Partitioning in Chlorinated-DNAPL Source Zones

    Science.gov (United States)

    Boroumand, A.; Ramsburg, A.; Christ, J.; Abriola, L.

    2009-12-01

    Metabolic reductive dechlorination degrades aqueous phase contaminant concentrations, increasing the driving force for DNAPL dissolution. Results from laboratory and field investigations suggest that accumulation of cis-dichloroethene (cis-DCE) and vinyl chloride (VC) may occur within DNAPL source zones. The lack of (or slow) degradation of cis-DCE and VC within bioactive DNAPL source zones may result in these dechlorination products becoming distributed among the solid, aqueous, and organic phases. Partitioning of cis-DCE and VC into the organic phase may reduce aqueous phase concentrations of these contaminants and result in the enrichment of these dechlorination products within the non-aqueous phase. Enrichment of degradation products within DNAPL may reduce some of the advantages associated with the application of bioremediation in DNAPL source zones. Thus, it is important to quantify how partitioning (between the aqueous and organic phases) influences the transport of cis-DCE and VC within bioactive DNAPL source zones. In this work, abiotic two-phase (PCE-water) one-dimensional column experiments are modeled using analytical and numerical methods to examine the rate of partitioning and the capacity of PCE-DNAPL to reversibly sequester cis-DCE. These models consider aqueous-phase, nonaqueous phase, and aqueous plus nonaqueous phase mass transfer resistance using linear driving force and spherical diffusion expressions. Model parameters are examined and compared for different experimental conditions to evaluate the mechanisms controlling partitioning. Biot number, a dimensionless number which is an index of the ratio of the aqueous phase mass transfer rate in boundary layer to the mass transfer rate within the NAPL, is used to characterize conditions in which either or both processes are controlling. Results show that application of a single aqueous resistance is capable to capture breakthrough curves when DNAPL is distributed in porous media as low

  10. 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

  11. Chaos game representation (CGR)-walk model for DNA sequences

    International Nuclear Information System (INIS)

    Jie, Gao; Zhen-Yuan, Xu

    2009-01-01

    Chaos game representation (CGR) is an iterative mapping technique that processes sequences of units, such as nucleotides in a DNA sequence or amino acids in a protein, in order to determine the coordinates of their positions in a continuous space. This distribution of positions has two features: one is unique, and the other is source sequence that can be recovered from the coordinates so that the distance between positions may serve as a measure of similarity between the corresponding sequences. A CGR-walk model is proposed based on CGR coordinates for the DNA sequences. The CGR coordinates are converted into a time series, and a long-memory ARFIMA (p, d, q) model, where ARFIMA stands for autoregressive fractionally integrated moving average, is introduced into the DNA sequence analysis. This model is applied to simulating real CGR-walk sequence data of ten genomic sequences. Remarkably long-range correlations are uncovered in the data, and the results from these models are reasonably fitted with those from the ARFIMA (p, d, q) model. (cross-disciplinary physics and related areas of science and technology)

  12. 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

  13. 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

  14. The genome sequence of the model ascomycete fungus Podospora anserina

    NARCIS (Netherlands)

    Espagne, Eric; Lespinet, Olivier; Malagnac, Fabienne; Da Silva, Corinne; Jaillon, Olivier; Porcel, Betina M; Couloux, Arnaud; Aury, Jean-Marc; Ségurens, Béatrice; Poulain, Julie; Anthouard, Véronique; Grossetete, Sandrine; Khalili, Hamid; Coppin, Evelyne; Déquard-Chablat, Michelle; Picard, Marguerite; Contamine, Véronique; Arnaise, Sylvie; Bourdais, Anne; Berteaux-Lecellier, Véronique; Gautheret, Daniel; de Vries, Ronald P; Battaglia, Evy; Coutinho, Pedro M; Danchin, Etienne Gj; Henrissat, Bernard; Khoury, Riyad El; Sainsard-Chanet, Annie; Boivin, Antoine; Pinan-Lucarré, Bérangère; Sellem, Carole H; Debuchy, Robert; Wincker, Patrick; Weissenbach, Jean; Silar, Philippe

    2008-01-01

    BACKGROUND: The dung-inhabiting ascomycete fungus Podospora anserina is a model used to study various aspects of eukaryotic and fungal biology, such as ageing, prions and sexual development. RESULTS: We present a 10X draft sequence of P. anserina genome, linked to the sequences of a large expressed

  15. Dislocation-free zone model of fracture comparison with experiments

    International Nuclear Information System (INIS)

    Ohr, S.M.; Chang, S.

    1982-01-01

    The dislocation-free zone (DFZ) model of fracture has been extended to study the relationship between the stress intensity factor, extent of plastic deformation, and crack tip geometry of an elastic-plastic crack as a function of applied stress. The results show that the stress intensity factor K decreases from the elastic value at first slowly, then goes rapidly to zero as the number of dislocations in the plastic zone increases. The crack with a zero stress intensity factor has its crack tip stress field completely relaxed by plastic deformation and hence is called a plastic crack. Between the elastic and plastic cracks, a wide range of elastic-plastic cracks having both a stress singularity and a plastic zone are possible. These elastic-plastic cracks with a DFZ are predicted if there is a critical stress intensity factor K/sub g/ required for the generation of dislocations at the crack tip. The expression for K/sub g/ is obtained from the crack tip dislocation nucleation model of Rice and Thomson. In most metals, the magnitude of K/sub g/ is less than the critical stress intensity factor for brittle fracture K/sub c/. The values of K are determined from electron microscope fracture experiments for various metals and they are found to be in good agreement with the K/sub g/ predicted from the model. It is concluded that for most ductile and semibrittle metals, the mechanism of dislocation generation is more important than the fracture surface energy in determining the stress intensity factor at the crack tip

  16. 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.

  17. 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.

  18. 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.

  19. Phase II, improved work zone design guidelines and enhanced model of traffic delays in work zones : executive summary report.

    Science.gov (United States)

    2009-03-01

    This project contains three major parts. In the first part a digital computer simulation model was developed with the aim to model the traffic through a freeway work zone situation. The model was based on the Arena simulation software and used cumula...

  20. Phase II, improved work zone design guidelines and enhanced model of traffic delays in work zones : final report, March 2009.

    Science.gov (United States)

    2009-03-01

    This project contains three major parts. In the first part a digital computer simulation model was developed with the aim to model the traffic through a freeway work zone situation. The model was based on the Arena simulation software and used cumula...

  1. Time-reversibility in seismic sequences: Application to the seismicity of Mexican subduction zone

    Science.gov (United States)

    Telesca, L.; Flores-Márquez, E. L.; Ramírez-Rojas, A.

    2018-02-01

    In this paper we investigate the time-reversibility of series associated with the seismicity of five seismic areas of the subduction zone beneath the Southwest Pacific Mexican coast, applying the horizontal visibility graph method to the series of earthquake magnitudes, interevent times, interdistances and magnitude increments. We applied the Kullback-Leibler divergence D that is a metric for quantifying the degree of time-irreversibility in time series. Our findings suggest that among the five seismic areas, Jalisco-Colima is characterized by time-reversibility in all the four seismic series. Our results are consistent with the peculiar seismo-tectonic characteristics of Jalisco-Colima, which is the closest to the Middle American Trench and belongs to the Mexican volcanic arc.

  2. 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.

  3. Joint Distributed Surf Zone Environmental Model: FY96 Modeling Procedure

    National Research Council Canada - National Science Library

    Allard, Richard

    1997-01-01

    ... to the modeling and simulation community. To test this proof of concept, a suite of models were identified and tested for Camp Pendelton, CA, during two 7 day periods in January and August 1995, in which data from the Coupled Ocean...

  4. Cohesive zone modeling of intergranular cracking in polycrystalline aggregates

    International Nuclear Information System (INIS)

    Simonovski, Igor; Cizelj, Leon

    2015-01-01

    Highlights: • Alternative approach to cohesive elements is proposed: cohesive-zone contact. • Applicability to measured and simulated grain structures is demonstrated. • Normal and normal/shear separation as a damage initialization is explored. • Normal/shear damage initialization significantly reduces ductility. • Little difference in Voronoi aggregate size on macroscopic response. - Abstract: Understanding and controlling early damage initiation and evolution are amongst the most important challenges in nuclear power plants, occurring in ferritic, austenitic steels and nickel based alloys. In this work a meso-scale approach to modeling initiation and evolution of early intergranular cracking is presented. This damage mechanism is present in a number of nuclear power plant components and depends on the material (e.g. composition, heat treatment, microstructure), environment and load. Finite element modeling is used to explicitly model the microstructure – both the grains and the grain boundaries. Spatial Voronoi tessellation is used to obtain the grain topology. In addition, measured topology of a 0.4 mm stainless steel wire is used. Anisotropic elasticity and crystal plasticity are used as constitutive laws for the grains. Grain boundaries are modeled using the cohesive zone approach. Different modeling assumptions/parameters are evaluated against the numerical stability criteria. The biggest positive contribution to numerical stability is the use of cohesive-type contact instead of cohesive elements. A small amount of viscous regularization should be also used along with the addition of a small amount of viscous forces to the global equilibrium equations. Two cases of grain boundary damage initiation are explored: (1) initiation due to normal separation and (2) initiation due to a combination of normal and shear separation. The second criterion significantly decreases the ductility of an aggregate and slightly improves the numerical stability

  5. 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

  6. Geodynamic Modeling of the Subduction Zone around the Japanese Islands

    Science.gov (United States)

    Honda, S.

    2017-06-01

    In this review, which focuses on our research, we describe the development of the thermomechanical modeling of subduction zones, paying special attention to those around the Japanese Islands. Without a sufficient amount of data and observations, models tended to be conceptual and general. However, the increasing power of computational tools has resulted in simple analytical and numerical models becoming more realistic, by incorporating the mantle flow around the subducting slab. The accumulation of observations and data has made it possible to construct regional models to understand the detail of the subduction processes. Recent advancements in the study of the seismic tomography and geology around the Japanese Islands has enabled new aspects of modeling the mantle processes. A good correlation between the seismic velocity anomalies and the finger-like distribution of volcanoes in northeast Japan has been recognized and small-scale convection (SSC) in the mantle wedge has been proposed to explain such a feature. The spatial and temporal evolution of the distribution of past volcanoes may reflect the characteristics of the flow in the mantle wedge, and points to the possibility of the flip-flopping of the finger-like pattern of the volcano distribution and the migration of volcanic activity from the back-arc side to the trench side. These observations are found to be qualitatively consistent with the results of the SSC model. We have also investigated the expected seismic anisotropy in the presence of SSC. The fast direction of the P-wave anisotropy generally shows the trench-normal direction with a reduced magnitude compared to the case without SSC. An analysis of full 3D seismic anisotropy is necessary to confirm the existence and nature of SSC. The 3D mantle flow around the subduction zone of plate-size scale has been modeled. It was found that the trench-parallel flow in the sub-slab mantle around the northern edge of the Pacific plate at the junction between

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

    DEFF Research Database (Denmark)

    Have, Christian Theil; Mørk, Søren

    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...... 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...... and are evaluated by the effect on prediction performance. Since bacterial gene finding to a large extent is a solved problem it forms an ideal proving ground for evaluating the explicit modeling of larger scale gene sequence composition of genomes. We conclude that the sequential composition of gene reading frames...

  8. 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.

  9. 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

  10. 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.

  11. Phase equilibria constraints on models of subduction zone magmatism

    Science.gov (United States)

    Myers, James D.; Johnston, Dana A.

    Petrologic models of subduction zone magmatism can be grouped into three broad classes: (1) predominantly slab-derived, (2) mainly mantle-derived, and (3) multi-source. Slab-derived models assume high-alumina basalt (HAB) approximates primary magma and is derived by partial fusion of the subducting slab. Such melts must, therefore, be saturated with some combination of eclogite phases, e.g. cpx, garnet, qtz, at the pressures, temperatures and water contents of magma generation. In contrast, mantle-dominated models suggest partial melting of the mantle wedge produces primary high-magnesia basalts (HMB) which fractionate to yield derivative HAB magmas. In this context, HMB melts should be saturated with a combination of peridotite phases, i.e. ol, cpx and opx, and have liquid-lines-of-descent that produce high-alumina basalts. HAB generated in this manner must be saturated with a mafic phase assemblage at the intensive conditions of fractionation. Multi-source models combine slab and mantle components in varying proportions to generate the four main lava types (HMB, HAB, high-magnesia andesites (HMA) and evolved lavas) characteristic of subduction zones. The mechanism of mass transfer from slab to wedge as well as the nature and fate of primary magmas vary considerably among these models. Because of their complexity, these models imply a wide range of phase equilibria. Although the experiments conducted on calc-alkaline lavas are limited, they place the following limitations on arc petrologic models: (1) HAB cannot be derived from HMB by crystal fractionation at the intensive conditions thus far investigated, (2) HAB could be produced by anhydrous partial fusion of eclogite at high pressure, (3) HMB liquids can be produced by peridotite partial fusion 50-60 km above the slab-mantle interface, (4) HMA cannot be primary magmas derived by partial melting of the subducted slab, but could have formed by slab melt-peridotite interaction, and (5) many evolved calc

  12. The normal zone propagation in ATLAS B00 model coil

    CERN Document Server

    Boxman, E W; ten Kate, H H J

    2002-01-01

    The B00 model coil has been successfully tested in the ATLAS Magnet Test Facility at CERN. The coil consists of two double pancakes wound with aluminum stabilized cables of the barrel- and end-cap toroids conductors for the ATLAS detector. The magnet current is applied up to 24 kA and quenches are induced by firing point heaters. The normal zone velocity is measured over a wide range of currents by using pickup coils, voltage taps and superconducting quench detectors. The signals coming from various sensors are presented and analyzed. The results extracted from the various detection methods are in good agreement. It is found that the characteristic velocities vary from 5 to 20 m/s at 15 and 24 kA respectively. In addition, the minimum quench energies at different applied magnet currents are presented. (6 refs).

  13. Modelling guided waves in the Alaskan-Aleutian subduction zone

    Science.gov (United States)

    Coulson, Sophie; Garth, Thomas; Reitbrock, Andreas

    2016-04-01

    Subduction zone guided wave arrivals from intermediate depth earthquakes (70-300 km depth) have a huge potential to tell us about the velocity structure of the subducting oceanic crust as it dehydrates at these depths. We see guided waves as the oceanic crust has a slower seismic velocity than the surrounding material, and so high frequency energy is retained and delayed in the crustal material. Lower frequency energy is not retained in this crustal waveguide and so travels at faster velocities of the surrounding material. This gives a unique observation at the surface with low frequency energy arriving before the higher frequencies. We constrain this guided wave dispersion by comparing the waveforms recorded in real subduction zones with simulated waveforms, produced using finite difference full waveform modelling techniques. This method has been used to show that hydrated minerals in the oceanic crust persist to much greater depths than accepted thermal petrological subduction zone models would suggest in Northern Japan (Garth & Rietbrock, 2014a), and South America (Garth & Rietbrock, in prep). These observations also suggest that the subducting oceanic mantle may be highly hydrated at intermediate depth by dipping normal faults (Garth & Rietbrock 2014b). We use this guided wave analysis technique to constrain the velocity structure of the down going ~45 Ma Pacific plate beneath Alaska. Dispersion analysis is primarily carried out on guided wave arrivals recorded on the Alaskan regional seismic network. Earthquake locations from global earthquake catalogues (ISC and PDE) and regional earthquake locations from the AEIC (Alaskan Earthquake Information Centre) catalogue are used to constrain the slab geometry and to identify potentially dispersive events. Dispersed arrivals are seen at stations close to the trench, with high frequency (>2 Hz) arrivals delayed by 2 - 4 seconds. This dispersion is analysed to constrain the velocity and width of the proposed waveguide

  14. TSPA Model for the Yucca Mountain Unsaturated Zone

    International Nuclear Information System (INIS)

    M.L. Wilson; C.K. Ho

    2001-01-01

    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

  15. A sequence-dependent rigid-base model of DNA

    Science.gov (United States)

    Gonzalez, O.; Petkevičiutė, D.; Maddocks, J. H.

    2013-02-01

    A novel hierarchy of coarse-grain, sequence-dependent, rigid-base models of B-form DNA in solution is introduced. The hierarchy depends on both the assumed range of energetic couplings, and the extent of sequence dependence of the model parameters. A significant feature of the models is that they exhibit the phenomenon of frustration: each base cannot simultaneously minimize the energy of all of its interactions. As a consequence, an arbitrary DNA oligomer has an intrinsic or pre-existing stress, with the level of this frustration dependent on the particular sequence of the oligomer. Attention is focussed on the particular model in the hierarchy that has nearest-neighbor interactions and dimer sequence dependence of the model parameters. For a Gaussian version of this model, a complete coarse-grain parameter set is estimated. The parameterized model allows, for an oligomer of arbitrary length and sequence, a simple and explicit construction of an approximation to the configuration-space equilibrium probability density function for the oligomer in solution. The training set leading to the coarse-grain parameter set is itself extracted from a recent and extensive database of a large number of independent, atomic-resolution molecular dynamics (MD) simulations of short DNA oligomers immersed in explicit solvent. The Kullback-Leibler divergence between probability density functions is used to make several quantitative assessments of our nearest-neighbor, dimer-dependent model, which is compared against others in the hierarchy to assess various assumptions pertaining both to the locality of the energetic couplings and to the level of sequence dependence of its parameters. It is also compared directly against all-atom MD simulation to assess its predictive capabilities. The results show that the nearest-neighbor, dimer-dependent model can successfully resolve sequence effects both within and between oligomers. For example, due to the presence of frustration, the model can

  16. A sequence-dependent rigid-base model of DNA.

    Science.gov (United States)

    Gonzalez, O; Petkevičiūtė, D; Maddocks, J H

    2013-02-07

    A novel hierarchy of coarse-grain, sequence-dependent, rigid-base models of B-form DNA in solution is introduced. The hierarchy depends on both the assumed range of energetic couplings, and the extent of sequence dependence of the model parameters. A significant feature of the models is that they exhibit the phenomenon of frustration: each base cannot simultaneously minimize the energy of all of its interactions. As a consequence, an arbitrary DNA oligomer has an intrinsic or pre-existing stress, with the level of this frustration dependent on the particular sequence of the oligomer. Attention is focussed on the particular model in the hierarchy that has nearest-neighbor interactions and dimer sequence dependence of the model parameters. For a Gaussian version of this model, a complete coarse-grain parameter set is estimated. The parameterized model allows, for an oligomer of arbitrary length and sequence, a simple and explicit construction of an approximation to the configuration-space equilibrium probability density function for the oligomer in solution. The training set leading to the coarse-grain parameter set is itself extracted from a recent and extensive database of a large number of independent, atomic-resolution molecular dynamics (MD) simulations of short DNA oligomers immersed in explicit solvent. The Kullback-Leibler divergence between probability density functions is used to make several quantitative assessments of our nearest-neighbor, dimer-dependent model, which is compared against others in the hierarchy to assess various assumptions pertaining both to the locality of the energetic couplings and to the level of sequence dependence of its parameters. It is also compared directly against all-atom MD simulation to assess its predictive capabilities. The results show that the nearest-neighbor, dimer-dependent model can successfully resolve sequence effects both within and between oligomers. For example, due to the presence of frustration, the model can

  17. Thermodynamic modeling of phase relations and metasomatism in shear zones

    Science.gov (United States)

    Goncalves, P.; Oliot, E.; Marquer, D.

    2009-04-01

    Ductile shear zones have been recognized for a long time as privileged sites of intense fluid-rock interactions in the crust. In most cases they induce focused changes in mineralogy and bulk chemical composition (metasomatism) which in turn may control the deformation and fluid-migration processes. Therefore understanding these processes requires in a first step to be able to model phase relations in such open system. In this contribution, emphasizes in placed on metasomatic aspects of the problem. Indeed , in many ductile shear zones reported in metagranites, deformation and fluid-rock interactions are associated with gain in MgO and losses of CaO and Na2O (K2O is also a mobile component but it can be either gained or lost). Although the mineralogical consequences of this so-called Mg-metasomatism are well-documented (replacement of K-feldspar into phengite, breakdown of plagioclase into ab + ep, crystallization of chlorite), the origin of this coupled mass-transfer is still unknown. We have performed a forward modeling of phase relationships using petrogenetic grids and pseudosections that consider variations in chemical potential (μ) of the mobile elements (MgO, CaO, Na2O). Chemical potential gradients being the driving force of mass transfer, μ-μ diagrams are the most appropriate diagrams to model open systems where fluid-rock interactions are prominent. Chemical potential diagrams are equivalent to activity diagrams but our approach differs from previous work because (1) solid solutions are taken into account (2) phase relations are modeled in a more realistic chemical system (Na2O-CaO-K2O-FeO-MgO-Al2O3-SiO2-H2O) and (3) the use of pseudosections allows to predict changes of the mineralogy (modes, composition) for the specific bulk composition studied. A particular attention is paid to the relationships between component concentrations and chemical potentials, which is not obvious in multi-component system. The studied shear zone is located in the Grimsel

  18. 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.

  19. Self-Exciting Point Process Modeling of Conversation Event Sequences

    Science.gov (United States)

    Masuda, Naoki; Takaguchi, Taro; Sato, Nobuo; Yano, Kazuo

    Self-exciting processes of Hawkes type have been used to model various phenomena including earthquakes, neural activities, and views of online videos. Studies of temporal networks have revealed that sequences of social interevent times for individuals are highly bursty. We examine some basic properties of event sequences generated by the Hawkes self-exciting process to show that it generates bursty interevent times for a wide parameter range. Then, we fit the model to the data of conversation sequences recorded in company offices in Japan. In this way, we can estimate relative magnitudes of the self excitement, its temporal decay, and the base event rate independent of the self excitation. These variables highly depend on individuals. We also point out that the Hawkes model has an important limitation that the correlation in the interevent times and the burstiness cannot be independently modulated.

  20. 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

  1. 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

  2. Validating a perceptual distraction model using 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. Originally, the distraction model was trained with music targets and interferers using a simple loudspeaker setup, consisting of only 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. The results show that the model performance is equally good in both zones, i.e., with both speech- on-music and music-on-speech stimuli...

  3. 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...

  4. 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).

  5. 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.

  6. 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

  7. Optimization and evaluation of probabilistic-logic sequence models

    DEFF Research Database (Denmark)

    Christiansen, Henning; Lassen, Ole Torp

    to, in principle, Turing complete languages. In general, such models are computationally far to complex for direct use, so optimization by pruning and approximation are needed. % The first steps are made towards a methodology for optimizing such models by approximations using auxiliary models......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...

  8. 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.

  9. 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.

  10. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Dinther van, Y.

    2013-07-01

    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

  12. 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 geological

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

    Indian Academy of Sciences (India)

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

    soil properties are studied by varying the unsaturated parameters α and n over a wide range. ... Keywords. Unsaturated zone; capillary fringe; finite element method. ... and radioactive wastes. Several .... The length (L) of the soil sample is 1 m.

  14. 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)

  15. Solar Luminosity on the Main Sequence, Standard Model and Variations

    Science.gov (United States)

    Ayukov, S. V.; Baturin, V. A.; Gorshkov, A. B.; Oreshina, A. V.

    2017-05-01

    Our Sun became Main Sequence star 4.6 Gyr ago according Standard Solar Model. At that time solar luminosity was 30% lower than current value. This conclusion is based on assumption that Sun is fueled by thermonuclear reactions. If Earth's albedo and emissivity in infrared are unchanged during Earth history, 2.3 Gyr ago oceans had to be frozen. This contradicts to geological data: there was liquid water 3.6-3.8 Gyr ago on Earth. This problem is known as Faint Young Sun Paradox. We analyze luminosity change in standard solar evolution theory. Increase of mean molecular weight in the central part of the Sun due to conversion of hydrogen to helium leads to gradual increase of luminosity with time on the Main Sequence. We also consider several exotic models: fully mixed Sun; drastic change of pp reaction rate; Sun consisting of hydrogen and helium only. Solar neutrino observations however exclude most non-standard solar models.

  16. Fatigue damage modeling in solder interconnects using a cohesive zone approach

    NARCIS (Netherlands)

    Abdul-Baqi, A.J.J.; Schreurs, P.J.G.; Geers, M.G.D.

    2005-01-01

    The objective of this work is to model the fatigue damage process in a solder bump subjected to cyclic loading conditions. Fatigue damage is simulated using the cohesive zone methodology. Damage is assumed to occur at interfaces modeled through cohesive zones in the material, while the bulk material

  17. Accident sequence precursor analysis level 2/3 model development

    International Nuclear Information System (INIS)

    Lui, C.H.; Galyean, W.J.; Brownson, D.A.

