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Sample records for modeling grain nitrogen

  1. Computing wheat nitrogen requirements from grain yield and protein maps

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Optical protein sensors and mass-flow yield monitors provide the opportunity to continuously measure grain quality and quantity during harvesting. This chapter illustrates how yield monitor and grain protein measurements may provide useful postharvest information for evaluating water or nitrogen (N)...

  2. Computing wheat nitrogen requirements from grain yield and protein maps

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Optical protein sensors and mass-flow yield monitors provide the opportunity to continuously measure grain quality and quantity during harvesting. This chapter illustrates how yield monitor and grain protein measurements may provide useful post-harvest information for evaluating water or nitrogen (...

  3. Lunar Nitrogen Problem: A peep at individual mineral grains

    NASA Astrophysics Data System (ADS)

    Sripada, V. S. Murty; Mahajan, R. R.

    2012-07-01

    The lunar surface is continuously receiving solar wind (SW) implantation, due to lack of atmosphere and intrinsic magnetic field. As a result, grains at the surface are loaded with SW nitrogen and noble gases, making the lunar soils an excellent means to understand the composition of these elements in the SW. A surprise finding since the Apollo era has been the over abundance of nitrogen in lunar soils by about an order of magnitude than expected from noble gases [ ^{14}N/ ^{36}Ar ˜ 360, as against 37 for SW]. In addition, the nitrogen isotopic composition of lunar soil ranges from -240 to +100 per mil, while pure SW nitrogen is -400 per mil. The excess N in lunar soils and its isotopic range still elude an explanation and termed as the ``Lunar Nitrogen Problem''. As would be expected, similar behavior of N and noble gases has been observed in lunar meteorites also. A simultaneous study of N and noble gases is necessary to better address this problem and such studies are sparse in literature. Also, lunar soil consists of an ensemble of different mineral grains, each receiving SW during multiple surface exposures due to regolith gardening and also each grain has different retentivity for SW implanted species. Bulk soil analysis will provide an average picture of the ensemble of grains it has. To better characterize the nitrogen components, it is more appropriate to analyse individual grains. We have developed a laser heating system with low blanks, attached with a mass spectrometer that can analyse all noble gases and nitrogen (in pico mole amounts) for isotopic composition, to investigate this problem. We have analysed individual mineral grains (weighing few hundred micro grams) from the lunar meteorite Y983885 for noble gases and nitrogen. So far we have studied ilmenite grains (analysis of other mineral grains is in progress) by stepwise heating method in an effort to resolve the multiple nitrogen components. The release pattern of N, δ ^{15}N and ^{14}N/ ^{36

  4. Grain metamorphism in polar nitrogen ice on Triton

    NASA Technical Reports Server (NTRS)

    Zent, Aaron P.; Mckay, Christopher P.; Pollack, James B.; Cruikshank, Dale P.

    1989-01-01

    The rate of nitrogen grain growth on putative N2-rich polar caps on Triton is calculated. For most plausible assumptions of independent variables, mean grain sizes in polar N2 are meter-scale. Triton's polar caps should constitute the definitive solar-system test bed for the process of ice grain metamorphism. Interpretation of data already in hand may require long path length through condensed N2, possibly due to grain growth. Upcoming Voyager data may clarify the situation, although possible complications in detecting a glaze of N2 ice exist.

  5. Effect of nitrogen and vanadium on austenite grain growth kinetics of a low alloy steel

    SciTech Connect

    Stasko, Renata . E-mail: rstasko@ap.Cracow.pl; Adrian, Henryk . E-mail: adrian@uci.agh.edu.pl; Adrian, Anna . E-mail: adrian@metal.agh.edu.pl

    2006-06-15

    Austenite grain growth kinetics in a steel containing 0.4% C, 1.8% Cr with different nitrogen contents (in the range 0.0038-0.0412%) and a micralloying addition of 0.078% V were investigated. The investigations were carried out in an austenitising temperature range of 840-1200 deg. C for 30 min. The results of investigations showed that N promotes the grain growth of austenite. The microalloying addition of vanadium protects the austenite grain growth because of carbonitride V(C,N) precipitation and the grain boundary pinning effect of undissolved particles of V(C,N). Using a thermodynamic model, the carbonitride V(C,N) content, undissolved at the austenitising temperature was calculated. At temperatures when a coarsening and dissolution of carbonitride occurs, the austenite grains start to growth. The effect of nitrogen on the type of chord length distribution of austenite grains was analysed.

  6. Relationship between grain crop yield potential and nitrogen response

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cereal grain fertilizer nitrogen (N) recommendations should conform to accepted theory. The objective of this study was to evaluate the relationship between yield potential (yield level) and N responsiveness in long-term winter wheat (Triticum aestivum L.) and maize (Zea mays L.) field experiments ...

  7. Modeling Grain Protein Formation in Relation to N Uptake and Remobilzation in Rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Grain protein concentration is an important quality index, and formation of grain protein largely depends on pre-anthesis nitrogen assimilation and post-anthesis nitrogen remobilization. In this study, we developed a simplified process model for simulating plant nitrogen uptake and remobilization a...

  8. [Nitrogen-containing mycotoxins of fungi of Aspergillus and Penicillium species infesting grain and its products].

    PubMed

    Reshetilova, T A; Vinokurova, N G; L'vova, L S

    1993-01-01

    The review summarizes the literature data on distribution of nitrogen-containing mycotoxins (alkaloids) among Penicillium and Aspergillus fungi infesting grain and products of grain processing. Particular attention in given to clavins (ergotalkaloids) and tremorgens (roquefortine, verruculogen, penitrems). PMID:8295871

  9. Organic Model of Interstellar Grains

    NASA Astrophysics Data System (ADS)

    Yabushita, S.; Inagaki, T.; Kawabe, T.; Wada, K.

    1987-04-01

    Extinction efficiency of grains is calculated from the Mie formula on the premise that the grains are of organic composition. The optical constants adopted for the calculations are those of E. coli, polystyrene and bovine albumin. The grain radius a is assumed to obey a distribution of the form N(a) ∝ a-α and the value of α is chosen so as to make the calculated extinction curve match the observed interstellar extinction curve. Although the calculated curve gives a reasonably good fit to the observed extinction curve for wavelengths less than 2100 Å, at longer wavelength regions, agreement is poor. It is concluded that another component is required for the organic model to be viable.

  10. Modeling Atmospheric Reactive Nitrogen

    EPA Science Inventory

    Nitrogen is an essential building block of all proteins and thus an essential nutrient for all life. Reactive nitrogen, which is naturally produced via enzymatic reactions, forest fires and lightning, is continually recycled and cascades through air, water, and soil media. Human ...

  11. The damaging effects of nitrogen ion beam implantation on upland cotton ( Gossypium hirsutum L.) pollen grains

    NASA Astrophysics Data System (ADS)

    Yu, Yanjie; Wu, Lijun; Wu, Yuejin; Wang, Qingya; Tang, Canming

    2008-09-01

    With the aim to study the effects of an ion beam on plant cells, upland cotton (Gossypium hirsutum L.) cultivar "Sumian 22" pollen grains were irradiated in vacuum (7.8 × 10-3 Pa) by low-energy nitrogen ions with an energy of 20 keV at various fluences ranging from 0.26 × 1016 to 0.78 × 1016 N+/cm2. The irradiation effects on pollen grains were tested, considering the ultrastructural changes in the exine and interior walls of pollen grains, their germination rate, the growth speed of the pollen tubes in the style, fertilization and boll development after the pistils were pollinated by the pollen grains which had been implanted with nitrogen ions. Nitrogen ions entered the pollen grains by etching and penetrating the exine and interior walls and destroying cell structures. A greater percentage of the pollen grains were destroyed as the fluence of N+ ions increased. Obviously, the nitrogen ion beam penetrated the exine and interior walls of the pollen grains and produced holes of different sizes. As the ion fluence increased, the amount and the density of pollen grain inclusions decreased and the size of the lacuna and starch granules increased. Pollen grain germination rates decreased with increasing ion fluence. The number of pollen tubes in the style declined with increased ion implantation into pollen grains, but the growth speed of the tubes did not change. All of the pollen tubes reached the end of the style at 13 h after pollination. This result was consistent with that of the control. Also, the weight and the diameter of the ovary decreased and shortened with increased ion beam implantation fluence. No evident change in the fecundation time of the ovule was observed. These results indicate that nitrogen ions can enter pollen grains and cause a series of biological changes in pollen grains of upland cotton.

  12. Nitrogen and Water Stress Impact on Hard Red Spring Wheat Crop Reflectance, Yield and Grain Quality

    NASA Astrophysics Data System (ADS)

    Reese, C. L.; Clay, D. E.; Beck, D.; Clay, S. A.; Seielstad, G.

    2007-12-01

    Water and nitrogen stress impact hard red spring wheat (Triticum aestivum) crop reflectance, yield and grain quality. To minimize yield losses from nitrogen (N) and water stress, it is essential to apply appropriate N in relation to water stress. The objective of this experiment was to determine the influence of N and water stress on hard red spring wheat crop reflectance, yield, and grain quality. Complete randomized block experiments were conducted in 2003, 2004 and 2004 in dryland and irrigated fields at three locations in central South Dakota. Treatments consisted of N rates and N application at different growth stages. Nitrogen fertilizer rates ranged from 0 to 200 kg ha-1. Nitrogen fertilizer application times were (1) planting; (2) planting and tillering (Feekes 2 -3) or (3) tillering (Feekes 2 -3). Reflectance data was collected using a Cropscan and a CropCircle radiometer. Reflectance data was collected at bare soil, tillering (Feekes 2-3) and flag leaf (Feekes 9-10). Carbon 13 isotopic discrimination (Ä) was used to determine yield loss to nitrogen or water stress. Reflectance data was compared to yield and Ä values or grain quality and Ä values. Correlation of crop reflectance (measured at the different growth stages and by the different radiometers) with yield loss to nitrogen or water and grain quality will be presented. Information presented will be used to make corrective nitrogen treatments and improve marketing decisions as related to grain quality.

  13. Evolutionary characteristics of a bimodal grain model. [interstellar grains

    NASA Technical Reports Server (NTRS)

    Greenberg, J. M.; Seung, S. H.

    1974-01-01

    A bimodal model of interstellar grains consisting of silicate cores of size approximately 0.06 micron with modified ice mantles of approximately 0.1 micron and very small particles of silicate and/or graphite of size approximately 0.005 micron is followed through various stages of evolution. Starting with a distribution of core-mantle cylinders producing average wavelength dependence of polarization and extinction, changes in physical and optical characteristics of the model are studied going first into regions of dense cloud condensation and coming out at the other end of star formation into young H2 regions. Physical justification is presented to show that not only in dense clouds must the core mantle grains be larger than normal, but also in young H2 regions.

  14. Interstellar Silicate Dust: Modeling and Grain Alignment

    NASA Astrophysics Data System (ADS)

    Das, Indrajit

    We examine some aspects of the alignment of silicate dust grains with respect to the interstellar magnetic field. First, we consider possible observational constraints on the magnetic properties of the grains. Second, we investigate the role of collisions with gas atoms and the production of H2 molecules on the grain surface in the alignment process when the grain is drifting in the gaseous medium. Paramagnetism associated with Fe content in the dust is thought to play a critical role in alignment. Min et al (2007) claimed that the Fe content of the silicate dust can be constrained by the shape of the 10 μm extinction feature. They found low Fe abundances, potentially posing problems for grain alignment theories. We revisit this analysis modeling the grains with irregularly shaped Gaussian Random Sphere (GRS). We give a comprehensive review of all the relevant constraints researchers apply and discuss their effects on the inferred mineralogy. Also, we extend this analysis to examine whether constraints can be placed on the presence of Fe-rich inclusions which could yield "super-paramagnetism". This possibility has long been speculated, but so far observational constraints are lacking. Every time a gas atom collides with a grain, the grain's angular momentum is slightly modified. Likewise when an H2 molecule forms on the surface and is ejected. Here also we model the grain with GRS shape and considered various scenarios about how the colliding gas particles depart the grain. We develop theoretical and computational tools to estimate the torques associated with these aforementioned events for a range of grain drift speeds---from low subsonic to high supersonic speeds. Code results were verified with spherical grain for which analytical results were available. Finally, the above torque results were used to study the grain rotational dynamics. Solving dynamical equations we examine how these torques influence the grain alignment process. Our analysis suggests that

  15. Investigating Nitrogen Pollution: Activities and Models.

    ERIC Educational Resources Information Center

    Green Teacher, 2000

    2000-01-01

    Introduces activities on nitrogen, nitrogen pollution from school commuters, nitrogen response in native and introduced species, and nutrient loading models. These activities help students determine the nitrogen contribution from their parents' cars, test native plant responses to nitrogen, and experiment with the results of removing water from…

  16. Nonequilibrium grain-boundary cosegregation of nitrogen and chromium in NiCrMoV steel

    NASA Astrophysics Data System (ADS)

    Zheng, Lei; Xu, Tingdong

    2005-12-01

    It is concluded in this article that nonequilibrium grain-boundary cosegregation (NCGS) of nitrogen and chromium occurs in NiCrMoV steel. That conclusion is reached from experimental observations of the parallel segregation isotherms and the maximum coverage of Cr and N at grain boundaries during the isotherms. This means that the nonequilibrium segregation of Cr induces that of N, in NiCrMoV steel.

  17. Influence of Nitrogen Content on Thermal Stability and Grain Growth Kinetics of Cryomilled Al Nanocomposites

    NASA Astrophysics Data System (ADS)

    Hashemi-Sadraei, L.; Mousavi, S. E.; Vogt, R.; Li, Y.; Zhang, Z.; Lavernia, E. J.; Schoenung, J. M.

    2012-02-01

    Nanocomposite powders of Al 5083/B4C were produced via cryogenic milling (cryomilling) of boron carbide (B4C) particles in Al 5083 matrix. The effect of milling time (up to 24 hours), and consequential nitrogen content, on grain growth in the nanocrystalline Al 5083 matrix was investigated. Thermal stability was studied at temperatures as high as ~0.96 T m and annealing times of up to 24 hours. Average grain sizes increased with time and temperature and tended to stabilize after longer annealing times, regardless of nitrogen content. Higher thermal stability was observed in samples with higher nitrogen content, with the average grain size remaining in the range of 30 nm, even after exposure to the most extreme annealing conditions. This behavior was attributed to the retarding effect that nitrides have on grain growth, as a result of pinning grain boundaries. Kinetic studies based on the Burke equation showed two thermally activated grain growth regimes—a low-temperature regime with an activation energy of 15 kJ/mol and a high-temperature regime with an activation energy of 58 kJ/mol.

  18. Nitrogen accumulation profiles of selected grain and vegetable crops: A bibliography (1940-1992)

    SciTech Connect

    Meischen, S.J.; Byrd, K.R.

    1994-10-01

    A bibliography of nitrogen accumulation profile data for 25 vegetable and grain crops reported between 1940 and 1992 is presented. The selected crops are asparagus, broccoli, brussels sprouts, cabbage, carrots, cauliflower, celery, corn, cotton, cucumber, field bean, field pea, garlic, lettuce, onions, and peppers.

  19. Utilizing existing sensor technology to predict spring wheat grain nitrogen concentration

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Obtaining optimum grain N concentration and yield in spring wheat (Triticum aestivum L.) can be problematic without proper nitrogen (N) fertilizer management. Sensor-based technologies have been used for an accurate and precise application of fertilizers. This technology has also been used to predic...

  20. Corn grain yield and nutrient uptake from application of enhanced-efficiency nitrogen fertilizers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Increasing demand for food and agricultural products directly impact the use of chemical fertilizers particularly nitrogen (N). This study examined corn grain yield and nutrient uptake resulting from applications of different N fertilizer sources, urea (U), urea-ammonium nitrate (UAN), ammonium nitr...

  1. Assessment of MARMOT Grain Growth Model

    SciTech Connect

    Fromm, B.; Zhang, Y.; Schwen, D.; Brown, D.; Pokharel, R.

    2015-12-01

    This report assesses the MARMOT grain growth model by comparing modeling predictions with experimental results from thermal annealing. The purpose here is threefold: (1) to demonstrate the validation approach of using thermal annealing experiments with non-destructive characterization, (2) to test the reconstruction capability and computation efficiency in MOOSE, and (3) to validate the grain growth model and the associated parameters that are implemented in MARMOT for UO2. To assure a rigorous comparison, the 2D and 3D initial experimental microstructures of UO2 samples were characterized using non-destructive Synchrotron x-ray. The same samples were then annealed at 2273K for grain growth, and their initial microstructures were used as initial conditions for simulated annealing at the same temperature using MARMOT. After annealing, the final experimental microstructures were characterized again to compare with the results from simulations. So far, comparison between modeling and experiments has been done for 2D microstructures, and 3D comparison is underway. The preliminary results demonstrated the usefulness of the non-destructive characterization method for MARMOT grain growth model validation. A detailed analysis of the 3D microstructures is in progress to fully validate the current model in MARMOT.

  2. Historical Synthesis-Analysis of Changes in Grain Nitrogen Dynamics in Sorghum

    PubMed Central

    Ciampitti, Ignacio A.; Prasad, P. V. Vara

    2016-01-01

    Unraveling the complexity underpinning nitrogen (N) use efficiency (NUE) can be physiologically approached via examining grain N sources and N internal efficiency (NIE) (yield to plant N content ratio). The main objective of this original research paper is to document and understand sorghum NUE and physiological mechanisms related to grain N dynamics. The study of different grain N sources, herein defined as the reproductive-stage shoot N remobilization (Remobilized N), reproductive-stage whole-plant N content (Reproductive N), and vegetative-stage whole-plant N content (Vegetative N), was pursued with the goal of synthesizing scientific literature for sorghum [Sorghum bicolor (L.) Moench] crop. A detailed literature review was performed and summarized on sorghum NUE (13 studies; >250 means) with three Eras, defined by the year of the study, named as Old Era (1965–1980); Transient Era (1981–2000); and New Era (2001–2014). The most remarkable outcomes from this synthesis were: (1) overall historical (1965–2014) cumulative yield gain was >0.5 Mg ha-1 (yields >7 Mg ha-1); (2) NIE did not change across the same time period; (3) grain N concentration (grain %N) accounted for a large proportion (63%) of the variation in NIE; (4) NIE increased as grain %N diminished, regardless of the Eras; (5) Remobilized N was strongly (>R2 0.6) and positively associated with Vegetative N, presenting a unique slope across Eras; and (6) a trade-off was documented for the Remobilized N and Reproductive N (with large variation, grain N demand, sink- (driven by grain number) and source-modulated (via restriction of grain N demand). PMID:27014299

  3. Fingerprints of carbon, nitrogen, and silicon isotopes in small interstellar SiC grains from the Murchison meteorite

    NASA Technical Reports Server (NTRS)

    Hoppe, Peter; Geiss, Johannes; Buehler, Fritz; Neuenschwander, Juerg; Amari, Sachiko; Lewis, Roy S.