    1997-01-01

    The US Nuclear Regulatory Commission's Accident Sequence Precursor (ASP) program currently uses simple Level 1 models to assess the conditional core damage probability for operational events occurring in commercial nuclear power plants (NPP). Since not all accident sequences leading to core damage will result in the same radiological consequences, it is necessary to develop simple Level 2/3 models that can be used to analyze the response of the NPP containment structure in the context of a core damage accident, estimate the magnitude of the resulting radioactive releases to the environment, and calculate the consequences associated with these releases. The simple Level 2/3 model development work was initiated in 1995, and several prototype models have been completed. Once developed, these simple Level 2/3 models are linked to the simple Level 1 models to provide risk perspectives for operational events. This paper describes the methods implemented for the development of these simple Level 2/3 ASP models, and the linkage process to the existing Level 1 models

  18. Using hidden Markov models to align multiple sequences.

    Science.gov (United States)

    Mount, David W

    2009-07-01

    A hidden Markov model (HMM) is a probabilistic model of a multiple sequence alignment (msa) of proteins. In the model, each column of symbols in the alignment is represented by a frequency distribution of the symbols (called a "state"), and insertions and deletions are represented by other states. One moves through the model along a particular path from state to state in a Markov chain (i.e., random choice of next move), trying to match a given sequence. The next matching symbol is chosen from each state, recording its probability (frequency) and also the probability of going to that state from a previous one (the transition probability). State and transition probabilities are multiplied to obtain a probability of the given sequence. The hidden nature of the HMM is due to the lack of information about the value of a specific state, which is instead represented by a probability distribution over all possible values. This article discusses the advantages and disadvantages of HMMs in msa and presents algorithms for calculating an HMM and the conditions for producing the best HMM.

  19. The 2012 Strike-slip Earthquake Sequence in Black Sea and its Link to the Caucasus Collision Zone

    Science.gov (United States)

    Tseng, T. L.; Hsu, C. H.; Legendre, C. P.; Jian, P. R.; Huang, B. S.; Karakhanian, A.; Chen, C. W.

    2016-12-01

    The Black Sea formed as a back-arc basin in Late Cretaceous to Paleogene with lots of extensional features. However, the Black Sea is now tectonically stable and absent of notable earthquakes except for the coastal region. In this study we invert regional waveforms of a new seismic array to constrain the focal mechanisms and depths of the 2012/12/23 earthquake sequence occurred in northeastern Black Sea basin that can provide unique estimates on the stress field in the region. The results show that the focal mechanisms for the main shock and 5 larger aftershocks are all strike-slip faulting and resembling with each other. The main rupture fall along the vertical dipping, NW-SE trending sinistral fault indicated by the lineation of most aftershocks. The fault strike and aftershock distribution are both consistent with the Shatsky Ridge, which is continental in nature but large normal faults was created by previous subsidence. The occurrence of 2012 earthquakes can be re-activated, as strike-slip, on one of the pre-existing normal fault cutting at depth nearly 20-30 km in the extended crust. Some of the aftershocks, including a larger one occurred 5 days later, are distributed toward NE direction 20 km away from main fault zone. Those events might be triggered by the main shock along a conjugate fault, which is surprisingly at the extension of proposed transform fault perpendicular to the rift axis of eastern Black Sea Basin. The focal mechanisms also indicate that the maximum compression in northeast Black Sea is at E-W direction, completely different from the N-S compression in the Caucasus and East Turkey controlled by Arabia-Eurasia collision. The origin of E-W maximum compression is probably the same as the secondary stress inferred from earthquakes in Racha region of the Greater Caucasus.

  20. 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

  1. 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

  2. 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...

  3. 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.

  4. Numerical Model for Solidification Zones Selection in the Large Ingots

    Directory of Open Access Journals (Sweden)

    Wołczyński W.

    2015-12-01

    Full Text Available A vertical cut at the mid-depth of the 15-ton forging steel ingot has been performed by curtesy of the CELSA - Huta Ostrowiec plant. Some metallographic studies were able to reveal not only the chilled undersized grains under the ingot surface but columnar grains and large equiaxed grains as well. Additionally, the structural zone within which the competition between columnar and equiaxed structure formation was confirmed by metallography study, was also revealed. Therefore, it seemed justified to reproduce some of the observed structural zones by means of numerical calculation of the temperature field. The formation of the chilled grains zone is the result of unconstrained rapid solidification and was not subject of simulation. Contrary to the equiaxed structure formation, the columnar structure or columnar branched structure formation occurs under steep thermal gradient. Thus, the performed simulation is able to separate both discussed structural zones and indicate their localization along the ingot radius as well as their appearance in term of solidification time.

  5. 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

  6. 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

  7. Modeling framework for crew decisions during accident sequences

    International Nuclear Information System (INIS)

    Lukic, Y.D.; Worledge, D.H.; Hannaman, G.W.; Spurgin, A.J.

    1986-01-01

    The ability to model the average behavior of operating crews in the course of accident sequences is vital in learning on how to prevent damage to power plants and to maintain safety. This paper summarizes the work carried out in support of a Human Reliability Model framework. This work develops the mathematical framework of the model and identifies the parameters which could be measured in some way, e.g., through simulator experience and/or small scale tests. Selected illustrative examples are presented, of the numerical experiments carried out in order to understand the model sensitivity to parameter variation. These examples ar discussed with the objective of deriving insights of general nature regarding operating of the model which may lead to enhanced understanding of man/machine interactions

  8. 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

  9. Minipig model of maxillary distraction osteogenesis: immunohistochemical and histomorphometric analysis of the sequence of osteogenesis.

    Science.gov (United States)

    Papadaki, Maria E; Kaban, Leonard B; Troulis, Maria J

    2012-11-01

    To document the sequence of bone formation in a minipig model of Le Fort I distraction osteogenesis (DO) using immunohistochemistry and histomorphometry. Female Yucatan minipigs (N = 9) in the mixed-dentition stage underwent bilateral maxillary DO. The distraction protocol was 0 days of latency, with a distraction rate of 1 mm/d for 12 days and 24 days of fixation. Specimens were harvested and divided between the central incisors (18 hemi-maxillae) at the end of DO (n = 6), at mid-fixation (n = 6), and at the end of fixation (n = 6). Sections, including the advancement zone, were stained with hematoxylin-eosin, collagen II, CD34, proliferating cell nuclear antigen, and tartrate-resistant acid phosphatase. Light and fluorescence microscope images (original magnification ×200) were obtained, and percentage of surface area (PSA) of the advancement zone occupied by fibrous tissue, vessels, proliferating cells, osteoid, and bone was determined. An intact maxilla served as the control. At the end of DO, in the advancement zone, the PSA (mean values) of proliferating cells was 33.16%; fibrous tissue, 52%; vessels, 4.35%; and new bone, 5.45%. At the end of fixation, the PSA of proliferating cells decreased to 10.53%, fibrous tissue to 2.3%, and vessels to 1.5% whereas the PSA of new bone increased to 44.9%. The results of this study indicate that the progression of osteogenesis in the maxillary DO wound begins with intense cellular proliferation and vascular fibrous tissue formation and progresses to mature, cancellous bone by the end of fixation. The PSA occupied by mature bone is significantly less than in the control maxilla at the end of fixation. This is consistent with the sequence in the mandibular DO wound. Published by Elsevier Inc.

  10. Two-zone model of coronal hole structure in the high corona

    International Nuclear Information System (INIS)

    Wang, Z.; Kundu, M.R.; Yoshimura, H.

    1988-01-01

    The two-zone coronal hole structure model presently proposed for the high corona at 1.5-1.7 solar radii emerges from a comparison of computation results for the potential magnetic fields of the corona and meter-decameter radio observations. The two zones of a coronal hole are defined by the configuration of magnetic field lines around a coronal hole: (1) the central hole of an open diverging magnetic field line system; and (2) the boundary zone between the central zone of the open field line system and the closed field line system or systems surrounding the open field line system. 19 references

  11. MODELING THE RED SEQUENCE: HIERARCHICAL GROWTH YET SLOW LUMINOSITY EVOLUTION

    International Nuclear Information System (INIS)

    Skelton, Rosalind E.; Bell, Eric F.; Somerville, Rachel S.

    2012-01-01

    We explore the effects of mergers on the evolution of massive early-type galaxies by modeling the evolution of their stellar populations in a hierarchical context. We investigate how a realistic red sequence population set up by z ∼ 1 evolves under different assumptions for the merger and star formation histories, comparing changes in color, luminosity, and mass. The purely passive fading of existing red sequence galaxies, with no further mergers or star formation, results in dramatic changes at the bright end of the luminosity function and color-magnitude relation. Without mergers there is too much evolution in luminosity at a fixed space density compared to observations. The change in color and magnitude at a fixed mass resembles that of a passively evolving population that formed relatively recently, at z ∼ 2. Mergers among the red sequence population ('dry mergers') occurring after z = 1 build up mass, counteracting the fading of the existing stellar populations to give smaller changes in both color and luminosity for massive galaxies. By allowing some galaxies to migrate from the blue cloud onto the red sequence after z = 1 through gas-rich mergers, younger stellar populations are added to the red sequence. This manifestation of the progenitor bias increases the scatter in age and results in even smaller changes in color and luminosity between z = 1 and z = 0 at a fixed mass. The resultant evolution appears much slower, resembling the passive evolution of a population that formed at high redshift (z ∼ 3-5), and is in closer agreement with observations. We conclude that measurements of the luminosity and color evolution alone are not sufficient to distinguish between the purely passive evolution of an old population and cosmologically motivated hierarchical growth, although these scenarios have very different implications for the mass growth of early-type galaxies over the last half of cosmic history.

  12. 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

  13. Bacterial DNA Sequence Compression Models Using Artificial Neural Networks

    Directory of Open Access Journals (Sweden)

    Armando J. Pinho

    2013-08-01

    Full Text Available It is widely accepted that the advances in DNA sequencing techniques have contributed to an unprecedented growth of genomic data. This fact has increased the interest in DNA compression, not only from the information theory and biology points of view, but also from a practical perspective, since such sequences require storage resources. Several compression methods exist, and particularly, those using finite-context models (FCMs have received increasing attention, as they have been proven to effectively compress DNA sequences with low bits-per-base, as well as low encoding/decoding time-per-base. However, the amount of run-time memory required to store high-order finite-context models may become impractical, since a context-order as low as 16 requires a maximum of 17.2 x 109 memory entries. This paper presents a method to reduce such a memory requirement by using a novel application of artificial neural networks (ANN to build such probabilistic models in a compact way and shows how to use them to estimate the probabilities. Such a system was implemented, and its performance compared against state-of-the art compressors, such as XM-DNA (expert model and FCM-Mx (mixture of finite-context models , as well as with general-purpose compressors. Using a combination of order-10 FCM and ANN, similar encoding results to those of FCM, up to order-16, are obtained using only 17 megabytes of memory, whereas the latter, even employing hash-tables, uses several hundreds of megabytes.

  14. 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.

  15. The Iquique earthquake sequence of April 2014: Bayesian modeling accounting for prediction uncertainty

    Science.gov (United States)

    Duputel, Zacharie; Jiang, Junle; Jolivet, Romain; Simons, Mark; Rivera, Luis; Ampuero, Jean-Paul; Riel, Bryan; Owen, Susan E; Moore, Angelyn W; Samsonov, Sergey V; Ortega Culaciati, Francisco; Minson, Sarah E.

    2016-01-01

    The subduction zone in northern Chile is a well-identified seismic gap that last ruptured in 1877. On 1 April 2014, this region was struck by a large earthquake following a two week long series of foreshocks. This study combines a wide range of observations, including geodetic, tsunami, and seismic data, to produce a reliable kinematic slip model of the Mw=8.1 main shock and a static slip model of the Mw=7.7 aftershock. We use a novel Bayesian modeling approach that accounts for uncertainty in the Green's functions, both static and dynamic, while avoiding nonphysical regularization. The results reveal a sharp slip zone, more compact than previously thought, located downdip of the foreshock sequence and updip of high-frequency sources inferred by back-projection analysis. Both the main shock and the Mw=7.7 aftershock did not rupture to the trench and left most of the seismic gap unbroken, leaving the possibility of a future large earthquake in the region.

  16. 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.

  17. 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......-layer height: friction velocity, kinematic heat flux near the ground and potential temperature gradient in the free atmosphere above the entrainment zone. When information is available on the horizontal divergence of the large-scale flow field, the model also takes into account the effect of subsidence...

  18. 2D and 3D Models of Convective Turbulence and Oscillations in Intermediate-Mass Main-Sequence Stars

    Science.gov (United States)

    Guzik, Joyce Ann; Morgan, Taylor H.; Nelson, Nicholas J.; Lovekin, Catherine; Kitiashvili, Irina N.; Mansour, Nagi N.; Kosovichev, Alexander

    2015-08-01

    We present multidimensional modeling of convection and oscillations in main-sequence stars somewhat more massive than the sun, using three separate approaches: 1) Applying the spherical 3D MHD ASH (Anelastic Spherical Harmonics) code to simulate the core convection and radiative zone. Our goal is to determine whether core convection can excite low-frequency gravity modes, and thereby explain the presence of low frequencies for some hybrid gamma Dor/delta Sct variables for which the envelope convection zone is too shallow for the convective blocking mechanism to drive g modes; 2) Using the 3D planar ‘StellarBox’ radiation hydrodynamics code to model the envelope convection zone and part of the radiative zone. Our goals are to examine the interaction of stellar pulsations with turbulent convection in the envelope, excitation of acoustic modes, and the role of convective overshooting; 3) Applying the ROTORC 2D stellar evolution and dynamics code to calculate evolution with a variety of initial rotation rates and extents of core convective overshooting. The nonradial adiabatic pulsation frequencies of these nonspherical models will be calculated using the 2D pulsation code NRO of Clement. We will present new insights into gamma Dor and delta Sct pulsations gained by multidimensional modeling compared to 1D model expectations.

  19. 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...... of changes in soil water content do not rely on a petrophysical relationship between the measured quantity and the water content but give a direct measure of the mass change in the soil. Only recently has the vadose zone been systematically incorporated when ground-based gravity data are used to infer...... 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...

  20. 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.

  1. Validation and sensitivity analysis of a two zone Diesel engine model for combustion and emissions prediction

    International Nuclear Information System (INIS)

    Rakopoulos, C.D.; Rakopoulos, D.C.; Giakoumis, E.G.; Kyritsis, D.C.

    2004-01-01

    The present two zone model of a direct injection (DI) Diesel engine divides the cylinder contents into a non-burning zone of air and another homogeneous zone in which fuel is continuously supplied from the injector and burned with entrained air from the air zone. The growth of the fuel spray zone, which comprises a number of fuel-air conical jets equal to the injector nozzle holes, is carefully modelled by incorporating jet mixing, thus determining the amount of oxygen available for combustion. The mass, energy and state equations are applied in each of the two zones to yield local temperatures and cylinder pressure histories. The concentration of the various constituents in the exhaust gases are calculated by adopting a chemical equilibrium scheme for the C-H-O system of the 11 species considered, together with chemical rate equations for the calculation of nitric oxide (NO). A model for evaluation of the soot formation and oxidation rates is included. The theoretical results from the relevant computer program are compared very favourably with the measurements from an experimental investigation conducted on a fully automated test bed, standard 'Hydra', DI Diesel engine installed at the authors' laboratory. In-cylinder pressure and temperature histories, nitric oxide concentration and soot density are among the interesting quantities tested for various loads and injection timings. As revealed, the model is sensitive to the selection of the constants of the fuel preparation and reaction sub-models, so that a relevant sensitivity analysis is undertaken. This leads to a better understanding of the physical mechanisms governed by these constants and also paves the way for construction of a reliable and relatively simple multi-zone model, which incorporates in each zone (packet) the philosophy of the present two zone model

  2. Validation and sensitivity analysis of a two zone diesel engine model for combustion and emissions prediction

    Energy Technology Data Exchange (ETDEWEB)

    Rakopoulos, C.D.; Rakopoulos, D.C.; Giakoumis, E.G. [National Technical University of Athens (Greece). Mechanical Engineering Dept.; Kyritsis, D.C. [University of Illinois at Urbana-Champaign, Urbana, IL (United States). Dept. of Mechanical and Industrial Engineering

    2004-06-01

    The present two zone model of a direct injection (DI) diesel engine divides the cylinder contents into a non-burning zone of air and another homogeneous zone in which fuel is continuously supplied from the injector and burned with entrained air from the air zone. The growth of the fuel spray zone, which comprises a number of fuel-air conical jets equal to the injector nozzle holes, is carefully modelled by incorporating jet mixing, thus determining the amount of oxygen available for combustion. The mass, energy and state equations are applied in each of the two zones to yield local temperatures and cylinder pressure histories. The concentration of the various constituents in the exhaust gases are calculated by adopting a chemical equilibrium scheme for the C-H-O system of the 11 species considered, together with chemical rate equations for the calculation of nitric oxide (NO). A model for evaluation of the soot formation and oxidation rates is included. The theoretical results from the relevant computer program are compared very favourably with the measurements from an experimental investigation conducted on a fully automated test bed, standard ''Hydra'', DI diesel engine installed at the authors' laboratory. In-cylinder pressure and temperature histories, nitric oxide concentration and soot density are among the interesting quantities tested for various loads and injection timings. As revealed, the model is sensitive to the selection of the constants of the fuel preparation and reaction sub-models, so that a relevant sensitivity analysis is undertaken. This leads to a better understanding of the physical mechanisms governed by these constants and also paves the way for construction of a reliable and relatively simple multi-zone model, which incorporates in each zone (packet) the philosophy of the present two zone model. (author)

  3. Analysis of correlations between sites in models of protein sequences

    International Nuclear Information System (INIS)

    Giraud, B.G.; Lapedes, A.; Liu, L.C.

    1998-01-01

    A criterion based on conditional probabilities, related to the concept of algorithmic distance, is used to detect correlated mutations at noncontiguous sites on sequences. We apply this criterion to the problem of analyzing correlations between sites in protein sequences; however, the analysis applies generally to networks of interacting sites with discrete states at each site. Elementary models, where explicit results can be derived easily, are introduced. The number of states per site considered ranges from 2, illustrating the relation to familiar classical spin systems, to 20 states, suitable for representing amino acids. Numerical simulations show that the criterion remains valid even when the genetic history of the data samples (e.g., protein sequences), as represented by a phylogenetic tree, introduces nonindependence between samples. Statistical fluctuations due to finite sampling are also investigated and do not invalidate the criterion. A subsidiary result is found: The more homogeneous a population, the more easily its average properties can drift from the properties of its ancestor. copyright 1998 The American Physical Society

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

    International Nuclear Information System (INIS)

    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

  5. 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.

  6. 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.

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

    DEFF Research Database (Denmark)

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

    2012-01-01

    metabolism against fast chemical reaction and mass transfer. Likewise, the analysis of the dynamics contributed to establish qualitatively the requirements for control of the reactors, both for regulation and for optimal operation. Work in progress on quantitatively analysing different control structure......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...

  8. 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.

  9. 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

  10. 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)

  11. Experimental verification of a weak zone model for timber in bending

    DEFF Research Database (Denmark)

    Källsner, B.; Ditlevsen, Ove Dalager; Salmela, K.

    1997-01-01

    In order to verify a stochastic model for the variation of bending strength within and between structural timber members, tests with long members subjected to constant bending moment have been performed. The span with constant moment contained between five and nine weak zones, i.e. zones...... with a cluster of knots. In a previous investigation test specimens, each containing one weak zone, have been tested in bending separately. Based on these tests a hierarchical model with two levels was formulated. The test results show that the bending strength of the long timber members on the average is 5...

  12. A Model of Ischemia-Induced Neuroblast Activation in the Adult Subventricular Zone

    OpenAIRE

    Vergni, Davide; Castiglione, Filippo; Briani, Maya; Middei, Silvia; Alberdi, Elena; Reymann, Klaus G.; Natalini, Roberto; Volont?, Cinzia; Matute, Carlos; Cavaliere, Fabio

    2009-01-01

    12 p. 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...

  13. Sensitivity of euphotic zone properties to CDOM variations in marine ecosystem models

    OpenAIRE

    Urtizberea, Agurtzane; Dupont, Nicolas; Rosland, Rune; Aksnes, Dag L.

    2013-01-01

    In marine ecosystem models, the underwater light intensity is commonly characterized by the shading of phytoplankton in addition to a background light attenuation coefficient. Colour dissolved organic matter (CDOM) is an important component of the background light attenuation, and we investigate how variation in CDOM attenuation affects euphotic zone properties in a general marine ecosystem model. Our results suggest that euphotic zone properties are highly sensitive to CDOM variations occurr...

  14. Evaluation of core modeling effect on transients for multi-flow zone design of SFR

    International Nuclear Information System (INIS)

    Shin, Andong; Choi, Yong Won

    2016-01-01

    SFR core is composed of different types of assemblies including fuel driver, reflector, blanket, control, safety drivers and other drivers. Modeling of different types of assemblies is inevitable in general. But modeling of core flow zones of with different channels needs a lot of effort and could be a challenge for system code modeling due to its limitation on the number of modeling components. In this study, core modeling effect on SFR transient was investigated with flow-zone model and averaged inner core channel model to improve modeling efficiency and validation of simplified core model for EBR-II loss of flow transient case with the modified TRACE code for SFRs. Core modeling effect on the loss flow transient was analyzed with flow-zoned channel model, single averaged inner core model and highest flow channel with averaged inner core channel model for EBR-II SHRT-17 test core. Case study showed that estimations of transient pump and channel flow as well as channel outlet temperatures were similar for all cases macroscopically. Comparing the result of the base case (flow-zone channel inner core model) and the case 2 (highest flow channel considered averaged inner core channel model), flow and channel outlet temperature response were closer than the case1 (single averaged inner core model)

  15. Evaluation of core modeling effect on transients for multi-flow zone design of SFR

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Andong; Choi, Yong Won [Korea Institute of Nuclear Safety, Daejeon (Korea, Republic of)

    2016-10-15

    SFR core is composed of different types of assemblies including fuel driver, reflector, blanket, control, safety drivers and other drivers. Modeling of different types of assemblies is inevitable in general. But modeling of core flow zones of with different channels needs a lot of effort and could be a challenge for system code modeling due to its limitation on the number of modeling components. In this study, core modeling effect on SFR transient was investigated with flow-zone model and averaged inner core channel model to improve modeling efficiency and validation of simplified core model for EBR-II loss of flow transient case with the modified TRACE code for SFRs. Core modeling effect on the loss flow transient was analyzed with flow-zoned channel model, single averaged inner core model and highest flow channel with averaged inner core channel model for EBR-II SHRT-17 test core. Case study showed that estimations of transient pump and channel flow as well as channel outlet temperatures were similar for all cases macroscopically. Comparing the result of the base case (flow-zone channel inner core model) and the case 2 (highest flow channel considered averaged inner core channel model), flow and channel outlet temperature response were closer than the case1 (single averaged inner core model)

  16. Modelling of just-in-sequence supply of manufacturing processes

    Directory of Open Access Journals (Sweden)

    Bányai Tamás

    2017-01-01

    Full Text Available The customer oriented production led to the growth of complexity of manufacturing and connected logistics processes. In many production companies one of the largest asset on balance sheet is inventory. To avoid inventory problems and to be the winners of today’s market situation manufacturing companies try to decrease heavy inventory levels through just-in-time based supply strategies. The aim of this research work is to analyse these supply strategies. The first part of the paper describes the just-in-time based supply and summarises the most important characteristics of them. The second part focuses on the modelling of just-in-sequence based in-plant supply. The models makes it possible to determine different in-plant supply strategies.

  17. 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

  18. 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...... block pavements. It is envisaged that the methodology implemented in this study can be extended and thereby contribute to the ongoing development of rational failure criteria that can replace the empirical formulas currently used in pavement engineering....

  19. Evaluation of using digital gravity field models for zoning map creation

    Science.gov (United States)

    Loginov, Dmitry

    2018-05-01

    At the present time the digital cartographic models of geophysical fields are taking a special significance into geo-physical mapping. One of the important directions to their application is the creation of zoning maps, which allow taking into account the morphology of geophysical field in the implementation automated choice of contour intervals. The purpose of this work is the comparative evaluation of various digital models in the creation of integrated gravity field zoning map. For comparison were chosen the digital model of gravity field of Russia, created by the analog map with scale of 1 : 2 500 000, and the open global model of gravity field of the Earth - WGM2012. As a result of experimental works the four integrated gravity field zoning maps were obtained with using raw and processed data on each gravity field model. The study demonstrates the possibility of open data use to create integrated zoning maps with the condition to eliminate noise component of model by processing in specialized software systems. In this case, for solving problem of contour intervals automated choice the open digital models aren't inferior to regional models of gravity field, created for individual countries. This fact allows asserting about universality and independence of integrated zoning maps creation regardless of detail of a digital cartographic model of geo-physical fields.

  20. 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

    Energy Technology Data Exchange (ETDEWEB)

    Danchi, William C. [Exoplanets and Stellar Astrophysics Laboratory, NASA Goddard Space Flight Center, Code 667, Greenbelt, MD 20771 (United States); Lopez, Bruno, E-mail: william.c.danchi@nasa.gov, E-mail: bruno.lopez@oca.eu [Observatoire de la Cote d' Azur, Laboratoire Lagrange UMR 7293, BP 4229, F-06034 Nice Cedex 4 (France)

    2013-05-20

    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{sub Sun} 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{sub Sun} 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 {approx}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.

  1. 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.

  2. 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

  3. 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

  4. Seismic-sequence stratigraphy and geologic structure of the Floridan aquifer system near "Boulder Zone" deep wells in Miami-Dade County, Florida

    Science.gov (United States)

    Cunningham, Kevin J.

    2015-01-01

    The U.S. Geological Survey, in cooperation with the Miami-Dade Water and Sewer Department, acquired, processed, and interpreted seismic-reflection data near the North and South District “Boulder Zone” Well Fields to determine if geologic factors may contribute to the upward migration of injected effluent into that upper part of the Floridan aquifer system designated by the U.S. Environmental Protection Agency as an underground source of drinking water. The depth of the Boulder Zone at the North and South District “Boulder Zone” Well Fields ranges from about 2,750 to 3,300 feet below land surface (ft bls), whereas overlying permeable zones used as alternative drinking water supply range in depth from about 825 to 1,580 ft bls at the North and South District “Boulder Zone” Well Fields. Seismic-sequence stratigraphy and geologic structures imaged on seismic-reflection profiles created for the study describe the part of the Floridan aquifer system overlying and within the Boulder Zone. Features of the Floridan aquifer system underlying the Boulder Zone were not studied because seismic-reflection profiles acquired near the North and South District “Boulder Zone” Well Fields lacked adequate resolution at such depths.

  5. Multi-zone thermodynamic modelling of spark-ignition engine combustion - An overview

    International Nuclear Information System (INIS)

    Verhelst, S.; Sheppard, C.G.W.

    2009-01-01

    'Multi-zone thermodynamic engine model' is a generic term adopted here for the type of model also referred to as quasi-dimensional, two-zone, three-zone, etc.; based on the laws of mass and energy conservation and using a mass burning rate sub-model (as opposed to a prescribed mass burning rate) to predict the in-cylinder pressure and temperature throughout the power cycle. Such models have been used for about three decades and provide valuable tools for rapid evaluation of the influence of key engine parameters. Numerous papers have been published on the development of models of varying complexity and their application. The current work is not intended as a comprehensive review of all these works, but presents an overview of multi-zone thermodynamic models for spark-ignition engines, their pros and cons, the model equations and sub-models used to account for various processes such as turbulent wrinkling, flame development, flame geometry, heat transfer, etc. It is suggested that some past terminology adopted to distinguish combustion models (e.g. 'entrainment' versus 'flamelet') is artificial and confusing; it can also be difficult to compare the different models used. Naturally, different models use varying underlying assumptions; however, the influence of several physical processes has frequently been incorporated into one term, not always well documented or clearly described. The authors propose a unified framework that can be used to compare different sub-models on the same basis, with particular focus on turbulent combustion models.

  6. 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.

  7. 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)

    Ahmad Mirmarghabi

    2015-02-01

    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.

  8. Large scale multi-zone creep finite element modelling of a main steam line branch intersection

    International Nuclear Information System (INIS)

    Payten, Warwick

    2006-01-01

    A number of papers detail the non-linear creep finite element analysis of branch pieces. Predominately these models have incorporated only a single material zone representing the parent material. Multi-zone models incorporating weld material and heat affected zones have primarily been two-dimensional analyses, in part due to the large number of elements required to adequately represent all of the zones. This paper describes a non-linear creep analysis of a main steam line branch intersection using creep properties to represent the parent metal, weld metal, and heat affected zone (HAZ), the stress redistribution over 100,000 h is examined. The results show that the redistribution leads to a complex stress state, particularly at the heat affected zone. Although, there is damage on the external surface of the branch piece as expected, the results indicate that the damage would be more widespread through extensive sections of the heat affected zone. This would appear to indicate that the time between damage indications on the surface using techniques such as replication and full thickness damage may be more limited then previously expected

  9. Calibrating vadose zone models with time-lapse gravity data: a forced infiltration experiment

    DEFF Research Database (Denmark)

    Christiansen, Lars; Hansen, Allan Bo; Zibar, Majken Caroline Looms

    A change in soil water content is a change in mass stored in the subsurface, and when large enough, can be measured with a gravity meter. Over the last few decades there has been increased use of ground-based time-lapse gravity measurements to infer hydrogeological parameters. These studies have...... focused on the saturated zone, with specific yield as the most prominent target parameter and with few exceptions, changes in storage in the vadose zone have been considered as noise. Here modeling results are presented suggesting that gravity changes will be measureable when soil moisture changes occur...... in the unsaturated zone. These results are confirmed by field measurements of gravity and georadar data at a forced infiltration experiment conducted over 14 days on a grassland area of 10 m by 10 m. An unsaturated zone infiltration model can be calibrated using the gravity data with good agreement to the field data...

  10. 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.

  11. Framework Model for Database Replication within the Availability Zones

    OpenAIRE

    Al-Mughrabi, Ala'a Atallah; Owaied, Hussein

    2013-01-01

    This paper presents a proposed model for database replication model in private cloud availability regions, which is an enhancement of the SQL Server AlwaysOn Layers of Protection Model presents by Microsoft in 2012. The enhancement concentrates in the database replication for private cloud availability regions through the use of primary and secondary servers. The processes of proposed model during the client send Write/Read Request to the server, in synchronous and semi synchronous replicatio...

  12. Experimental modeling of weld thermal cycle of the heat affected zone (HAZ

    Directory of Open Access Journals (Sweden)

    J. Kulhánek

    2016-10-01

    Full Text Available Contribution deals with experimental modeling of quick thermal cycles of metal specimens. In the introduction of contribution will be presented measured graphs of thermal cycle of heat affected zone (HAZ of weld. Next will be presented experimental simulation of measured thermal cycle on the standard specimens, useable for material testing. This approach makes possible to create material structures of heat affected zone of weld, big enough for standard material testing.

  13. 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.

  14. 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.

  15. Modeling Interdependent and Periodic Real-World Action Sequences

    Science.gov (United States)

    Kurashima, Takeshi; Althoff, Tim; Leskovec, Jure

    2018-01-01

    Mobile health applications, including those that track activities such as exercise, sleep, and diet, are becoming widely used. Accurately predicting human actions in the real world is essential for targeted recommendations that could improve our health and for personalization of these applications. However, making such predictions is extremely difficult due to the complexities of human behavior, which consists of a large number of potential actions that vary over time, depend on each other, and are periodic. Previous work has not jointly modeled these dynamics and has largely focused on item consumption patterns instead of broader types of behaviors such as eating, commuting or exercising. In this work, we develop a novel statistical model, called TIPAS, for Time-varying, Interdependent, and Periodic Action Sequences. Our approach is based on personalized, multivariate temporal point processes that model time-varying action propensities through a mixture of Gaussian intensities. Our model captures short-term and long-term periodic interdependencies between actions through Hawkes process-based self-excitations. We evaluate our approach on two activity logging datasets comprising 12 million real-world actions (e.g., eating, sleep, and exercise) taken by 20 thousand users over 17 months. We demonstrate that our approach allows us to make successful predictions of future user actions and their timing. Specifically, TIPAS improves predictions of actions, and their timing, over existing methods across multiple datasets by up to 156%, and up to 37%, respectively. Performance improvements are particularly large for relatively rare and periodic actions such as walking and biking, improving over baselines by up to 256%. This demonstrates that explicit modeling of dependencies and periodicities in real-world behavior enables successful predictions of future actions, with implications for modeling human behavior, app personalization, and targeting of health interventions. PMID

  16. 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.

  17. Availability analysis of a syngas fueled spark ignition engine using a multi-zone combustion model

    International Nuclear Information System (INIS)

    Rakopoulos, C.D.; Michos, C.N.; Giakoumis, E.G.

    2008-01-01

    A previously developed and validated zero-dimensional, multi-zone, thermodynamic combustion model for the prediction of spark ignition (SI) engine performance and nitric oxide (NO) emissions has been extended to include second-law analysis. The main characteristic of the model is the division of the burned gas into several distinct zones, in order to account for the temperature and chemical species stratification developed in the burned gas during combustion. Within the framework of the multi-zone model, the various availability components constituting the total availability of each of the multiple zones of the simulation are identified and calculated separately. The model is applied to a multi-cylinder, four-stroke, turbocharged and aftercooled, natural gas (NG) SI gas engine running on synthesis gas (syngas) fuel. The major part of the unburned mixture availability consists of the chemical contribution, ranging from 98% at the inlet valve closing (IVC) event to 83% at the ignition timing of the total availability for the 100% load case, which is due to the presence of the combustible fuel. On the contrary, the multiple burned zones possess mainly thermomechanical availability. Specifically, again for the 100% load case, the total availability of the first burned zone at the exhaust valve opening (EVO) event consists of thermomechanical availability approximately by 90%, with similar percentages for all other burned zones. Two definitions of the combustion exergetic efficiency are used to explore the degree of reversibility of the combustion process in each of the multiple burned zones. It is revealed that the crucial factor determining the thermodynamic perfection of combustion in each burned zone is the level of the temperatures at which combustion occurs in the zone, with minor influence of the whole temperature history of the zone during the complete combustion phase. The availability analysis is extended to various engine loads. The engine in question is

  18. Multiphasic modeling of charged solute transport across articular cartilage: Application of multi-zone finite-bath model.

    Science.gov (United States)

    Arbabi, Vahid; Pouran, Behdad; Weinans, Harrie; Zadpoor, Amir A

    2016-06-14

    Charged and uncharged solutes penetrate through cartilage to maintain the metabolic function of chondrocytes and to possibly restore or further breakdown the cartilage tissue in different stages of osteoarthritis. In this study the transport of charged solutes across the various zones of cartilage was quantified, taken into account the physicochemical interactions between the solute and the cartilage constituents. A multiphasic finite-bath finite element (FE) model was developed to simulate equine cartilage diffusion experiments that used a negatively charged contrast agent (ioxaglate) in combination with serial micro-computed tomography (micro-CT) to measure the diffusion. By comparing the FE model with the experimental data both the diffusion coefficient of ioxaglate and the fixed charge density (FCD) were obtained. In the multiphasic model, cartilage was divided into multiple (three) zones to help understand how diffusion coefficient and FCD vary across cartilage thickness. The direct effects of charged solute-FCD interaction on diffusion were investigated by comparing the diffusion coefficients derived from the multiphasic and biphasic-solute models. We found a relationship between the FCD obtained by the multiphasic model and ioxaglate partitioning obtained from micro-CT experiments. Using our multi-zone multiphasic model, diffusion coefficient of the superficial zone was up to ten-fold higher than that of the middle zone, while the FCD of the middle zone was up to almost two-fold higher than that of the superficial zone. In conclusion, the developed finite-bath multiphasic model provides us with a non-destructive method by which we could obtain both diffusion coefficient and FCD of different cartilage zones. The outcomes of the current work will also help understand how charge of the bath affects the diffusion of a charged molecule and also predict the diffusion behavior of a charged solute across articular cartilage. Copyright © 2016 Elsevier Ltd. All

  19. 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

    , 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......In this paper, a multi-zone modeling concept is proposed based on a simplified energy balance formulation to provide a better prediction of the indoor horizontal temperature variation inside the livestock building. The developed mathematical models reflect the influences from the weather...... 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....

  20. A modified hydrodynamic model for routing unsteady flow in a river having piedmont zone

    Directory of Open Access Journals (Sweden)

    Patowary Sudarshan

    2017-03-01

    Full Text Available Existence of piedmont zone in a river bed is a critical parameter from among numerous variations of topographical, geological and geographical conditions that can significantly influence the river flow scenario. Downstream flow situation assessed by routing of upstream hydrograph may yield higher flow depth if existence of such high infiltration zone is ignored and therefore it is a matter of concern for water resources planning and flood management. This work proposes a novel modified hydrodynamic model that has the potential to accurately determine the flow scenario in presence of piedmont zone. The model has been developed using unsteady free surface flow equations, coupled with Green-Ampt infiltration equation as governing equation. For solution of the governing equations Beam and Warming implicit finite difference scheme has been used. The proposed model was first validated from the field data of Trout Creek River showing excellent agreement. The validated model was then applied to a hypothetical river reach commensurate with the size of major tributaries of Brahmaputra Basin of India. Results indicated a 10% and 14% difference in the maximum value of discharge and depth hydrograph in presence and absence of piedmont zone respectively. Overall this model was successfully used to accurately predict the effect of piedmont zone on the unsteady flow in a river.

  1. Mathematical modeling of the mixing zone for getting bimetallic compound

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Stanislav L. [Institute of Applied Mechanics, Ural Branch, Izhevsk (Russian Federation)

    2011-07-01

    A mathematical model of the formation of atomic bonds in metals and alloys, based on the electrostatic interaction between the outer electron shells of atoms of chemical elements. Key words: mathematical model, the interatomic bonds, the electron shell of atoms, the potential, the electron density, bimetallic compound.

  2. Dimensionless model to determine spontaneous combustion danger zone in the longwall gob

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xin-hai; DENG Jun; WEN Hu

    2011-01-01

    According to spontaneous combustion propensity,the longwall gob is divided into three zones,including heat dissipation zone,self-heating zone and the choking zone.Only in the self-heating zone can temperature of coal rise due to oxidation.Studying the distribution of the “Three Zones” in gob is important for predicting and preventing spontaneous combustion in coalmine.In normal mining operations,temperature of coal is roughly constant.The process of mass transfer in the gob is considered to be steady.Based on mass conservation,gas species conservation,darcy' s law,Ficks law of diffusion and coal oxidation 1-grade reaction rule,governing equation for air leakage intensity and species concentration are deduced.With critical value of coal spontaneous combustion and the size of longwall workface as basic dimension,a dimensionless steady coupled model of air flow diffusion and chemical reaction in loose coal of Fully Mechanized Top-Coal Caving Mining Workface (FMTCCMW) is setup.By solving the model numerically,regulation of three zones' distribution and spontaneous combustion in the gob can be obtained.The results can be easily popularized to prediction of spontaneous combustion in other coalmines' longwall gob.

  3. Cohesive zone model for direct silicon wafer bonding

    Science.gov (United States)

    Kubair, D. V.; Spearing, S. M.

    2007-05-01

    Direct silicon wafer bonding and decohesion are simulated using a spectral scheme in conjunction with a rate-dependent cohesive model. The cohesive model is derived assuming the presence of a thin continuum liquid layer at the interface. Cohesive tractions due to the presence of a liquid meniscus always tend to reduce the separation distance between the wafers, thereby opposing debonding, while assisting the bonding process. In the absence of the rate-dependence effects the energy needed to bond a pair of wafers is equal to that needed to separate them. When rate-dependence is considered in the cohesive law, the experimentally observed asymmetry in the energetics can be explained. The derived cohesive model has the potential to form a bridge between experiments and a multiscale-modelling approach to understand the mechanics of wafer bonding.

  4. TRANSFoRm: a flexible zone model of a data privacy framework for Primary Care research.

    NARCIS (Netherlands)

    Kuchinke, W.; Veen, E.B. van; Delaney, B.C.; Verheij, R.; Taweel, A.; Ohmann, C.

    2011-01-01

    As part of the TRANSFoRm project a flexible zone model for data privacy in Primary Care research was developed. The model applies different privacy generating methods to different aspects of the research data flow and allows in this way for only minimal hindrance of research activities. This is

  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. 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.

  7. 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.

  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. Permafrost Degradation Risk Zone Assessment using Simulation Models

    DEFF Research Database (Denmark)

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

    2011-01-01

    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...... to climate change in a region generally underlain by permafrost. We present the current and future state of permafrost in Greenland as modelled numerically with the GIPL model driven by HIRHAM climate projections up to 2080. We develop a concept called Permafrost Thaw Potential (PTP), defined...... 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...

  10. 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.)

  11. The Normal Zone Propagation in ATLAS B00 Model Coil

    NARCIS (Netherlands)

    Boxman, E.W.; Dudarev, A.V.; ten Kate, Herman H.J.

    2002-01-01

    The B00 model coil has been successfully tested in the ATLAS Magnet Test Facility at CERN. The coil consists of two double pancakes wound with aluminum stabilized cables of the barrel- and end-cap toroids conductors for the ATLAS detector. The magnet current is applied up to 24 kA and quenches are

  12. Using a cylindrical vortex model to assess the induction zone infront of aligned and yawed rotors

    DEFF Research Database (Denmark)

    Branlard, Emmanuel Simon Pierre; Meyer Forsting, Alexander Raul

    2015-01-01

    . The mean relative error is estimated in the induction zone and foundto be below 0.4% for the aligned flows tested and below 1.3% for the yawed test cases. Thecomputational time required by the analytical model is in the order of thousands of timesless than the one required by the actuator disk simulation.......Analytical formulae for the velocity field induced by a cylindrical vortex wake model areapplied to assess the induction zone in front of aligned and yawed rotors. The results arecompared to actuator disk (AD) simulations for different operating conditions, includingfinite tip-speed ratios...

  13. 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

    A new multi-zone model is proposed that explains how porosity forms in various regions of a casting under different conditions and leads to distinct zonal differences in pore shape, size and distribution. This model was developed by considering the effect of cooling rate on solidification......) a central zone where the thermal gradient is low and equiaxed dendritic grains and eutectic cells grow at the centre of the casting and larger, rounded pores tend to form. The paper discusses how Si content, modification type and cooling conditions influence the location and size (i.e. depth) of each...

  14. Flood Zoning Simulation by HEC-RAS Model (Case Study: Johor River-Kota Tinggi Region)

    OpenAIRE

    ShahiriParsa, Ahmad; Heydari, Mohammad; Sadeghian, Mohammad Sadegh; Moharrampour, Mahdi

    2015-01-01

    Flooding of rivers has caused many human and financial losses. Hence, studies and research on the nature of the river is inevitable.However, the behavior of rivers hasmany complexities and in this respect, computer models are efficient tools in order to study and simulate the behavior of rivers with the least possible cost. In this paper, one-dimensional model HEC-RAS was used to simulate the flood zoning in the Kota Tinggi district in Johor state. Implementation processes of the zoning on ca...

  15. 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

  16. 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

  17. Data-driven modelling of protein synthesis : A sequence perspective

    NARCIS (Netherlands)

    Gritsenko, A.

    2017-01-01

    Recent advances in DNA sequencing, synthesis and genetic engineering have enabled the introduction of choice DNA sequences into living cells. This is an exciting prospect for the field of industrial biotechnology, which aims at using microorganisms to produce foods, beverages, pharmaceuticals and

  18. Stochastic model and method of zoning water networks

    OpenAIRE

    Тевяшев, Андрей Дмитриевич; Матвиенко, Ольга Ивановна

    2014-01-01

    Water consumption at different time of the day is uneven. The model of steady flow distribution in water-supply networks is calculated for maximum consumption and effectively used in the network design and reconstruction. Quasi-stationary modes, in which the parameters are random variables and vary relative to their mean values are more suitable for operational management and planning of rational network operation modes.Leaks, which sometimes exceed 50 % of the volume of water supplied, are o...

  19. 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.

  20. Variation of b and p values from aftershocks sequences along the Mexican subduction zone and their relation to plate characteristics

    Science.gov (United States)

    Ávila-Barrientos, L.; Zúñiga, F. R.; Rodríguez-Pérez, Q.; Guzmán-Speziale, M.

    2015-11-01

    Aftershock sequences along the Mexican subduction margin (between coordinates 110ºW and 91ºW) were analyzed by means of the p value from the Omori-Utsu relation and the b value from the Gutenberg-Richter relation. We focused on recent medium to large (Mw > 5.6) events considered susceptible of generating aftershock sequences suitable for analysis. The main goal was to try to find a possible correlation between aftershock parameters and plate characteristics, such as displacement rate, age and segmentation. The subduction regime of Mexico is one of the most active regions of the world with a high frequency of occurrence of medium to large events and plate characteristics change along the subduction margin. Previous studies have observed differences in seismic source characteristics at the subduction regime, which may indicate a difference in rheology and possible segmentation. The results of the analysis of the aftershock sequences indicate a slight tendency for p values to decrease from west to east with increasing of plate age although a statistical significance is undermined by the small number of aftershocks in the sequences, a particular feature distinctive of the region as compared to other world subduction regimes. The b values show an opposite, increasing trend towards the east even though the statistical significance is not enough to warrant the validation of such a trend. A linear regression between both parameters provides additional support for the inverse relation. Moreover, we calculated the seismic coupling coefficient, showing a direct relation with the p and b values. While we cannot undoubtedly confirm the hypothesis that aftershock generation depends on certain tectonic characteristics (age, thickness, temperature), our results do not reject it thus encouraging further study into this question.

  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. Modeling of geochemical processes in the submarine discharge zone of hydrothermal solutions

    Directory of Open Access Journals (Sweden)

    С. М. Судариков

    2017-06-01

    Full Text Available The paper reviews the main methods and analyzes modeling results for geochemical processes in the submarine discharge zone of hydrothermal solutions of mid-ocean ridges. Initial data for modeling have been obtained during several marine expeditions, including Russian-French expedition SERPENTINE on the research vessel «Pourquoi Рas?» (2007. Results of field observations, laboratory experiments and theoretical developments are supported by the analysis of regression model of mixing between hydrothermal solutions and sea water. Verification of the model has been carried out and the quality of chemical analysis has been assessed; degree and character of participation of solution components in the hydrothermal process have been defined; the content of end members has been calculated basing on reverse forecasting of element concentration, depending on regression character; data for thermodynamic modeling have been prepared. Regression model of acid-base properties and chloridity of mineralizing thermal springs confirms adequacy of the model of double-diffusive convection for forming the composition of hydrothermal solutions.  Differentiation of solutions according to concentrations of chloride-ion, depending on temperature and pH indicator within this model, is associated with phase conversions and mixing of fluids from two convection cells, one of which is a zone of brine circulation. In order to carry out computer thermodynamic modeling, hydro-geochemical and physicochemical models of hydrothermal discharge zone have been created. Verification of the model has been carried out basing on changes of Mn concentration in the hydrothermal plume. Prevailing forms of Mn migration in the plume are Mn2+, MnCl+, MnCl2. Two zones have been identified in the geochemical structure of the plume: 1 high-temperature zone (350-100 °С with prevalence of chloride complexes – ascending plume; 2 low-temperature zone (100-2 °С, where predominant form of

  3. Reference genome sequence of the model plant Setaria.

    Science.gov (United States)

    Bennetzen, Jeffrey L; Schmutz, Jeremy; Wang, Hao; Percifield, Ryan; Hawkins, Jennifer; Pontaroli, Ana C; Estep, Matt; Feng, Liang; Vaughn, Justin N; Grimwood, Jane; Jenkins, Jerry; Barry, Kerrie; Lindquist, Erika; Hellsten, Uffe; Deshpande, Shweta; Wang, Xuewen; Wu, Xiaomei; Mitros, Therese; Triplett, Jimmy; Yang, Xiaohan; Ye, Chu-Yu; Mauro-Herrera, Margarita; Wang, Lin; Li, Pinghua; Sharma, Manoj; Sharma, Rita; Ronald, Pamela C; Panaud, Olivier; Kellogg, Elizabeth A; Brutnell, Thomas P; Doust, Andrew N; Tuskan, Gerald A; Rokhsar, Daniel; Devos, Katrien M

    2012-05-13

    We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ∼400-Mb assembly covers ∼80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).

  4. Reference genome sequence of the model plant Setaria

    Energy Technology Data Exchange (ETDEWEB)

    Bennetzen, Jeffrey L [ORNL; Schmutz, Jeremy [Hudson Alpha Institute of Biotechnology; Wang, Hao [University of Georgia, Athens, GA; Percifield, Ryan [University of Georgia, Athens, GA; Hawkins, Jennifer [University of Georgia, Athens, GA; Pontaroli, Ana C. [University of Georgia, Athens, GA; Estep, Matt [University of Georgia, Athens, GA; Feng, Liang [University of Georgia, Athens, GA; Vaughn, Justin N [ORNL; Grimwood, Jane [Hudson Alpha Institute of Biotechnology; Jenkins, Jerry [Hudson Alpha Institute of Biotechnology; Barry, Kerrie [U.S. Department of Energy, Joint Genome Institute; Lindquist, Erika [U.S. Department of Energy, Joint Genome Institute; Hellsten, Uffe [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Wang, Xuewen [University of Georgia, Athens, GA; Wu, Xiaomei [University of Georgia, Athens, GA; Mitros, Therese [University of California, Berkeley; Triplett, Jimmy [University of Missouri, St. Louis; Yang, Xiaohan [ORNL; Ye, Chuyu [ORNL; Mauro-Herrera, Margarita [Oklahoma State University; Wang, Lin [Cornell University; Li, Pinghua [Cornell University; Sharma, Manoj [University of California, Davis; Sharma, Rita [University of California, Davis; Ronald, Pamela [University of California, Davis; Panaud, Olivier [Universite de Perpignan, Perpignan, France; Kellogg, Elizabeth A. [University of Missouri, St. Louis; Brutnell, Thomas P. [Cornell University; Doust, Andrew N. [Oklahoma State University; Tuskan, Gerald A [ORNL; Rokhsar, Daniel [U.S. Department of Energy, Joint Genome Institute; Devos, Katrien M [ORNL

    2012-01-01

    We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ~400-Mb assembly covers ~80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).

  5. Reference genome sequence of the model plant Setaria

    Energy Technology Data Exchange (ETDEWEB)

    Bennetzen, Jeffrey L [ORNL; Yang, Xiaohan [ORNL; Ye, Chuyu [ORNL; Tuskan, Gerald A [ORNL

    2012-01-01

    We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The {approx}400-Mb assembly covers {approx}80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).

  6. 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)

  7. Robust multi-model predictive control of multi-zone thermal plate system

    Directory of Open Access Journals (Sweden)

    Poom Jatunitanon

    2018-02-01

    Full Text Available A modern controller was designed by using the mathematical model of a multi–zone thermal plate system. An important requirement for this type of controller is that it must be able to keep the temperature set-point of each thermal zone. The mathematical model used in the design was determined through a system identification process. The results showed that when the operating condition is changed, the performance of the controller may be reduced as a result of the system parameter uncertainties. This paper proposes a weighting technique of combining the robust model predictive controller for each operating condition into a single robust multi-model predictive control. Simulation and experimental results showed that the proposed method performed better than the conventional multi-model predictive control in rise time of transient response, when used in a system designed to work over a wide range of operating conditions.