    1993-01-01

    We report ion microprobe determinations of the carbon, nitrogen, and silicon isotopic compositions of small SiC grains from the Murchison CM2 chondrite. Analyses were made on samples containing variable numbers of grains and on 14 individual grains. In some cases the multiple-grain sample compositions were probably dominated by only one or two grains. Total ranges observed are given. Only a few grains show values near the range limits. Both the total ranges of carbon and nitrogen isotopic compositions, and even the narrower ranges typical for the majority of the grains, are similar to those observed for larger SiC grains. Two rare components appear to be present in the smaller-size fraction, one characterized by C-12/C-13 about 12-16 and the other by very heavy nitrogen. The carbon and nitrogen isotopic compositions qualitatively may reflect hydrostatic H-burning via the CNO cycle and He-burning in red giants, as well as explosive H-burning in novae. The silicon isotopic compositions of most grains qualitatively show what is the signature of He-burning. The silicon isotopic composition of one grain, however, suggests a different process.

  4. Coarse-grained modelling of surface nanobubbles

    NASA Astrophysics Data System (ADS)

    Grosfils, Patrick

    2013-05-01

    Surface nanobubbles are nanoscale gaseous objects that form on hydrophobic surfaces in contact with water. Understanding nanobubble formation and stability remains challenging due to the lack of appropriate theoretical framework and adequate modelling. Here we present a non-equilibrium coarse-grained model for nanobubbles at hydrophobic surfaces. The model is based on a lattice-gas model that has been proposed to understand the hydrophobic effect to which dynamical properties are added. The results presented demonstrate the ability of the model to reproduce the basic features of stable surface nanobubbles, which, thereby, supports the dynamical origin of these objects.

  5. Within-Leaf Nitrogen Allocation in Adaptation to Low Nitrogen Supply in Maize during Grain-Filling Stage

    PubMed Central

    Mu, Xiaohuan; Chen, Qinwu; Chen, Fanjun; Yuan, Lixing; Mi, Guohua

    2016-01-01

    Nitrogen (N) plays a vital role in photosynthesis and crop productivity. Maize plants may be able to increase physiological N utilization efficiency (NUtE) under low-N stress by increasing photosynthetic rate (Pn) per unit leaf N, that is, photosynthetic N-use efficiency (PNUE). In this study, we analyzed the relationship between PNUE and N allocation in maize ear-leaves during the grain-filling stage under low N (no N application) and high N (180 kg N ha-1) in a 2-year field experiment. Under low N, grain yield decreased while NUtE increased. Low-N treatment reduced the specific N content of ear leaves by 38% without significant influencing Pn, thereby increasing PNUE by 54%. Under low-N stress, maize plants tended to invest relatively more N into bioenergetics to sustain electron transport. In contrast, N allocated to chlorophyll and light-harvesting proteins was reduced to control excess electron production. Soluble proteins were reduced to shrink the N storage reservoir. We conclude that optimization of N allocation within leaves is a key adaptive mechanism to maximize Pn and crop productivity when N is limited during the grain-filling stage in maize under low-N conditions. PMID:27252716

  6. A new model of composite interstellar grains

    NASA Astrophysics Data System (ADS)

    Voshchinnikov, N. V.; Il'in, V. B.; Henning, Th.; Dubkova, D. N.

    The approach to model composite interstellar dust grains using the exact solution to the light scattering problem for multi-layered spheras suggested by Voshchinnikov & Mathis (1999) is further developed. Heterogeneous scatterers are represented by particles with very large numof shells each including a homogeneous layer per material considered (here amorphous carbon, astronomical silicate and vacuum). It is demonstrated that the scattering characteristics (cross-sections, albedo, asymmetry factor, etc.) well converge with the increase of the number of shells (layers) and each of the characteristics has the same limit independent of the layer order in the shells. The limit obviously corresponds to composite particles consisting of several well mixed materials. However, our results indicate that layered particles with even a few shells (layers) have the characteristics close enough to these limits. The applicability of the effective medium theory (EMT) mostly utilized earlier to approximate inhomogeneous interstellar grains is examined on the base of the model. It is shown that the used EMT rules generally have the accuracy of several percents in the whole range of particle sizes provided the porosity does not exceed about 50%. For larger porosity, the rules give wrong results. Using the model we reanalyze basics of interpretation of various manifestations of cosmic dust --- interstellar extinction, scattered radiation, infrared radiation, radiation pressure, etc. It is found that an increase of porosity typically leads to the increase of cross-sections, albedo and the sweeping efficiency of small grains as well as to the decrease of dust temperature and the strength of infrared bands (the EMT fails to produce these effects). We also conclude that pure iron even in negligible amount (<˜1 % by the volume fractis unlikely to form a layer on or inside a grain because of peculiar absorption of radiation by such particles. As an example of the potential of the model, it

  7. Coarse-grained modelling of supercoiled RNA

    NASA Astrophysics Data System (ADS)

    Matek, Christian; Šulc, Petr; Randisi, Ferdinando; Doye, Jonathan P. K.; Louis, Ard A.

    2015-12-01

    We study the behaviour of double-stranded RNA under twist and tension using oxRNA, a recently developed coarse-grained model of RNA. Introducing explicit salt-dependence into the model allows us to directly compare our results to data from recent single-molecule experiments. The model reproduces extension curves as a function of twist and stretching force, including the buckling transition and the behaviour of plectoneme structures. For negative supercoiling, we predict denaturation bubble formation in plectoneme end-loops, suggesting preferential plectoneme localisation in weak base sequences. OxRNA exhibits a positive twist-stretch coupling constant, in agreement with recent experimental observations.

  8. Predicting grain protein content of winter wheat using remote sensing data based on nitrogen status and water stress

    NASA Astrophysics Data System (ADS)

    Zhao, Chunjiang; Liu, Liangyun; Wang, Jihua; Huang, Wenjiang; Song, Xiaoyu; Li, Cunjun

    2005-05-01

    Advanced site-specific knowledge of grain protein content of winter wheat from remote sensing data would provide opportunities to manage grain harvest differently, and to maximize output by adjusting input in fields. In this study, remote sensing data were utilized to predict grain protein content. Firstly, the leaf nitrogen content at winter wheat anthesis stage was proved to be significantly correlated with grain protein content ( R2 = 0.36), and spectral indices significantly correlated to leaf nitrogen content at anthesis stage were potential indicators for grain protein content. The vegetation index, VI green, derived from the canopy spectral reflectance at green and red bands, was significantly correlated to the leaf nitrogen content at anthesis stage, and also highly significantly correlated to the final grain protein content ( R2 = 0.46). Secondly, the external conditions, such as irrigation, fertilization and temperature, had important influence on grain quality. Water stress at grain filling stage can increase grain protein content, and leaf water content is closely related to irrigation levels, therefore, the spectral indices correlated to leaf water content can be potential indicators for grain protein content. The spectral reflectance of TM channel 5 derived from canopy spectra or image data at grain filling stage was all significantly correlated to grain protein content ( R2 = 0.31 and 0.37, respectively). Finally, not only this study proved the feasibility of using remote sensing data to predict grain protein content, but it also provided a tentative prediction of the grain protein content in Beijing area using the reflectance image of TM channel 5.

  9. The strategy of the wheat plant in acclimating growth and grain production to nitrogen availability.

    PubMed

    Oscarson, P

    2000-11-01

    Two cultivars of spring wheat (Triticum aestivum L.) were grown to maturity in hydroponic cultures. Nitrogen accumulation was controlled by daily growth-limiting additions of nitrate together with all other nutrients in excess. Six different curves of N accumulation were used, with the same relative changes from day to day, but with different amplitudes. These curves were obtained by using the same mathematic formula of the N accumulation curves but varying the value of initial N content. The total amount of nitrogen added varied from 20 mg plant(-1) to 65 mg plant(-1). Plant bioproductivity showed a linear response to accumulated N. The number of grains per plant increased linearly with increased N availability whereas grain weights were essentially unaffected. Grain N concentrations and N content varied slightly, with highest values generally at the lower N availability levels. The quantitatively most important response to increased N availability was an increased number of earbearing tillers per plant. This varied from 0.1 tiller plant(-1) at maturity when given 20 mg N plant(-1), up to about 2 tillers plant(-1) when given 65 mg N plant(-1). Not all tillers that were initiated developed ears. The reduction of tillers seems to be one important mechanism in adapting plant productivity to N availability. Other individual characters influenced by N availability were straw height and the number of spikelets per spike. The two cultivars behaved in a qualitatively similar manner over the range of N availability even though they quantitatively differed in grain size, N concentrations and yield. PMID:11113170

  10. Sublimating grains model of cometary coma.

    NASA Astrophysics Data System (ADS)

    Faggi, S.; Tozzi, G. P.; Brucato, J. R.

    between organic and water icy grains by measuring their color and spectra. To understand solid cometary coma environment from observations it has been necessary to construct a theoretical model to connect each other the observational Sigma Af profiles with a theoretical profile achived from physical laws. In this talk we will present the architecture of the model and the results obtained from the comparison between theoretical Sigma Af profiles and observations of differents new Oort cloud comtes, in order to understand the nature of sublimating grains.

  11. Modeling Nitrogen Isotopes in the Global Ocean

    NASA Astrophysics Data System (ADS)

    Somes, C.; Schmittner, A.

    2008-12-01

    The nitrogen isotopic signal measured in marine sediments has the potential to be a valuable paleoceanographic proxy. It captures the response of different biological processes in the marine ecosystem including photosynthesis, nitrogen fixation, denitrification as well as processes within the food chain. A simple marine ecosystem model that includes the interactive cycling of nitrogen, phosphorus, and oxygen is augmented to record nitrogen isotopes in the University of Victoria Earth System Climate Model. New nitrogen isotopic tracers are employed at all trophic levels of the ecosystem. This includes the δ15N of nitrate, both classes of phytoplankton (nitrogen fixers and all other phytoplankton), zooplankton, and detritus. Despite a few shortcomings, it is shown that the nitrogen isotope model can capture the major trends observed in the modern climate. The ability to model nitrogen isotopes in a global coupled ocean- atmosphere-sea ice-ecosystem model gives us a unique opportunity to directly infer what physical and biological changes in the climate system are driving the δ15N signal on spatial and temporal scales. This is a valuable tool giving us tremendous insight on how to interpret the nitrogen isotopic signal.

  12. Coarse-Grain Modeling of Energetic Materials

    NASA Astrophysics Data System (ADS)

    Brennan, John

    2015-06-01

    Mechanical and thermal loading of energetic materials can incite responses over a wide range of spatial and temporal scales due to inherent nano- and microscale features. Many energy transfer processes within these materials are atomistically governed, yet the material response is manifested at the micro- and mesoscale. The existing state-of-the-art computational methods include continuum level approaches that rely on idealized field-based formulations that are empirically based. Our goal is to bridge the spatial and temporal modeling regimes while ensuring multiscale consistency. However, significant technical challenges exist, including that the multiscale methods linking the atomistic and microscales for molecular crystals are immature or nonexistent. To begin addressing these challenges, we have implemented a bottom-up approach for deriving microscale coarse-grain models directly from quantum mechanics-derived atomistic models. In this talk, a suite of computational tools is described for particle-based microscale simulations of the nonequilibrium response of energetic solids. Our approach builds upon recent advances both in generating coarse-grain models under high strains and in developing a variant of dissipative particle dynamics that includes chemical reactions.

  13. NEMA, a functional–structural model of nitrogen economy within wheat culms after flowering. II. Evaluation and sensitivity analysis

    PubMed Central

    Bertheloot, Jessica; Wu, Qiongli; Cournède, Paul-Henry; Andrieu, Bruno

    2011-01-01

    Background and Aims Simulating nitrogen economy in crop plants requires formalizing the interactions between soil nitrogen availability, root nitrogen acquisition, distribution between vegetative organs and remobilization towards grains. This study evaluates and analyses the functional–structural and mechanistic model of nitrogen economy, NEMA (Nitrogen Economy Model within plant Architecture), developed for winter wheat (Triticum aestivum) after flowering. Methods NEMA was calibrated for field plants under three nitrogen fertilization treatments at flowering. Model behaviour was investigated and sensitivity to parameter values was analysed. Key Results Nitrogen content of all photosynthetic organs and in particular nitrogen vertical distribution along the stem and remobilization patterns in response to fertilization were simulated accurately by the model, from Rubisco turnover modulated by light intercepted by the organ and a mobile nitrogen pool. This pool proved to be a reliable indicator of plant nitrogen status, allowing efficient regulation of nitrogen acquisition by roots, remobilization from vegetative organs and accumulation in grains in response to nitrogen treatments. In our simulations, root capacity to import carbon, rather than carbon availability, limited nitrogen acquisition and ultimately nitrogen accumulation in grains, while Rubisco turnover intensity mostly affected dry matter accumulation in grains. Conclusions NEMA enabled interpretation of several key patterns usually observed in field conditions and the identification of plausible processes limiting for grain yield, protein content and root nitrogen acquisition that could be targets for plant breeding; however, further understanding requires more mechanistic formalization of carbon metabolism. Its strong physiological basis and its realistic behaviour support its use to gain insights into nitrogen economy after flowering. PMID:21685429

  14. Coarse-grained modeling of DNA curvature

    NASA Astrophysics Data System (ADS)

    Freeman, Gordon S.; Hinckley, Daniel M.; Lequieu, Joshua P.; Whitmer, Jonathan K.; de Pablo, Juan J.

    2014-10-01

    The interaction of DNA with proteins occurs over a wide range of length scales, and depends critically on its local structure. In particular, recent experimental work suggests that the intrinsic curvature of DNA plays a significant role on its protein-binding properties. In this work, we present a coarse grained model of DNA that is capable of describing base-pairing, hybridization, major and minor groove widths, and local curvature. The model represents an extension of the recently proposed 3SPN.2 description of DNA [D. M. Hinckley, G. S. Freeman, J. K. Whitmer, and J. J. de Pablo, J. Chem. Phys. 139, 144903 (2013)], into which sequence-dependent shape and mechanical properties are incorporated. The proposed model is validated against experimental data including melting temperatures, local flexibilities, dsDNA persistence lengths, and minor groove width profiles.

  15. AEROBIC DENITRIFICATION: IMPLICATIONS FOR NITROGEN FATE MODELING

    EPA Science Inventory

    In the Mississippi, as well as most nitrogen-degraded rivers and streams, NO3- is the dominant N species and therefore understanding its biogeochemical behavior is critical for accurate nitrogen fate modeling. To our knowledge this is the first work to report aerobic denitrificat...

  16. Model exchange-spring nanocomposite magnetic grains

    NASA Astrophysics Data System (ADS)

    Szlaferek, A.

    2004-05-01

    The magnetization reversal in nanocomposite two-phase grains embedded in a soft magnetic matrix is calculated using Brown's equation. The grains are spherical, consisting of a soft core surrounded by a hard shell. The calculation yields nonlinear algebraic expressions whose solutions describe the nucleation field as a function of the geometrical and magnetic parameters of the grains. The magnetization reversal depends not only on the total grain size but also on the shell thickness.

  17. Modeling nitrogen fluxes in Germany - where does the nitrogen go?

    NASA Astrophysics Data System (ADS)

    Klement, Laura; Bach, Martin; Breuer, Lutz

    2016-04-01

    According to the latest inventory of the EU Water Framework Directive, 26.3% of German groundwater bodies are in a poor chemical state regarding nitrate. Additionally, the EU initiated infringement proceedings against Germany for not meeting the quality standards of the EU Nitrate Directive. Agriculture has been determined as the main source of nitrate pollution due to over-fertilization and regionally high density of livestock farming. The nitrogen balance surplus is commonly used as an indicator characterizing the potential of nitrate leaching into groundwater bodies and thus also serves as a foundation to introduce legislative restrictions or to monitor the success of mitigation measures. Currently, there is an ongoing discussion which measures are suitable for reducing the risk of nitrate leaching and also to what extent. However, there is still uncertainty about just how much the nitrogen surplus has to be reduced to meet the groundwater quality standards nationwide. Therefore, the aims of our study were firstly to determine the level of the nitrogen surplus that would be acceptable at the utmost and secondly whether the currently discussed target value of 30 kg N per hectare agricultural land for the soil surface nitrogen balance would be sufficient. The models MONERIS (Modeling Nutrient Emissions in River System) and MoRE (Modelling of Regionalized Emissions), the latter based on the first, are commonly used for estimating nitrogen loads into the river system in Germany at the mesoscale, as well as the effect of mitigation measures in the context of the EU directive 2008/105/EC (Environmental quality standards applicable to surface water). We used MoRE to calculate nitrate concentration for 2759 analytical units in Germany. Main factors are the surplus of the soil surface nitrogen balance, the percolation rate and an exponent representing the denitrification in the vadose zone. The modeled groundwater nitrate concentrations did not correspond to the regional

  18. Optimizing nitrogen management for soft red winter wheat yield, grain protein, and grain quality using precision agriculture and remote sensing techniques

    NASA Astrophysics Data System (ADS)

    Farrer, Dianne Carter

    The purpose of this research was to improve the management of soft red winter wheat (Triticum aestivum L.) in North Carolina. There were three issues addressed; the quality of the grain as affected by delayed harvest, explaining grain protein variability through nitrogen (N) management, and developing N recommendations at growth stage (GS) 30 using aerial color infrared (CIR) photography. The impact of delayed harvest on grain yield, test weight, grain protein, and 20 milling and baking quality parameters was studied in three trials in 2002 and three trials in 2003. Yield was significantly reduced in three out of five trials due to dry, warm environments, possibly indicating shattering. Test weights were significantly reduced in five out of six trials and were positively correlated to the number of precipitation events and to the number of days between harvests, indicating the negative effects of wetting and drying cycles. Grain protein was not affected by delayed harvest. Of the 20 quality parameters investigated, flour falling number, clear flour, and farinograph breakdown times were significantly reduced due to delayed harvest, while grain deoxynivalenol (DON) levels increased with a delayed harvest. Grain protein content in soft red winter wheat is highly variable across years and environments. A second study examined the effects of different nitrogen (N) fertilizer rates and times of application on grain protein variability. Seven different environments were utilized in this study. Though environment contributed about 23% of grain protein variability, the majority of that variability (52%) was attributed to N management. It was found that as grain protein levels increased at higher N rates, so did overall protein variability as indicated by the three stability indexes employed. In addition, applying the majority of total N at growth stage (GS) 30 decreased grain protein stability. Site-specific N management systems using remote sensing techniques can

  19. Kinetic Modeling of Sunflower Grain Filling and Fatty Acid Biosynthesis.

    PubMed

    Durruty, Ignacio; Aguirrezábal, Luis A N; Echarte, María M

    2016-01-01

    Grain growth and oil biosynthesis are complex processes that involve various enzymes placed in different sub-cellular compartments of the grain. In order to understand the mechanisms controlling grain weight and composition, we need mathematical models capable of simulating the dynamic behavior of the main components of the grain during the grain filling stage. In this paper, we present a non-structured mechanistic kinetic model developed for sunflower grains. The model was first calibrated for sunflower hybrid ACA855. The calibrated model was able to predict the theoretical amount of carbohydrate equivalents allocated to the grain, grain growth and the dynamics of the oil and non-oil fraction, while considering maintenance requirements and leaf senescence. Incorporating into the model the serial-parallel nature of fatty acid biosynthesis permitted a good representation of the kinetics of palmitic, stearic, oleic, and linoleic acids production. A sensitivity analysis showed that the relative influence of input parameters changed along grain development. Grain growth was mostly affected by the specific growth parameter (μ') while fatty acid composition strongly depended on their own maximum specific rate parameters. The model was successfully applied to two additional hybrids (MG2 and DK3820). The proposed model can be the first building block toward the development of a more sophisticated model, capable of predicting the effects of environmental conditions on grain weight and composition, in a comprehensive and quantitative way. PMID:27242809

  20. Kinetic Modeling of Sunflower Grain Filling and Fatty Acid Biosynthesis

    PubMed Central

    Durruty, Ignacio; Aguirrezábal, Luis A. N.; Echarte, María M.