  8. 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

  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. 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.

  11. 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.

  12. Development and testing of a compartmentalized reaction network model for redox zones in contaminated aquifers

    Science.gov (United States)

    Abrams , Robert H.; Loague, Keith; Kent, Douglas B.

    1998-01-01

    The work reported here is the first part of a larger effort focused on efficient numerical simulation of redox zone development in contaminated aquifers. The sequential use of various electron acceptors, which is governed by the energy yield of each reaction, gives rise to redox zones. The large difference in energy yields between the various redox reactions leads to systems of equations that are extremely ill-conditioned. These equations are very difficult to solve, especially in the context of coupled fluid flow, solute transport, and geochemical simulations. We have developed a general, rational method to solve such systems where we focus on the dominant reactions, compartmentalizing them in a manner that is analogous to the redox zones that are often observed in the field. The compartmentalized approach allows us to easily solve a complex geochemical system as a function of time and energy yield, laying the foundation for our ongoing work in which we couple the reaction network, for the development of redox zones, to a model of subsurface fluid flow and solute transport. Our method (1) solves the numerical system without evoking a redox parameter, (2) improves the numerical stability of redox systems by choosing which compartment and thus which reaction network to use based upon the concentration ratios of key constituents, (3) simulates the development of redox zones as a function of time without the use of inhibition factors or switching functions, and (4) can reduce the number of transport equations that need to be solved in space and time. We show through the use of various model performance evaluation statistics that the appropriate compartment choice under different geochemical conditions leads to numerical solutions without significant error. The compartmentalized approach described here facilitates the next phase of this effort where we couple the redox zone reaction network to models of fluid flow and solute transport.

  13. Linear-stability theory of thermocapillary convection in a model of float-zone crystal growth

    Science.gov (United States)

    Neitzel, G. P.; Chang, K.-T.; Jankowski, D. F.; Mittelmann, H. D.

    1992-01-01

    Linear-stability theory has been applied to a basic state of thermocapillary convection in a model half-zone to determine values of the Marangoni number above which instability is guaranteed. The basic state must be determined numerically since the half-zone is of finite, O(1) aspect ratio with two-dimensional flow and temperature fields. This, in turn, means that the governing equations for disturbance quantities will remain partial differential equations. The disturbance equations are treated by a staggered-grid discretization scheme. Results are presented for a variety of parameters of interest in the problem, including both terrestrial and microgravity cases.

  14. 20 cool facts about the New Madrid Seismic Zone-Commemorating the bicentennial of the New Madrid earthquake sequence, December 1811-February 1812 [poster

    Science.gov (United States)

    Williams, R.A.; McCallister, N.S.; Dart, R.L.

    2011-01-01

    This poster summarizes a few of the more significant facts about the series of large earthquakes that struck the New Madrid seismic zone of southeastern Missouri, northeastern Arkansas, and adjacent parts of Tennessee and Kentucky from December 1811 to February 1812. Three earthquakes in this sequence had a magnitude (M) of 7.0 or greater. The first earthquake occurred on December 16, 1811, at 2:15 a.m.; the second on January 23, 1812, at 9 a.m.; and the third on February 7, 1812, at 3:45 a.m. These three earthquakes were among the largest to strike North America since European settlement. The mainshocks were followed by many hundreds of aftershocks that occurred over the next decade. Many of the aftershocks were major earthquakes themselves. The area that was strongly shaken by the three main shocks was 2-3 times as large as the strongly shaken area of the 1964 M9.2 Alaskan earthquake and 10 times as large as that of the 1906 M7.8 San Francisco earthquake. Geologic studies show that the 1811-1812 sequence was not an isolated event in the New Madrid region. The 1811-1812 New Madrid earthquake sequence was preceded by at least two other similar sequences in about A.D. 1450 and A.D. 900. Research also indicates that other large earthquakes have occurred in the region surrounding the main New Madrid seismicity trends in the past 5,000 years or so.

  15. Toward a consistent model for strain accrual and release for the New Madrid Seismic Zone, central United States

    Science.gov (United States)

    Hough, S.E.; Page, M.

    2011-01-01

    At the heart of the conundrum of seismogenesis in the New Madrid Seismic Zone is the apparently substantial discrepancy between low strain rate and high recent seismic moment release. In this study we revisit the magnitudes of the four principal 1811–1812 earthquakes using intensity values determined from individual assessments from four experts. Using these values and the grid search method of Bakun and Wentworth (1997), we estimate magnitudes around 7.0 for all four events, values that are significantly lower than previously published magnitude estimates based on macroseismic intensities. We further show that the strain rate predicted from postglacial rebound is sufficient to produce a sequence with the moment release of one Mmax6.8 every 500 years, a rate that is much lower than previous estimates of late Holocene moment release. However, Mw6.8 is at the low end of the uncertainty range inferred from analysis of intensities for the largest 1811–1812 event. We show that Mw6.8 is also a reasonable value for the largest main shock given a plausible rupture scenario. One can also construct a range of consistent models that permit a somewhat higher Mmax, with a longer average recurrence rate. It is thus possible to reconcile predicted strain and seismic moment release rates with alternative models: one in which 1811–1812 sequences occur every 500 years, with the largest events being Mmax∼6.8, or one in which sequences occur, on average, less frequently, with Mmax of ∼7.0. Both models predict that the late Holocene rate of activity will continue for the next few to 10 thousand years.

  16. 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...... impact on near surface density. In the lower percolation zone, the mass change associated with a temperature anomaly in respect to the mean climate may for example amount to as little as 10 percent of the observed, simultaneous surface elevation change. Moreover, significant surface elevation change may...

  17. An Extended Multi-Zone Model for the MCG-6-30-15 Warm Absorber

    Science.gov (United States)

    Morales, R.; Fabian, A. C.; Reynolds, C. S.

    2000-01-01

    The variable warm absorber seen with ASCA in the X-ray spectrum of MCG 6-30-15 shows complex time behaviour in which the optical depth of O VIII anticorrelates with the flux whereas that of O VII is unchanging. The explanation in terms of a two zone absorber has since been challenged by BeppoSAX observations. These present a more complicated behaviour for the O VII edge. The explanation we offer for both ASCA and BeppoSAX observations requires a very simple photoionization model together with the presence of a third, intermediate, zone and a period of very low luminosity. In practice warm absorbers are likely to be extended, multi-zone regions of which only part causes directly observable absorption edges at any given time depending on the value of the luminosity.

  18. 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).

  19. Flood Risk Zoning by Using 2D Hydrodynamic Modeling: A Case Study in Jinan City

    Directory of Open Access Journals (Sweden)

    Tao Cheng

    2017-01-01

    Full Text Available Climate change and rapid urbanization have aggravated the rainstorm flood in Jinan City during the past decades. Jinan City is higher in the south and lower in the north with a steep slope inclined from the south to the north. This results in high-velocity overland flow and deep waterlogging, which poses a tremendous threat to pedestrians and vehicles. Therefore, it is vital to investigate the rainstorm flood and further perform flood risk zoning. This study is carried out in the “Sponge City Construction” pilot area of Jinan City, where the InfoWorks ICM 2D hydrodynamic model is utilized for simulating historical and designed rainfall events. The model is validated with observations, and the causes for errors are analyzed. The simulated water depth and flow velocity are recorded for flood risk zoning. The result shows that the InfoWorks ICM 2D model performed well. The flood risk zoning result shows that rainfalls with larger recurrence intervals generate larger areas of moderate to extreme risk. Meanwhile, the zoning results for the two historical rainfalls show that flood with a higher maximum hourly rainfall intensity is more serious. This study will provide scientific support for the flood control and disaster reduction in Jinan City.

  20. 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

  1. 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.

  2. Thermal and microstructural modelling in weld heat-affected zones: microstructural development

    International Nuclear Information System (INIS)

    Ribera, J.M.; Prado, J.M.

    1996-01-01

    After having analysed in Part 2 of this work the thermal effects caused by a welding process, a metallurgical model which uses those results is proposed to predict the hardness and the microstructure resulting in weld heat affected zones. This model simulates the decomposition of austenite to its various products: martensite, bainite, pearlite and ferrite. Thus, it allows one to optimize welding process parameters to achieve the best microstructure possible. (Author) 5 refs

  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. Conceptual Model and Numerical Approaches for Unsaturated Zone Flow and Transport

    International Nuclear Information System (INIS)

    H.H. Liu

    2004-01-01

    The purpose of this model report is to document the conceptual and numerical models used for modeling unsaturated zone (UZ) fluid (water and air) flow and solute transport processes. This work was planned in ''Technical Work Plan for: Unsaturated Zone Flow Model and Analysis Report Integration'' (BSC 2004 [DIRS 169654], Sections 1.2.5, 2.1.1, 2.1.2 and 2.2.1). The conceptual and numerical modeling approaches described in this report are mainly used for models of UZ flow and transport in fractured, unsaturated rock under ambient conditions. Developments of these models are documented in the following model reports: (1) UZ Flow Model and Submodels; (2) Radionuclide Transport Models under Ambient Conditions. Conceptual models for flow and transport in unsaturated, fractured media are discussed in terms of their applicability to the UZ at Yucca Mountain. The rationale for selecting the conceptual models used for modeling of UZ flow and transport is documented. Numerical approaches for incorporating these conceptual models are evaluated in terms of their representation of the selected conceptual models and computational efficiency; and the rationales for selecting the numerical approaches used for modeling of UZ flow and transport are discussed. This report also documents activities to validate the active fracture model (AFM) based on experimental observations and theoretical developments. The AFM is a conceptual model that describes the fracture-matrix interaction in the UZ of Yucca Mountain. These validation activities are documented in Section 7 of this report regarding use of an independent line of evidence to provide additional confidence in the use of the AFM in the UZ models. The AFM has been used in UZ flow and transport models under both ambient and thermally disturbed conditions. Developments of these models are documented

  6. Sequence Tree Modeling for Combined Accident and Feed-and-Bleed Operation

    International Nuclear Information System (INIS)

    Kim, Bo Gyung; Kang Hyun Gook; Yoon, Ho Joon

    2016-01-01

    In order to address this issue, this study suggests the sequence tree model to analyze accident sequence systematically. Using the sequence tree model, all possible scenarios which need a specific safety action to prevent the core damage can be identified and success conditions of safety action under complicated situation such as combined accident will be also identified. Sequence tree is branch model to divide plant condition considering the plant dynamics. Since sequence tree model can reflect the plant dynamics, arising from interaction of different accident timing and plant condition and from the interaction between the operator action, mitigation system, and the indicators for operation, sequence tree model can be used to develop the dynamic event tree model easily. Target safety action for this study is a feed-and-bleed (F and B) operation. A F and B operation directly cools down the reactor cooling system (RCS) using the primary cooling system when residual heat removal by the secondary cooling system is not available. In this study, a TLOFW accident and a TLOFW accident with LOCA were the target accidents. Based on the conventional PSA model and indicators, the sequence tree model for a TLOFW accident was developed. If sampling analysis is performed, practical accident sequences can be identified based on the sequence analysis. If a realistic distribution for the variables can be obtained for sampling analysis, much more realistic accident sequences can be described. Moreover, if the initiating event frequency under a combined accident can be quantified, the sequence tree model can translate into a dynamic event tree model based on the sampling analysis results

  7. Sequence Tree Modeling for Combined Accident and Feed-and-Bleed Operation

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Bo Gyung; Kang Hyun Gook [KAIST, Daejeon (Korea, Republic of); Yoon, Ho Joon [Khalifa University of Science, Abu Dhabi (United Arab Emirates)

    2016-05-15

    In order to address this issue, this study suggests the sequence tree model to analyze accident sequence systematically. Using the sequence tree model, all possible scenarios which need a specific safety action to prevent the core damage can be identified and success conditions of safety action under complicated situation such as combined accident will be also identified. Sequence tree is branch model to divide plant condition considering the plant dynamics. Since sequence tree model can reflect the plant dynamics, arising from interaction of different accident timing and plant condition and from the interaction between the operator action, mitigation system, and the indicators for operation, sequence tree model can be used to develop the dynamic event tree model easily. Target safety action for this study is a feed-and-bleed (F and B) operation. A F and B operation directly cools down the reactor cooling system (RCS) using the primary cooling system when residual heat removal by the secondary cooling system is not available. In this study, a TLOFW accident and a TLOFW accident with LOCA were the target accidents. Based on the conventional PSA model and indicators, the sequence tree model for a TLOFW accident was developed. If sampling analysis is performed, practical accident sequences can be identified based on the sequence analysis. If a realistic distribution for the variables can be obtained for sampling analysis, much more realistic accident sequences can be described. Moreover, if the initiating event frequency under a combined accident can be quantified, the sequence tree model can translate into a dynamic event tree model based on the sampling analysis results.

  8. 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

  9. A computational model of pile vertical vibration in saturated soil based on the radial disturbed zone of pile driving

    International Nuclear Information System (INIS)

    Li Qiang; Shi Qian; Wang Kuihua

    2010-01-01

    In this study, a simplified computational model of pile vertical vibration was developed. The model was based on the inhomogeneous radial disturbed zone of soil in the vicinity of a pile disturbed by pile driving. The model contained two regions: the disturbed zone, which was located in the immediate vicinity of the pile, and the undisturbed region, external to the disturbed zone. In the model, excess pore pressure in the disturbed zone caused by pile driving was assumed to follow a logarithmic distribution. The relationships of stress and strain in the disturbed zone were based on the principle of effective stress under plain strain conditions. The external zone was governed by the poroelastic theory proposed by Biot. With the use of a variable separation method, an analytical solution in the frequency domain was obtained. Furthermore, a semi-analytical solution was attained by employing a numerical convolution method. Numerical results from the frequency and time domain indicated that the equivalent radius of the disturbed zone and the ratio of excess pore pressure had a significant effect on pile dynamic response. However, actual interactions between pile and soil will be weaker due to the presence of the radial disturbed zone, which is caused by pile driving. Consequently, the ideal undisturbed model overestimates the interaction between pile and soil; however, the proposed model reflects the interaction of pile and soil better than the perfect contact model. Numerical results indicate that the model can account for the time effect of pile dynamic tests.

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

    Energy Technology Data Exchange (ETDEWEB)

    Park, Chung Kyun; Lee, Jaek Wang; Baik, Min Hoon; Jeong, Jong Tae [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2012-02-15

    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.

  11. 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...... that the model performance is equally good in both zones, i.e., with both speech-on-music and music-on-speech stimuli, and comparable to the previous validation round (RMSE approximately 10%). The results further confirm that the distraction model can be used as a valuable tool in evaluating and optimizing...

  12. 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.

  13. Probabilistic topic modeling for the analysis and classification of genomic sequences

    Science.gov (United States)

    2015-01-01

    Background Studies on genomic sequences for classification and taxonomic identification have a leading role in the biomedical field and in the analysis of biodiversity. These studies are focusing on the so-called barcode genes, representing a well defined region of the whole genome. Recently, alignment-free techniques are gaining more importance because they are able to overcome the drawbacks of sequence alignment techniques. In this paper a new alignment-free method for DNA sequences clustering and classification is proposed. The method is based on k-mers representation and text mining techniques. Methods The presented method is based on Probabilistic Topic Modeling, a statistical technique originally proposed for text documents. Probabilistic topic models are able to find in a document corpus the topics (recurrent themes) characterizing classes of documents. This technique, applied on DNA sequences representing the documents, exploits the frequency of fixed-length k-mers and builds a generative model for a training group of sequences. This generative model, obtained through the Latent Dirichlet Allocation (LDA) algorithm, is then used to classify a large set of genomic sequences. Results and conclusions We performed classification of over 7000 16S DNA barcode sequences taken from Ribosomal Database Project (RDP) repository, training probabilistic topic models. The proposed method is compared to the RDP tool and Support Vector Machine (SVM) classification algorithm in a extensive set of trials using both complete sequences and short sequence snippets (from 400 bp to 25 bp). Our method reaches very similar results to RDP classifier and SVM for complete sequences. The most interesting results are obtained when short sequence snippets are considered. In these conditions the proposed method outperforms RDP and SVM with ultra short sequences and it exhibits a smooth decrease of performance, at every taxonomic level, when the sequence length is decreased. PMID:25916734

  14. 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

  15. A saturated zone site-scale flow model for Yucca Mountain

    International Nuclear Information System (INIS)

    Eddebbarh, Al Aziz

    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

  16. 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

  17. Hollow Cylinder Tests on Boom Clay: Modelling of Strain Localization in the Anisotropic Excavation Damaged Zone

    Science.gov (United States)

    François, Bertrand; Labiouse, Vincent; Dizier, Arnaud; Marinelli, Ferdinando; Charlier, Robert; Collin, Frédéric

    2014-01-01

    Boom Clay is extensively studied as a potential candidate to host underground nuclear waste disposal in Belgium. To guarantee the safety of such a disposal, the mechanical behaviour of the clay during gallery excavation must be properly predicted. In that purpose, a hollow cylinder experiment on Boom Clay has been designed to reproduce, in a small-scale test, the Excavation Damaged Zone (EDZ) as experienced during the excavation of a disposal gallery in the underground. In this article, the focus is made on the hydro-mechanical constitutive interpretation of the displacement (experimentally obtained by medium resolution X-ray tomography scanning). The coupled hydro-mechanical response of Boom Clay in this experiment is addressed through finite element computations with a constitutive model including strain hardening/softening, elastic and plastic cross-anisotropy and a regularization method for the modelling of strain localization processes. The obtained results evidence the directional dependency of the mechanical response of the clay. The softening behaviour induces transient strain localization processes, addressed through a hydro-mechanical second grade model. The shape of the obtained damaged zone is clearly affected by the anisotropy of the materials, evidencing an eye-shaped EDZ. The modelling results agree with experiments not only qualitatively (in terms of the shape of the induced damaged zone), but also quantitatively (for the obtained displacement in three particular radial directions).

  18. 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)

  19. 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.

  20. Dynamic model of forest area on flood zone of Padang City, West Sumatra Province-Indonesia

    Science.gov (United States)

    Dewata, Indang; Iswandi, U.

    2018-05-01

    The flood disaster has caused many harm to human life, and the change of watershed characteristic is one of the factors causing the flood disaster. The increase of deforestation due to the increase of water causes the occurrence of flood disaster in the rainy season. The research objective was to develop a dynamic model of forest on flood hazard zone using powersim 10.1. In model development, there are three scenarios: optimistic, moderate, and pessimistic. The study shows that in Padang there are about 13 percent of high flood hazard zones. Deforestation of 4.5 percent/year is one cause that may increased the flooding intensity in Padang. There will be 14 percent of total forest area when management policy of forest absence in 2050.

  1. [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)

  2. 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.

  3. 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.)

  4. 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.

  5. 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.

  6. 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 ...

  7. Conceptual hydrologic model of flow in the unsaturated zone, Yucca Mountain, Nevada

    International Nuclear Information System (INIS)

    Montazer, P.; Wilson, W.E.

    1984-01-01

    The purpose of this report is to propose a conceptual hydrologic model that reasonably describes the flow of fluids through the unsaturated zone at Yucca Mountain, for use as a basis for preliminary site-performance assessment and as a guide to further investigations. Scott and others (1983) presented an initial conceptual hydrogeologic model for the unsaturated zone at Yucca Mountain, based on detailed geologic, but very limited hydrologic, information. In this report, some of their concepts are examined and either supported or modified, and new concepts are developed. The model describes the manner in which flow probably occurs at Yucca Mountain and is based on: (1) current understanding of the hydrogeologic framework; (2) application of the principles of unsaturated flow; and (3) interpretation of some preliminary data from ongoing field and laboratory investigations. Included are extensive geologic information but relatively few hydrologic data that currently exist from the unsaturated zone in the Yucca Mountain area. Many uncertainties remain to be resolved concerning hydrologic conditions and processes. As a result, most of the concepts presented are intentionally descriptive and conjectural, with little quantitative basis provided. However, for the sake of directness and simplicity of expression, the model is presented as if it were a true expression of the facts. The authors recognize, and the reader should be aware, that the proposed model probably is not the only reasonable description that could be made at this point, and it certainly is subject to revision and quantification as more data become available. Although various alternative models probably could be developed, the one described in this report seems to fit current understanding of the unsaturated flow through a section of layered, fractured-rock formations with contrasting hydrologic properties, such as occurs at Yucca Mountain. 41 refs., 14 figs., 1 tab

  8. 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

  9. 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

  10. 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.

  11. Parametric analysis of a TOUGH2 model for the unsaturated zone at Yucca Mountain

    Energy Technology Data Exchange (ETDEWEB)

    Xiang, Y.; Mishra, S.; Dunlap, B. [CRWMS M& O/INTERA, Inc., Las Vegas, NV (United States)

    1995-03-01

    Yucca Mountain in Nevada is currently being investigated for suitability as a potential site for the disposal of high-level radioactive waste and spent nuclear fuel. As the most important natural barrier against radionuclide migration to the accessible environment, the unsaturated zone at Yucca mountain is a key constituent in assessing the ambient geohydrology. A three-dimensional site-scale TOUGH2 model of the unsaturated zone is currently under development by Lawrence Berkeley Laboratory (LBL) and the United States Geological Survey (USGS) consists of six hydrogeologic units - TCw (Tiva Canyon welded), PTn (Paintbrush nonwelded), TSw (Topopah Spring welded), TSv (Topopah Spring welded-vitrophyre), CHnz (Calico Hills nonwelded-vitric), and CHnz (Calico Hills nonwelded-zeolitic), which are further subdivided into seventeen layers to represent additional lithologic detail. Based on the work of Klavetter and Peters, the fractured units TCw and TSw are treated as equivalent continua with specified threshold saturation for triggering fracture flow.

  12. Finite Element Multibody Simulation of a Breathing Crack in a Rotor with a Cohesive Zone Model

    OpenAIRE

    Liong, Rugerri Toni; Proppe, Carsten

    2013-01-01

    The breathing mechanism of a transversely cracked shaft and its influence on a rotor system that appears due to shaft weight and inertia forces is studied. The presence of a crack reduces the stiffness of the rotor system and introduces a stiffness variation during the revolution of the shaft. Here, 3D finite element (FE) model and multibody simulation (MBS) are introduced to predict and to analyse the breathing mechanism on a transverse cracked shaft. It is based on a cohesive zone model (CZ...

  13. Galactic evolution with self-regulated star formation - Stability of a simple one-zone model

    International Nuclear Information System (INIS)

    Parravano, A.; Rosenzweig, P.; Teran, M.

    1990-01-01

    In a simple one-zone model of mass exchange between three components (stars, clouds, and diffused gas), a self-regulating mechanism based on the sensitivity of the condensation of small cool clouds upon the radiation density in the 912-1100 A band is presently included. This mechanism is capable of affecting the large-scale structure of the galaxies due to the fact that it acts at a large scale in a very short time. Even in the most favorable models for the production of nonlinear oscillations, the inclusion of this mechanism of self-regulation leads, in many cases, to the progressive damping of the oscillations. 26 refs

  14. 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....... Since the EKF is sensitive to the initial guess, in the following the estimation process is split up into simple parts and approximate parameters are found with a non recursive least squares method in order to provide good initial values. Results based on experiments from a real life stable facility...

  15. An Updated Site Scale Saturated Zone Ground Water Transport Model For Yucca Mountain

    International Nuclear Information System (INIS)

    S. Kelkar; H. Viswanathan; A. Eddebbarrh; M. Ding; P. Reimus; B. Robinson; B. Arnold; A. Meijer

    2006-01-01

    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 Kd distributions for radionuclides of interest, and updated retardation factor distributions for colloid filtration. 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 14 C-based age estimates. The transport model includes the processes of advection, dispersion, fracture flow, matrix diffusion, 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 coefficient and matrix diffusion coefficients. Model breakthrough curves for various radionuclides at the compliance boundary are presented along with their sensitivity to various parameters

  16. Validating the Performance of the FHWA Work Zone Model Version 1.0: A Case Study Along I-91 in Springfield, Massachusetts

    Science.gov (United States)

    2017-08-01

    Central to the effective design of work zones is being able to understand how drivers behave as they approach and enter a work zone area. States use simulation tools in modeling freeway work zones to predict work zone impacts and to select optimal de...

  17. The use of synthetic input sequences in time series modeling

    International Nuclear Information System (INIS)

    Oliveira, Dair Jose de; Letellier, Christophe; Gomes, Murilo E.D.; Aguirre, Luis A.

    2008-01-01

    In many situations time series models obtained from noise-like data settle to trivial solutions under iteration. This Letter proposes a way of producing a synthetic (dummy) input, that is included to prevent the model from settling down to a trivial solution, while maintaining features of the original signal. Simulated benchmark models and a real time series of RR intervals from an ECG are used to illustrate the procedure

  18. 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

  19. Residence-time framework for modeling multicomponent reactive transport in stream hyporheic zones

    Science.gov (United States)

    Painter, S. L.; Coon, E. T.; Brooks, S. C.