    2016-01-01

    Grain growth and oil biosynthesis are complex processes that involve various enzymes placed in different sub-cellular compartments of the grain. In order to understand the mechanisms controlling grain weight and composition, we need mathematical models capable of simulating the dynamic behavior of the main components of the grain during the grain filling stage. In this paper, we present a non-structured mechanistic kinetic model developed for sunflower grains. The model was first calibrated for sunflower hybrid ACA855. The calibrated model was able to predict the theoretical amount of carbohydrate equivalents allocated to the grain, grain growth and the dynamics of the oil and non-oil fraction, while considering maintenance requirements and leaf senescence. Incorporating into the model the serial-parallel nature of fatty acid biosynthesis permitted a good representation of the kinetics of palmitic, stearic, oleic, and linoleic acids production. A sensitivity analysis showed that the relative influence of input parameters changed along grain development. Grain growth was mostly affected by the specific growth parameter (μ′) while fatty acid composition strongly depended on their own maximum specific rate parameters. The model was successfully applied to two additional hybrids (MG2 and DK3820). The proposed model can be the first building block toward the development of a more sophisticated model, capable of predicting the effects of environmental conditions on grain weight and composition, in a comprehensive and quantitative way. PMID:27242809

  1. 3D modeling of metallic grain growth

    SciTech Connect

    George, D.; Carlson, N.; Gammel, J.T.; Kuprat, A.

    1999-06-01

    This paper will describe simulating metallic grain growth using the Gradient Weighted Moving Finite Elements code, GRAIN3D. The authors also describe the set of mesh topology change operations developed to respond to changes in the physical topology such as the collapse of grains and to maintain uniform calculational mesh quality. Validation of the method is demonstrated by comparison to analytic calculations. The authors present results of multigrain simulations where grain boundaries evolve by mean curvature motion and include results which incorporate grain boundary orientation dependence.

  2. Ion Implantation into Presolar Grains: A Theoretical Model

    NASA Astrophysics Data System (ADS)

    Verchovsky, A. B.; Wright, I. P.; Pillinger, C. T.

    A numerical model for ion implantation into spherical grains in free space has been developed. It can be applied to single grains or collections of grains with known grain-size distributions. Ion-scattering effects were taken into account using results of computer simulations. Possible isotope and element fractionation of the implanted species was investigated using this model. The astrophysical significance of the model lies in the possible identification of energetically different components (such as noble gases) implanted into presolar grains (such as diamond and SiC) and in establishing implantation energies of the components.

  3. Coarse-grained models for biological simulations

    NASA Astrophysics Data System (ADS)

    Wu, Zhe; Cui, Qiang; Yethiraj, Arun

    2011-03-01

    The large timescales and length-scales of interest in biophysics preclude atomistic study of many systems and processes. One appealing approach is to use coarse-grained (CG) models where several atoms are grouped into a single CG site. In this work we describe a new CG force field for lipids, surfactants, and amino acids. The topology of CG sites is the same as in the MARTINI force field, but the new model is compatible with a recently developed CG electrostatic water (Big Multiple Water, BMW) model. The model not only gives correct structural, elastic properties and phase behavior for lipid and surfactants, but also reproduces electrostatic properties at water-membrane interface that agree with experiment and atomistic simulations, including the potential of mean force for charged amino acid residuals at membrane. Consequently, the model predicts stable attachment of cationic peptides (i.e., poly-Arg) on lipid bilayer surface, which is not shown in previous models with non-electrostatic water.

  4. Visible injury and nitrogen metabolism of rice leaves under ozone stress, and effect on sugar and protein contents in grain

    NASA Astrophysics Data System (ADS)

    Huang, Y. Z.; Sui, L. H.; Wang, W.; Geng, C. M.; Yin, B. H.

    2012-12-01

    Effect of ozone on the visible injury, nitrogen metabolism of rice leaves, and sugar and protein contents in rice grain was carried out by the open-top chamber. The results indicated that ozone stress caused obvious injury in rice leaves. The increase in ozone concentration had significant influence on the nitrate reductase activity in rice leaves. At the ozone concentration of 40, 80 and 120 nL L-1, the nitrate reductase activities in rice leaves in the tillering stage, the jointing stage, the heading stage and milk stage were separately reduced by 25.3-86.3%, 57.4-97.8%, 91.0-99.3% and 89.5-96.7% compared with those in the control treatment. As ozone concentration increased, the contents of ammonium nitrogen and nitrate nitrogen in rice leaves were obviously reduced. Ozone stress also had an influence on the contents of sugar and protein in rice grain. The stress of high ozone concentration (120 nL L-1) caused the starch content in grain to reduce by 15.8% than that in the control treatment, but total soluble sugars in grain was actually enhanced by 47.5% compared to that in the control treatment. The contents of albumin and glutenin in rice grain increased with increasing the ozone concentration, and prolamin and crude protein contents in rice grain increased only at the higher ozone concentration. Under ozone concentration of 120 nL L-1, the contents of albumin, glutenin and crude protein in rice grain were increased respectively by 23.1%, 21.0% and 21.1% compared with those in the control treatment. The result suggested that ozone tress has an influence on nitrogen metabolism of rice leaves and grain quality.

  5. Grain size modeling and optimization of rotary forged Alloy 718

    SciTech Connect

    Domblesky, J.P.; Shivpuri, R.

    1997-04-01

    The study presented describes the simulation procedure and methodology used to develop two models for predicting recrystallized grain size in Alloy 718 billet. To simulate multiple pass forging of billet, controlled, high temperature compression testing was used to apply alternate deformation and dwell cycles to Alloy 718 specimens. Grain size obtained by simulation was found to be in excellent agreement with grain size from forged billet when cooling rate was included. The study also revealed that strain per pass and forging temperature were the predominant factors in controlling the recrystallized grain size. Both models were found to accurately predict the recrystallized grain size obtained by compression tests performed at super-solvus temperatures.

  6. Use of the Stable Nitrogen Isotope to Reveal the Source-Sink Regulation of Nitrogen Uptake and Remobilization during Grain Filling Phase in Maize.

    PubMed

    Yang, Lan; Guo, Song; Chen, Qinwu; Chen, Fanjun; Yuan, Lixing; Mi, Guohua

    2016-01-01

    Although the remobilization of vegetative nitrogen (N) and post-silking N both contribute to grain N in maize (Zea mays L.), their regulation by grain sink strength is poorly understood. Here we use 15N labeling to analyze the dynamic behaviors of both pre- and post-silking N in relation to source and sink manipulation in maize plants. The results showed that the remobilization of pre-silking N started immediately after silking and the remobilized pre-silking N had a greater contribution to grain N during early grain filling, with post-silking N importance increasing during the later filling stage. The amount of post-silking N uptake was largely driven by post-silking dry matter accumulation in both grain as well as vegetative organs. Prevention of pollination during silking had less effect on post-silking N uptake, as a consequence of compensatory growth of stems, husk + cob and roots. Also, leaves continuously export N even though grain sink was removed. The remobilization efficiency of N in the leaf and stem increased with increasing grain yield (hence N requirement). It is suggested that the remobilization of N in the leaf is controlled by sink strength but not the leaf per se. Enhancing post-silking N uptake rather than N remobilization is more likely to increase grain N accumulation. PMID:27606628

  7. Genetic Basis for Variation in Wheat Grain Yield in Response to Varying Nitrogen Application

    PubMed Central

    Mahjourimajd, Saba; Taylor, Julian; Sznajder, Beata; Timmins, Andy; Shahinnia, Fahimeh; Rengel, Zed; Khabaz-Saberi, Hossein; Kuchel, Haydn; Okamoto, Mamoru

    2016-01-01

    Nitrogen (N) is a major nutrient needed to attain optimal grain yield (GY) in all environments. Nitrogen fertilisers represent a significant production cost, in both monetary and environmental terms. Developing genotypes capable of taking up N early during development while limiting biomass production after establishment and showing high N-use efficiency (NUE) would be economically beneficial. Genetic variation in NUE has been shown previously. Here we describe the genetic characterisation of NUE and identify genetic loci underlying N response under different N fertiliser regimes in a bread wheat population of doubled-haploid lines derived from a cross between two Australian genotypes (RAC875 × Kukri) bred for a similar production environment. NUE field trials were carried out at four sites in South Australia and two in Western Australia across three seasons. There was genotype-by-environment-by-treatment interaction across the sites and also good transgressive segregation for yield under different N supply in the population. We detected some significant Quantitative Trait Loci (QTL) associated with NUE and N response at different rates of N application across the sites and years. It was also possible to identify lines showing positive N response based on the rankings of their Best Linear Unbiased Predictions (BLUPs) within a trial. Dissecting the complexity of the N effect on yield through QTL analysis is a key step towards elucidating the molecular and physiological basis of NUE in wheat. PMID:27459317

  8. Genetic Basis for Variation in Wheat Grain Yield in Response to Varying Nitrogen Application.

    PubMed

    Mahjourimajd, Saba; Taylor, Julian; Sznajder, Beata; Timmins, Andy; Shahinnia, Fahimeh; Rengel, Zed; Khabaz-Saberi, Hossein; Kuchel, Haydn; Okamoto, Mamoru; Langridge, Peter

    2016-01-01

    Nitrogen (N) is a major nutrient needed to attain optimal grain yield (GY) in all environments. Nitrogen fertilisers represent a significant production cost, in both monetary and environmental terms. Developing genotypes capable of taking up N early during development while limiting biomass production after establishment and showing high N-use efficiency (NUE) would be economically beneficial. Genetic variation in NUE has been shown previously. Here we describe the genetic characterisation of NUE and identify genetic loci underlying N response under different N fertiliser regimes in a bread wheat population of doubled-haploid lines derived from a cross between two Australian genotypes (RAC875 × Kukri) bred for a similar production environment. NUE field trials were carried out at four sites in South Australia and two in Western Australia across three seasons. There was genotype-by-environment-by-treatment interaction across the sites and also good transgressive segregation for yield under different N supply in the population. We detected some significant Quantitative Trait Loci (QTL) associated with NUE and N response at different rates of N application across the sites and years. It was also possible to identify lines showing positive N response based on the rankings of their Best Linear Unbiased Predictions (BLUPs) within a trial. Dissecting the complexity of the N effect on yield through QTL analysis is a key step towards elucidating the molecular and physiological basis of NUE in wheat. PMID:27459317

  9. The Grain Structure of Castings: Some Aspects of Modelling

    NASA Technical Reports Server (NTRS)

    Hellawell, A.

    1995-01-01

    The efficacy of the modelling of the solidification of castings is typically tested against observed cooling curves and the final grain structures and sizes. Without thermo solutal convection, equiaxed grain formation is promoted by introduction of heterogeneous substrates into the melt, as grain refiners. With efficient thermo solutal convection, dendrite fragments from the mushy zone can act as an intrinsic source of equiaxed grains and resort to grain refining additions is unnecessary. The mechanisms of dendrite fragmentation and transport of these fragments are briefly considered.

  10. Grain formation around carbon stars. 1: Stationary outflow models

    NASA Technical Reports Server (NTRS)

    Egan, Michael P.; Leung, Chun Ming

    1995-01-01

    Asymptotic giant branch (AGB) stars are known to be sites of dust formation and undergo significant mass loss. The outflow is believed to be driven by radiation pressure on grains and momentum coupling between the grains and gas. While the physics of shell dynamics and grain formation are closely coupled, most previous models of circumstellar shells have treated the problem separately. Studies of shell dynamics typically assume the existence of grains needed to drive the outflow, while most grain formation models assume a constant veolcity wind in which grains form. Furthermore, models of grain formation have relied primarily on classical nucleation theory instead of using a more realistic approach based on chemical kinetics. To model grain formation in carbon-rich AGB stars, we have coupled the kinetic equations governing small cluster growth to moment equations which determine the growth of large particles. Phenomenological models assuming stationary outflow are presented to demonstrate the differences between the classical nucleation approach and the kinetic equation method. It is found that classical nucleation theory predicts nucleation at a lower supersaturation ratio than is predicted by the kinetic equations, resulting in significant differences in grain properties. Coagulation of clusters larger than monomers is unimportant for grain formation in high mass-loss models but becomes more important to grain growth in low mass-loss situations. The properties of the dust grains are altered considerably if differential drift velocities are ignored in modeling grain formation. The effect of stellar temperature, stellar luminosity, and different outflow velocities are investigated. The models indicate that changing the stellar temperature while keeping the stellar luminosity constant has little effect on the physical parameters of the dust shell formed. Increasing the stellar luminosity while keeping the stellar temperature constant results in large differences in

  11. A First Look at Graphite Grains from Orgueil: Morphology, Carbon, Nitrogen and Neon Isotopic Compositions of Individual, Chemically Separated Grains

    NASA Technical Reports Server (NTRS)

    Pravdivtseva, O.; Zinner, E.; Meshik, A. P.; Hohenberg, C. M.; Walker, R. W.

    2004-01-01

    Presolar graphite in Murchison has been extensively studied. It is characterized by a unique Ne isotopic composition, known as the Ne-E(L) component. According to studies by Huss and Lewis, the concentration of Ne-E(L) in Orgueil is about one order of magnitude higher than in Murchison, when normalized to the matrix. This could be due to a higher presolar graphite abundance in Orgueil, or due to a higher Ne-E concentrations per grain. The Ne isotopic compositions in individual presolar graphite grains from Murchison have been measured before. It was shown, that a third of the grains have detectable excesses in 22Ne, characteristic of the Ne-E(L) component. One grain in a hundred had a Ne-22 concentration two orders of magnitude higher than blank.

  12. [Effects of water-nitrogen interaction on the contents and components of protein and starch in wheat grains].

    PubMed

    Fu, Xue-Li; Wang, Chen-Yang; Guo, Tian-Cai; Zhu, Yun-Ji; Ma, Dong-Yun; Wang, Yong-Hua

    2008-02-01

    With wheat cultivars Yumai 34 (strong-gluten wheat) and Yumai 50 (weak-gluten wheat) as test materials, a field experiment was conducted to study the effects of three irrigation treatments (irrigation at jointing stage, at jointing and grain-filling stages, and at jointing, grain-filling, and pre-maturing stages), three nitrogen application rates (0, 150, and 270 kg x hm(-2)), and their combinations on the contents and components of protein and starch in wheat grains. The results showed that for strong-gluten wheat cultivar Yumai 34, applying 270 kg x hm(-2) of N increased the total content of protein and the contents of albumin, gliadin and glutelin, and enhanced the glutelin/gliadin ratio. This application rate of nitrogen also increased the total content of starch and the content of amylopectin, and decreased the amylose/amylopetin ratio. For weak-gluten wheat cultivar Yumai 50, applying 150 kg x hm(-2) of N increased the contents of albumin and gliadin, and decreased the contents of globulin and glutelin and the glutelin/gliadin ratio. The amylopectin and starch contents also increased when the N application rate was 150 kg x hm(-2). Non-N fertilization or applying 270 kg x hm(-2) of N decreased the accumulation of protein and starch, and resulted in a decrease of grain yield. Among the irrigation treatments, irrigation at jointing and grain-filling stages promoted the accumulation of protein and starch in grains and increased the grain yield, while the other two treatments were unbeneficial to the accumulation of protein and starch and decreased the grain yield. Applying 270 kg x hm(-2) and 150 kg x hm(-2) of N combined with irrigation at jointing and grain-filling stages was the ideal management regime for the high yield and good quality of strong- and weak-gluten wheat cultivars, respectively. PMID:18464637

  13. Phase field modeling of grain growth in porous polycrystalline solids

    NASA Astrophysics Data System (ADS)

    Ahmed, Karim E.

    The concurrent evolution of grain size and porosity in porous polycrystalline solids is a technically important problem. All the physical properties of such materials depend strongly on pore fraction and pore and grain sizes and distributions. Theoretical models for the pore-grain boundary interactions during grain growth usually employ restrictive, unrealistic assumptions on the pore and grain shapes and motions to render the problem tractable. However, these assumptions limit the models to be only of qualitative nature and hence cannot be used for predictions. This has motivated us to develop a novel phase field model to investigate the process of grain growth in porous polycrystalline solids. Based on a dynamical system of coupled Cahn-Hilliard and All en-Cahn equations, the model couples the curvature-driven grain boundary motion and the migration of pores via surface diffusion. As such, the model accounts for all possible interactions between the pore and grain boundary, which highly influence the grain growth kinetics. Through a formal asymptotic analysis, the current work demonstrates that the phase field model recovers the corresponding sharp-interface dynamics of the co-evolution of grain boundaries and pores; this analysis also fixes the model kinetic parameters in terms of real materials properties. The model was used to investigate the effect of porosity on the kinetics of grain growth in UO2 and CeO2 in 2D and 3D. It is shown that the model captures the phenomenon of pore breakaway often observed in experiments. Pores on three- and four- grain junctions were found to transform to edge pores (pores on two-grain junction) before complete separation. The simulations demonstrated that inhomogeneous distribution of pores and pore breakaway lead to abnormal grain growth. The simulations also showed that grain growth kinetics in these materials changes from boundary-controlled to pore-controlled as the amount of porosity increases. The kinetic growth

  14. A meteorologically driven grain sorghum stress indicator model

    NASA Technical Reports Server (NTRS)

    Taylor, T. W.; Ravet, F. W. (Principal Investigator)

    1981-01-01

    A grain sorghum soil moisture and temperature stress model is described. It was developed to serve as a meteorological data filter to alert commodity analysts to potential stress conditions and crop phenology in selected grain sorghum production areas. The model also identifies optimum conditions on a daily basis and planting/harvest problems associated with poor tractability.

  15. Wheat (Triticum aestivum) NAM proteins regulate the translocation of iron, zinc, and nitrogen compounds from vegetative tissues to grain.