    2017-12-01

    Process-based models for transport and transformation of nutrients and contaminants in streams require tractable representations of solute exchange between the stream channel and biogeochemically active hyporheic zones. Residence-time based formulations provide an alternative to detailed three-dimensional simulations and have had good success in representing hyporheic exchange of non-reacting solutes. We extend the residence-time formulation for hyporheic transport to accommodate general multicomponent reactive transport. To that end, the integro-differential form of previous residence time models is replaced by an equivalent formulation based on a one-dimensional advection dispersion equation along the channel coupled at each channel location to a one-dimensional transport model in Lagrangian travel-time form. With the channel discretized for numerical solution, the associated Lagrangian model becomes a subgrid model representing an ensemble of streamlines that are diverted into the hyporheic zone before returning to the channel. In contrast to the previous integro-differential forms of the residence-time based models, the hyporheic flowpaths have semi-explicit spatial representation (parameterized by travel time), thus allowing coupling to general biogeochemical models. The approach has been implemented as a stream-corridor subgrid model in the open-source integrated surface/subsurface modeling software ATS. We use bedform-driven flow coupled to a biogeochemical model with explicit microbial biomass dynamics as an example to show that the subgrid representation is able to represent redox zonation in sediments and resulting effects on metal biogeochemical dynamics in a tractable manner that can be scaled to reach scales.

  20. An introduction to hidden Markov models for biological sequences

    DEFF Research Database (Denmark)

    Krogh, Anders Stærmose

    1998-01-01

    A non-matematical tutorial on hidden Markov models (HMMs) plus a description of one of the applications of HMMs: gene finding.......A non-matematical tutorial on hidden Markov models (HMMs) plus a description of one of the applications of HMMs: gene finding....

  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. Geological modeling of a fault zone in clay rocks at the Mont-Terri laboratory (Switzerland)

    Science.gov (United States)

    Kakurina, M.; Guglielmi, Y.; Nussbaum, C.; Valley, B.

    2016-12-01

    Clay-rich formations are considered to be a natural barrier for radionuclides or fluids (water, hydrocarbons, CO2) migration. However, little is known about the architecture of faults affecting clay formations because of their quick alteration at the Earth's surface. The Mont Terri Underground Research Laboratory provides exceptional conditions to investigate an un-weathered, perfectly exposed clay fault zone architecture and to conduct fault activation experiments that allow explore the conditions for stability of such clay faults. Here we show first results from a detailed geological model of the Mont Terri Main Fault architecture, using GoCad software, a detailed structural analysis of 6 fully cored and logged 30-to-50m long and 3-to-15m spaced boreholes crossing the fault zone. These high-definition geological data were acquired within the Fault Slip (FS) experiment project that consisted in fluid injections in different intervals within the fault using the SIMFIP probe to explore the conditions for the fault mechanical and seismic stability. The Mont Terri Main Fault "core" consists of a thrust zone about 0.8 to 3m wide that is bounded by two major fault planes. Between these planes, there is an assembly of distinct slickensided surfaces and various facies including scaly clays, fault gouge and fractured zones. Scaly clay including S-C bands and microfolds occurs in larger zones at top and bottom of the Mail Fault. A cm-thin layer of gouge, that is known to accommodate high strain parts, runs along the upper fault zone boundary. The non-scaly part mainly consists of undeformed rock block, bounded by slickensides. Such a complexity as well as the continuity of the two major surfaces are hard to correlate between the different boreholes even with the high density of geological data within the relatively small volume of the experiment. This may show that a poor strain localization occurred during faulting giving some perspectives about the potential for

  3. Revised sequence components power system models for unbalanced power system studies

    Energy Technology Data Exchange (ETDEWEB)

    Abdel-Akher, M. [Tunku Abdul Rahman Univ., Kuala Lumpur (Malaysia); Nor, K.-M. [Univ. of Technology Malaysia, Johor (Malaysia); Rashid, A.H.A. [Univ. of Malaya, Kuala Lumpur (Malaysia)

    2007-07-01

    The principle method of analysis using positive, negative, and zero-sequence networks has been used to examine the balanced power system under both balanced and unbalanced loading conditions. The significant advantage of the sequence networks is that the sequence networks become entirely uncoupled in the case of balanced three-phase power systems. The uncoupled sequence networks then can be solved in independent way such as in fault calculation programs. However, the hypothesis of balanced power systems cannot be considered in many cases due to untransposed transmission lines; multiphase line segments in a distribution power system; or transformer phase shifts which cannot be incorporated in the existing models. A revised sequence decoupled power system models for analyzing unbalanced power systems based on symmetrical networks was presented in this paper. These models included synchronous machines, transformers, transmission lines, and voltage regulators. The models were derived from their counterpart's models in phase coordinates frame of reference. In these models, the three sequence networks were fully decoupled with a three-phase coordinates features such as transformer phase shifts and transmission line coupling. The proposed models were used to develop an unbalanced power-flow program for analyzing both balanced and unbalanced networks. The power flow solution was identical to results obtained from a full phase coordinate three-phase power-flow program. 11 refs., 3 tabs.

  4. 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...

  5. 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.

  6. 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).

  7. DYNAMIC MIXING MODEL OF THE CHIGNAHUAPAN THERMAL SPRING IN THE GEOTHERMAL ZONE OF THE ACOCULCO CALDERA, PUEBLA, MEXICO

    Science.gov (United States)

    Gutierrez-Cirlos, A.; Torres-Rodriguez, V.

    2009-12-01

    The Acoculco Caldera, of Pliocenic age, is located within the limits of the Transmexican Volcanic Belt (CVT) and the Sierra Madre Oriental (SMOr). The Acoculco geothermal zone consists of a 790m thick igneous sequence, related to a volcanic complex formed by andesites and rhyolitic domes emplaced in an 18 Km diameter annular fracture. It unconformably overlies a 5000 m thick section of folded and faulted Jurassic-Cretaceous carbonate rocks. The Chignahuapan Spring, located in the extreme eastern part of the Geothermal Zone of the Acoculco Caldera, yields temperatures of 49°C and discharges an estimated of 98 lps from the karstified Lower Cretaceous limestone. Both major and trace element geochemical analysis were carried out, and results were interpreted using Piper and Stiff diagrams, as well as geothermometry. The results indicate that water belongs to the calcium-bicarbonate type and yield temperatures in a range of 70-80°C at depth, which suggest an extensive lateral flow from the main reservoir and mixing with shallow groundwaters. The spring suffers significant variations in its temperature throughout the year, especially during the rainy season, when water temperature decreases up to 10°C. Analyzing the hot spring water temperature data from of the last 10 years and comparing it with the precipitation and air temperature curves of the region, we expect to develop a dynamic mixing model which depicts the relation between these factors and the importance of each one in the water temperature variation. We also look forward to be able to forecast water temperature trends for the next several years and correlate it with climate change in the area.

  8. Structure of the Koyna-Warna Seismic Zone, Maharashtra, India: A possible model for large induced earthquakes elsewhere

    Science.gov (United States)

    Catchings, Rufus D.; Dixit, M.M.; Goldman, Mark R.; Kumar, S.

    2015-01-01

    The Koyna-Warna area of India is one of the best worldwide examples of reservoir-induced seismicity, with the distinction of having generated the largest known induced earthquake (M6.3 on 10 December 1967) and persistent moderate-magnitude (>M5) events for nearly 50 years. Yet, the fault structure and tectonic setting that has accommodated the induced seismicity is poorly known, in part because the seismic events occur beneath a thick sequence of basalt layers. On the basis of the alignment of earthquake epicenters over an ~50 year period, lateral variations in focal mechanisms, upper-crustal tomographic velocity images, geophysical data (aeromagnetic, gravity, and magnetotelluric), geomorphic data, and correlation with similar structures elsewhere, we suggest that the Koyna-Warna area lies within a right step between northwest trending, right-lateral faults. The sub-basalt basement may form a local structural depression (pull-apart basin) caused by extension within the step-over zone between the right-lateral faults. Our postulated model accounts for the observed pattern of normal faulting in a region that is dominated by north-south directed compression. The right-lateral faults extend well beyond the immediate Koyna-Warna area, possibly suggesting a more extensive zone of seismic hazards for the central India area. Induced seismic events have been observed many places worldwide, but relatively large-magnitude induced events are less common because critically stressed, preexisting structures are a necessary component. We suggest that releasing bends and fault step-overs like those we postulate for the Koyna-Warna area may serve as an ideal tectonic environment for generating moderate- to large- magnitude induced (reservoir, injection, etc.) earthquakes.

  9. 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.

  10. 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.

  11. Secondary structure classification of amino-acid sequences using state-space modeling

    OpenAIRE

    Brunnert, Marcus; Krahnke, Tillmann; Urfer, Wolfgang

    2001-01-01

    The secondary structure classification of amino acid sequences can be carried out by a statistical analysis of sequence and structure data using state-space models. Aiming at this classification, a modified filter algorithm programmed in S is applied to data of three proteins. The application leads to correct classifications of two proteins even when using relatively simple estimation methods for the parameters of the state-space models. Furthermore, it has been shown that the assumed initial...

  12. A Double Zone Dynamical Model For The Tidal Evolution Of The Obliquity

    Science.gov (United States)

    Damiani, Cilia

    2017-10-01

    It is debated wether close-in giants planets can form in-situ and if not, which mechanisms are responsible for their migration. One of the observable tests for migration theories is the current value of the obliquity. But after the main migration mechanism has ended, the combined effects of tidal dissipation and the magnetic braking of the star lead to the evolution of both the obliquity and the semi-major axis. The observed correlation between effective temperature and measured projected obliquity has been taken as evidence of such mechanisms being at play. Here I present an improved model for the tidal evolution of the obliquity. It includes all the components of the dynamical tide for circular misaligned systems. It uses an analytical formulation for the frequency-averaged dissipation for each mode, depending only on global stellar parameters, giving a measure of the dissipative properties of the convective zone of the host as it evolves in time. The model also includes the effect of magnetic braking in the framework of the double zone model. This results in the estimation of different tidal evolution timescales for the evolution of the planet's semi-major axis and obliquity depending on the properties of the stellar host. This model can be used to test migration theories, provided that a good determination of stellar radii, masses and ages can be obtained.

  13. Quantifying the relevance of adaptive thermal comfort models in moderate thermal climate zones

    Energy Technology Data Exchange (ETDEWEB)

    Hoof, Joost van; Hensen, Jan L.M. [Faculty of Architecture, Building and Planning, Technische Universiteit Eindhoven, Vertigo 6.18, P.O. Box 513, 5600 MB Eindhoven (Netherlands)

    2007-01-15

    Standards governing thermal comfort evaluation are on a constant cycle of revision and public review. One of the main topics being discussed in the latest round was the introduction of an adaptive thermal comfort model, which now forms an optional part of ASHRAE Standard 55. Also on a national level, adaptive thermal comfort guidelines come into being, such as in the Netherlands. This paper discusses two implementations of the adaptive comfort model in terms of usability and energy use for moderate maritime climate zones by means of literature study, a case study comprising temperature measurements, and building performance simulation. It is concluded that for moderate climate zones the adaptive model is only applicable during summer months, and can reduce energy for naturally conditioned buildings. However, the adaptive thermal comfort model has very limited application potential for such climates. Additionally we suggest a temperature parameter with a gradual course to replace the mean monthly outdoor air temperature to avoid step changes in optimum comfort temperatures. (author)

  14. 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

  15. Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling.

    Science.gov (United States)

    Schudoma, Christian; May, Patrick; Nikiforova, Viktoria; Walther, Dirk

    2010-01-01

    The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct clusters based on structural and sequence similarity. We detected clear evidence of the hallmark of homology present in the sequence-structure relationships in loops. Loops differing by structures. Thus, our results support the application of homology modeling for RNA loop model building. We established a threshold that may guide the sequence divergence-based selection of template structures for RNA loop homology modeling. Of all possible sequences that are, under the assumption of isosteric relationships, theoretically compatible with actual sequences observed in RNA structures, only a small fraction is contained in the Rfam database of RNA sequences and classes implying that the actual RNA loop space may consist of a limited number of unique loop structures and conserved sequences. The loop-structure data sets are made available via an online database, RLooM. RLooM also offers functionalities for the modeling of RNA loop structures in support of RNA engineering and design efforts.

  16. 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

  17. 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.

  18. 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

  19. Mechanical evolution of transpression zones affected by fault interactions: Insights from 3D elasto-plastic finite element models

    Science.gov (United States)

    Nabavi, Seyed Tohid; Alavi, Seyed Ahmad; Mohammadi, Soheil; Ghassemi, Mohammad Reza

    2018-01-01

    The mechanical evolution of transpression zones affected by fault interactions is investigated by a 3D elasto-plastic mechanical model solved with the finite-element method. Ductile transpression between non-rigid walls implies an upward and lateral extrusion. The model results demonstrate that a, transpression zone evolves in a 3D strain field along non-coaxial strain paths. Distributed plastic strain, slip transfer, and maximum plastic strain occur within the transpression zone. Outside the transpression zone, fault slip is reduced because deformation is accommodated by distributed plastic shear. With progressive deformation, the σ3 axis (the minimum compressive stress) rotates within the transpression zone to form an oblique angle to the regional transport direction (∼9°-10°). The magnitude of displacement increases faster within the transpression zone than outside it. Rotation of the displacement vectors of oblique convergence with time suggests that transpression zone evolves toward an overall non-plane strain deformation. The slip decreases along fault segments and with increasing depth. This can be attributed to the accommodation of bulk shortening over adjacent fault segments. The model result shows an almost symmetrical domal uplift due to off-fault deformation, generating a doubly plunging fold and a 'positive flower' structure. Outside the overlap zone, expanding asymmetric basins subside to 'negative flower' structures on both sides of the transpression zone and are called 'transpressional basins'. Deflection at fault segments causes the fault dip fall to less than 90° (∼86-89°) near the surface (∼1.5 km). This results in a pure-shear-dominated, triclinic, and discontinuous heterogeneous flow of the transpression zone.

  20. Sequence-based model of gap gene regulatory network.

    Science.gov (United States)

    Kozlov, Konstantin; Gursky, Vitaly; Kulakovskiy, Ivan; Samsonova, Maria

    2014-01-01

    The detailed analysis of transcriptional regulation is crucially important for understanding biological processes. The gap gene network in Drosophila attracts large interest among researches studying mechanisms of transcriptional regulation. It implements the most upstream regulatory layer of the segmentation gene network. The knowledge of molecular mechanisms involved in gap gene regulation is far less complete than that of genetics of the system. Mathematical modeling goes beyond insights gained by genetics and molecular approaches. It allows us to reconstruct wild-type gene expression patterns in silico, infer underlying regulatory mechanism and prove its sufficiency. We developed a new model that provides a dynamical description of gap gene regulatory systems, using detailed DNA-based information, as well as spatial transcription factor concentration data at varying time points. We showed that this model correctly reproduces gap gene expression patterns in wild type embryos and is able to predict gap expression patterns in Kr mutants and four reporter constructs. We used four-fold cross validation test and fitting to random dataset to validate the model and proof its sufficiency in data description. The identifiability analysis showed that most model parameters are well identifiable. We reconstructed the gap gene network topology and studied the impact of individual transcription factor binding sites on the model output. We measured this impact by calculating the site regulatory weight as a normalized difference between the residual sum of squares error for the set of all annotated sites and for the set with the site of interest excluded. The reconstructed topology of the gap gene network is in agreement with previous modeling results and data from literature. We showed that 1) the regulatory weights of transcription factor binding sites show very weak correlation with their PWM score; 2) sites with low regulatory weight are important for the model output; 3

  1. 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....

  2. 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

  3. Hidden Markov models for sequence analysis: extension and analysis of the basic method

    DEFF Research Database (Denmark)

    Hughey, Richard; Krogh, Anders Stærmose

    1996-01-01

    -maximization training procedure is relatively straight-forward. In this paper,we review the mathematical extensions and heuristics that move the method from the theoreticalto the practical. Then, we experimentally analyze the effectiveness of model regularization,dynamic model modification, and optimization strategies......Hidden Markov models (HMMs) are a highly effective means of modeling a family of unalignedsequences or a common motif within a set of unaligned sequences. The trained HMM can then beused for discrimination or multiple alignment. The basic mathematical description of an HMMand its expectation....... Finally it is demonstrated on the SH2domain how a domain can be found from unaligned sequences using a special model type. Theexperimental work was completed with the aid of the Sequence Alignment and Modeling softwaresuite....

  4. 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

  5. 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.

  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

    In this paper we propose a method for whole brain parcellation using the type of generative parametric models typically used in tissue classification. Compared to the non-parametric, multi-atlas segmentation techniques that have become popular in recent years, our method obtains state-of-the-art ...

  7. Trace Elements in Basalts From the Siqueiros Fracture Zone: Implications for Melt Migration Models

    Science.gov (United States)

    Pickle, R. C.; Forsyth, D. W.; Saal, A. E.; Nagle, A. N.; Perfit, M. R.

    2008-12-01

    Incompatible trace element (ITE) ratios in MORB from a variety of locations may provide insights into the melt migration process by constraining aggregated melt compositions predicted by mantle melting and flow models. By using actual plate geometries to create a 3-D thermodynamic mantle model, melt volumes and compositions at all depths and locations may be calculated and binned into cubes using the pHMELTS algorithm [Asimow et al., 2004]. These melts can be traced from each cube to the surface assuming several migration models, including a simplified pressure gradient model and one in which melt is guided upwards by a low permeability compacted layer. The ITE ratios of all melts arriving at the surface are summed, averaged, and compared to those of the actual sample compositions from the various MOR locales. The Siqueiros fracture zone at 8° 20' N on the East Pacific Rise (EPR) comprises 4 intra-transform spreading centers (ITSCs) across 140 km of offset between two longer spreading ridges, and is an excellent study region for several reasons. First, an abundance of MORB data is readily available, and the samples retrieved from ITSCs are unlikely to be aggregated in a long-lived magma chamber or affected by along-axis transport, so they represent melts extracted locally from the mantle. Additionally, samples at Siqueiros span a compositional range from depleted to normal MORB within the fracture zone yet have similar isotopic compositions to samples collected from the 9-10° EPR. This minimizes the effect of assuming a uniform source composition in our melting model despite a heterogeneous mantle, allowing us to consistently compare the actual lava composition with that predicted by our model. Finally, it has been demonstrated with preliminary migration models that incipient melts generated directly below an ITSC may not necessarily erupt at that ITSC but migrate laterally towards a nearby ridge due to enhanced pressure gradients. The close proximity of the

  8. Spatio-Temporal Modelling of Dust Transport over Surface Mining Areas and Neighbouring Residential Zones

    Directory of Open Access Journals (Sweden)

    Eva Gulikova

    2008-06-01

    Full Text Available Projects focusing on spatio-temporal modelling of the living environment need to manage a wide range of terrain measurements, existing spatial data, time series, results of spatial analysis and inputs/outputs from numerical simulations. Thus, GISs are often used to manage data from remote sensors, to provide advanced spatial analysis and to integrate numerical models. In order to demonstrate the integration of spatial data, time series and methods in the framework of the GIS, we present a case study focused on the modelling of dust transport over a surface coal mining area, exploring spatial data from 3D laser scanners, GPS measurements, aerial images, time series of meteorological observations, inputs/outputs form numerical models and existing geographic resources. To achieve this, digital terrain models, layers including GPS thematic mapping, and scenes with simulation of wind flows are created to visualize and interpret coal dust transport over the mine area and a neighbouring residential zone. A temporary coal storage and sorting site, located near the residential zone, is one of the dominant sources of emissions. Using numerical simulations, the possible effects of wind flows are observed over the surface, modified by natural objects and man-made obstacles. The coal dust drifts with the wind in the direction of the residential zone and is partially deposited in this area. The simultaneous display of the digital map layers together with the location of the dominant emission source, wind flows and protected areas enables a risk assessment of the dust deposition in the area of interest to be performed. In order to obtain a more accurate simulation of wind flows over the temporary storage and sorting site, 3D laser scanning and GPS thematic mapping are used to create a more detailed digital terrain model. Thus, visualization of wind flows over the area of interest combined with 3D map layers enables the exploration of the processes of coal dust

  9. 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.

  10. Subduction zone and crustal dynamics of western Washington; a tectonic model for earthquake hazards evaluation

    Science.gov (United States)

    Stanley, Dal; Villaseñor, Antonio; Benz, Harley

    1999-01-01

    The Cascadia subduction zone is extremely complex in the western Washington region, involving local deformation of the subducting Juan de Fuca plate and complicated block structures in the crust. It has been postulated that the Cascadia subduction zone could be the source for a large thrust earthquake, possibly as large as M9.0. Large intraplate earthquakes from within the subducting Juan de Fuca plate beneath the Puget Sound region have accounted for most of the energy release in this century and future such large earthquakes are expected. Added to these possible hazards is clear evidence for strong crustal deformation events in the Puget Sound region near faults such as the Seattle fault, which passes through the southern Seattle metropolitan area. In order to understand the nature of these individual earthquake sources and their possible interrelationship, we have conducted an extensive seismotectonic study of the region. We have employed P-wave velocity models developed using local earthquake tomography as a key tool in this research. Other information utilized includes geological, paleoseismic, gravity, magnetic, magnetotelluric, deformation, seismicity, focal mechanism and geodetic data. Neotectonic concepts were tested and augmented through use of anelastic (creep) deformation models based on thin-plate, finite-element techniques developed by Peter Bird, UCLA. These programs model anelastic strain rate, stress, and velocity fields for given rheological parameters, variable crust and lithosphere thicknesses, heat flow, and elevation. Known faults in western Washington and the main Cascadia subduction thrust were incorporated in the modeling process. Significant results from the velocity models include delineation of a previously studied arch in the subducting Juan de Fuca plate. The axis of the arch is oriented in the direction of current subduction and asymmetrically deformed due to the effects of a northern buttress mapped in the velocity models. This

  11. 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

  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. CLEAR: a model for the calculation of evacuation-time estimates in Emergency Planning Zones

    International Nuclear Information System (INIS)

    McLean, M.A.; Moeller, M.P.; Desrosiers, A.E.

    1983-01-01

    This paper describes the methodology and application of the computer model CLEAR (Calculates Logical Evacuation And Response) which estimates the time required for a specific population density and distribution to evacuate an area using a specific transportation network. The CLEAR model simulates vehicle departure and movement on a transportation network according to the conditions and consequences of traffice flow. These include handling vehicles at intersecting road segments, calculating the velocity of travel on a road segment as a function of its vehicle density, and accounting for the delay of vehicles in traffice queues. The program also models the distribution of times required by individuals to prepare for an evacuation. CLEAR can calculate realistic evacuation time estimates using site specific data and can identify troublesome areas within an Emergency Planning Zone

  14. Stochastic Petri Net Modeling of Wave Sequences in Cardiac Arrhythmias.

    Science.gov (United States)

    1987-11-01

    Wolff - Parkinson - White syndrome . The ventricles are divided into two parts. One of these is excited normally and produces R...example, in a condition called the Wolff - Parkinson - White syn- drome the ECG displays an abnormally early onset of the ventricular activity. It also...8217. , ’ ", -’ , .’ %,,? .’ ,; ’ .- ’ ’ -’ € ’ , . ’ - I. 32 Wolfe- Parkinson - White Syndrome (Fig. 8c) This model uses "basic" elements for the

  15. Situation models and memory: the effects of temporal and causal information on recall sequence.

    Science.gov (United States)

    Brownstein, Aaron L; Read, Stephen J

    2007-10-01

    Participants watched an episode of the television show Cheers on video and then reported free recall. Recall sequence followed the sequence of events in the story; if one concept was observed immediately after another, it was recalled immediately after it. We also made a causal network of the show's story and found that recall sequence followed causal links; effects were recalled immediately after their causes. Recall sequence was more likely to follow causal links than temporal sequence, and most likely to follow causal links that were temporally sequential. Results were similar at 10-minute and 1-week delayed recall. This is the most direct and detailed evidence reported on sequential effects in recall. The causal network also predicted probability of recall; concepts with more links and concepts on the main causal chain were most likely to be recalled. This extends the causal network model to more complex materials than previous research.

  16. 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.

  17. Finite element models of earthquake cycles in mature strike-slip fault zones

    Science.gov (United States)

    Lynch, John Charles

    The research presented in this dissertation is on the subject of strike-slip earthquakes and the stresses that build and release in the Earth's crust during earthquake cycles. Numerical models of these cycles in a layered elastic/viscoelastic crust are produced using the finite element method. A fault that alternately sticks and slips poses a particularly challenging problem for numerical implementation, and a new contact element dubbed the "Velcro" element was developed to address this problem (Appendix A). Additionally, the finite element code used in this study was bench-marked against analytical solutions for some simplified problems (Chapter 2), and the resolving power was tested for the fault region of the models (Appendix B). With the modeling method thus developed, there are two main questions posed. First, in Chapter 3, the effect of a finite-width shear zone is considered. By defining a viscoelastic shear zone beneath a periodically slipping fault, it is found that shear stress concentrates at the edges of the shear zone and thus causes the stress tensor to rotate into non-Andersonian orientations. Several methods are used to examine the stress patterns, including the plunge angles of the principal stresses and a new method that plots the stress tensor in a manner analogous to seismic focal mechanism diagrams. In Chapter 4, a simple San Andreas-like model is constructed, consisting of two great earthquake producing faults separated by a freely-slipping shorter fault. The model inputs of lower crustal viscosity, fault separation distance, and relative breaking strengths are examined for their effect on fault communication. It is found that with a lower crustal viscosity of 1018 Pa s (in the lower range of estimates for California), the two faults tend to synchronize their earthquake cycles, even in the cases where the faults have asymmetric breaking strengths. These models imply that postseismic stress transfer over hundreds of kilometers may play a

  18. Estimated damage from the Cascadia Subduction Zone tsunami: A model comparisons using fragility curves

    Science.gov (United States)

    Wiebe, D. M.; Cox, D. T.; Chen, Y.; Weber, B. A.; Chen, Y.