    PubMed

    Waters, Brian M; Uauy, Cristobal; Dubcovsky, Jorge; Grusak, Michael A

    2009-01-01

    The NAM-B1 gene is a NAC transcription factor that affects grain nutrient concentrations in wheat (Triticum aestivum). An RNAi line with reduced expression of NAM genes has lower grain protein, iron (Fe), and zinc (Zn) concentrations. To determine whether decreased remobilization, lower plant uptake, or decreased partitioning to grain are responsible for this phenotype, mineral dynamics were quantified in wheat tissues throughout grain development. Control and RNAi wheat were grown in potting mix and hydroponics. Mineral (Ca, Cu, Fe, K, Mg, Mn, P, S, and Zn) and nitrogen (N) contents of organs were determined at regular intervals to quantify the net remobilization from vegetative tissues and the accumulation of nutrients in grain. Total nutrient accumulation was similar between lines, but grain Fe, Zn, and N were at lower concentrations in the NAM knockdown line. In potting mix, net remobilization of N, Fe, and Zn from vegetative tissues was impaired in the RNAi line. In hydroponics with ample nutrients, net remobilization was not observed, but grain Fe and Zn contents and concentrations remained lower in the RNAi line. When Fe or Zn was withheld post-anthesis, both lines demonstrated remobilization. These results suggest that a major effect of the NAM genes is an increased efflux of nutrients from the vegetative tissues and a higher partitioning of nutrients to grain. PMID:19858116

  16. Physiological Mechanisms Underlying the High-Grain Yield and High-Nitrogen Use Efficiency of Elite Rice Varieties under a Low Rate of Nitrogen Application in China

    PubMed Central

    Wu, Lilian; Yuan, Shen; Huang, Liying; Sun, Fan; Zhu, Guanglong; Li, Guohui; Fahad, Shah; Peng, Shaobing; Wang, Fei

    2016-01-01

    Selecting rice varieties with a high nitrogen (N) use efficiency (NUE) is the best approach to reduce N fertilizer application in rice production and is one of the objectives of the Green Super Rice (GSR) Project in China. However, the performance of elite candidate GSR varieties under low N supply remains unclear. In the present study, differences in the grain yield and NUE of 13 and 14 candidate varieties with two controls were determined at a N rate of 100 kg ha−1 in field experiments in 2014 and 2015, respectively. The grain yield for all of the rice varieties ranged from 8.67 to 11.09 t ha−1, except for a japonica rice variety YG29, which had a grain yield of 6.42 t ha−1. HY549 and YY4949 produced the highest grain yield, reflecting a higher biomass production and harvest index in 2014 and 2015, respectively. Total N uptake at maturity (TNPM) ranged from 144 to 210 kg ha−1, while the nitrogen use efficiency for grain production (NUEg) ranged from 35.2 to 62.0 kg kg−1. Both TNPM and NUEg showed a significant quadratic correlation with grain yield, indicating that it is possible to obtain high grain yield and NUEg with the reduction of TNPM. The correlation between N-related parameters and yield-related traits suggests that promoting pre-heading growth could increase TNPM, while high biomass accumulation during the grain filling period and large panicles are important for a higher NUEg. In addition, there were significant and negative correlations between the NUEg and N concentrations in leaf, stem, and grain tissues at maturity. Further improvements in NUEg require a reduction in the stem N concentration but not the leaf N concentration. The daily grain yield was the only parameter that significantly and positively correlated with both TNPMand NUEg. This study determined variations in the grain yield and NUE of elite candidate GSR rice varieties and provided plant traits that could be used as selection criteria in breeding N-efficient rice varieties

  17. Physiological Mechanisms Underlying the High-Grain Yield and High-Nitrogen Use Efficiency of Elite Rice Varieties under a Low Rate of Nitrogen Application in China.

    PubMed

    Wu, Lilian; Yuan, Shen; Huang, Liying; Sun, Fan; Zhu, Guanglong; Li, Guohui; Fahad, Shah; Peng, Shaobing; Wang, Fei

    2016-01-01

    Selecting rice varieties with a high nitrogen (N) use efficiency (NUE) is the best approach to reduce N fertilizer application in rice production and is one of the objectives of the Green Super Rice (GSR) Project in China. However, the performance of elite candidate GSR varieties under low N supply remains unclear. In the present study, differences in the grain yield and NUE of 13 and 14 candidate varieties with two controls were determined at a N rate of 100 kg ha(-1) in field experiments in 2014 and 2015, respectively. The grain yield for all of the rice varieties ranged from 8.67 to 11.09 t ha(-1), except for a japonica rice variety YG29, which had a grain yield of 6.42 t ha(-1). HY549 and YY4949 produced the highest grain yield, reflecting a higher biomass production and harvest index in 2014 and 2015, respectively. Total N uptake at maturity (TNPM) ranged from 144 to 210 kg ha(-1), while the nitrogen use efficiency for grain production (NUEg) ranged from 35.2 to 62.0 kg kg(-1). Both TNPM and NUEg showed a significant quadratic correlation with grain yield, indicating that it is possible to obtain high grain yield and NUEg with the reduction of TNPM. The correlation between N-related parameters and yield-related traits suggests that promoting pre-heading growth could increase TNPM, while high biomass accumulation during the grain filling period and large panicles are important for a higher NUEg. In addition, there were significant and negative correlations between the NUEg and N concentrations in leaf, stem, and grain tissues at maturity. Further improvements in NUEg require a reduction in the stem N concentration but not the leaf N concentration. The daily grain yield was the only parameter that significantly and positively correlated with both TNPMand NUEg. This study determined variations in the grain yield and NUE of elite candidate GSR rice varieties and provided plant traits that could be used as selection criteria in breeding N-efficient rice varieties

  18. [Effects of nitrogen application rates and straw returning on nutrient balance and grain yield of late sowing wheat in rice-wheat rotation].

    PubMed

    Zhang, Shan; Shi, Zu-liang; Yang, Si-jun; Gu, Ke-jun; Dai, Ting-bo; Wang, Fei; Li, Xiang; Sun, Ren-hua

    2015-09-01

    Field experiments were conducted to study the effects of nitrogen application rates and straw returning on grain yield, nutrient accumulation, nutrient release from straw and nutrient balance in late sowing wheat. The results showed that straw returning together with appropriate application of nitrogen fertilizer improved the grain yield. Dry matter, nitrogen, phosphorus and potassium accumulation increased significantly as the nitrogen application rate increased. At the same nitrogen application rate (270 kg N · hm(-2)), the dry matter, phosphorus and potassium accumulation of the treatment with straw returning were higher than that without straw returning, but the nitrogen accumulation was lower. Higher-rate nitrogen application promoted straw decomposition and nutrient release, and decreased the proportion of the nutrient released from straw after jointing. The dry matter, phosphorus and potassium release from straw showed a reverse 'N' type change with the wheat growing, while nitrogen release showed a 'V' type change. The nutrient surplus increased significantly with the nitrogen application rate. At the nitrogen application rate for the highest grain yield, nitrogen and potassium were surplus significantly, and phosphorus input could keep balance. It could be concluded that as to late sowing wheat with straw returning, applying nitrogen at 257 kg · hm(-2) and reducing potassium fertilizer application could improve grain yield and reduce nutrients loss. PMID:26785553

  19. Film grain noise modeling in advanced video coding

    NASA Astrophysics Data System (ADS)

    Oh, Byung Tae; Kuo, C.-C. Jay; Sun, Shijun; Lei, Shawmin

    2007-01-01

    A new technique for film grain noise extraction, modeling and synthesis is proposed and applied to the coding of high definition video in this work. The film grain noise is viewed as a part of artistic presentation by people in the movie industry. On one hand, since the film grain noise can boost the natural appearance of pictures in high definition video, it should be preserved in high-fidelity video processing systems. On the other hand, video coding with film grain noise is expensive. It is desirable to extract film grain noise from the input video as a pre-processing step at the encoder and re-synthesize the film grain noise and add it back to the decoded video as a post-processing step at the decoder. Under this framework, the coding gain of the denoised video is higher while the quality of the final reconstructed video can still be well preserved. Following this idea, we present a method to remove film grain noise from image/video without distorting its original content. Besides, we describe a parametric model containing a small set of parameters to represent the extracted film grain noise. The proposed model generates the film grain noise that is close to the real one in terms of power spectral density and cross-channel spectral correlation. Experimental results are shown to demonstrate the efficiency of the proposed scheme.

  20. Modelling grain growth in the framework of Rational Extended Thermodynamics

    NASA Astrophysics Data System (ADS)

    Kertsch, Lukas; Helm, Dirk

    2016-05-01

    Grain growth is a significant phenomenon for the thermomechanical processing of metals. Since the mobility of the grain boundaries is thermally activated and energy stored in the grain boundaries is released during their motion, a mutual interaction with the process conditions occurs. To model such phenomena, a thermodynamic framework for the representation of thermomechanical coupling phenomena in metals including a microstructure description is required. For this purpose, Rational Extended Thermodynamics appears to be a useful tool. We apply an entropy principle to derive a thermodynamically consistent model for grain coarsening due to the growth and shrinkage of individual grains. Despite the rather different approaches applied, we obtain a grain growth model which is similar to existing ones and can be regarded as a thermodynamic extension of that by Hillert (1965) to more general systems. To demonstrate the applicability of the model, we compare our simulation results to grain growth experiments in pure copper by different authors, which we are able to reproduce very accurately. Finally, we study the implications of the energy release due to grain growth on the energy balance. The present unified approach combining a microstructure description and continuum mechanics is ready to be further used to develop more elaborate material models for complex thermo-chemo-mechanical coupling phenomena.

  1. Plant Nitrogen Uptake in Terrestrial Biogeochemical Models

    NASA Astrophysics Data System (ADS)

    Marti Donati, A.; Cox, P.; Smith, M. J.; Purves, D.; Sitch, S.; Jones, C. D.

    2013-12-01

    Most terrestrial biogeochemical models featured in the last Intergovernmental Panel on Climate Change (IPPC) Assessment Report highlight the importance of the terrestrial Carbon sequestration and feedbacks between the terrestrial Carbon cycle and the climate system. However, these models have been criticized for overestimating predicted Carbon sequestration and its potential climate feedback when calculating the rate of future climate change because they do not account for the Carbon sequestration constraints caused by nutrient limitation, particularly Nitrogen (N). This is particularly relevant considering the existence of a substantial deficit of Nitrogen for plants in most areas of the world. To date, most climate models assume that plants have access to as much Nitrogen as needed, but ignore the nutrient requirements for new vegetation growth. Determining the natural demand and acquisition for Nitrogen and its associated resource optimization is key when accounting for the Carbon sequestration constrains caused by nutrient limitation. The few climate models that include C-N dynamics have illustrated that the stimulation of plant growth over the coming century may be significantly smaller than previously predicted. However, models exhibit wide differences in their predictive accuracy and lead to widely diverging and inconsistent projections accounting for an uncertain Carbon sequestration decrease due to Nitrogen limitation ranging from 7 to 64%. This reduction in growth is partially offset by an increase in the availability of nutrients resulting from an accelerated rate of decomposition of dead plants and other organic matter that occurring with a rise in temperature. However, this offset does not counterbalance the reduced level of plant growth calculated by natural nutrient limitations. Additionally, Nitrogen limitation is also expected to become more pronounced in some ecosystems as atmospheric CO2 concentration increases; resulting in less new growth and

  2. A Madurella mycetomatis Grain Model in Galleria mellonella Larvae.

    PubMed

    Kloezen, Wendy; van Helvert-van Poppel, Marilyn; Fahal, Ahmed H; van de Sande, Wendy W J

    2015-01-01

    Eumycetoma is a chronic granulomatous subcutaneous infectious disease, endemic in tropical and subtropical regions and most commonly caused by the fungus Madurella mycetomatis. Interestingly, although grain formation is key in mycetoma, its formation process and its susceptibility towards antifungal agents are not well understood. This is because grain formation cannot be induced in vitro; a mammalian host is necessary to induce its formation. Until now, invertebrate hosts were never used to study grain formation in M. mycetomatis. In this study we determined if larvae of the greater wax moth Galleria mellonella could be used to induce grain formation when infected with M. mycetomatis. Three different M. mycetomatis strains were selected and three different inocula for each strain were used to infect G. mellonella larvae, ranging from 0.04 mg/larvae to 4 mg/larvae. Larvae were monitored for 10 days. It appeared that most larvae survived the lowest inoculum, but at the highest inoculum all larvae died within the 10 day observation period. At all inocula tested, grains were formed within 4 hours after infection. The grains produced in the larvae resembled those formed in human and in mammalian hosts. In conclusion, the M. mycetomatis grain model in G. mellonella larvae described here could serve as a useful model to study the grain formation and therapeutic responses towards antifungal agents in the future. PMID:26173126

  3. A Madurella mycetomatis Grain Model in Galleria mellonella Larvae

    PubMed Central

    Kloezen, Wendy; van Helvert-van Poppel, Marilyn; Fahal, Ahmed H.; van de Sande, Wendy W. J.

    2015-01-01

    Eumycetoma is a chronic granulomatous subcutaneous infectious disease, endemic in tropical and subtropical regions and most commonly caused by the fungus Madurella mycetomatis. Interestingly, although grain formation is key in mycetoma, its formation process and its susceptibility towards antifungal agents are not well understood. This is because grain formation cannot be induced in vitro; a mammalian host is necessary to induce its formation. Until now, invertebrate hosts were never used to study grain formation in M. mycetomatis. In this study we determined if larvae of the greater wax moth Galleria mellonella could be used to induce grain formation when infected with M. mycetomatis. Three different M. mycetomatis strains were selected and three different inocula for each strain were used to infect G. mellonella larvae, ranging from 0.04 mg/larvae to 4 mg/larvae. Larvae were monitored for 10 days. It appeared that most larvae survived the lowest inoculum, but at the highest inoculum all larvae died within the 10 day observation period. At all inocula tested, grains were formed within 4 hours after infection. The grains produced in the larvae resembled those formed in human and in mammalian hosts. In conclusion, the M. mycetomatis grain model in G. mellonella larvae described here could serve as a useful model to study the grain formation and therapeutic responses towards antifungal agents in the future. PMID:26173126

  4. A Phase-Field Model for Grain Growth

    SciTech Connect

    Chen, L.Q.; Fan, D.N.; Tikare, V.

    1998-12-23

    A phase-field model for grain growth is briefly described. In this model, a poly-crystalline microstructure is represented by multiple structural order parameter fields whose temporal and spatial evolutions follow the time-dependent Ginzburg-Landau (TDGL) equations. Results from phase-field simulations of two-dimensional (2D) grain growth will be summarized and preliminary results on three-dimensional (3D) grain growth will be presented. The physical interpretation of the structural order parameter fields and the efficient and accurate semi-implicit Fourier spectral method for solving the TDGL equations will be briefly discussed.

  5. Thermal spike model of ion-induced grain growth

    SciTech Connect

    Alexander, D.E. ); Was, G.S. . Dept. of Nuclear Engineering)

    1990-11-01

    A thermal spike model has been developed to describe the phenomenon of ion irradiation-induced grain growth in metal alloy thin films. In single phase films where the driving force for grain growth is the reduction of grain boundary curvature, the model shows that ion-induced grain boundary mobility, M{sub ion}, is proportional to the quantity F{sub D}{sup 2}/{Delta}H{sub coh}{sup 3}, where F{sub D} is the deposited ion damage energy and {Delta}H{sub coh} is the cohesive energy of the element or alloy. Experimental strain growth results from ion irradiated coevaporated binary alloy films compare favorably with model predictions. 11 refs., 1 fig., 1 tab.

  6. Effect of Grain Refinement on the Mechanical Properties of a Nickel- and Manganese-Free High Nitrogen Austenitic Stainless Steel

    NASA Astrophysics Data System (ADS)

    Akbari, Alireza; Mohammadzadeh, Roghayeh

    2015-04-01

    Grain coarsening due to the high temperature exposure deteriorates mechanical properties of the high nitrogen austenitic stainless steels (HNASSs) produced by solution nitriding. To improve mechanical properties, the grains of nickel and manganese-free Fe-23Cr-2.4Mo-1.2N HNASS plates fabricated by pressurized solution nitriding were refined using a two-stage heat treatment process. Structural and mechanical properties were investigated using X-ray diffraction, optical microscopy, scanning and transmission electron microscopy, hardness and tensile testing and compared with that of the conventional AISI 316L steel. The results show that the as-produced HNASS exhibits uniform deformation up to failure without necking and brittle inter-granular fracture. By grain refinement, the yield and tensile strengths as well as the elongation to failure are increased by 17.8, 21.2, and 108.3 pct, respectively, as compared to the as-produced HNASS. However, despite more than a double increase in tensile toughness and elongation to failure, the brittle inter-granular fracture is not suppressed. The HNASSs plastically deform through formation of straight slip bands. TEM observations indicate development of planar arrays of dislocations in tensile-deformed HNASSs. The enhancement in tensile strength and toughness by grain refinement is discussed on the basis of straight slip bands formation, number of dislocations in pile-ups, and incompatibility strain developed between adjacent grains.

  7. Physics-Based Reactive Burn Model: Grain Size Effects

    NASA Astrophysics Data System (ADS)

    Lu, X.; Hamate, Y.; Horie, Y.

    2007-12-01

    We have been developing a physics-based reactive burn (PBRB) model, which was formulated based on the concept of a statistical hot spot cell. In the model, essential thermomechanics and physiochemical features are explicitly modeled. In this paper, we have extended the statistical hot spot model to explicitly describe the ignition and growth of hot spots. In particular, grain size effects are explicitly delineated through introduction of grain size-dependent, thickness of the hot-region, energy deposition criterion, and specific surface area. Besides the linear relationships between the run distance to detonation and the critical diameter with respect to the reciprocal specific surface area of heterogeneous explosives (HE), which is based on the original model and discussed in a parallel paper of this meeting, parametric studies have shown that the extended PBRB model can predict a non-monotonic variation of shock sensitivity with grain size, as observed by Moulard et al.

  8. Modeling the Role of Small Scale Physics in Sediment Transport From Grain Size to Grain Shape

    NASA Astrophysics Data System (ADS)

    Calantoni, J.; Holland, K. T.

    2007-12-01

    In recent years work has focused on the detailed physics of sediment transport at or near the grain scale. Although computational resources often restrict the domain size, deterministic models for sediment motions can prove useful in improving our understanding of sediment dynamics. Using a discrete particle model (DPM), we have performed computer simulations that describe the collective and individual motions of sediment grains immersed in fluid in an effort to emulate the physics of the sea floor, at the fluid-sediment interface, in shallow water under forcing from waves and currents. Examples of our DPM (briefly described) are shown for research applications at a range scales from millimeters to meters involving fluid flow models from simple one- dimensional eddy viscosity up to three-dimensional direct numerical simulation. Based on hundreds of different simulations over the past decade, our findings have shown: how a parameterization of pressure gradients or equivalently fluid accelerations on particle motions under waves influences sand bar migration in the surf zone; how grain shape changes bulk bedload transport rates; how efforts to model sediment particle motions in the swash zone can yield insight toward models for shoreline erosion and accretion; how recently simulated bedload transport using bimodal size distributions has uncovered a new power law; how upcoming work focuses on simulating the role of grain size distributions in small-scale sand ripple dynamics. Good agreement is found between comparisons of model output for both bulk transport rates and time dependent concentration profiles with laboratory data. Likewise, parameterizations obtained from simulation results have demonstrated skill in hindcast applications to both field and laboratory measurements. Conclusions will discuss the future role of reductionism in sediment transport modeling.

  9. Zinc, iron, manganese and copper uptake requirement in response to nitrogen supply and the increased grain yield of summer maize.

    PubMed

    Xue, Yanfang; Yue, Shanchao; Zhang, Wei; Liu, Dunyi; Cui, Zhenling; Chen, Xinping; Ye, Youliang; Zou, Chunqin

    2014-01-01

    The relationships between grain yields and whole-plant accumulation of micronutrients such as zinc (Zn), iron (Fe), manganese (Mn) and copper (Cu) in maize (Zea mays L.) were investigated by studying their reciprocal internal efficiencies (RIEs, g of micronutrient requirement in plant dry matter per Mg of grain). Field experiments were conducted from 2008 to 2011 in North China to evaluate RIEs and shoot micronutrient accumulation dynamics during different growth stages under different yield and nitrogen (N) levels. Fe, Mn and Cu RIEs (average 64.4, 18.1 and 5.3 g, respectively) were less affected by the yield and N levels. ZnRIE increased by 15% with an increased N supply but decreased from 36.3 to 18.0 g with increasing yield. The effect of cultivars on ZnRIE was similar to that of yield ranges. The substantial decrease in ZnRIE may be attributed to an increased Zn harvest index (from 41% to 60%) and decreased Zn concentrations in straw (a 56% decrease) and grain (decreased from 16.9 to 12.2 mg kg-1) rather than greater shoot Zn accumulation. Shoot Fe, Mn and Cu accumulation at maturity tended to increase but the proportions of pre-silking shoot Fe, Cu and Zn accumulation consistently decreased (from 95% to 59%, 90% to 71% and 91% to 66%, respectively). The decrease indicated the high reproductive-stage demands for Fe, Zn and Cu with the increasing yields. Optimized N supply achieved the highest yield and tended to increase grain concentrations of micronutrients compared to no or lower N supply. Excessive N supply did not result in any increases in yield or micronutrient nutrition for shoot or grain. These results indicate that optimized N management may be an economical method of improving micronutrient concentrations in maize grain with higher grain yield. PMID:24705926

  10. [Hyperspectral remote sensing estimation models for snow grain size].

    PubMed

    Wang, Jian-Geng; Feng, Xue-Zhi; Xiao, Peng-Feng; Liang, Ji; Zhang, Xue-Liang; Li, Hai-Xing; Li, Yun

    2013-01-01

    Snow grain size is a key parameter not only to affect the energy budget of the global or local region but also characterizing the status of snow vapor transport and temperature gradient. It is significant to monitor and estimate the snow grain size in large area for global or local climate change and water resource management. Recently, remote sensing technology has become a useful tool for snow grain size monitoring and estimating. In the present paper, the estimate models were built based on simulating the snow surface spectral reflectance curve in visible-infrared region and the sensitive bands and snow indices for snow grain size were selected. These models help estimate snow grain size by hyperspectral remote sensing. Through validating with ground true data, the results show that these models have higher explorative accuracy using 1 030, 1 260 nm and normalized difference snow index (460 and 1 030 nm). In addition, the correlation slopes of estimated and observed valves are 1.37, 0.61 and 0.62, respectively. R2 are 0.82, 0.86 and 0.93 and RMSE are 55.65, 50.83 and 35.91 microm, respectively. The result can provide a scientific basis for snow grain size monitoring and estimating. PMID:23586251

  11. Bayesian parametrization of coarse-grain dissipative dynamics models

    NASA Astrophysics Data System (ADS)

    Dequidt, Alain; Solano Canchaya, Jose G.

    2015-08-01

    We introduce a new bottom-up method for the optimization of dissipative coarse-grain models. The method is based on Bayesian optimization of the likelihood to reproduce a coarse-grained reference trajectory obtained from analysis of a higher resolution molecular dynamics trajectory. This new method is related to force matching techniques, but using the total force on each grain averaged on a coarse time step instead of instantaneous forces. It has the advantage of not being limited to pairwise short-range interactions in the coarse-grain model and also yields an estimation of the friction parameter controlling the dynamics. The theory supporting the method is exposed in a practical perspective, with an analytical solution for the optimal set of parameters. The method was first validated by using it on a system with a known optimum. The new method was then tested on a simple system: n-pentane. The local molecular structure of the optimized model is in excellent agreement with the reference system. An extension of the method allows to get also an excellent agreement for the equilibrium density. As for the dynamic properties, they are also very satisfactory, but more sensitive to the choice of the coarse-grain representation. The quality of the final force field depends on the definition of the coarse grain degrees of freedom and interactions. We consider this method as a serious alternative to other methods like iterative Boltzmann inversion, force matching, and Green-Kubo formulae.

  12. Modelling Nitrogen from soil to sea in Denmark: Concept and major results using a new national Nitrogen model.

    NASA Astrophysics Data System (ADS)

    Tornbjerg, Henrtik; Windolf, Jørgen; Kronvang, Brian; Blicher-Mathiesen, Gitte; Duus Børgensen, Christen; Lajer Højberg, Anker; Troldborg, Lars

    2016-04-01

    In order to improve the information on the variations and trends in sources and sinks of nitrogen a new national model linking nitrogen from Soil to Sea has recently been developed in Denmark. The strategic perspectives of the newly developed model include: On a 15 km2 scale to aggregate modelled data for the hydrological and nitrogen cycle. To model the Nitrogen sources and sinks by coupling of submodels and then include these models in an overall model. To link the sources, transport and sinks of Nitrogen for obtaining the resulting net nitrogen load to the Danish estuaries and coastal waters To evaluate the modelled Nitrogen transport on measured nitrogen loads from around 300 gauging stations in Danish streams. To combine modelled and measured Nitrogen loads thereby providing new time series and geographically distributed data for land based Nitrogen loadings to Danish coastal waters The general modelling concept and overall results will be described. The modelled nitrogen transport on coastal gauging stations will be compared to measured data from the period 1990-2010. For some catchments the model fails to satisfactory estimate the measured nitrogen load or the relative trend in these measurements. This includes some catchments rich on lakes and some catchments in areas where oxidized groundwater are present in deeper aquifers.

  13. Two-temperature models for nitrogen dissociation

    NASA Astrophysics Data System (ADS)

    da Silva, M. Lino; Guerra, V.; Loureiro, J.

    2007-12-01

    Accurate sets of nitrogen state-resolved dissociation rates have been reduced to two-temperature (translational T and vibrational Tv) dissociation rates. The analysis of such two-temperature dissociation rates shows evidence of two different dissociation behaviors. For Tv < 0.3 T dissociation proceeds predominantly from the lower-lying vibrational levels, whereas for Tv > 0.3 T dissociation proceeds predominantly form the near-dissociative vibrational levels, with an abrupt change of behavior at Tv = 0.3 T. These two-temperature sets have then been utilized as a benchmark for the comparison against popular multitemperature dissociation models (Park, Hansen, Marrone-Treanor, Hammerling, Losev-Shatalov, Gordiets, Kuznetsov, and Macheret-Fridman). This has allowed verifying the accuracy of each theoretical model, and additionally proposing adequate values for any semi-empirical parameters present in the different theories. The Macheret-Fridman model, who acknowledges the existence of the two aforementioned dissociation regimes, has been found to provide significantly more accurate results than the other models. Although these different theoretical approaches have been tested and validated solely for nitrogen dissociation processes, it is reasonable to expect that the general conclusions of this work, regarding the adequacy of the different dissociation models, could be extended to the description of arbitrary diatomic dissociation processes.

  14. Multiscale Modeling of Grain-Boundary Fracture: Cohesive Zone Models Parameterized From Atomistic Simulations

    NASA Technical Reports Server (NTRS)

    Glaessgen, Edward H.; Saether, Erik; Phillips, Dawn R.; Yamakov, Vesselin

    2006-01-01

    A multiscale modeling strategy is developed to study grain boundary fracture in polycrystalline aluminum. Atomistic simulation is used to model fundamental nanoscale deformation and fracture mechanisms and to develop a constitutive relationship for separation along a grain boundary interface. The nanoscale constitutive relationship is then parameterized within a cohesive zone model to represent variations in grain boundary properties. These variations arise from the presence of vacancies, intersticies, and other defects in addition to deviations in grain boundary angle from the baseline configuration considered in the molecular dynamics simulation. The parameterized cohesive zone models are then used to model grain boundaries within finite element analyses of aluminum polycrystals.

  15. Soil Carbon and Nitrogen Cycle Modeling

    NASA Astrophysics Data System (ADS)

    Woo, D.; Chaoka, S.; Kumar, P.; Quijano, J. C.

    2012-12-01

    Second generation bioenergy crops, such as miscanthus (Miscantus × giganteus) and switchgrass (Panicum virgatum), are regarded as clean energy sources, and are an attractive option to mitigate the human-induced climate change. However, the global climate change and the expansion of perennial grass bioenergy crops have the power to alter the biogeochemical cycles in soil, especially, soil carbon storages, over long time scales. In order to develop a predictive understanding, this study develops a coupled hydrological-soil nutrient model to simulate soil carbon responses under different climate scenarios such as: (i) current weather condition, (ii) decreased precipitation by -15%, and (iii) increased temperature up to +3C for four different crops, namely miscanthus, switchgrass, maize, and natural prairie. We use Precision Agricultural Landscape Modeling System (PALMS), version 5.4.0, to capture biophysical and hydrological components coupled with a multilayer carbon and ¬nitrogen cycle model. We apply the model at daily time scale to the Energy Biosciences Institute study site, located in the University of Illinois Research Farms, in Urbana, Illinois. The atmospheric forcing used to run the model was generated stochastically from parameters obtained using available data recorded in Bondville Ameriflux Site. The model simulations are validated with observations of drainage and nitrate and ammonium concentrations recorded in drain tiles during 2011. The results of this study show (1) total soil carbon storage of miscanthus accumulates most noticeably due to the significant amount of aboveground plant carbon, and a relatively high carbon to nitrogen ratio and lignin content, which reduce the litter decomposition rate. Also, (2) the decreased precipitation contributes to the enhancement of total soil carbon storage and soil nitrogen concentration because of the reduced microbial biomass pool. However, (3) an opposite effect on the cycle is introduced by the increased

  16. Kinetic model of particle-inhibited grain growth

    NASA Astrophysics Data System (ADS)

    Thompson, Gary Scott

    The effects of second phase particles on matrix grain growth kinetics were investigated using Al2O3-SiC as a model system. In particular, the validity of the conclusion drawn from a previous kinetic analysis that the kinetics of particle-inhibited grain growth in Al2 O3-SiC samples with an intermediate volume fraction of second phase could be well quantified by a modified-Zener model was investigated. A critical analysis of assumptions made during the previous kinetic analysis revealed oversimplifications which affect the validity of the conclusion. Specifically, the degree of interaction between particles and grain boundaries was assumed to be independent of the mean second phase particle size and size distribution. In contrast, current measurements indicate that the degree of interaction in Al2O3-SiC is dependent on these parameters. An improved kinetic model for particle-inhibited grain growth in Al 2O3-SiC was developed using a modified-Zener approach. The comparison of model predictions with experimental grain growth data indicated that significant discrepancies (as much as 4--5 orders of magnitude) existed. Based on this, it was concluded that particles had a much more significant effect on grain growth kinetics than that caused by a simple reduction of the boundary driving force due to the removal of boundary area. Consequently, it was also concluded that the conclusion drawn from the earlier kinetic analysis regarding the validity of a modified-Zener model was incorrect. Discrepancies between model and experiment were found to be the result of a significant decrease in experimental growth rate constant not predicted by the model. Possible physical mechanisms for such a decrease were investigated. The investigation of a small amount of SiO2 on grain growth in Al2O3 indicated that the decrease was not the result of a decrease in grain boundary mobility due to impurity contamination by particles. By process of elimination and based on previous observations

  17. Carbon, nitrogen, magnesium, silicon, and titanium isotopic compositions of single interstellar silicon carbide grains from the Murchison carbonaceous chondrite

    NASA Technical Reports Server (NTRS)

    Hoppe, Peter; Amari, Sachiko; Zinner, Ernst; Ireland, Trevor; Lewis, Roy S.

    1994-01-01

    . The C- and N-isotopic compositions of most grains are consistent with H-burning in the CNO cycle. These and s-process Kr, Xe, Ba, and Nd suggest asymptotic giant branch (AGB) or Wolf-Rayet stars as likely sources for the grains, but existing models of nucleosynthesis in these stellar sites fail to account in detail for all the observed isotopic compositions. Special problems are posed by grains with C-12/C-13 less than 10 and almost normal and heavy N-isotopic compositions. Also the Si- and Ti-isotopic compositions, with excesses in Si-29 and Si-30 relative to Si-28 and excesses in all Ti isotopes relative to Ti-48, do not precisely conform with the compositions predicted for slow neutron capture. Additional theoretical efforts are needed to achieve an understanding of the isotopic composition of the SiC grains and their stellar sources.

  18. [Research advances in soil nitrogen cycling models and their simulation].

    PubMed

    Tang, Guoyong; Huang, Daoyou; Tong, Chengli; Zhang, Wenju; Wu, Jinshui

    2005-11-01

    Nitrogen is one of the necessary nutrients for plant, and also a primary element leading to environmental pollution. Many researches have been concerned about the contribution of agricultural activities to environmental pollution by nitrogenous compounds, and the focus is how to simulate soil nitrogen cycling processes correctly. In this paper, the primary soil nitrogen cycling processes were reviewed in brief, with 13 cycling models and 6 simulated cycling processes introduced, and the parameterization of models discussed. PMID:16471369

  19. 3D reconstruction of grains in polycrystalline materials using a tessellation model with curved grain boundaries

    NASA Astrophysics Data System (ADS)

    Šedivý, Ondřej; Brereton, Tim; Westhoff, Daniel; Polívka, Leoš; Beneš, Viktor; Schmidt, Volker; Jäger, Aleš

    2016-06-01

    A compact and tractable representation of the grain structure of a material is an extremely valuable tool when carrying out an empirical analysis of the material's microstructure. Tessellations have proven to be very good choices for such representations. Most widely used tessellation models have convex cells with planar boundaries. Recently, however, a new tessellation model - called the generalised balanced power diagram (GBPD) - has been developed that is very flexible and can incorporate features such as curved boundaries and non-convexity of cells. In order to use a GBPD to describe the grain structure observed in empirical image data, the parameters of the model must be chosen appropriately. This typically involves solving a difficult optimisation problem. In this paper, we describe a method for fitting GBPDs to tomographic image data. This method uses simulated annealing to solve a suitably chosen optimisation problem. We then apply this method to both artificial data and experimental 3D electron backscatter diffraction (3D EBSD) data obtained in order to study the properties of fine-grained materials with superplastic behaviour. The 3D EBSD data required new alignment and segmentation procedures, which we also briefly describe. Our numerical experiments demonstrate the effectiveness of the simulated annealing approach (compared to heuristic fitting methods) and show that GBPDs are able to describe the structures of polycrystalline materials very well.

  20. Solid Solution Model for Interstellar Dust Grains and Their Organics

    NASA Astrophysics Data System (ADS)

    Freund, Minoru M.; Freund, Friedemann T.

    2006-03-01

    We present a dust grain model based on the fundamental principle of solid solutions. The model is applicable to the mineral (silicate) component of the dust in the interstellar medium (ISM). We show that nanometer-sized mineral grains, which condense in the gas-rich outflow of late-stage stars or expanding gas shells of supernova explosions, do not consist of just high melting point oxides or silicates. Instead they form solid solutions with gas-phase components H2O, CO, and CO2 that are omnipresent in environments where the grains condense. Through a series of thermodynamically well-understood solid-state processes, these solid solutions become ``parents'' of organic matter that precipitates inside the grains. Thus, the mineral dust grains and their organics become part of the same thermodynamically defined solid phase and, hence, physically inseparable. This model can account for many astronomical observations, which no prior model can adequately address, specifically: (1) Organics in the diffuse ISM are identified by a 3.4 μm IR band, characteristic of aliphatic hydrocarbons composed of CH2 and of CH3 groups. (2) The methylene-to-methyl ratio is nearly constant, implying a CH2:CH3 ratio of ~5:2. (3) The intensity ratio between the 9.7 and the 3.4 μm band is nearly constant, implying a silicate-to-organics ratio of ~10:1. (4) In dense clouds the complex 3.4 μm band is replaced by a weak, featureless 3.47 μm band. (5) Whereas silicate grains identified by their 9.7 μm band tend to align in magnetic fields, grains with a strong 3.4 μm organic signature do not tend to align.

  1. The Genetic Control of Grain Protein Content under Variable Nitrogen Supply in an Australian Wheat Mapping Population

    PubMed Central

    Mahjourimajd, Saba; Taylor, Julian; Rengel, Zed; Khabaz-Saberi, Hossein; Kuchel, Haydn; Okamoto, Mamoru

    2016-01-01

    Genetic variation has been observed in both protein concentration in wheat grain and total protein content (protein yield). Here we describe the genetic analysis of variation for grain protein in response to nitrogen (N) supply and locate significant genomic regions controlling grain protein components in a spring wheat population. In total, six N use efficiency (NUE) field trials were carried out for the target traits in a sub-population of doubled haploid lines derived from a cross between two Australian varieties, RAC875 and Kukri, in Southern and Western Australia from 2011 to 2013. Twenty-four putative Quantitative Trait Loci (QTL) for protein-related traits were identified at high and low N supply and ten QTL were identified for the response to N for the traits studied. These loci accounted for a significant proportion of the overall effect of N supply. Several of the regions were co-localised with grain yield QTL and are promising targets for further investigation and selection in breeding programs. PMID:27438012

  2. The Genetic Control of Grain Protein Content under Variable Nitrogen Supply in an Australian Wheat Mapping Population.

    PubMed

    Mahjourimajd, Saba; Taylor, Julian; Rengel, Zed; Khabaz-Saberi, Hossein; Kuchel, Haydn; Okamoto, Mamoru; Langridge, Peter

    2016-01-01

    Genetic variation has been observed in both protein concentration in wheat grain and total protein content (protein yield). Here we describe the genetic analysis of variation for grain protein in response to nitrogen (N) supply and locate significant genomic regions controlling grain protein components in a spring wheat population. In total, six N use efficiency (NUE) field trials were carried out for the target traits in a sub-population of doubled haploid lines derived from a cross between two Australian varieties, RAC875 and Kukri, in Southern and Western Australia from 2011 to 2013. Twenty-four putative Quantitative Trait Loci (QTL) for protein-related traits were identified at high and low N supply and ten QTL were identified for the response to N for the traits studied. These loci accounted for a significant proportion of the overall effect of N supply. Several of the regions were co-localised with grain yield QTL and are promising targets for further investigation and selection in breeding programs. PMID:27438012

  3. Coarse-grained dynamics of alignment in animal group models

    NASA Astrophysics Data System (ADS)

    Moon, Sung Joon; Levin, Simon; Kevrekidis, Yannis

    2006-03-01

    Coordinated motion in animal groups, such as bird flocks and fish schools, and their models gives rise to remarkable coherent structures. Using equation-free computational tools we explore the coarse-grained dynamics of a model for the orientational movement decision in animal groups, consisting of a small number of informed "leaders" and a large number of uninformed, nonidentical ``followers.'' The direction in which each group member is headed is characterized by a phase angle of a limit-cycle oscillator, whose dynamics are nonlinearly coupled with those of all the other group members. We identify a small number of proper coarse-grained variables (using uncertainty quantification methods) that describe the collective dynamics, and perform coarse projective integration and equation-free bifurcation analysis of the coarse-grained model behavior in these variables.