    2012-12-01

    Building damage from a hypothetical Cascadia Subduction Zone tsunami was estimated using two methods and applied at the community scale. The first method applies proposed guidelines for a new ASCE 7 standard to calculate the flow depth, flow velocity, and momentum flux from a known runup limit and estimate of the total tsunami energy at the shoreline. This procedure is based on a potential energy budget, uses the energy grade line, and accounts for frictional losses. The second method utilized numerical model results from previous studies to determine maximum flow depth, velocity, and momentum flux throughout the inundation zone. The towns of Seaside and Canon Beach, Oregon, were selected for analysis due to the availability of existing data from previously published works. Fragility curves, based on the hydrodynamic features of the tsunami flow (inundation depth, flow velocity, and momentum flux) and proposed design standards from ASCE 7 were used to estimate the probability of damage to structures located within the inundations zone. The analysis proceeded at the parcel level, using tax-lot data to identify construction type (wood, steel, and reinforced-concrete) and age, which was used as a performance measure when applying the fragility curves and design standards. The overall probability of damage to civil buildings was integrated for comparison between the two methods, and also analyzed spatially for damage patterns, which could be controlled by local bathymetric features. The two methods were compared to assess the sensitivity of the results to the uncertainty in the input hydrodynamic conditions and fragility curves, and the potential advantages of each method discussed. On-going work includes coupling the results of building damage and vulnerability to an economic input output model. This model assesses trade between business sectors located inside and outside the induction zone, and is used to measure the impact to the regional economy. Results highlight

  19. A compartmentalized solute transport model for redox zones in contaminated aquifers: 1. Theory and development

    Science.gov (United States)

    Abrams , Robert H.; Loague, Keith

    2000-01-01

    This paper, the first of two parts [see Abrams and Loague, this issue], takes the compartmentalized approach for the geochemical evolution of redox zones presented by Abrams et al. [1998] and embeds it within a solute transport framework. In this paper the compartmentalized approach is generalized to facilitate the description of its incorporation into a solute transport simulator. An equivalent formulation is developed which removes any discontinuities that may occur when switching compartments. Rate‐limited redox reactions are modeled with a modified Monod relationship that allows either the organic substrate or the electron acceptor to be the rate‐limiting reactant. Thermodynamic constraints are used to inhibit lower‐energy redox reactions from occurring under infeasible geochemical conditions without imposing equilibrium on the lower‐energy reactions. The procedure used allows any redox reaction to be simulated as being kinetically limited or thermodynamically limited, depending on local geochemical conditions. Empirical reaction inhibition methods are not needed. The sequential iteration approach (SIA), a technique which allows the number of solute transport equations to be reduced, is adopted to solve the coupled geochemical/solute transport problem. When the compartmentalized approach is embedded within the SIA, with the total analytical concentration of each component as the dependent variable in the transport equation, it is possible to reduce the number of transport equations even further than with the unmodified SIA. A one‐dimensional, coupled geochemical/solute transport simulation is presented in which redox zones evolve dynamically in time and space. The compartmentalized solute transport (COMPTRAN) model described in this paper enables the development of redox zones to be simulated under both kinetic and thermodynamic constraints. The modular design of COMPTRAN facilitates the use of many different, preexisting solute transport and

  20. 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

  1. Sequence Modeling for Analysing Student Interaction with Educational Systems

    DEFF Research Database (Denmark)

    Hansen, Christian; Hansen, Casper; Hjuler, Niklas Oskar Daniel

    2017-01-01

    as exhibiting unproductive student behaviour. Based on our results this student representation is promising, especially for educational systems offering many different learning usages, and offers an alternative to common approaches like modelling student behaviour as a single Markov chain often done......The analysis of log data generated by online educational systems is an important task for improving the systems, and furthering our knowledge of how students learn. This paper uses previously unseen log data from Edulab, the largest provider of digital learning for mathematics in Denmark...

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  3. 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.

  4. 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.

  5. 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

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

    KAUST Repository

    Zhang, Zhang; Yu, Jun

    2010-01-01

    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.

  7. 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.

  8. 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.

  9. Modeling mesoscale diffusion and transport processes for releases within coastal zones during land/sea breezes

    International Nuclear Information System (INIS)

    Lyons, W.A.; Keen, C.S.; Schuh, J.A.

    1983-12-01

    This document discusses the impacts of coastal mesoscale regimes (CMRs) upon the transport and diffusion of potential accidental radionuclide releases from a shoreline nuclear power plant. CMRs exhibit significant spatial (horizontal and vertical) and temporal variability. Case studies illustrate land breezes, sea/lake breeze inflows and return flows, thermal internal boundary layers, fumigation, plume trapping, coastal convergence zones, thunderstorms and snow squalls. The direct application of a conventional Gaussian straight-line dose assessment model, initialized only by on-site tower data, can potentially produce highly misleading guidance as to plume impact locations. Since much is known concerning CMRs, there are many potential improvements to modularized dose assessment codes, such as by proper parameterization of TIBLs, forecasting the inland penetration of convergence zones, etc. A three-dimensional primitive equation prognostic model showed excellent agreement with detailed lake breeze field measurements, giving indications that such codes can be used in both diagnostic and prognostic studies. The use of relatively inexpensive supplemental meteorological data especially from remote sensing systems (Doppler sodar, radar, lightning strike tracking) and computerized data bases should save significantly on software development costs. Better quality assurance of emergency response codes could include systems of flags providing personnel with confidence levels as to the applicability of a code being used during any given CMR

  10. 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.

  11. A branch-heterogeneous model of protein evolution for efficient inference of ancestral sequences.

    Science.gov (United States)

    Groussin, M; Boussau, B; Gouy, M

    2013-07-01

    Most models of nucleotide or amino acid substitution used in phylogenetic studies assume that the evolutionary process has been homogeneous across lineages and that composition of nucleotides or amino acids has remained the same throughout the tree. These oversimplified assumptions are refuted by the observation that compositional variability characterizes extant biological sequences. Branch-heterogeneous models of protein evolution that account for compositional variability have been developed, but are not yet in common use because of the large number of parameters required, leading to high computational costs and potential overparameterization. Here, we present a new branch-nonhomogeneous and nonstationary model of protein evolution that captures more accurately the high complexity of sequence evolution. This model, henceforth called Correspondence and likelihood analysis (COaLA), makes use of a correspondence analysis to reduce the number of parameters to be optimized through maximum likelihood, focusing on most of the compositional variation observed in the data. The model was thoroughly tested on both simulated and biological data sets to show its high performance in terms of data fitting and CPU time. COaLA efficiently estimates ancestral amino acid frequencies and sequences, making it relevant for studies aiming at reconstructing and resurrecting ancestral amino acid sequences. Finally, we applied COaLA on a concatenate of universal amino acid sequences to confirm previous results obtained with a nonhomogeneous Bayesian model regarding the early pattern of adaptation to optimal growth temperature, supporting the mesophilic nature of the Last Universal Common Ancestor.

  12. 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.

  13. GPS measurements and finite element modeling of the earthquake cycle along the Middle America subduction zone

    Science.gov (United States)

    Correa Mora, Francisco

    We model surface deformation recorded by GPS stations along the Pacific coasts of Mexico and Central America to estimate the magnitude of and variations in frictional locking (coupling) along the subduction interface, toward a better understanding of seismic hazard in these earthquake-prone regions. The first chapter describes my primary analysis technique, namely 3-dimensional finite element modeling to simulate subduction and bounded-variable inversions that optimize the fit to the GPS velocity field. This chapter focuses on and describes interseismic coupling of the Oaxaca segment of the Mexican subduction zone and introduces an analysis of transient slip events that occur in this region. Our results indicate that coupling is strong within the rupture zone of the 1978 Ms=7.8 Oaxaca earthquake, making this region a potential source of a future large earthquake. However, we also find evidence for significant variations in coupling on the subduction interface over distances of only tens of kilometers, decreasing toward the outer edges of the 1978 rupture zone. In the second chapter, we study in more detail some of the slow slip events that have been recorded over a broad area of southern Mexico, with emphasis on their space-time behavior. Our modeling indicates that transient deformation beneath southern Mexico is focused in two distinct slip patches mostly located downdip from seismogenic areas beneath Guerrero and Oaxaca. Contrary to conclusions reached in one previous study, we find no evidence for a spatial or temporal correlation between transient slip that occurs in these two widely separated source regions. Finally, chapter three extends the modeling techniques to new GPS data in Central America, where subduction coupling is weak or zero and the upper plate deformation is much more complex than in Mexico. Cocos-Caribbean plate convergence beneath El Salvador and Nicaragua is accompanied by subduction and trench-parallel motion of the forearc. Our GPS

  14. 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

  15. Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing.

    Science.gov (United States)

    Seoane-Zonjic, Pedro; Cañas, Rafael A; Bautista, Rocío; Gómez-Maldonado, Josefa; Arrillaga, Isabel; Fernández-Pozo, Noé; Claros, M Gonzalo; Cánovas, Francisco M; Ávila, Concepción

    2016-02-27

    In the era of DNA throughput sequencing, assembling and understanding gymnosperm mega-genomes remains a challenge. Although drafts of three conifer genomes have recently been published, this number is too low to understand the full complexity of conifer genomes. Using techniques focused on specific genes, gene models can be established that can aid in the assembly of gene-rich regions, and this information can be used to compare genomes and understand functional evolution. In this study, gene capture technology combined with BAC isolation and sequencing was used as an experimental approach to establish de novo gene structures without a reference genome. Probes were designed for 866 maritime pine transcripts to sequence genes captured from genomic DNA. The gene models were constructed using GeneAssembler, a new bioinformatic pipeline, which reconstructed over 82% of the gene structures, and a high proportion (85%) of the captured gene models contained sequences from the promoter regulatory region. In a parallel experiment, the P. pinaster BAC library was screened to isolate clones containing genes whose cDNA sequence were already available. BAC clones containing the asparagine synthetase, sucrose synthase and xyloglucan endotransglycosylase gene sequences were isolated and used in this study. The gene models derived from the gene capture approach were compared with the genomic sequences derived from the BAC clones. This combined approach is a particularly efficient way to capture the genomic structures of gene families with a small number of members. The experimental approach used in this study is a valuable combined technique to study genomic gene structures in species for which a reference genome is unavailable. It can be used to establish exon/intron boundaries in unknown gene structures, to reconstruct incomplete genes and to obtain promoter sequences that can be used for transcriptional studies. A bioinformatics algorithm (GeneAssembler) is also provided as a

  16. 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)

  17. Assimilation of a thermal remote sensing-based soil moisture proxy into a root-zone water balance model

    Science.gov (United States)

    Crow, W. T.; Kustas, W. P.

    2006-05-01

    Two types of Soil Vegetation Atmosphere Transfer (SVAT) modeling approaches are commonly applied to monitoring root-zone soil water availability. Water and Energy Balance (WEB) SVAT modeling are based forcing a prognostic water balance model with precipitation observations. In constrast, thermal Remote Sensing (RS) observations of canopy radiometric temperatures can be integrated into purely diagnostic SVAT models to predict the onset of vegetation water stress due to low root-zone soil water availability. Unlike WEB-SVAT models, RS-SVAT models do not require observed precipitation. Using four growings seasons (2001 to 2004) of profile soil moisture, micro-meteorology, and surface radiometric temperature observations at the USDA's OPE3 site, root-zone soil moisture predictions made by both WEB- and RS-SVAT modeling approaches are intercompared with each other and availible root- zone soil moisture observations. Results indicate that root-zone soil moisture estimates derived from a WEB- SVAT model have slightly more skill in detecting soil moisture anomalies at the site than comporable predictions from a competing RS-SVAT modeling approach. However, the relative advantage of the WEB-SVAT model disappears when it is forced with lower-quality rainfall information typical of continental and global-scale rainfall data sets. Most critically, root-zone soil moisture errors associated with both modeling approaches are sufficiently independent such that the merger of both information from both proxies - using either simple linear averaging or an Ensemble Kalman filter - creates a merge soil moisture estimate that is more accurate than either of its parent components.

  18. 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

  19. 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

  20. 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.

  1. PRECISION MEASUREMENTS OF THE CLUSTER RED SEQUENCE USING AN ERROR-CORRECTED GAUSSIAN MIXTURE MODEL

    International Nuclear Information System (INIS)

    Hao Jiangang; Annis, James; Koester, Benjamin P.; Mckay, Timothy A.; Evrard, August; Gerdes, David; Rykoff, Eli S.; Rozo, Eduardo; Becker, Matthew; Busha, Michael; Wechsler, Risa H.; Johnston, David E.; Sheldon, Erin

    2009-01-01

    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.

  2. 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

  3. 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

  4. 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.

  5. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    K. Rehfeldt

    2004-10-08

    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

  7. Model-based quality assessment and base-calling for second-generation sequencing data.

    Science.gov (United States)

    Bravo, Héctor Corrada; Irizarry, Rafael A

    2010-09-01

    Second-generation sequencing (sec-gen) technology can sequence millions of short fragments of DNA in parallel, making it capable of assembling complex genomes for a small fraction of the price and time of previous technologies. In fact, a recently formed international consortium, the 1000 Genomes Project, plans to fully sequence the genomes of approximately 1200 people. The prospect of comparative analysis at the sequence level of a large number of samples across multiple populations may be achieved within the next five years. These data present unprecedented challenges in statistical analysis. For instance, analysis operates on millions of short nucleotide sequences, or reads-strings of A,C,G, or T's, between 30 and 100 characters long-which are the result of complex processing of noisy continuous fluorescence intensity measurements known as base-calling. The complexity of the base-calling discretization process results in reads of widely varying quality within and across sequence samples. This variation in processing quality results in infrequent but systematic errors that we have found to mislead downstream analysis of the discretized sequence read data. For instance, a central goal of the 1000 Genomes Project is to quantify across-sample variation at the single nucleotide level. At this resolution, small error rates in sequencing prove significant, especially for rare variants. Sec-gen sequencing is a relatively new technology for which potential biases and sources of obscuring variation are not yet fully understood. Therefore, modeling and quantifying the uncertainty inherent in the generation of sequence reads is of utmost importance. In this article, we present a simple model to capture uncertainty arising in the base-calling procedure of the Illumina/Solexa GA platform. Model parameters have a straightforward interpretation in terms of the chemistry of base-calling allowing for informative and easily interpretable metrics that capture the variability in

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

    Energy Technology Data Exchange (ETDEWEB)

    Roostapour, A. [Craft and Hawkins Department of Petroleum Engineering, Louisiana State University, Baton Rouge, LA 70803 (United States); Kam, S.I., E-mail: kam@lsu.edu [Craft and Hawkins Department of Petroleum Engineering, Louisiana State University, Baton Rouge, LA 70803 (United States)

    2012-12-15

    Highlights: Black-Right-Pointing-Pointer A new mathematical framework established for vadose-zone foam remediation. Black-Right-Pointing-Pointer Graphical solutions presented by Method of Characteristics quantitatively. Black-Right-Pointing-Pointer Effects of design parameters in the field applications thoroughly investigated. Black-Right-Pointing-Pointer 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{sub 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

  9. 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

  10. 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

  11. 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

  12. Construction sequence scale model: an aid to productivity and quality assurance

    International Nuclear Information System (INIS)

    Clothier, W.A. Sr.

    1978-01-01

    The natural tendencies of an engineering scale model to promote a high level of quality by error prevention during design and construction stages of a project are studied. A brief section on the basic history of engineering modeling is used to describe TVA's usage of the model. The basic design model is explored in an overview touching the highlights of that form of modeling. A detailed look at the construction sequence model, a relatively new form of model, is presented to demonstrate quality and productivity awareness

  13. 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

  14. Groundwater and solute transport modeling at Hyporheic zone of upper part Citarum River

    Science.gov (United States)

    Iskandar, Irwan; Farazi, Hendy; Fadhilah, Rahmat; Purnandi, Cipto; Notosiswoyo, Sudarto

    2017-06-01

    Groundwater and surface water interaction is an interesting topic to be studied related to the water resources and environmental studies. The study of interaction between groundwater and river water at the Upper Part Citarum River aims to know the contribution of groundwater to the river or reversely and also solute transport of dissolved ions between them. Analysis of drill logs, vertical electrical sounding at the selected sections, measurement of dissolved ions, and groundwater modeling were applied to determine the flow and solute transport phenomena at the hyporheic zone. It showed the hyporheic zone dominated by silt and clay with hydraulic conductivity range from 10-4∼10-8 m/s. The groundwater flowing into the river with very low gradient and it shows that the Citarum River is a gaining stream. The groundwater modeling shows direct seepage of groundwater into the Citarum River is only 186 l/s, very small compared to the total discharge of the river. Total dissolved ions of the groundwater ranged from 200 to 480 ppm while the river water range from 200 to 2,000 ppm. Based on solute transport modeling it indicates dissolved ions dispersion of the Citarum River into groundwater may occur in some areas such as Bojongsoang-Dayeuh Kolot and Nanjung. This situation would increase the dissolved ions in groundwater in the region due to the contribution of the Citarum River. The results of the research can be a reference for further studies related to the mechanism of transport of the pollutants in the groundwater around the Citarum River.

  15. 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.

  16. How Models Simulate the Radiative Effect in the Transition Zone of the Aerosol-Cloud Continuum

    Science.gov (United States)

    Calbo Angrill, J.; González, J. A.; Long, C. N.; McComiskey, A. C.

    2017-12-01

    Several studies have pointed towards dealing with clouds and aerosols as two manifestations of what is essentially the same physical phenomenon: a suspension of tiny particles in the air. Although the two extreme cases (i.e., pure aerosol and well-defined cloud) are easily distinguished, and obviously produce different radiative effects, there are many situations in the transition (or "twilight") zone. In a recent paper [Calbó et al., Atmos. Res. 2017, j.atmosres.2017.06.010], the authors of the current communication estimated that about 10% of time there might be a suspension of particles in the air that is difficult to distinguish as either cloud or aerosol. Radiative transfer models, however, simulate the effect of clouds and aerosols with different modules, routines, or parameterizations. In this study, we apply a sensitivity analysis approach to assess the ability of two radiative transfer models (SBDART and RRTM) in simulating the radiative effect of a suspension of particles with characteristics in the boundary between cloud and aerosol. We simulate this kind of suspension either in "cloud mode" or in "aerosol mode" and setting different values of optical depth, droplet size, water path, aerosol type, cloud height, etc. Irradiances both for solar and infrared bands are studied, both at ground level and at the top of the atmosphere, and all analyses are repeated for different solar zenith angles. We obtain that (a) water clouds and ice clouds have similar radiative effects if they have the same optical depth; (b) the spread of effects regarding different aerosol type/aerosol characteristics is remarkable; (c) radiative effects of an aerosol layer and of a cloud layer are different, even if they have similar optical depth; (d) for a given effect on the diffuse component, the effect on the direct component is usually greater (more extinction of direct beam) by aerosols than by clouds; (e) radiative transfer models are somewhat limited when simulating the

  17. 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.

  18. Structured prediction models for RNN based sequence labeling in clinical text.

    Science.gov (United States)

    Jagannatha, Abhyuday N; Yu, Hong

    2016-11-01

    Sequence labeling is a widely used method for named entity recognition and information extraction from unstructured natural language data. In clinical domain one major application of sequence labeling involves extraction of medical entities such as medication, indication, and side-effects from Electronic Health Record narratives. Sequence labeling in this domain, presents its own set of challenges and objectives. In this work we experimented with various CRF based structured learning models with Recurrent Neural Networks. We extend the previously studied LSTM-CRF models with explicit modeling of pairwise potentials. We also propose an approximate version of skip-chain CRF inference with RNN potentials. We use these methodologies for structured prediction in order to improve the exact phrase detection of various medical entities.

  19. A consistency assessment of coupled cohesive zone models for mixed-mode debonding problems

    Directory of Open Access Journals (Sweden)

    R. Dimitri

    2014-07-01

    Full Text Available Due to their simplicity, cohesive zone models (CZMs are very attractive to describe mixed-mode failure and debonding processes of materials and interfaces. Although a large number of coupled CZMs have been proposed, and despite the extensive related literature, little attention has been devoted to ensuring the consistency of these models for mixed-mode conditions, primarily in a thermodynamical sense. A lack of consistency may affect the local or global response of a mechanical system. This contribution deals with the consistency check for some widely used exponential and bilinear mixed-mode CZMs. The coupling effect on stresses and energy dissipation is first investigated and the path-dependance of the mixed-mode debonding work of separation is analitically evaluated. Analytical predictions are also compared with results from numerical implementations, where the interface is described with zero-thickness contact elements. A node-to-segment strategy is here adopted, which incorporates decohesion and contact within a unified framework. A new thermodynamically consistent mixed-mode CZ model based on a reformulation of the Xu-Needleman model as modified by van den Bosch et al. is finally proposed and derived by applying the Coleman and Noll procedure in accordance with the second law of thermodynamics. The model holds monolithically for loading and unloading processes, as well as for decohesion and contact, and its performance is demonstrated through suitable examples.

  20. Three-dimensional shear transformation zone dynamics model for amorphous metals

    International Nuclear Information System (INIS)

    Homer, Eric R; Schuh, Christopher A

    2010-01-01

    A fully three-dimensional (3D) mesoscale modeling framework for the mechanical behavior of amorphous metals is proposed. The model considers the coarse-grained action of shear transformation zones (STZs) as the fundamental deformation event. The simulations are controlled through the kinetic Monte Carlo algorithm and the mechanical response of the system is captured through finite-element analysis, where STZs are mapped onto a 3D finite-element mesh and are allowed to shear in any direction in three dimensions. Implementation of the technique in uniaxial creep tests over a wide range of conditions validates the model's ability to capture the expected behaviors of an amorphous metal, including high temperature flow conforming to the expected constitutive law and low temperature localization in the form of a nascent shear band. The simulation results are combined to construct a deformation map that is comparable to experimental deformation maps. The flexibility of the modeling framework is illustrated by performing a contact test (simulated nanoindentation) in which the model deforms through STZ activity in the region experiencing the highest shear stress

  1. Implications of emission zone limits for the Ruderman-Sutherland pulsar model

    International Nuclear Information System (INIS)

    Matese, J.J.; Whitmire, D.P.

    1980-01-01

    In the Ruderman-Sutherland (RS) pulsar model the frequency at which coherent radiation is emitted depends upon the source location, v=v (r). In the oblique rotator version of this model the time-averaged tangential velocities of the magnetosphere sources must increase linearly with radius, and this leads to a frequency-dependent aberration and retardation time delay in which higher frequencies lag behind lower frequencies. As previously noted by Cordes, within the context of a given model which specifies v (r), the absence of any anomalous time delay in dispersion measurements allows limits to be placed on the radial position of the source of a given frequency. In this paper we (a) give a time-delay analysis (similar to that of Cordes) appropriate for the RS model and show that existing dispersion measurements are incompatible with RS emission mechanism. If the basic RS emission mechanism is applicable to pulsars, we find that the most plausible modification consistent with the dispersion data is a reduction in the low-energy plasma density by a factor approx.10 -4 to 10 -5 . This has the effect of bringing the radio emission zone closer to the stellar surface, thereby making the model consistent with the dispersion data. In addition, this modification results in a significant decrease in the predicted maximum cone angle and an increase in the predicted maximum frequency by factors which bring these predictions more in line with observation. We also consider implications of a reduced plasma density for radio luminosity

  2. 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.

  3. Assessment of vulnerability zones for ground water pollution using GIS-DRASTIC-EC model: A field-based approach

    Science.gov (United States)

    Anantha Rao, D.; Naik, Pradeep K.; Jain, Sunil K.; Vinod Kumar, K.; Dhanamjaya Rao, E. N.

    2018-06-01

    Assessment of groundwater vulnerability to pollution is an essential pre-requisite for better planning of an area. We present the groundwater vulnerability assessment in parts of the Yamuna Nagar District, Haryana State, India in an area of about 800 km2, considered to be a freshwater zone in the foothills of the Siwalik Hill Ranges. Such areas in the Lower Himalayas form good groundwater recharge zones, and should always be free from contamination. But, the administration has been trying to promote industrialization along these foothill zones without actually assessing the environmental consequences such activities may invite in the future. GIS-DRASTIC model has been used with field based data inputs for studying the vulnerability assessment. But, we find that inclusion electrical conductivity (EC) as a model parameter makes it more robust. Therefore, we rename it as GIS-DRASTIC-EC model. The model identifies three vulnerability zones such as low, moderate and high with an areal extent of 5%, 80% and 15%, respectively. On the basis of major chemical parameters alone, the groundwater in the foothill zones apparently looks safe, but analysis with the help of GIS-DRASTIC-EC model gives a better perspective of the groundwater quality in terms of identifying the vulnerable areas.

  4. Creys-Malville nuclear plant. Simulation of the cold plenum thermal-hydraulics. 12 zone model presentation

    International Nuclear Information System (INIS)

    Faulot, J.P.

    1990-05-01

    The CRUSIFI code has been developed by SEPTEN (Engineering and Construction Division) with SICLE software during 1983-1985 in order to study the CREYS-MALVILLE dynamic behavior. At the time, the version was based on project data (version 2.3). It includes a 2 zones model for the cold plenum thermal-hydraulics, modelling which does not allow to reproduce accurately dissymetries apt to occur as well in usual operating (hydraulic dissymetries bound to one or many systems out of order), as during incidentally operating (hydraulic dissymetries bound to primary pump working back or thermal dissymetries after a transient on one or many secondary loops). Moreover, a 2 zones model cannot simulate axial temperature gradients which appear during double stratification phenomenon (upper and lower part of the plenum) produced by alternating thermal shock. A 12 zones model (4 sectors with 3 axial zones each) such as model developed by R$DD (Research and Development Division) allows to satisfy correctly these problems. This report is a specification of the chosen modelling. This model is now operational after qualifying with experimental transients on mockup and reactor. It is to-day connected with the EDF general operating code CRUSIFI (calibrating version 3.0). It could be easily integrated in a four loops plant modelling such as the CREYS-MALVILLE simulator in a four loops plant modelling such as the CREYS-MALVILLE simulator under construction at the present time by THOMSON

  5. 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

  6. 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.

  7. 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

  8. Spatially explicit modeling of conflict zones between wildlife and snow sports: prioritizing areas for winter refuges.

    Science.gov (United States)

    Braunisch, Veronika; Patthey, Patrick; Arlettaz, Raphaël

    2011-04-01

    Outdoor winter recreation exerts an increasing pressure upon mountain ecosystems, with unpredictable, free-ranging activities (e.g., ski mountaineering, snowboarding, and snowshoeing) representing a major source of stress for wildlife. Mitigating anthropogenic disturbance requires the spatially explicit prediction of the interference between the activities of humans and wildlife. We applied spatial modeling to localize conflict zones between wintering Black Grouse (Tetrao tetrix), a declining species of Alpine timberline ecosystems, and two free-ranging winter sports (off-piste skiing [including snow-boarding] and snowshoeing). Track data (snow-sports and birds' traces) obtained from aerial photographs taken over a 585-km transect running along the timberline, implemented within a maximum entropy model, were used to predict the occurrence of snow sports and Black Grouse as a function of landscape characteristics. By modeling Black Grouse presence in the theoretical absence of free-ranging activities and ski infrastructure, we first estimated the amount of habitat reduction caused by these two factors. The models were then extrapolated to the altitudinal range occupied by Black Grouse, while the spatial extent and intensity of potential conflict were assessed by calculating the probability of human-wildlife co-occurrence. The two snow-sports showed different distribution patterns. Skiers' occurrence was mainly determined by ski-lift presence and a smooth terrain, while snowshoers' occurrence was linked to hiking or skiing routes and moderate slopes. Wintering Black Grouse avoided ski lifts and areas frequented by free-ranging snow sports. According to the models, Black Grouse have faced a substantial reduction of suitable wintering habitat along the timberline transect: 12% due to ski infrastructure and another 16% when adding free-ranging activities. Extrapolating the models over the whole study area results in an overall habitat loss due to ski infrastructure of

  9. Cohesive zone modelling of wafer bonding and fracture: effect of patterning and toughness variations

    Science.gov (United States)

    Kubair, D. V.; Spearing, S. M.

    2006-03-01

    Direct wafer bonding has increasingly become popular in the manufacture of microelectromechanical systems and semiconductor microelectronics components. The success of the bonding process is controlled by variables such as wafer flatness and surface preparation. In order to understand the effects of these variables, spontaneous planar crack propagation simulations were performed using the spectral scheme in conjunction with a cohesive zone model. The fracture-toughness on the bond interface is varied to simulate the effect of surface roughness (nanotopography) and patterning. Our analysis indicated that the energetics of crack propagation is sensitive to the local surface property variations. The patterned wafers are tougher (well bonded) than the unpatterned ones of the same average fracture-toughness.

  10. 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

  11. 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

  12. 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.

  13. Multilevel modeling of micromechanics and phase formation for microstructural evolution of magnetic zones

    International Nuclear Information System (INIS)

    Suwa, Yoshihiro; Aizawa, Tatsuhiko; Takaya, Shigeru; Nagae, Yuji; Aoto, Kazumi

    2005-03-01

    The present research aims at a proposal of theoretical treatise to describe the local phase transformation from austenite to ferrite in the stainless steels under hot cyclic fatigue conditions. In experiments, this local phase transformation is detected as a magnetized region in the non-magnetic matrix after low-cycle fatigue test at the elevated temperature. The theoretical frame proposed here is composed of two methodologies. In the first approach, microstructure evolution with γ → α transformation is described by the phase field method. In the second approach, micromechanical method on the basis of the unit cell modeling is proposed to develop a new micromechanical analysis. The details of two approached are summarized in the following. (1) Phase formation simulation by the phase field method. Most of reports have started that γ-α phase transformation as a creep damage is induced by dechromization, which comes from carbide precipitation around grain boundaries. A new theoretical treatise is proposed for simulating this γ → α transformation in Fe-Cr-Ni system. Stabilities of both phases are investigated for various chemical compositions. Furthermore, in order to investigate dechromization phenomena in Fe-Cr-Ni-C system, a new theoretical frame is also proposed to handle an interstitial element in phase field method. (2) Low cycle fatigue elasto-plastic analysis by the unit-cell modeling. In experiments, the magnetized zones are generated to distribute at the vicinity of the hard, delta-phase inclusion in the austenitic matrix. The cumulative plastic region advances in the surroundings of this hard inclusion with increasing the number of cycles in the controlled strain range. This predicted profile of cumulative plastic regions corresponds to the experimentally measured, magnetized zones. In addition, the effect of geometric configuration of this inclusion on the plastic region evolution has close relationship of creep damage advancement in experiments

  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. Time-varying mixed logit model for vehicle merging behavior in work zone merging areas.

    Science.gov (United States)

    Weng, Jinxian; Du, Gang; Li, Dan; Yu, Yao

    2018-08-01

    This study aims to develop a time-varying mixed logit model for the vehicle merging behavior in work zone merging areas during the merging implementation period from the time of starting a merging maneuver to that of completing the maneuver. From the safety perspective, vehicle crash probability and severity between the merging vehicle and its surrounding vehicles are regarded as major factors influencing vehicle merging decisions. Model results show that the model with the use of vehicle crash risk probability and severity could provide higher prediction accuracy than previous models with the use of vehicle speeds and gap sizes. It is found that lead vehicle type, through lead vehicle type, through lag vehicle type, crash probability of the merging vehicle with respect to the through lag vehicle, crash severities of the merging vehicle with respect to the through lead and lag vehicles could exhibit time-varying effects on the merging behavior. One important finding is that the merging vehicle could become more and more aggressive in order to complete the merging maneuver as quickly as possible over the elapsed time, even if it has high vehicle crash risk with respect to the through lead and lag vehicles. Copyright © 2018 Elsevier Ltd. All rights reserved.

  16. A New Paradigm For Modeling Fault Zone Inelasticity: A Multiscale Continuum Framework Incorporating Spontaneous Localization and Grain Fragmentation.

    Science.gov (United States)

    Elbanna, A. E.

    2015-12-01

    The brittle portion of the crust contains structural features such as faults, jogs, joints, bends and cataclastic zones that span a wide range of length scales. These features may have a profound effect on earthquake nucleation, propagation and arrest. Incorporating these existing features in modeling and the ability to spontaneously generate new one in response to earthquake loading is crucial for predicting seismicity patterns, distribution of aftershocks and nucleation sites, earthquakes arrest mechanisms, and topological changes in the seismogenic zone structure. Here, we report on our efforts in modeling two important mechanisms contributing to the evolution of fault zone topology: (1) Grain comminution at the submeter scale, and (2) Secondary faulting/plasticity at the scale of few to hundreds of meters. We use the finite element software Abaqus to model the dynamic rupture. The constitutive response of the fault zone is modeled using the Shear Transformation Zone theory, a non-equilibrium statistical thermodynamic framework for modeling plastic deformation and localization in amorphous materials such as fault gouge. The gouge layer is modeled as 2D plane strain region with a finite thickness and heterogeenous distribution of porosity. By coupling the amorphous gouge with the surrounding elastic bulk, the model introduces a set of novel features that go beyond the state of the art. These include: (1) self-consistent rate dependent plasticity with a physically-motivated set of internal variables, (2) non-locality that alleviates mesh dependence of shear band formation, (3) spontaneous evolution of fault roughness and its strike which affects ground motion generation and the local stress fields, and (4) spontaneous evolution of grain size and fault zone fabric.

  17. 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.

  18. 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.)

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

    International Nuclear Information System (INIS)

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

    2015-01-01

    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.)

  20. 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

  1. 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

  2. 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

  3. The Lower Main Sequence of Stars in the Solar Neighborhood: Model Predictions Versus Observation

    Directory of Open Access Journals (Sweden)

    Bartašiūtė S.

    2012-09-01

    Full Text Available We have used the Simbad database and VizieR catalogue access tools to construct the observational color-absolute magnitude diagrams of nearby K-M dwarfs with precise Hipparcos parallaxes (σπ/π ≤ 0:05. Particular attention has been paid to removing unresolved double/multiple stars and variables. In addition to archival data, we have made use of nearly 2000 new radial-velocity measurements of K-M dwarfs to identify spectroscopic binary candidates. The main sequences, cleaned from unresolved binaries, variable stars, and old population stars which can also widen the sequence due to their presumably lower metallicity, were compared to available solar-metallicity models. Significant offsets of most of the model main-sequence lines are seen with respect to observational data, especially for the lower-mass stars. Only the location and slope of the Victoria-Regina and, partly, BaSTI isochrones match the data quite well.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. Modeling of macrosegregation caused by volumetric deformation in a coherent mushy zone

    Science.gov (United States)

    Nicolli, Lilia C.; Mo, Asbjørn; M'hamdi, Mohammed

    2005-02-01

    A two-phase volume-averaged continuum model is presented that quantifies macrosegregation formation during solidification of metallic alloys caused by deformation of the dendritic network and associated melt flow in the coherent part of the mushy zone. Also, the macrosegregation formation associated with the solidification shrinkage (inverse segregation) is taken into account. Based on experimental evidence established elsewhere, volumetric viscoplastic deformation (densification/dilatation) of the coherent dendritic network is included in the model. While the thermomechanical model previously outlined (M. M’Hamdi, A. Mo, and C.L. Martin: Metall. Mater. Trans. A, 2002, vol. 33A, pp. 2081-93) has been used to calculate the temperature and velocity fields associated with the thermally induced deformations and shrinkage driven melt flow, the solute conservation equation including both the liquid and a solid volume-averaged velocity is solved in the present study. In modeling examples, the macrosegregation formation caused by mechanically imposed as well as by thermally induced deformations has been calculated. The modeling results for an Al-4 wt pct Cu alloy indicate that even quite small volumetric strains (≈2 pct), which can be associated with thermally induced deformations, can lead to a macroscopic composition variation in the final casting comparable to that resulting from the solidification shrinkage induced melt flow. These results can be explained by the relatively large volumetric viscoplastic deformation in the coherent mush resulting from the applied constitutive model, as well as the relatively large difference in composition for the studied Al-Cu alloy in the solid and liquid phases at high solid fractions at which the deformation takes place.

  10. A Model for Organizational Intelligence in Islamic Azad University (Zone 8

    Directory of Open Access Journals (Sweden)

    Masoumeh Erfani Khanghahi

    2013-08-01

    Full Text Available Today organizations are faced with the rapidly changeable events in economical, technological, social, cultural and political environment. Successful and dynamic reaction of organizations depends on their ability to provide relevant information and to find, at the same time, adequate solutions to the problems they are faced with. In that sense, the attention of organizational theoreticians is focused on designing of intellectual abilities of organization and new concept in organizational theory has developed organizational intelligence (OI. In two decades ago, theoretical models have been developed and little research has been conducted. Having a model for defining and assessing the organizational status of an organization can be very helpful but the key questions facing every manager are; how can the level of collective intelligence be promoted? And what factors influence OI? Therefore this research carried out in order to assess OI and its factors influencing I.A.U. and provide a structural equation model. The subject of the study was 311 faculty members of I.A.U (Zone 8. Faculty members completed OI questionnaire (Cronbach's alpha=0.98, learning climate (Cronbach's alpha=0.94, multifactor leadership questionnaire (Cronbach's alpha =0.92 and organizational learning audit (Cronbach's alpha =0.94. Findings of this research showed that mean of organizational intelligence, organizational learning and learning culture were less than mean and transformational leadership was more than mean of questionnaire. Lisrel project software was applied for confirmatory factor analysis (CFA and structural equation modeling (SEM. Based on the tested structural equation model, transformational leadership style had direct impact on learning culture $(eta=0.78$, learning culture had a direct impact on OI $(eta=0.46$, organizational learning had a direct impact on OI $(eta=0.34$ and learning culture had a direct impact on organizational learning $(eta=0.96$. The

  11. 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

  12. 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.

  13. 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.

  14. Development of a Fatigue Model for Low Alloy Steels Using a Cycle-Dependent Cohesive Zone Law

    Directory of Open Access Journals (Sweden)

    Kyungmok Kim

    2014-03-01

    Full Text Available A fatigue model for SAE 4130 steels is developed using a cycle-dependent cohesive zone law. Reduction of fracture energy and degradation of stiffness are considered to describe failure resistance after certain number of cycles. The reduction rate of fracture energy is determined with experimental stress (S- number of cycles to failure (N scatter found in the literature. Three-dimensional finite element models containing a cohesive zone are generated with commercial software (ABAQUS. Calculated fatigue lives at different stress ratios are in good agreement with experimental ones. In addition, fatigue behavior of hardened SAE 4130 steels is predicted with that of normalized material.

  15. 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.)

  16. Determination of the relationship between major fault and zinc mineralization using fractal modeling in the Behabad fault zone, central Iran

    Science.gov (United States)

    Adib, Ahmad; Afzal, Peyman; Mirzaei Ilani, Shapour; Aliyari, Farhang

    2017-10-01

    The aim of this study is to determine a relationship between zinc mineralization and a major fault in the Behabad area, central Iran, using the Concentration-Distance to Major Fault (C-DMF), Area of Mineralized Zone-Distance to Major Fault (AMZ-DMF), and Concentration-Area (C-A) fractal models for Zn deposit/mine classification according to their distance from the Behabad fault. Application of the C-DMF and the AMZ-DMF models for Zn mineralization classification in the Behabad fault zone reveals that the main Zn deposits have a good correlation with the major fault in the area. The distance from the known zinc deposits/mines with Zn values higher than 29% and the area of the mineralized zone of more than 900 m2 to the major fault is lower than 1 km, which shows a positive correlation between Zn mineralization and the structural zone. As a result, the AMZ-DMF and C-DMF fractal models can be utilized for the delineation and the recognition of different mineralized zones in different types of magmatic and hydrothermal deposits.

  17. Distinct Element Method modelling of fold-related fractures in a multilayer sequence

    Science.gov (United States)

    Kaserer, Klemens; Schöpfer, Martin P. J.; Grasemann, Bernhard

    2017-04-01

    Natural fractures have a significant impact on the performance of hydrocarbon systems/reservoirs. In a multilayer sequence, both the fracture density within the individual layers and the type of fracture intersection with bedding contacts are key parameters controlling fluid pathways. In the present study the influence of layer stacking and interlayer friction on fracture density and connectivity within a folded sequence is systematically investigated using 2D Distinct Element Method modelling. Our numerical approach permits forward modelling of both fracture nucleation/propagation/arrest and (contemporaneous) frictional slip along bedding planes in a robust and mechanically sound manner. Folding of the multilayer sequence is achieved by enforcing constant curvature folding by means of a velocity boundary condition at the model base, while a constant overburden pressure is maintained at the model top. The modelling reveals that with high bedding plane friction the multilayer stack behaves mechanically as a single layer so that the neutral surface develops in centre of the sequence and fracture spacing is controlled by the total thickness of the folded sequence. In contrast, low bedding plane friction leads to decoupling of the individual layers (flexural slip folding) so that a neutral surface develops in the centre of each layer and fracture spacing is controlled by the thickness of the individual layers. The low interfacial friction models illustrate that stepping of fractures across bedding planes is a common process, which can however have two contrasting origins: The mechanical properties of the interface cause fracture stepping during fracture propagation. Originally through-going fractures are later offset by interfacial slip during folding. A combination of these two different origins may lead to (apparently) inconsistent fracture offsets across bedding planes within a flexural slip fold.

  18. 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.

  19. 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...

  20. Bayesian clustering of DNA sequences using Markov chains and a stochastic partition model.

    Science.gov (United States)

    Jääskinen, Väinö; Parkkinen, Ville; Cheng, Lu; Corander, Jukka

    2014-02-01

    In many biological applications it is necessary to cluster DNA sequences into groups that represent underlying organismal units, such as named species or genera. In metagenomics this grouping needs typically to be achieved on the basis of relatively short sequences which contain different types of errors, making the use of a statistical modeling approach desirable. Here we introduce a novel method for this purpose by developing a stochastic partition model that clusters Markov chains of a given order. The model is based on a Dirichlet process prior and we use conjugate priors for the Markov chain parameters which enables an analytical expression for comparing the marginal likelihoods of any two partitions. To find a good candidate for the posterior mode in the partition space, we use a hybrid computational approach which combines the EM-algorithm with a greedy search. This is demonstrated to be faster and yield highly accurate results compared to earlier suggested clustering methods for the metagenomics application. Our model is fairly generic and could also be used for clustering of other types of sequence data for which Markov chains provide a reasonable way to compress information, as illustrated by experiments on shotgun sequence type data from an Escherichia coli strain.

  1. 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...

  2. A nonlinear model for fluid flow in a multiple-zone composite reservoir including the quadratic gradient term

    International Nuclear Information System (INIS)

    Wang, Xiao-Lu; Fan, Xiang-Yu; Nie, Ren-Shi; Huang, Quan-Hua; He, Yong-Ming

    2013-01-01

    Based on material balance and Darcy's law, the governing equation with the quadratic pressure gradient term was deduced. Then the nonlinear model for fluid flow in a multiple-zone composite reservoir including the quadratic gradient term was established and solved using a Laplace transform. A series of standard log–log type curves of 1-zone (homogeneous), 2-zone and 3-zone reservoirs were plotted and nonlinear flow characteristics were analysed. The type curves governed by the coefficient of the quadratic gradient term (β) gradually deviate from those of a linear model with time elapsing. Qualitative and quantitative analyses were implemented to compare the solutions of the linear and nonlinear models. The results showed that differences of pressure transients between the linear and nonlinear models increase with elapsed time and β. At the end, a successful application of the theoretical model data against the field data shows that the nonlinear model will be a good tool to evaluate formation parameters more accurately. (paper)

  3. A study on in-situ measuring method and modeling technique of an unsaturated zone

    Energy Technology Data Exchange (ETDEWEB)

    Imai, Hisashi [Hazama Corp., Tsukuba, Ibaraki (Japan). Technical Research Inst.; Amemiya, Kiyoshi; Nishida, Kaoru; Lin, Weiren; Lei, Xinglin

    1997-03-01

    It is generally considered that an unsaturated zone is generated in the vicinity of a drift after excavation. In such a zone, invasion of air containing oxygen possibly changes geochemical environment (redox condition) of the rock mass. However, no measurement technique for quantitative understanding of this unsaturated zone is currently available. This study has been started to develop the measuring method in the several years. This year, fundamental information has been obtained through analysis, laboratory experiments using homogeneous rock samples and field measurement described below. (1) experiments on the mechanism of undersaturation in rock. (2) experiments on the measuring method of the extend of unsaturated zone. (author)

  4. 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.

  5. 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

  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. Adapting Better Interpolation Methods to Model Amphibious MT Data Along the Cascadian Subduction Zone.

    Science.gov (United States)

    Parris, B. A.; Egbert, G. D.; Key, K.; Livelybrooks, D.

    2016-12-01

    Magnetotellurics (MT) is an electromagnetic technique used to model the inner Earth's electrical conductivity structure. MT data can be analyzed using iterative, linearized inversion techniques to generate models imaging, in particular, conductive partial melts and aqueous fluids that play critical roles in subduction zone processes and volcanism. For example, the Magnetotelluric Observations of Cascadia using a Huge Array (MOCHA) experiment provides amphibious data useful for imaging subducted fluids from trench to mantle wedge corner. When using MOD3DEM(Egbert et al. 2012), a finite difference inversion package, we have encountered problems inverting, particularly, sea floor stations due to the strong, nearby conductivity gradients. As a work-around, we have found that denser, finer model grids near the land-sea interface produce better inversions, as characterized by reduced data residuals. This is partly to be due to our ability to more accurately capture topography and bathymetry. We are experimenting with improved interpolation schemes that more accurately track EM fields across cell boundaries, with an eye to enhancing the accuracy of the simulated responses and, thus, inversion results. We are adapting how MOD3DEM interpolates EM fields in two ways. The first seeks to improve weighting functions for interpolants to better address current continuity across grid boundaries. Electric fields are interpolated using a tri-linear spline technique, where the eight nearest electrical field estimates are each given weights determined by the technique, a kind of weighted average. We are modifying these weights to include cross-boundary conductivity ratios to better model current continuity. We are also adapting some of the techniques discussed in Shantsev et al (2014) to enhance the accuracy of the interpolated fields calculated by our forward solver, as well as to better approximate the sensitivities passed to the software's Jacobian that are used to generate a new

  8. Modeling pH-zone refining countercurrent chromatography: a dynamic approach.

    Science.gov (United States)

    Kotland, Alexis; Chollet, Sébastien; Autret, Jean-Marie; Diard, Catherine; Marchal, Luc; Renault, Jean-Hugues

    2015-04-24

    A model based on mass transfer resistances and acid-base equilibriums at the liquid-liquid interface was developed for the pH-zone refining mode when it is used in countercurrent chromatography (CCC). The binary separation of catharanthine and vindoline, two alkaloids used as starting material for the semi-synthesis of chemotherapy drugs, was chosen for the model validation. Toluene/CH3CN/water (4/1/5, v/v/v) was selected as biphasic solvent system. First, hydrodynamics and mass transfer were studied by using chemical tracers. Trypan blue only present in the aqueous phase allowed the determination of the parameters τextra and Pe for hydrodynamic characterization whereas acetone, which partitioned between the two phases, allowed the determination of the transfer parameter k0a. It was shown that mass transfer was improved by increasing both flow rate and rotational speed, which is consistent with the observed mobile phase dispersion. Then, the different transfer parameters of the model (i.e. the local transfer coefficient for the different species involved in the process) were determined by fitting experimental concentration profiles. The model accurately predicted both equilibrium and dynamics factors (i.e. local mass transfer coefficients and acid-base equilibrium constant) variation with the CCC operating conditions (cell number, flow rate, rotational speed and thus stationary phase retention). The initial hypotheses (the acid-base reactions occurs instantaneously at the interface and the process is mainly governed by mass transfer) are thus validated. Finally, the model was used as a tool for catharanthine and vindoline separation prediction in the whole experimental domain that corresponded to a flow rate between 20 and 60 mL/min and rotational speeds from 900 and 2100 rotation per minutes. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. 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

  10. 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

  11. 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

  12. 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

  13. Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity

    DEFF Research Database (Denmark)

    Asti, Lorenzo; Uguzzoni, Guido; Marcatili, Paolo

    2016-01-01

    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...... 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....

  14. Key Issues in Modeling of Complex 3D Structures from Video Sequences

    Directory of Open Access Journals (Sweden)

    Shengyong Chen

    2012-01-01

    Full Text Available Construction of three-dimensional structures from video sequences has wide applications for intelligent video analysis. This paper summarizes the key issues of the theory and surveys the recent advances in the state of the art. Reconstruction of a scene object from video sequences often takes the basic principle of structure from motion with an uncalibrated camera. This paper lists the typical strategies and summarizes the typical solutions or algorithms for modeling of complex three-dimensional structures. Open difficult problems are also suggested for further study.

  15. 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)

  16. 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.

  17. 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.

  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. A Comparison of Models Describing Heat Transfer in the Primary Cooling Zone of a Continuous Casting Machine

    Directory of Open Access Journals (Sweden)

    Miłkowska-Piszczek K.

    2015-04-01

    Full Text Available This paper presents the findings of research conducted concerning the determination of thermal boundary conditions for the steel continuous casting process within the primary cooling zone. A cast slab - with dimensions of 1100 mm×220 mm - was analysed, and models described in references were compared with the authors’ model. The presented models were verified on the basis of an industrial database. The research problem was solved with the finite element method using the ProCAST software package.

  20. 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.

  1. 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.

  2. Three-dimensional modelling of thermal stress in floating zone silicon crystal growth

    Science.gov (United States)

    Plate, Matiss; Krauze, Armands; Virbulis, Jānis

    2018-05-01

    During the growth of large diameter silicon single crystals with the industrial floating zone method, undesirable level of thermal stress in the crystal is easily reached due to the inhomogeneous expansion as the crystal cools down. Shapes of the phase boundaries, temperature field and elastic material properties determine the thermal stress distribution in the solid mono crystalline silicon during cylindrical growth. Excessive stress can lead to fracture, generation of dislocations and altered distribution of intrinsic point defects. Although appearance of ridges on the crystal surface is the decisive factor of a dislocation-free growth, the influence of these ridges on the stress field is not completely clear. Here we present the results of thermal stress analysis for 4” and 5” diameter crystals using a quasi-stationary three dimensional mathematical model including the material anisotropy and the presence of experimentally observed ridges which cannot be addressed with axis-symmetric models. The ridge has a local but relatively strong influence on thermal stress therefore its relation to the origin of fracture is hypothesized. In addition, thermal stresses at the crystal rim are found to increase for a particular position of the crystal radiation reflector.