  4. NEMA, a functional–structural model of nitrogen economy within wheat culms after flowering. I. Model description

    PubMed Central

    Bertheloot, Jessica; Cournède, Paul-Henry; Andrieu, Bruno

    2011-01-01

    Background and Aims Models simulating nitrogen use by plants are potentially efficient tools to optimize the use of fertilizers in agriculture. Most crop models assume that a target nitrogen concentration can be defined for plant tissues and formalize a demand for nitrogen, depending on the difference between the target and actual nitrogen concentrations. However, the teleonomic nature of the approach has been criticized. This paper proposes a mechanistic model of nitrogen economy, NEMA (Nitrogen Economy Model within plant Architecture), which links nitrogen fluxes to nitrogen concentration and physiological processes. Methods A functional–structural approach is used: plant aerial parts are described in a botanically realistic way and physiological processes are expressed at the scale of each aerial organ or root compartment as a function of local conditions (light and resources). Key Results NEMA was developed for winter wheat (Triticum aestivum) after flowering. The model simulates the nitrogen (N) content of each photosynthetic organ as regulated by Rubisco turnover, which depends on intercepted light and a mobile N pool shared by all organs. This pool is enriched by N acquisition from the soil and N release from vegetative organs, and is depleted by grain uptake and protein synthesis in vegetative organs; NEMA accounts for the negative feedback from circulating N on N acquisition from the soil, which is supposed to follow the activities of nitrate transport systems. Organ N content and intercepted light determine dry matter production via photosynthesis, which is distributed between organs according to a demand-driven approach. Conclusions NEMA integrates the main feedbacks known to regulate plant N economy. Other novel features are the simulation of N for all photosynthetic tissues and the use of an explicit description of the plant that allows how the local environment of tissues regulates their N content to be taken into account. We believe this represents

  5. A Transferable Coarse-Grained Model for Hydrogen Bonding Liquids

    PubMed Central

    Golubkov, Pavel A.; Wu, Johnny C.; Ren, Pengyu

    2008-01-01

    We present here a recent development of a generalized coarse-grained model for use in molecular simulations. In this model, interactions between coarse-grained particles consist of both van der Waals and explicit electrostatic components. As a result, the coarse-grained model offers the transferability that is lacked by most current effectivepotential based approaches. The previous center-of-mass framework1 is generalized here to include arbitrary off-center interaction sites for both Gay-Berne and multipoles. The new model has been applied to molecular dynamic simulations of neat methanol liquid. By placing a single point multipole at the oxygen atom rather than at the center of mass of methanol, there is a significant improvement in the ability to capture hydrogen-bonding. The critical issue of transferability of the coarse-grained model is verified on methanol-water mixtures, using parameters derived from neat liquids without any modification. The mixture density and internal energy from coarse-grained molecular dynamics simulations show good agreement with experimental measurements, on a par with what has been obtained from more detailed atomic models. By mapping the dynamics trajectory from the coarse-grained simulation into the all-atom counterpart, we are able to investigate atomic .level structure and interaction. Atomic radial distribution functions of neat methanol, neat water and mixtures compare favorably to experimental measurements. Furthermore, hydrogen-bonded 6- and 7-molecule chains of water and methanol observed in the mixture are in agreement with previous atomic simulations. PMID:18688358

  6. Toward a mechanistic modeling of nitrogen limitation for photosynthesis

    NASA Astrophysics Data System (ADS)

    Xu, C.; Fisher, R. A.; Travis, B. J.; Wilson, C. J.; McDowell, N. G.

    2011-12-01

    The nitrogen limitation is an important regulator for vegetation growth and global carbon cycle. Most current ecosystem process models simulate nitrogen effects on photosynthesis based on a prescribed relationship between leaf nitrogen and photosynthesis; however, there is a large amount of variability in this relationship with different light, temperature, nitrogen availability and CO2 conditions, which can affect the reliability of photosynthesis prediction under future climate conditions. To account for the variability in nitrogen-photosynthesis relationship under different environmental conditions, in this study, we developed a mechanistic model of nitrogen limitation for photosynthesis based on nitrogen trade-offs among light absorption, electron transport, carboxylization and carbon sink. Our model shows that strategies of nitrogen storage allocation as determined by tradeoff among growth and persistence is a key factor contributing to the variability in relationship between leaf nitrogen and photosynthesis. Nitrogen fertilization substantially increases the proportion of nitrogen in storage for coniferous trees but much less for deciduous trees, suggesting that coniferous trees allocate more nitrogen toward persistence compared to deciduous trees. The CO2 fertilization will cause lower nitrogen allocation for carboxylization but higher nitrogen allocation for storage, which leads to a weaker relationship between leaf nitrogen and maximum photosynthesis rate. Lower radiation will cause higher nitrogen allocation for light absorption and electron transport but less nitrogen allocation for carboxylyzation and storage, which also leads to weaker relationship between leaf nitrogen and maximum photosynthesis rate. At the same time, lower growing temperature will cause higher nitrogen allocation for carboxylyzation but lower allocation for light absorption, electron transport and storage, which leads to a stronger relationship between leaf nitrogen and maximum

  7. Modeling Nitrogen Oxides in the Lower Stratosphere

    NASA Technical Reports Server (NTRS)

    Kawa, S. Randy; Einaudi, Franco (Technical Monitor)

    2001-01-01

    This talk will focus on the status of current understanding (not a historical review) as regards modeling nitrogen oxides (NOy) in the lower stratosphere (LS). The presentation will be organized around three major areas of process understanding: 1) NOy sources, sinks, and transport to the LS, 2) NOy species partitioning, and 3) polar multiphase processes. In each area, process topics will be identified with an estimate of the degree of confidence associated with their representation in numerical models. Several exotic and/or speculative processes will also be discussed. Those topics associated with low confidence or knowledge gaps, weighted by their prospective importance in stratospheric chemical modeling, will be collected into recommendations for further study. Suggested approaches to further study will be presented for discussion.

  8. Abscisic acid and aldehyde oxidase activity in maize ear leaf and grain relative to post-flowering photosynthetic capacity and grain-filling rate under different water/nitrogen treatments.

    PubMed

    Qin, Shujun; Zhang, Zongzheng; Ning, Tangyuan; Ren, Shizhong; Su, Licheng; Li, Zengjia

    2013-09-01

    This study investigated changes in leaf abscisic acid (ABA) concentrations and grain ABA concentrations in two maize cultivars and analyzed the following relationships under different water/nitrogen treatments: leaf ABA concentrations and photosynthetic parameters; leaf ABA concentrations and grain ABA concentrations; leaf/grain ABA concentrations and grain-filling parameters; and aldehyde oxidase (AO, EC 1.2.3.1) activities and ABA concentrations. The ear leaf average AO activities and ABA concentrations were lower in the controlled release urea treatments compared with the conventional urea treatments. The average AO activities in the grains were higher in the controlled release urea treatments, and the ABA concentrations were significantly increased at 11-30 DAF. The Pn and ABA concentrations in ear leaves were negatively correlated. And the Gmean were positively correlated with the grain ABA concentrations at 11-30 DAF and negatively correlated with the leaf ABA concentrations at 20 and 40-50 DAF. The grain ABA concentrations and leaf ABA concentrations were positively correlated. Thus, the Gmean were closely related to the AO activities and to the ear leaf and grain ABA concentrations. As compared to other treatments, the subsoiling and controlled release urea treatment promoted the uptake of water and nitrogen by maize, increased the photosynthetic capacity of the ear leaves, increased the grain-filling rate, and improved the movement of photosynthetic assimilates toward the developing grains. In the cultivar Z958, higher ABA concentrations in grains at 11-30 DAF and lower ABA concentrations in ear leaves during the late grain-filling stage, resulted in higher grain-filling rate and increased accumulation of photosynthetic products (relative to the cultivar D3). PMID:23770596

  9. Coarse-Grained and Atomistic Modeling of Polyimides

    NASA Technical Reports Server (NTRS)

    Clancy, Thomas C.; Hinkley, Jeffrey A.

    2004-01-01

    A coarse-grained model for a set of three polyimide isomers is developed. Each polyimide is comprised of BPDA (3,3,4,4' - biphenyltetracarboxylic dianhydride) and one of three APB isomers: 1,3-bis(4-aminophenoxy)benzene, 1,4-bis(4-aminophenoxy)benzene or 1,3-bis(3-aminophenoxy)benzene. The coarse-grained model is constructed as a series of linked vectors following the contour of the polymer backbone. Beads located at the midpoint of each vector define centers for long range interaction energy between monomer subunits. A bulk simulation of each coarse-grained polyimide model is performed with a dynamic Monte Carlo procedure. These coarsegrained models are then reverse-mapped to fully atomistic models. The coarse-grained models show the expected trends in decreasing chain dimensions with increasing meta linkage in the APB section of the repeat unit, although these differences were minor due to the relatively short chains simulated here. Considerable differences are seen among the dynamic Monte Carlo properties of the three polyimide isomers. Decreasing relaxation times are seen with increasing meta linkage in the APB section of the repeat unit.

  10. Toward a mechanistic modeling of nitrogen limitation on vegetation dynamics

    SciTech Connect

    Xu, Chonggang; Fisher, Rosie; Wullschleger, Stan D; Wilson, Cathy; Cai, Michael; McDowell, Nathan

    2012-01-01

    Nitrogen is a dominant regulator of vegetation dynamics, net primary production, and terrestrial carbon cycles; however, most ecosystem models use a rather simplistic relationship between leaf nitrogen content and photosynthetic capacity. Such an approach does not consider how patterns of nitrogen allocation may change with differences in light intensity, growing-season temperature and CO{sub 2} concentration. To account for this known variability in nitrogen-photosynthesis relationships, we develop a mechanistic nitrogen allocation model based on a trade-off of nitrogen allocated between growth and storage, and an optimization of nitrogen allocated among light capture, electron transport, carboxylation, and respiration. The developed model is able to predict the acclimation of photosynthetic capacity to changes in CO{sub 2} concentration, temperature, and radiation when evaluated against published data of V{sub c,max} (maximum carboxylation rate) and J{sub max} (maximum electron transport rate). A sensitivity analysis of the model for herbaceous plants, deciduous and evergreen trees implies that elevated CO{sub 2} concentrations lead to lower allocation of nitrogen to carboxylation but higher allocation to storage. Higher growing-season temperatures cause lower allocation of nitrogen to carboxylation, due to higher nitrogen requirements for light capture pigments and for storage. Lower levels of radiation have a much stronger effect on allocation of nitrogen to carboxylation for herbaceous plants than for trees, resulting from higher nitrogen requirements for light capture for herbaceous plants. As far as we know, this is the first model of complete nitrogen allocation that simultaneously considers nitrogen allocation to light capture, electron transport, carboxylation, respiration and storage, and the responses of each to altered environmental conditions. We expect this model could potentially improve our confidence in simulations of carbon-nitrogen interactions

  11. Protoplanetary Disk Structure with Grain Evolution: The ANDES Model

    NASA Astrophysics Data System (ADS)

    Akimkin, V.; Zhukovska, S.; Wiebe, D.; Semenov, D.; Pavlyuchenkov, Ya.; Vasyunin, A.; Birnstiel, T.; Henning, Th.

    2013-03-01

    We present a self-consistent model of a protoplanetary disk: "ANDES" ("AccretioN disk with Dust Evolution and Sedimentation"). ANDES is based on a flexible and extendable modular structure that includes (1) a 1+1D frequency-dependent continuum radiative transfer module, (2) a module to calculate the chemical evolution using an extended gas-grain network with UV/X-ray-driven processes and surface reactions, (3) a module to calculate the gas thermal energy balance, and (4) a 1+1D module that simulates dust grain evolution. For the first time, grain evolution and time-dependent molecular chemistry are included in a protoplanetary disk model. We find that grain growth and sedimentation of large grains onto the disk midplane lead to a dust-depleted atmosphere. Consequently, dust and gas temperatures become higher in the inner disk (R <~ 50 AU) and lower in the outer disk (R >~ 50 AU), in comparison with the disk model with pristine dust. The response of disk chemical structure to the dust growth and sedimentation is twofold. First, due to higher transparency a partly UV-shielded molecular layer is shifted closer to the dense midplane. Second, the presence of big grains in the disk midplane delays the freeze-out of volatile gas-phase species such as CO there, while in adjacent upper layers the depletion is still effective. Molecular concentrations and thus column densities of many species are enhanced in the disk model with dust evolution, e.g., CO2, NH2CN, HNO, H2O, HCOOH, HCN, and CO. We also show that time-dependent chemistry is important for a proper description of gas thermal balance.

  12. PROTOPLANETARY DISK STRUCTURE WITH GRAIN EVOLUTION: THE ANDES MODEL

    SciTech Connect

    Akimkin, V.; Wiebe, D.; Pavlyuchenkov, Ya.; Zhukovska, S.; Semenov, D.; Henning, Th.; Vasyunin, A.; Birnstiel, T. E-mail: dwiebe@inasan.ru E-mail: zhukovska@mpia.de E-mail: henning@mpia.de E-mail: tbirnstiel@cfa.harvard.edu

    2013-03-20

    We present a self-consistent model of a protoplanetary disk: 'ANDES' ('AccretioN disk with Dust Evolution and Sedimentation'). ANDES is based on a flexible and extendable modular structure that includes (1) a 1+1D frequency-dependent continuum radiative transfer module, (2) a module to calculate the chemical evolution using an extended gas-grain network with UV/X-ray-driven processes and surface reactions, (3) a module to calculate the gas thermal energy balance, and (4) a 1+1D module that simulates dust grain evolution. For the first time, grain evolution and time-dependent molecular chemistry are included in a protoplanetary disk model. We find that grain growth and sedimentation of large grains onto the disk midplane lead to a dust-depleted atmosphere. Consequently, dust and gas temperatures become higher in the inner disk (R {approx}< 50 AU) and lower in the outer disk (R {approx}> 50 AU), in comparison with the disk model with pristine dust. The response of disk chemical structure to the dust growth and sedimentation is twofold. First, due to higher transparency a partly UV-shielded molecular layer is shifted closer to the dense midplane. Second, the presence of big grains in the disk midplane delays the freeze-out of volatile gas-phase species such as CO there, while in adjacent upper layers the depletion is still effective. Molecular concentrations and thus column densities of many species are enhanced in the disk model with dust evolution, e.g., CO{sub 2}, NH{sub 2}CN, HNO, H{sub 2}O, HCOOH, HCN, and CO. We also show that time-dependent chemistry is important for a proper description of gas thermal balance.

  13. Particle models for discrete element modeling of bulk grain properties of wheat kernels

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent research has shown the potential of discrete element method (DEM) in simulating grain flow in bulk handling systems. Research has also revealed that simulation of grain flow with DEM requires establishment of appropriate particle models for each grain type. This research completes the three-p...

  14. A nucleotide-level coarse-grained model of RNA

    SciTech Connect

    Šulc, Petr; Ouldridge, Thomas E.; Louis, Ard A.; Romano, Flavio; Doye, Jonathan P. K.

    2014-06-21

    We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical, and thermodynamic properties of RNA, and the coarse-graining level aims to retain the relevant physics for RNA hybridization and the structure of single- and double-stranded RNA. In order to explore its strengths and weaknesses, we test the model in a range of nanotechnological and biological settings. Applications explored include the folding thermodynamics of a pseudoknot, the formation of a kissing loop complex, the structure of a hexagonal RNA nanoring, and the unzipping of a hairpin motif. We argue that the model can be used for efficient simulations of the structure of systems with thousands of base pairs, and for the assembly of systems of up to hundreds of base pairs. The source code implementing the model is released for public use.

  15. Coarse-graining of proteins based on elastic network models

    NASA Astrophysics Data System (ADS)

    Sinitskiy, Anton V.; Voth, Gregory A.

    2013-08-01

    To simulate molecular processes on biologically relevant length- and timescales, coarse-grained (CG) models of biomolecular systems with tens to even hundreds of residues per CG site are required. One possible way to build such models is explored in this article: an elastic network model (ENM) is employed to define the CG variables. Free energy surfaces are approximated by Taylor series, with the coefficients found by force-matching. CG potentials are shown to undergo renormalization due to roughness of the energy landscape and smoothing of it under coarse-graining. In the case study of hen egg-white lysozyme, the entropy factor is shown to be of critical importance for maintaining the native structure, and a relationship between the proposed ENM-mode-based CG models and traditional CG-bead-based models is discussed. The proposed approach uncovers the renormalizable character of CG models and offers new opportunities for automated and computationally efficient studies of complex free energy surfaces.

  16. A nucleotide-level coarse-grained model of RNA

    NASA Astrophysics Data System (ADS)

    Šulc, Petr; Romano, Flavio; Ouldridge, Thomas E.; Doye, Jonathan P. K.; Louis, Ard A.

    2014-06-01

    We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical, and thermodynamic properties of RNA, and the coarse-graining level aims to retain the relevant physics for RNA hybridization and the structure of single- and double-stranded RNA. In order to explore its strengths and weaknesses, we test the model in a range of nanotechnological and biological settings. Applications explored include the folding thermodynamics of a pseudoknot, the formation of a kissing loop complex, the structure of a hexagonal RNA nanoring, and the unzipping of a hairpin motif. We argue that the model can be used for efficient simulations of the structure of systems with thousands of base pairs, and for the assembly of systems of up to hundreds of base pairs. The source code implementing the model is released for public use.

  17. Time Dependent Models of Grain Formation Around Carbon Stars

    NASA Technical Reports Server (NTRS)

    Egan, M. P.; Shipman, R. F.

    1996-01-01

    Carbon-rich Asymptotic Giant Branch stars are sites of dust formation and undergo mass loss at rates ranging from 10(exp -7) to 10(exp -4) solar mass/yr. The state-of-the-art in modeling these processes is time-dependent models which simultaneously solve the grain formation and gas dynamics problem. We present results from such a model, which also includes an exact solution of the radiative transfer within the system.

  18. Probabilistic modeling of solidification grain structure in investment castings

    SciTech Connect

    Upadhya, G.K.; Yu, K.O.; Layton, M.A.; Paul, A.J.

    1995-12-31

    A probabilistic approach for modeling the evolution of grain structure in investment castings has been developed. The approach differs from the classical Monte Carlo simulations of microstructural evolution in that it uses the results from a heat transfer simulation of the investment casting process for determining the probabilities of nucleation and growth. The model was used to predict the solidification grain structure in castings. The model is quasi-3D, since it uses the information from a 3D simulation of heat transfer to predict the grain structure developed in any 2D-section of the casting. Structural transitions such as columnar/equiaxed transition can also be predicted, using suitable transition criteria. Results from the model have been validated by comparison with actual micrographs from experimental investment castings. In the first case, simulations were performed for a simple plate shaped casting of superalloy Rene 77. The effects of mold insulation as well as metal pour and mold preheat temperatures on the grain size of the casting were studied. In the second example, the casting of a complex-shaped jet engine component made of superalloy IN718 was simulated. Simulation results were seen to match very well with experiments.

  19. Models for the Microwave Dielectric Properties of Grain and Seed

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Based on microwave dielectric properties of wheat, corn, barley, oats, grain sorghum, soybeans, canola, shelled peanuts and pod peanuts measured over ranges of frequency and moisture content, models are developed for predicting the dielectric constant and loss factor of these commodities. Nearly li...