  3. 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

  4. 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.

  5. 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.

  6. 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

  7. 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

  8. New Conceptual Model for Soil Treatment Units: Formation of Multiple Hydraulic Zones during Unsaturated Wastewater Infiltration.

    Science.gov (United States)

    Geza, Mengistu; Lowe, Kathryn S; Huntzinger, Deborah N; McCray, John E

    2013-07-01

    Onsite wastewater treatment systems are commonly used in the United States to reclaim domestic wastewater. A distinct biomat forms at the infiltrative surface, causing resistance to flow and decreasing soil moisture below the biomat. To simulate these conditions, previous modeling studies have used a two-layer approach: a thin biomat layer (1-5 cm thick) and the native soil layer below the biomat. However, the effect of wastewater application extends below the biomat layer. We used numerical modeling supported by experimental data to justify a new conceptual model that includes an intermediate zone (IZ) below the biomat. The conceptual model was set up using Hydrus 2D and calibrated against soil moisture and water flux measurements. The estimated hydraulic conductivity value for the IZ was between biomat and the native soil. The IZ has important implications for wastewater treatment. When the IZ was not considered, a loading rate of 5 cm d resulted in an 8.5-cm ponding. With the IZ, the same loading rate resulted in a 9.5-cm ponding. Without the IZ, up to 3.1 cm d of wastewater could be applied without ponding; with the IZ, only up to 2.8 cm d could be applied without ponding. The IZ also plays a significant role in soil moisture distribution. Without the IZ, near-saturation conditions were observed only within the biomat, whereas near-saturation conditions extended below the biomat with the IZ. Accurate prediction of ponding is important to prevent surfacing of wastewater. The degree of water and air saturation influences pollutant treatment efficiency through residence time, volatility, and biochemical reactions. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

  9. Hydrological functioning of West-African inland valleys explored with a critical zone model

    Science.gov (United States)

    Hector, B.; Cohard, J. M.; Séguis, L.; Peugeot, C.; Galle, S.

    2017-12-01

    In west Africa, recurrent floods are still a major issue, and hydropower has been recognized as an important development pathway. Furthermore, inland valleys carry an important agronomic potential, which could meet the necessary increase of the crop production associated with the strong demographic rates of the region. This can lead to land cover and subsequent hydrologic changes. However, the hydrological role of the inland valleys in the humid, hard rock-dominated Sudanian area is not yet well understood, specifically for streamflow (Q) generation processes. We address both the questions of the hydrological functioning of inland valleys in the Sudanian area of West-Africa and the impact of land cover changes on these systems through deterministic sensitivity experiments using a physically-based critical zone model (ParFlow-CLM) applied on a synthetic catchment which comprises an inland valley. The conceptual lithological/pedological model for the catchment includes the main features of such a hydrological elementary unit derived from the literature and from a previously published model based on data from a highly instrumented elementary catchment. Model forcings and parameters are based on data from the AMMA-CATCH observation service and multiple field experiments. We found yearly water budgets were much more sensitive to vegetation distribution than lithology features of the inland valley (presence of the low permeability layer commonly found below the inland valley and the hydrodynamic properties of upstream and lateral areas). Yearly evapotranspiration budget between a fully tree-covered and an herbaceous-covered catchment increases between 6 and 21% of the precipitation of the year (depending on the tested cases) which reduces considerably the yearly streamflow budgets ( 30%). On the other hand, the lithology distribution has clear impacts on the spatial distribution of water storage dynamics.

  10. Numerical Modeling of Water Fluxes in the Root Zone of Irrigated Pecan

    Science.gov (United States)

    Shukla, M. K.; Deb, S.

    2010-12-01

    Information is still limited on the coupled liquid water, water vapor, heat transport and root water uptake for irrigated pecan. Field experiments were conducted in a sandy loam mature pecan field in Las Cruces, New Mexico. Three pecan trees were chosen to monitor diurnal soil water content under the canopy (approximately half way between trunk and the drip line) and outside the drip line (bare spot) along a transect at the depths of 5, 10, 20, 40, and 60 cm using TDR sensors. Soil temperature sensors were installed at an under-canopy locations and bare spot to monitor soil temperature data at depths of 5, 10, 20, and 40 cm. Simulations of the coupled transport of liquid water, water vapor, and heat with and without root water uptake were carried out using the HYDRUS-1D code. Measured soil hydraulic and thermal properties, continuous meteorological data, and pecan characteristics, e.g. rooting depth, leaf area index, were used in the model simulations. Model calibration was performed for a 26-day period from DOY 204 through DOY 230, 2009 based on measured soil water content and soil temperature data at different soil depths, while the model was validated for a 90-day period from DOY 231 through DOY 320, 2009 at bare spot. Calibrated parameters were also used to apply the model at under-canopy locations for a 116-day period from DOY 204 to 320. HYDRUS-1D simulated water contents and soil temperatures correlated well with the measured data at each depth. Numerical assessment of various transport mechanisms and quantitative estimates of isothermal and thermal water fluxes with and without root water uptake in the unsaturated zone within canopy and bare spot is in progress and will be presented in the conference.

  11. Structure and Deformation in the Transpressive Zone of Southern California Inferred from Seismicity, Velocity, and Qp Models

    Science.gov (United States)

    Hauksson, E.; Shearer, P.

    2004-12-01

    We synthesize relocated regional seismicity and 3D velocity and Qp models to infer structure and deformation in the transpressive zone of southern California. These models provide a comprehensive synthesis of the tectonic fabric of the upper to middle crust, and the brittle ductile transition zone that in some cases extends into the lower crust. The regional seismicity patterns in southern California are brought into focus when the hypocenters are relocated using the double difference method. In detail, often the spatial correlation between background seismicity and late Quaternary faults is improved as the hypocenters become more clustered, and the spatial patterns are more sharply defined. Along some of the strike-slip faults the seismicity clusters decrease in width and form alignments implying that in many cases the clusters are associated with a single fault. In contrast, the Los Angeles Basin seismicity remains mostly scattered, reflecting a 3D distribution of the tectonic compression. We present the results of relocating 327,000 southern California earthquakes that occurred between 1984 and 2002. In particular, the depth distribution is improved and less affected by layer boundaries in velocity models or other similar artifacts, and thus improves the definition of the brittle ductile transition zone. The 3D VP and VP/VS models confirm existing tectonic interpretations and provide new insights into the configuration of the geological structures in southern California. The models extend from the US-Mexico border in the south to the Coast Ranges and Sierra Nevada in the north, and have 15 km horizontal grid spacing and an average vertical grid spacing of 4 km, down to 22 km depth. The heterogeneity of the crustal structure as imaged in both the VP and VP/VS models is larger within the Pacific than the North America plate, reflecting regional asymmetric variations in the crustal composition and past tectonic processes. Similarly, the relocated seismicity is

  12. 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.

  13. 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.

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

    Science.gov (United States)

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

    2015-02-01

    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. • MRI helps find prostate cancer in the anterior of the gland • Logistic regression models based on mp-MRI can classify prostate cancer • Computers can help confirm cancer in areas doctors are uncertain about.

  15. 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

  16. Improved work zone design guidelines and enhanced model of travel delays in work zones : Phase I, portability and scalability of interarrival and service time probability distribution functions for different locations in Ohio and the establishment of impr

    Science.gov (United States)

    2006-01-01

    The project focuses on two major issues - the improvement of current work zone design practices and an analysis of : vehicle interarrival time (IAT) and speed distributions for the development of a digital computer simulation model for : queues and t...

  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. 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.

  19. The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies.

    Science.gov (United States)

    Li, Guotian; Jain, Rashmi; Chern, Mawsheng; Pham, Nikki T; Martin, Joel A; Wei, Tong; Schackwitz, Wendy S; Lipzen, Anna M; Duong, Phat Q; Jones, Kyle C; Jiang, Liangrong; Ruan, Deling; Bauer, Diane; Peng, Yi; Barry, Kerrie W; Schmutz, Jeremy; Ronald, Pamela C

    2017-06-01

    The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitate functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake ( Oryza sativa ssp japonica ), which completes its life cycle in 9 weeks. We sequenced 1504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single-base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportion of loss-of-function mutations. We identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line. This result reveals the usefulness of the resource for efficient, cost-effective identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. This population complements other available mutant collections and gene-editing technologies. This work demonstrates how inexpensive next-generation sequencing can be applied to generate a high-density catalog of mutations. © 2017 American Society of Plant Biologists. All rights reserved.

  20. Novel expressed sequences identified in a model of androgen independent prostate cancer

    Directory of Open Access Journals (Sweden)

    Jones Steven JM

    2007-01-01

    Full Text Available Abstract Background Prostate cancer is the most frequently diagnosed cancer in American men, and few effective treatment options are available to patients who develop hormone-refractory prostate cancer. The molecular changes that occur to allow prostate cells to proliferate in the absence of androgens are not fully understood. Results Subtractive hybridization experiments performed with samples from an in vivo model of hormonal progression identified 25 expressed sequences representing novel human transcripts. Intriguingly, these 25 sequences have small open-reading frames and are not highly conserved through evolution, suggesting many of these novel expressed sequences may be derived from untranslated regions of novel transcripts or from non-coding transcripts. Examination of a large metalibrary of human Serial Analysis of Gene Expression (SAGE tags demonstrated that only three of these novel sequences had been previously detected. RT-PCR experiments confirmed that the 6 sequences tested were expressed in specific human tissues, as well as in clinical samples of prostate cancer. Further RT-PCR experiments for five of these fragments indicated they originated from large untranslated regions of unannotated transcripts. Conclusion This study underlines the value of using complementary techniques in the annotation of the human genome. The tissue-specific expression of 4 of the 6 clones tested indicates the expression of these novel transcripts is tightly regulated, and future work will determine the possible role(s these novel transcripts may play in the progression of prostate cancer.

  1. 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.

  2. 2-dimensional triplicated waveform modeling of the mantle transition zone beneath Northeast Asia

    Science.gov (United States)

    Lai, Y.; Chen, L.; Wang, T.

    2017-12-01

    The Mantle Transition Zone (MTZ) of Northeast Asia has long been investigated by geoscientists for its critical importance where the subducted Pacific slab is stagnant above the 660km discontinuity, accompanied by complicated mantle processes. Taking advantages of the frequent occurrent deep earthquakes in subduction zone and dense seismic arrays in Northeast China, we successfully constructed the fine-scale P and SH velocity structure of a narrow azimuthal fan area based on 2-Dimensional (2D) triplicated waveform modeling for three deep close earthquakes, in which the triplicated waveforms are very sensitive to MTZ velocity structure in general, particularly the morphology of the stagnant slab in Northeast Asia. In our 2D triplication study, for the first time, we show a quite consistent feature of a high velocity layer for both Vp and Vs with the thickness of 140km and the length of 1200km just atop the 660km discontinuity, the western edge of the stagnant slab intersect with the North-South Gravity Lineament in China and has the subducting age of 30 Ma. Compared with a quite normal Vp, the Shear wave velocity reduction of -0.5% in the slab and -2.5% in the upper MTZ is required to reconcile the SH waves featured by the broad BOD. The high Vp/Vs ratio beneath Northeast Asia may imply a water-rich MTZ with the H2O content of 0.1-0.3 wt%. Particularly, a low velocity anomaly of about 150km wide was detected in the overall high-velocity stagnant slab by both P and SH triplicated waveform modeling, with the velocity anomaly value of -1% and -3%, respectively. The gap/window in the stagnant slab may provide a passage for hot deeper mantle materials to penetrate through the thick slab and feed the surface Changbaishan volcano. We also speculate that the existence of such a gap can be the manifestation of the original heterogeneity in the subducted slab and will further exacerbatethe impending gravitational instability and speed up mantle avalanche.

  3. 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

  4. Using SST and land cover data from EO Missions for improved mesoscale modelling of the coastal zone

    DEFF Research Database (Denmark)

    Karagali, Ioanna; Floors, Rogier Ralph; Lea, Guillaume

    was to evaluate the uncertainty of the modelled wind in the coastal zone and further improve it. Moreover LIDAR measurements were used to evaluate the wind speed retrieval from high resolution SAR systems (Sentinel-1 and TerraSAR-X). The WRF model used a high-resolution satellite SST reanalysis product from...... be implemented in the meso-scale model to better represent the actual conditions in the study area. Such improvements are expected to strengthen the model’s ability to represent land- sea and air-sea interactions, the atmospheric stability and the local topographic features that partly affect the coastal zone......Existing wind measurements in near-shore and offshore areas are sparse and scarce, therefore simulations from state-of-the-art meso-scale models are used for wind resource predictions. In coastal and near-shore areas, models are inaccurate and uncertain, mainly because of numerical approximations...

  5. A self-adaptive finite element approach for simulation of mixed-mode delamination using cohesive zone models

    NARCIS (Netherlands)

    Samimi, M.; Dommelen, van J.A.W.; Geers, M.G.D.

    2011-01-01

    Oscillations observed in the load–displacement response of brittle interfaces modeled by cohesive zone elements in a quasi-static finite element framework are artifacts of the discretization. The typical limit points in this oscillatory path can be traced by application of path-following techniques,

  6. Dutch distribution zones of stable iodine tablets based on atmospheric dispersion modelling of accidental releases from nuclear power plants.

    NARCIS (Netherlands)

    Kok-Palma, Y.S.; Leenders, M.; Meulenbelt, J.

    2010-01-01

    Rapid administration of stable iodine is essential for the saturation and subsequent protection of the thyroid gland against the potential harm caused by radioiodines. This paper proposes the Dutch risk analysis that uses an atmospheric dispersion model to calculate the size of the zones around

  7. Development of Pipeline Database and CAD Model for Selection of Core Security Zone in Nuclear Power Plants

    International Nuclear Information System (INIS)

    Choi, Seong Soo; Kwon, Tae Gyun; Baek, Hun Hyun; Kwon, Min Jin

    2008-07-01

    The objective of the project is to develop the pipeline database which can be used for selection of core security zones considering safety significance of pipes and to develop CAD model for 3-dimensional visualization of core security zones, for the purpose of minimizing damage and loss, enforcing security and protection on important facilities, and improving plant design preparing against emergency situations such as physical terrors in nuclear power plants. In this study, the pipeline database is developed for selection of core security zones considering safety significance of safety class 1 and 2 pipes. The database includes the information on 'pipe-room information-surrogate component' mapping, initiating events which may occur and accident mitigation functions which may be damaged by the pipe failure, and the drawing information related to 2,270 pipe segments of 30 systems. For the 3-dimensional visualization of core security zones, the CAD models on the containment building and the auxiliary building are developed using 3-D MAX tool and the demo program which can visualize the direct-X model converted from the 3-D MAX model is also developed. In addition to this, the coordinate information of all the buildings and their rooms is generated using AUTO CAD tool in order to be used as an input for 3-dimensional browsing of the VIP program

  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. Modeling coding-sequence evolution within the context of residue solvent accessibility.

    Science.gov (United States)

    Scherrer, Michael P; Meyer, Austin G; Wilke, Claus O

    2012-09-12

    Protein structure mediates site-specific patterns of sequence divergence. In particular, residues in the core of a protein (solvent-inaccessible residues) tend to be more evolutionarily conserved than residues on the surface (solvent-accessible residues). Here, we present a model of sequence evolution that explicitly accounts for the relative solvent accessibility of each residue in a protein. Our model is a variant of the Goldman-Yang 1994 (GY94) model in which all model parameters can be functions of the relative solvent accessibility (RSA) of a residue. We apply this model to a data set comprised of nearly 600 yeast genes, and find that an evolutionary-rate ratio ω that varies linearly with RSA provides a better model fit than an RSA-independent ω or an ω that is estimated separately in individual RSA bins. We further show that the branch length t and the transition-transverion ratio κ also vary with RSA. The RSA-dependent GY94 model performs better than an RSA-dependent Muse-Gaut 1994 (MG94) model in which the synonymous and non-synonymous rates individually are linear functions of RSA. Finally, protein core size affects the slope of the linear relationship between ω and RSA, and gene expression level affects both the intercept and the slope. Structure-aware models of sequence evolution provide a significantly better fit than traditional models that neglect structure. The linear relationship between ω and RSA implies that genes are better characterized by their ω slope and intercept than by just their mean ω.

  10. Modeling coding-sequence evolution within the context of residue solvent accessibility

    Directory of Open Access Journals (Sweden)

    Scherrer Michael P

    2012-09-01

    Full Text Available Abstract Background Protein structure mediates site-specific patterns of sequence divergence. In particular, residues in the core of a protein (solvent-inaccessible residues tend to be more evolutionarily conserved than residues on the surface (solvent-accessible residues. Results Here, we present a model of sequence evolution that explicitly accounts for the relative solvent accessibility of each residue in a protein. Our model is a variant of the Goldman-Yang 1994 (GY94 model in which all model parameters can be functions of the relative solvent accessibility (RSA of a residue. We apply this model to a data set comprised of nearly 600 yeast genes, and find that an evolutionary-rate ratio ω that varies linearly with RSA provides a better model fit than an RSA-independent ω or an ω that is estimated separately in individual RSA bins. We further show that the branch length t and the transition-transverion ratio κ also vary with RSA. The RSA-dependent GY94 model performs better than an RSA-dependent Muse-Gaut 1994 (MG94 model in which the synonymous and non-synonymous rates individually are linear functions of RSA. Finally, protein core size affects the slope of the linear relationship between ω and RSA, and gene expression level affects both the intercept and the slope. Conclusions Structure-aware models of sequence evolution provide a significantly better fit than traditional models that neglect structure. The linear relationship between ω and RSA implies that genes are better characterized by their ω slope and intercept than by just their mean ω.

  11. 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

  12. Generation of 3-D hydrostratigraphic zones from dense airborne electromagnetic data to assess groundwater model prediction error

    Science.gov (United States)

    Christensen, N. K.; Minsley, B. J.; Christensen, S.

    2017-02-01

    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.

  13. 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.

  14. 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.

  15. 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

  16. From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems.

    Science.gov (United States)

    Garza, Daniel R; Dutilh, Bas E

    2015-11-01

    Microorganisms and the viruses that infect them are the most numerous biological entities on Earth and enclose its greatest biodiversity and genetic reservoir. With strength in their numbers, these microscopic organisms are major players in the cycles of energy and matter that sustain all life. Scientists have only scratched the surface of this vast microbial world through culture-dependent methods. Recent developments in generating metagenomes, large random samples of nucleic acid sequences isolated directly from the environment, are providing comprehensive portraits of the composition, structure, and functioning of microbial communities. Moreover, advances in metagenomic analysis have created the possibility of obtaining complete or nearly complete genome sequences from uncultured microorganisms, providing important means to study their biology, ecology, and evolution. Here we review some of the recent developments in the field of metagenomics, focusing on the discovery of genetic novelty and on methods for obtaining uncultured genome sequences, including through the recycling of previously published datasets. Moreover we discuss how metagenomics has become a core scientific tool to characterize eco-evolutionary patterns of microbial ecosystems, thus allowing us to simultaneously discover new microbes and study their natural communities. We conclude by discussing general guidelines and challenges for modeling the interactions between uncultured microorganisms and viruses based on the information contained in their genome sequences. These models will significantly advance our understanding of the functioning of microbial ecosystems and the roles of microbes in the environment.

  17. 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.

  18. 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

  19. Impacts of Quaternary History on Critical Zone Structure and Processes: Examples and a Conceptual Model from the Intensively Managed Landscapes Critical Zone Observatory

    Science.gov (United States)

    Anders, Alison M.; Bettis, E. Arthur; Grimley, David A.; Stumpf, Andrew J.; Kumar, Praveen

    2018-03-01

    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 alteration in

  20. 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

  1. Predictive modelling of fault related fracturing in carbonate damage-zones: analytical and numerical models of field data (Central Apennines, Italy)

    Science.gov (United States)

    Mannino, Irene; Cianfarra, Paola; Salvini, Francesco

    2010-05-01

    Permeability in carbonates is strongly influenced by the presence of brittle deformation patterns, i.e pressure-solution surfaces, extensional fractures, and faults. Carbonate rocks achieve fracturing both during diagenesis and tectonic processes. Attitude, spatial distribution and connectivity of brittle deformation features rule the secondary permeability of carbonatic rocks and therefore the accumulation and the pathway of deep fluids (ground-water, hydrocarbon). This is particularly true in fault zones, where the damage zone and the fault core show different hydraulic properties from the pristine rock as well as between them. To improve the knowledge of fault architecture and faults hydraulic properties we study the brittle deformation patterns related to fault kinematics in carbonate successions. In particular we focussed on the damage-zone fracturing evolution. Fieldwork was performed in Meso-Cenozoic carbonate units of the Latium-Abruzzi Platform, Central Apennines, Italy. These units represent field analogues of rock reservoir in the Southern Apennines. We combine the study of rock physical characteristics of 22 faults and quantitative analyses of brittle deformation for the same faults, including bedding attitudes, fracturing type, attitudes, and spatial intensity distribution by using the dimension/spacing ratio, namely H/S ratio where H is the dimension of the fracture and S is the spacing between two analogous fractures of the same set. Statistical analyses of structural data (stereonets, contouring and H/S transect) were performed to infer a focussed, general algorithm that describes the expected intensity of fracturing process. The analytical model was fit to field measurements by a Montecarlo-convergent approach. This method proved a useful tool to quantify complex relations with a high number of variables. It creates a large sequence of possible solution parameters and results are compared with field data. For each item an error mean value is

  2. Effect of Hydrogen Addition on Methane HCCI Engine Ignition Timing and Emissions Using a Multi-zone Model

    Science.gov (United States)

    Wang, Zi-han; Wang, Chun-mei; Tang, Hua-xin; Zuo, Cheng-ji; Xu, Hong-ming

    2009-06-01

    Ignition timing control is of great importance in homogeneous charge compression ignition engines. The effect of hydrogen addition on methane combustion was investigated using a CHEMKIN multi-zone model. Results show that hydrogen addition advances ignition timing and enhances peak pressure and temperature. A brief analysis of chemical kinetics of methane blending hydrogen is also performed in order to investigate the scope of its application, and the analysis suggests that OH radical plays an important role in the oxidation. Hydrogen addition increases NOx while decreasing HC and CO emissions. Exhaust gas recirculation (EGR) also advances ignition timing; however, its effects on emissions are generally the opposite. By adjusting the hydrogen addition and EGR rate, the ignition timing can be regulated with a low emission level. Investigation into zones suggests that NOx is mostly formed in core zones while HC and CO mostly originate in the crevice and the quench layer.

  3. 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...

  4. Characterizing and modelling the radionuclide transport properties of fracture zones in plutonic rocks of the Canadian Shield

    International Nuclear Information System (INIS)

    Davison, C.C.; Kozak, E.T.; Frost, L.H.; Everitt, R.A.; Brown, A.; Gascoyne, M.; Scheier, N.W.

    1999-01-01

    Plutonic rocks of the Canadian Shield were investigated as a potential host medium for nuclear fuel waste disposal of used CANDU nuclear fuel. Field investigations at several geologic research areas on the Shield have shown that major fracture zones are the dominant pathways for the large scale movement of groundwater and solutes through plutonic rock bodies. Because of this, a significant amount of the geoscience work has focused on methods to identify, characterize and model the radionuclide transport properties of major fracture zones in the fractured plutonic rocks of the Shield. In order to quantify the transport properties of such fracture zones a series of, groundwater tracer tests were performed over a period of several years in several major, low dipping fracture zones. Sixteen tracer tests were performed using dipole recirculation methods to evaluate transport over distance scales ranging from 17 m to 700 m. It was concluded that only tracer tests can provide useful estimates of the effective porosity and dispersivity characteristics of these large fracture zones in plutonic rocks of the Canadian Shield. (author)

  5. Real-time ultrasound imaging of irreversible electroporation in a porcine liver model adequately characterizes the zone of cellular necrosis.

    Science.gov (United States)

    Schmidt, Carl R; Shires, Peter; Mootoo, Mary

    2012-02-01

      Irreversible electroporation (IRE) is a largely non-thermal method for the ablation of solid tumours. The ability of ultrasound (US) to measure the size of the IRE ablation zone was studied in a porcine liver model.   Three normal pig livers were treated in vivo with a total of 22 ablations using IRE. Ultrasound was used within minutes after ablation and just prior to liver harvest at either 6 h or 24 h after the procedure. The area of cellular necrosis was measured after staining with nitroblue tetrazolium and the percentage of cell death determined by histomorphometry.   Visible changes in the hepatic parenchyma were apparent by US after all 22 ablations using IRE. The mean maximum diameter of the ablation zone measured by US during the procedure was 20.1 ± 2.7 mm. This compared with a mean cellular necrosis zone maximum diameter of 20.3 ± 2.9 mm as measured histologically. The mean percentage of dead cells within the ablation zone was 77% at 6 h and 98% at 24 h after ablation.   Ultrasound is a useful modality for measuring the ablation zone within minutes of applying IRE to normal liver tissue. The area of parenchymal change measured by US correlates with the area of cellular necrosis. © 2011 International Hepato-Pancreato-Biliary Association.

  6. 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.