  20. Coarse-grained models for aqueous polyethylene glycol solutions.

    PubMed

    Choi, Eunsong; Mondal, Jagannath; Yethiraj, Arun

    2014-01-01

    A new coarse-grained force field is developed for polyethylene glycol (PEG) in water. The force field is based on the MARTINI model but with the big multipole water (BMW) model for the solvent. The polymer force field is reparameterized using the MARTINI protocol. The new force field removes the ring-like conformations seen in simulations of short chains with the MARTINI force field; these conformations are not observed in atomistic simulations. We also investigate the effect of using parameters for the end-group that are different from those for the repeat units, with the MARTINI and BMW/MARTINI models. We find that the new BMW/MARTINI force field removes the ring-like conformations seen in the MARTINI models and has more accurate predictions for the density of neat PEG. However, solvent-separated-pairs between chain ends and slow dynamics of the PEG reflect its own artifacts. We also carry out fine-grained simulations of PEG with bundled water clusters and show that the water bundling can lead to ring-like conformations of the polymer molecules. The simulations emphasize the pitfalls of coarse-graining several molecules into one site and suggest that polymer-solvent systems might be a stringent test for coarse-grained force fields. PMID:24350686

  1. Microwave Dielectric Properties Models for Grain and Seed

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Based on microwave dielectric properties of wheat, corn, barley, oats, grain sorghum, soybeans, canola, shelled peanuts and pod peanuts measured over ranges of frequency and moisture content, models are developed for predicting the dielectric constant and loss factor of these commodities. Nearly lin...

  2. Release of noble gases and nitrogen from grain-surface sites in lunar ilmenite by closed-system oxidation

    NASA Technical Reports Server (NTRS)

    Frick, U.; Becker, R. H.; Pepin, R. O.

    1986-01-01

    Noble gases and nitrogen were extracted from a 100 to 150 microns ilmenite separate from lunar soil 71501 by closed system stepped heating in approx. 10 torr O2 at 300 C, 400 C, 500 C, 600 C and 630 C, followed by stepped pyrolysis at ten temperatures between 680 C and approx. 1500 C. The five oxidation steps together liberated approx. 65% of the total He-4, 45% of the Ne-20, 23% of the N-14 and Ar-36, 12% of the Kr-84 and 8% of the Xe-132 in the sample; Ne-20/Ar-36 and Ne-20/Ne-22 ratios agree with the solar wind composition experiment, and Kr-84/Ar-36 and Xe-132/Ar-36 are within approx. 10% of Cameron's estimates for the sun and solar wind. The remaining gases, released above 630 C by pyrolysis, are strongly fractionated with respect to the SWC-Cameron solar wind elemental composition. Large concentrations of fractionated noble gases in grain interiors, their virtual absence in the relatively unfractionated surface gas reservoir, and the high N/noble gas ratio all imply that most of the solar wind noble gases initially implanted in grain surfaces are eventually lost by diffusion. Loss limits can be estimated by considering two given scenarios. It is concluded tat approx. 70 to 97% or more of the Ar implanted in 71501 ilmenite grains has diffusively escaped.

  3. Variations in Protein Concentration and Nitrogen Sources in Different Positions of Grain in Wheat

    PubMed Central

    Li, Xiangnan; Zhou, Longjing; Liu, Fulai; Zhou, Qin; Cai, Jian; Wang, Xiao; Dai, Tingbo; Cao, Weixing; Jiang, Dong

    2016-01-01

    The distribution patterns of total protein and protein components in different layers of wheat grain were investigated using the pearling technique, and the sources of different protein components and pearling fractions were identified using 15N isotope tracing methods. It was found that N absorbed from jointing to anthesis (JA) and remobilized to the grain after anthesis was the principal source of grain N, especially in the outer layer. For albumin and globulin, the amount of N absorbed during different stages all showed a decreasing trend from the surface layer to the center part. Whereas, for globulin and glutenin, the N absorbed after anthesis accounted for the main part indicating that for storage protein, the utilization of N assimilated after anthesis is greater than that of the stored N assimilated before anthesis. It is concluded that manipulation of the N application rate during different growth stages could be an effective approach to modulate the distribution of protein fractions in pearled grains for specific end-uses. PMID:27446169

  4. Crop rotation affects corn, grain sorghum, and soybean yields and nitrogen recovery

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Long-term cropping system and fertilizer N studies are essential towards understanding production potential and yield stability of corn (Zea mays L.), grain sorghum [Sorghum bicolor (L.) Moench], and soybean [Glycine max (L.) Merr.] in rain-fed environments. A no-till experiment (2007-13) was conduc...

  5. Optimization of Analytical Potentials for Coarse-Grained Biopolymer Models.

    PubMed

    Mereghetti, Paolo; Maccari, Giuseppe; Spampinato, Giulia Lia Beatrice; Tozzini, Valentina

    2016-08-25

    The increasing trend in the recent literature on coarse grained (CG) models testifies their impact in the study of complex systems. However, the CG model landscape is variegated: even considering a given resolution level, the force fields are very heterogeneous and optimized with very different parametrization procedures. Along the road for standardization of CG models for biopolymers, here we describe a strategy to aid building and optimization of statistics based analytical force fields and its implementation in the software package AsParaGS (Assisted Parameterization platform for coarse Grained modelS). Our method is based on the use and optimization of analytical potentials, optimized by targeting internal variables statistical distributions by means of the combination of different algorithms (i.e., relative entropy driven stochastic exploration of the parameter space and iterative Boltzmann inversion). This allows designing a custom model that endows the force field terms with a physically sound meaning. Furthermore, the level of transferability and accuracy can be tuned through the choice of statistical data set composition. The method-illustrated by means of applications to helical polypeptides-also involves the analysis of two and three variable distributions, and allows handling issues related to the FF term correlations. AsParaGS is interfaced with general-purpose molecular dynamics codes and currently implements the "minimalist" subclass of CG models (i.e., one bead per amino acid, Cα based). Extensions to nucleic acids and different levels of coarse graining are in the course. PMID:27150459

  6. Green manures in continuous wheat systems affect grain yield and nitrogen content

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Continuous winter wheat (Triticum aestivum L. em Thell.) is the foundation for most U.S. southern Great Plains (SGP) agriculture. Inorganic nitrogen (N) fertilizers are important to wheat production, but increasing N prices have caused farmers to reconsider growing legumes during summer fallow for ‘...

  7. Response of corn grain, cellulosic biomass, and ethanol yields to nitrogen fertilization

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Corn (Zea mays L.) stover will likely play an integral role in near-term attempts to produce renewable cellulosic transportation fuels. However, little is known regarding the influence of nitrogen (N) fertilization on biomass and ethanol yields of stover and cobs. The objectives were to evaluate the...

  8. Modelling the ecosystem effects of nitrogen deposition: Model of Ecosystem Retention and Loss of Inorganic Nitrogen (MERLIN

    NASA Astrophysics Data System (ADS)

    Cosby, B. J.; Ferrier, R. C.; Jenkins, A.; Emmett, B. A.; Wright, R. F.; Tietema, A.

    A catchment-scale mass-balance model of linked carbon and nitrogen cycling in ecosystems has been developed for simulating leaching losses of inorganic nitrogen. The model (MERLIN) considers linked biotic and abiotic processes affecting the cycling and storage of nitrogen. The model is aggregated in space and time and contains compartments intended to be observable and/or interpretable at the plot or catchment scale. The structure of the model includes the inorganic soil, a plant compartment and two soil organic compartments. Fluxes in and out of the ecosystem and between compartments are regulated by atmospheric deposition, hydrological discharge, plant uptake, litter production, wood production, microbial immobilization, mineralization, nitrification, and denitrification. Nitrogen fluxes are controlled by carbon productivity, the C:N ratios of organic compartments and inorganic nitrogen in soil solution. Inputs required are: 1) temporal sequences of carbon fluxes and pools- 2) time series of hydrological discharge through the soils, 3) historical and current external sources of inorganic nitrogen; 4) current amounts of nitrogen in the plant and soil organic compartments; 5) constants specifying the nitrogen uptake and immobilization characteristics of the plant and soil organic compartments; and 6) soil characteristics such as depth, porosity, bulk density, and anion/cation exchange constants. Outputs include: 1) concentrations and fluxes of NO3 and NH4 in soil solution and runoff; 2) total nitrogen contents of the organic and inorganic compartments; 3) C:N ratios of the aggregated plant and soil organic compartments; and 4) rates of nitrogen uptake and immobilization and nitrogen mineralization. The behaviour of the model is assessed for a combination of land-use change and nitrogen deposition scenarios in a series of speculative simulations. The results of the simulations are in broad agreement with observed and hypothesized behaviour of nitrogen dynamics in

  9. Coarse-Grained Model of SNARE-Mediated Docking

    PubMed Central

    Fortoul, Nicole; Singh, Pankaj; Hui, Chung-Yuen; Bykhovskaia, Maria; Jagota, Anand

    2015-01-01

    Synaptic transmission requires that vesicles filled with neurotransmitter molecules be docked to the plasma membrane by the SNARE protein complex. The SNARE complex applies attractive forces to overcome the long-range repulsion between the vesicle and membrane. To understand how the balance between the attractive and repulsive forces defines the equilibrium docked state we have developed a model that combines the mechanics of vesicle/membrane deformation with an apparently new coarse-grained model of the SNARE complex. The coarse-grained model of the SNARE complex is calibrated by comparison with all-atom molecular dynamics simulations as well as by force measurements in laser tweezer experiments. The model for vesicle/membrane interactions includes the forces produced by membrane deformation and hydration or electrostatic repulsion. Combining these two parts, the coarse-grained model of the SNARE complex with membrane mechanics, we study how the equilibrium docked state varies with the number of SNARE complexes. We find that a single SNARE complex is able to bring a typical synaptic vesicle to within a distance of ∼3 nm from the membrane. Further addition of SNARE complexes shortens this distance, but an overdocked state of >4–6 SNAREs actually increases the equilibrium distance. PMID:25954883

  10. Coarse-Grained Model of SNARE-Mediated Docking.

    PubMed

    Fortoul, Nicole; Singh, Pankaj; Hui, Chung-Yuen; Bykhovskaia, Maria; Jagota, Anand

    2015-05-01

    Synaptic transmission requires that vesicles filled with neurotransmitter molecules be docked to the plasma membrane by the SNARE protein complex. The SNARE complex applies attractive forces to overcome the long-range repulsion between the vesicle and membrane. To understand how the balance between the attractive and repulsive forces defines the equilibrium docked state we have developed a model that combines the mechanics of vesicle/membrane deformation with an apparently new coarse-grained model of the SNARE complex. The coarse-grained model of the SNARE complex is calibrated by comparison with all-atom molecular dynamics simulations as well as by force measurements in laser tweezer experiments. The model for vesicle/membrane interactions includes the forces produced by membrane deformation and hydration or electrostatic repulsion. Combining these two parts, the coarse-grained model of the SNARE complex with membrane mechanics, we study how the equilibrium docked state varies with the number of SNARE complexes. We find that a single SNARE complex is able to bring a typical synaptic vesicle to within a distance of ∼ 3 nm from the membrane. Further addition of SNARE complexes shortens this distance, but an overdocked state of >4-6 SNAREs actually increases the equilibrium distance. PMID:25954883

  11. The Grain Evolution Model for Icy Grains Ejected from 9P/Tempel 1 by Deep Impact

    NASA Astrophysics Data System (ADS)

    Beer, E.; Wooden, D. H.; Schulz, R.

    The GEM (Grain Evolution Model) is a unique model which follows the cometary icy grains from the moment of ejection until complete sublimation. The model takes into accounts the different forces acting on each and every grain from the initial distribution, as they are passing through the coma and sublimating. The GEM is sensitive to the wavelength and composition of the grains and therefore can anticipate which grains can better match the observations at a certain wavelength. The GEM can predict the brightness of the entire coma in steady state, or as in the Deep Impact Mission it can calculate the coma brightness at different cross sections of time while differentiating between the contribution of the nucleus and that of the grains. In this paper we will show that nearly pure ice grains, i.e. 1-5% of Pyroxene, match the observations from the Deep Impact Mission since they can give a reasonable explanation for the UV enhanced rapid and decline after 20-30 minutes. Furthermore nearly pure ice grains explain the sustained brightness in the UV that lasts 7-14 hours[20

  12. Coarse-Grained Models for Protein-Cell Membrane Interactions

    PubMed Central

    Bradley, Ryan; Radhakrishnan, Ravi

    2015-01-01

    The physiological properties of biological soft matter are the product of collective interactions, which span many time and length scales. Recent computational modeling efforts have helped illuminate experiments that characterize the ways in which proteins modulate membrane physics. Linking these models across time and length scales in a multiscale model explains how atomistic information propagates to larger scales. This paper reviews continuum modeling and coarse-grained molecular dynamics methods, which connect atomistic simulations and single-molecule experiments with the observed microscopic or mesoscale properties of soft-matter systems essential to our understanding of cells, particularly those involved in sculpting and remodeling cell membranes. PMID:26613047

  13. Modeling Nitrogen Losses under Rapid Infiltration Basins

    NASA Astrophysics Data System (ADS)

    Akhavan, M.; Imhoff, P. T.; Andres, A. S.; Finsterle, S.

    2011-12-01

    Rapid Infiltration Basin System (RIBS) is one of the major land treatment techniques used for wastewater treatment and reuse of recovered treated wastewater. In this system, wastewater that is treated using primary, secondary, or advanced treatment techniques is applied at high rates to shallow basins constructed in permeable deposits of soil or sand, with further treatment occurring in soil and the vadose zone before the water recharges groundwater. Because the influent wastewater is usually enriched in nitrogen (N) compounds, there is particular concern that RIBS may contaminant groundwater or nearby surface waters if not designed and operated properly. In most of the new sequenced batch reactor (SBR) wastewater treatment plants, N is found in the form of nitrate in the discharged wastewater, so denitrification (DNF) is the main reaction in N removal. The absence of molecular oxygen is one of the required conditions for DNF. During RIBS operation, application of wastewater is cyclic and typically consists of a flooding period followed by days or weeks of drying. Key operational parameters include the ratio of wetting to drying time and the hydraulic loading rate, which affect water saturation and air content in the vadose zone and as a result have an impact on DNF. Wastewater is typically distributed at a limited number of discharge points in RIBS and basins are not usually completely flooded which result in non-homogeneous distribution of wastewater and unusual surface water flow patterns. For this reason, we couple overland flow within RIBS with subsurface flow to investigate the influence of non-uniform application of wastewater on DNF. No modeling effort has been done for understanding this aspect of RIBS performance previously. TOUGH2/ iTOUGH2, a general-purpose numerical simulation program for multi-phase fluid flow in porous media, is used for modeling fluid movement. Water saturation is used as a surrogate parameter to evaluate oxygen limitations in the

  14. Acceleration of the rate of ethanol fermentation by addition of nitrogen in high tannin grain sorghum

    SciTech Connect

    Mullins, J.T.; NeSmith, C.C.

    1987-01-01

    In this communication, the authors show that accelerated rates of ethanol production, comparable to sorghum varieties containing low levels of tannins and to corn, can occur without the removal of the tannins. The basis of the inhibition appears to be a lack of sufficient nitrogen in the mash for protein synthesis required to support an accelerated fermentative metabolism in Saccharomyces. No inhibition of the enzymes used for starch hydrolysis was found.

  15. Polarimetric Models of Circumstellar Discs Including Aggregate Dust Grains

    NASA Astrophysics Data System (ADS)

    Mohan, Mahesh

    The work conducted in this thesis examines the nature of circumstellar discs by investigating irradiance and polarization of scattered light. Two circumstellar discs are investigated. Firstly, H-band high contrast imaging data on the transitional disc of the Herbig Ae/Be star HD169142 are presented. The images were obtained through the polarimetric differential imaging (PDI) technique on the Very Large Telescope (VLT) using the adaptive optics system NACO. Our observations use longer exposure times, allowing us to examine the edges of the disc. Analysis of the observations shows distinct signs of polarization due to circumstellar material, but due to excessive saturation and adaptive optics errors further information on the disc could not be inferred. The HD169142 disc is then modelled using the 3D radiative transfer code Hyperion. Initial models were constructed using a two disc structure, however recent PDI has shown the existence of an annular gap. In addition to this the annular gap is found not to be devoid of dust. This then led to the construction of a four-component disc structure. Estimates of the mass of dust in the gap (2.10E-6 Msun) are made as well as for the planet (1.53E-5 Msun (0.016 Mjupiter)) suspected to be responsible for causing the gap. The predicted polarization was also estimated for the disc, peaking at ~14 percent. The use of realistic dust grains (ballistic aggregate particles) in Monte Carlo code is also examined. The fortran code DDSCAT is used to calculate the scattering properties for aggregates which are used to replace the spherical grain models used by the radiative transfer code Hyperion. Currently, Hyperion uses four independent elements to define the scattering matrix, therefore the use of rotational averaging and a 50/50 percent population of grains and their enantiomers were explored to reduce the number of contributing scattering elements from DDSCAT. A python script was created to extract the scattering data from the DDSCAT

  16. Chesapeake Bay nitrogen fluxes derived from a land-estuarine ocean biogeochemical modeling system: Model description, evaluation, and nitrogen budgets

    NASA Astrophysics Data System (ADS)

    Feng, Yang; Friedrichs, Marjorie A. M.; Wilkin, John; Tian, Hanqin; Yang, Qichun; Hofmann, Eileen E.; Wiggert, Jerry D.; Hood, Raleigh R.

    2015-08-01

    The Chesapeake Bay plays an important role in transforming riverine nutrients before they are exported to the adjacent continental shelf. Although the mean nitrogen budget of the Chesapeake Bay has been previously estimated from observations, uncertainties associated with interannually varying hydrological conditions remain. In this study, a land-estuarine-ocean biogeochemical modeling system is developed to quantify Chesapeake riverine nitrogen inputs, within-estuary nitrogen transformation processes and the ultimate export of nitrogen to the coastal ocean. Model skill was evaluated using extensive in situ and satellite-derived data, and a simulation using environmental conditions for 2001-2005 was conducted to quantify the Chesapeake Bay nitrogen budget. The 5 year simulation was characterized by large riverine inputs of nitrogen (154 × 109 g N yr-1) split roughly 60:40 between inorganic:organic components. Much of this was denitrified (34 × 109 g N yr-1) and buried (46 × 109 g N yr-1) within the estuarine system. A positive net annual ecosystem production for the bay further contributed to a large advective export of organic nitrogen to the shelf (91 × 109 g N yr-1) and negligible inorganic nitrogen export. Interannual variability was strong, particularly for the riverine nitrogen fluxes. In years with higher than average riverine nitrogen inputs, most of this excess nitrogen (50-60%) was exported from the bay as organic nitrogen, with the remaining split between burial, denitrification, and inorganic export to the coastal ocean. In comparison to previous simulations using generic shelf biogeochemical model formulations inside the estuary, the estuarine biogeochemical model described here produced more realistic and significantly greater exports of organic nitrogen and lower exports of inorganic nitrogen to the shelf.

  17. Moving Beyond Watson-Crick Models of Coarse Grained DNA

    NASA Astrophysics Data System (ADS)

    Dorfman, Kevin; Linak, Margaret; Tourdot, Richard

    2012-02-01

    DNA structure possesses several levels of complexity, ranging from the sequence of bases (primary structure) to base pairing (secondary structure) to its three-dimensional shape (tertiary structure) and can produce a wide variety of conformations in addition to canonical double stranded DNA. By including non-Watson-Crick interactions in a coarse-grained model, we developed a system that not only can capture the traditional B-form double helix, but also can adopt a wide variety of other DNA conformations. In our experimentally parameterized, coarse-grained DNA model we are able to reproduce the microscopic features of double-stranded DNA without the need for explicit constraints and capture experimental melting curves for a number of short DNA hairpins. We demonstrate the utility of the model by simulating more complex tertiary structures such as the folding of the thrombin aptamer, which includes G-quartets, and strand invasion during triplex formation. Our results highlight the importance of non-canonical interactions in DNA coarse- grained models.

  18. Insights on protein-DNA recognition by coarse grain modelling

    PubMed Central

    Poulain, Pierre; Saladin, Adrien; Hartmann, Brigitte; Prévost, Chantal

    2008-01-01

    Coarse grain modelling of macromolecules is a new approach potentially well adapted to answer numerous issues, ranging from physics to biology. We propose here an original DNA coarse grain model specifically dedicated to protein–DNA docking, a crucial, but still largely unresolved, question in molecular biology. Using a representative set of protein–DNA complexes, we first show that our model is able to predict the interaction surface between the macromolecular partners taken in their bound form. In a second part, the impact of the DNA sequence and electrostatics, together with the DNA and protein conformations on docking is investigated. Our results strongly suggest that the overall DNA structure mainly contributes in discriminating the interaction site on cognate proteins. Direct electrostatic interactions between phosphate groups and amino acids side chains strengthen the binding. Overall, this work demonstrates that coarse grain modelling can reveal itself a precious auxiliary for a general and complete description and understanding of protein–DNA association mechanisms. PMID:18478582

  19. Modeling grain-scale thermoelastic stresses on airless bodies

    NASA Astrophysics Data System (ADS)

    Molaro, J.; Byrne, S.

    2013-12-01

    Thermal stress weathering is the mechanical breakdown of rock from expansion and contraction caused by changes in temperature. Damage occurs in the form of microscopic cracks that result from a thermal cycle or thermal shock. This process may play an important role in the evolution of airless landscapes, by contributing to regolith production and crater degradation. Without the presence of an atmosphere, rock surfaces experience very dramatic temperature changes that induce high thermoelastic stresses in the near sub-surface. The thermoelastic behavior of each surface is primarily controlled by its distance to the sun and its solar day length, providing a unique experience on each body. For example, slowly rotating bodies that are close to the sun (such as Mercury) experience a very wide diurnal temperature range. Bodies further from the sun (such as NEAs) have a much smaller range, but rotate quickly and experience rapid temperature 'shocks' during sunrise/set. While many studies suggest stresses induced by these temperature changes may cause rock breakdown, the extent of the damage produced as a result is unknown. In this study, we modeled thermoelastic stresses produced on airless surfaces at the mineral grain scale. Finite Element Analysis of Microstructures (OOF2) is a 2-D finite element modeling program, developed at NIST and designed to help scientists calculate macroscopic properties of real or simulated microstructures. This allows us to model thermal behavior of microstructures with varying grain sizes and thermophysical properties, and to explore the relationship between the spatial and temporal temperature gradients and stress. Using OOF2, we imposed the solar and conductive fluxes calculated by our 1-D thermal model at the surface and at 5mm depth on a microstructure. The microstructure has bulk properties typical of a basalt, and a grain size of ~0.3 mm. We assigned 20% and 80% of the grains a thermal conductivity of 1 and 3 W/mK, respectively. The

  20. [Effects of controlled-release fertilizers on summer maize grain yield, field ammonia volatilization, and fertilizer nitrogen use efficiency].

    PubMed

    Zhao, Bin; Dong, Shu-Ting; Wang, Kong-Jun; Zhang, Ji-Wang; Liu, Peng

    2009-11-01

    A field experiment with colophony-coated fertilizer (CRF) and sulfur-coated fertilizer (SCF) showed that under the same application rates of N, P and K, applying CRF and SCF increased the summer maize grain yield by 13.15% and 14.15%, respectively, compared to the application of common compound fertilizer CCF. When the applied amount of CRF and SCF was decreased by 25%, the yield increment was 9.69% and 10.04%, respectively; and when the applied amount of CRF and SCF was decreased by 50%, the yield had less difference with that under CCF application. The field ammonia volatilization rate in treatments CRF and SCF increased slowly, with a peak appeared 7 days later than that in treatment CCF, and the total amount of ammonia volatilization in treatments CRF and SCF was ranged from 0.78 kg N x hm(-2) to 4.43 kg N x hm(-2), with a decrement of 51.34%-91.34% compared to that in treatment CCF. The fertilizer nitrogen use efficiency and agronomic nitrogen use efficiency of CRF and SCF were also significantly higher than those of CCF. PMID:20136000

  1. [Modelling nitrogen and phosphorus transfer in Potamogeton malaianus Miq. decompostion].

    PubMed

    Han, Hong-Juan; Zhai, Shui-Jing; Hu, Wei-Ping

    2010-06-01

    Potamogeton malaianus Miq. is one of the dominant species of submerged aquatic vegetations in Lake Taihu, China. The decomposition of its debris and metabolic detritus is an important part of nutrients cycling in the lake water. Nitrogen and phosphorus transfer model in P. malaianus Miq. decomposition has been set up based on an indoor P. malaianus Miq. decomposition experiment to quantitatively characterize the decomposition process. It mainly focuses on the dissolving process of inorganic nitrogen and phosphorus in P. malaianus Miq., the degradation process of its organic nitrogen and phosphorus, and the boundary's adsorbing process of nitrogen and phosphorus in water. There are eight state variables in the model, including inorganic and organic nitrogen in P. malaianus Miq., inorganic and organic phosphorus in P. malaianus Miq., total nitrogen and total phosphorus in water, and nitrogen and phosphorus adsorbed on container boundary. The model calibration showed a good accordance with the observed results of P. malaianus Miq. decomposition experiment. The dissolve rates of inorganic nitrogen and phosphorus in P. malaianus Miq. are 0.04 d(-1) and 0.06 d(-1) respectively. And the decompose rates of these two state variables are 0.005 25 d(-1) and 0.010 44 d(-1) respectively. Model outputs show that 6.7% nitrogen and 35.8% phosphorus can release from P. malaianus Miq. in the former 5 days. Phosphorus release is prior to nitrogen due to the bigger inorganic/organic ratio of phosphorus than that of nitrogen in P. malaianus Miq., Decomposition of P. malaianus Miq. could be affected by water temperature, and the affection is slight when water temperature is lower according to the model. The model also showed that P. malaianus Miq. decomposition process has influences on water quality in the former days, which can be eliminated by adsorbing process later. PMID:20698260

  2. Effects of grain models on UV penetration into clouds

    NASA Astrophysics Data System (ADS)

    Chlewicki, G.; Greenberg, J. M.

    1984-12-01

    A derivation of the average scattering characteristics of interstellar grains in the ultraviolet based mainly on observations of extinction is shown to be more reliable than a determination from direct measures of scattered light. Several representative scattering models are constructed and their consequences for the transfer of UV radiation in clouds are discussed using the spherical harmonic expansion method (Flannery, Roberge and Rybicki 1980). Because of the presence of large grains (of about 0.15 microns) in the size distribution, all models are characterized by strongly anisotropic scattering throughout UV range (from about 0.7 to 0.9) with a relatively low albedo (less than 0.4 for wavelength greater than 2500 A) resulting from the presence of very small grains (no greater than 0.01 microns). An approximate algorithm replacing the exact solution of the radiative transfer equation by a greatly simplified solution for g = 1 is presented. It is shown to be accurate to within less than 10 percent at low and intermediate optical depths for values of g greater than 0.7 and albedos lower than 0.4 and to give a deviation of less than a factor of 2 for g as low as 0.5.

  3. Entrainment of coarse grains using a discrete particle model

    SciTech Connect

    Valyrakis, Manousos; Arnold, Roger B. Jr.

    2014-10-06

    Conventional bedload transport models and incipient motion theories relying on a time-averaged boundary shear stress are incapable of accounting for the effects of fluctuating near-bed velocity in turbulent flow and are therefore prone to significant errors. Impulse, the product of an instantaneous force magnitude and its duration, has been recently proposed as an appropriate criterion for quantifying the effects of flow turbulence in removing coarse grains from the bed surface. Here, a discrete particle model (DPM) is used to examine the effects of impulse, representing a single idealized turbulent event, on particle entrainment. The results are classified according to the degree of grain movement into the following categories: motion prior to entrainment, initial dislodgement, and energetic displacement. The results indicate that in all three cases the degree of particle motion depends on both the force magnitude and the duration of its application and suggest that the effects of turbulence must be adequately accounted for in order to develop a more accurate method of determining incipient motion. DPM is capable of simulating the dynamics of grain entrainment and is an appropriate tool for further study of the fundamental mechanisms of sediment transport.

  4. First principles modeling of grain boundaries in CdTe

    NASA Astrophysics Data System (ADS)

    Chan, Maria K. Y.; Sen, Fatih; Buurma, Christopher; Paulauskas, Tadas; Sun, Ce; Kim, Moon; Klie, Robert

    The role of extended defects is of significant interest for semiconductors, especially photovoltaics since energy conversion efficiencies are often affected by such defects. In particular, grain boundaries in CdTe photovoltaics are enigmatic since the achievable efficiencies of CdTe photovoltaics are higher in polycrystalline devices as compared to single crystalline devices. Yet, despite recent advances, the efficiency of poly-CdTe devices are still substantially below the theoretical maximum. We carry out an atomistic-level study using Scanning Transmission Electron Microscopy (STEM), together with first principles density functional theory (DFT) modeling, in order to understand the properties of specific bicrystals, i.e. artificial grain boundaries, constructed using wafer bonding. We discuss examples of bicrystals, including some involving large scale DFT calculations, and trends in defect and electronic properties. This work was funded by DOE SunShot BRIDGE program.

  5. Investigating the impact of representation upon coarse-grained models

    NASA Astrophysics Data System (ADS)

    Foley, Thomas; Shell, M. Scott; Noid, William

    The first step in building a coarse-grained (CG) model is choosing a representation or `mapping' of the original system at a reduced resolution. In practice, the mapping is often chosen on the basis of `physical intuition.' Consequently this crucial step would greatly benefit from the development of systematic and principled methodologies. Accordingly, we have studied the relationship between the mapping and the resulting CG model. As a starting point, we have analytically derived, as a function of the CG mapping, the exact many-body potential of mean force (PMF) for the simple Gaussian Network Model (GNM) of protein fluctuations. We use this as a simple model for investigating the effect of the CG mapping upon the information loss and quality of the CG model. Moreover, by considering the GNM's for different proteins, we investigate the significance of high resolution structural features for the quality of the CG model. We acknowledge support from the NSF, Alfred P. Sloan Foundation, and KITP.

  6. Model of evolution of surface grain structure under ion bombardment

    SciTech Connect

    Knyazeva, Anna G.; Kryukova, Olga N.

    2014-11-14

    Diffusion and chemical reactions in multicomponent systems play an important role in numerous technology applications. For example, surface treatment of materials and coatings by particle beam leads to chemical composition and grain structure change. To investigate the thermal-diffusion and chemical processes affecting the evolution of surface structure, the mathematical modeling is efficient addition to experiment. In this paper two-dimensional model is discussed to describe the evolution of titanium nitride coating on the iron substrate under implantation of boron and carbon. The equation for diffusion fluxes and reaction rate are obtained using Gibbs energy expansion into series with respect to concentration and their gradients.

  7. Modeling nitrogen cycling in forested watersheds of Chesapeake Bay

    SciTech Connect

    Hunsaker, C.T.; Garten, C.T.; Mulholland, P.J.

    1995-03-01

    The Chesapeake Bay Agreement calls for a 40% reduction of controllable phosphorus and nitrogen to the tidal Bay by the year 2000. To accomplish this goal the Chesapeake Bay Program needs accurate estimates of nutrient loadings, including atmospheric deposition, from various land uses. The literature was reviewed on forest nitrogen pools and fluxes, and nitrogen data from research catchments in the Chesapeake Basin were identified. The structure of a nitrogen module for forests is recommended for the Chesapeake Bay Watershed Model along with the possible functional forms for fluxes.

  8. Effects of corn processing method and dietary inclusion of wet distiller's grain with solubles on carbon-nitrogen balance of finishing cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The growing ethanol industry in the Southern Great Plains has increased the use of wet distiller's grains with solubles (WDGS) in beef cattle finishing diets. Effects of corn processing method and WDGS on carbon (C) and nitrogen (N) balance were evaluated in four Jersey steers using respiration calo...

  9. The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

    PubMed Central

    Noid, W. G.; Liu, Pu; Wang, Yanting; Chu, Jhih-Wei; Ayton, Gary S.; Izvekov, Sergei; Andersen, Hans C.; Voth, Gregory A.

    2008-01-01

    The multiscale coarse-graining (MS-CG) method [S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 (2005);J. Chem. Phys. 123, 134105 (2005)] employs a variational principle to determine an interaction potential for a CG model from simulations of an atomically detailed model of the same system. The companion paper proved that, if no restrictions regarding the form of the CG interaction potential are introduced and if the equilibrium distribution of the atomistic model has been adequately sampled, then the MS-CG variational principle determines the exact many-body potential of mean force (PMF) governing the equilibrium distribution of CG sites generated by the atomistic model. In practice, though, CG force fields are not completely flexible, but only include particular types of interactions between CG sites, e.g., nonbonded forces between pairs of sites. If the CG force field depends linearly on the force field parameters, then the vector valued functions that relate the CG forces to these parameters determine a set of basis vectors that span a vector subspace of CG force fields. The companion paper introduced a distance metric for the vector space of CG force fields and proved that the MS-CG variational principle determines the CG force force field that is within that vector subspace and that is closest to the force field determined by the many-body PMF. The present paper applies the MS-CG variational principle for parametrizing molecular CG force fields and derives a linear least squares problem for the parameter set determining the optimal approximation to this many-body PMF. Linear systems of equations for these CG force field parameters are derived and analyzed in terms of equilibrium structural correlation functions. Numerical calculations for a one-site CG model of methanol and a molecular CG model of the EMIM+∕NO3− ionic liquid are provided to illustrate the method. PMID:18601325

  10. Modeling Nitrogen Leaching With A Biogeochemical Model Coupled With Soil Hydrology Model

    NASA Astrophysics Data System (ADS)

    Barman, R.; Yang, X.; Jain, A.; Post, W. M.; Sivapalan, M.

    2008-12-01

    Land use changes for cropland, excessive application of fertilizers in agriculture, and increase in anthropogenic activities such as fossil fuel burning have lead to widespread increases in anthropogenic production of reactive N and NH3 emissions, and N deposition rates. An important consequence of these processes is intensification of soil nutrient leaching activities, leading to serious ground water contamination problems. The current study focuses on the issue of nitrogen (nitrate and ammonium) leaching due to land cover changes for cropland, excess N fertilizer application, and atmospheric nitrogen deposition on nitrogen leaching at a global scale. Simulations of nitrogen leaching require integration of processes involving soil hydrology and biogeochemical cycles. An existing terrestrial coupled carbon-nitrogen cycle model, Integrated Science Assessment Model (ISAM), was used to estimate nitrogen leaching. The N-cycle in ISAM includes the major processes associated with nitrogen (immobilization, mineralization, nitrification, denitrification, leaching, nitrogen fixation, and vegetation nitrogen uptake). ISAM also considers how carbon and nitrogen dynamics are influenced by the effects of human perturbations to the N cycle including atmospheric deposition and fertilizer application, and the fate of N in land use activities, i.e., deforestation and agricultural harvest. In this study, the ISAM soil hydrology was extended and improved with CLM 3.5 hydrology processes and algorithms, which extended the modeling capabilities to consider the prediction of nitrogen leaching. The model performance was evaluated with flow and nutrient data at several locations within the Upper Sangamon River Basin in Illinois, and flow data in contrasting watersheds in Oklahoma. This talk will focus on describing the results of a series of modeling experiments examining the influence of land management changes for cropland and nitrogen deposition on nitrogen leaching at a global scale

  11. A coarse-grained model of microtubule self-assembly

    NASA Astrophysics Data System (ADS)

    Regmi, Chola; Cheng, Shengfeng

    Microtubules play critical roles in cell structures and functions. They also serve as a model system to stimulate the next-generation smart, dynamic materials. A deep understanding of their self-assembly process and biomechanical properties will not only help elucidate how microtubules perform biological functions, but also lead to exciting insight on how microtubule dynamics can be altered or even controlled for specific purposes such as suppressing the division of cancer cells. Combining all-atom molecular dynamics (MD) simulations and the essential dynamics coarse-graining method, we construct a coarse-grained (CG) model of the tubulin protein, which is the building block of microtubules. In the CG model a tubulin dimer is represented as an elastic network of CG sites, the locations of which are determined by examining the protein dynamics of the tubulin and identifying the essential dynamic domains. Atomistic MD modeling is employed to directly compute the tubulin bond energies in the surface lattice of a microtubule, which are used to parameterize the interactions between CG building blocks. The CG model is then used to study the self-assembly pathways, kinetics, dynamics, and nanomechanics of microtubules.

  12. Simultaneous Modeling of Transient Creep and Grain Boundary Sliding

    NASA Astrophysics Data System (ADS)

    Cooper, R. F.; Sundberg, M.

    2009-12-01

    Grain boundary sliding (GBS) has been identified as an important contributor to the plastic deformation of polycrystalline solids. This phenomenon, whether accommodated by grain boundary diffusion or dislocation slip, has implications for rheological behavior and microstructural evolution during creep. Because GBS is not an independent deformation mechanism, but rather acts in kinetic series with some other (typically) rate-limiting process, direct investigation of the precise sliding mechanism(s) is difficult during conventional large-strain creep testing. Direct observations of grain boundary sliding can be obtained, however, by: (1) observing the mechanical response of a polycrystalline solid to an oscillating load as a function of frequency using the internal friction technique, and (2) studying the short duration transient response of a polycrystalline solid to a step-function change in stress. To this end, we have conducted an experimental study of low-frequency (10-2.25grained (d~5μm) aggregate of olivine and orthopyroxene (39 vol%). The attenuation spectra reveal “high-temperature background” behavior at low to moderate frequencies where attenuation diminishes smoothly and mildly with increasing frequency (QG-1 ~ f -0.3). At higher frequencies (f >10-0.5 Hz), the attenuation spectra reveal the onset of an apparent Debye peak in the attenuation spectra, likely due to elastically-accommodated GBS (GBS being rate-limiting). Previous experimental studies have demonstrated that the Andrade viscoelastic model can accurately predict both the transient creep response and

  13. Incorporating nitrogen fixing cyanobacteria in the global biogeochemical model HAMOCC

    NASA Astrophysics Data System (ADS)

    Paulsen, Hanna; Ilyina, Tatiana; Six, Katharina

    2015-04-01

    Nitrogen fixation by marine diazotrophs plays a fundamental role in the oceanic nitrogen and carbon cycle as it provides a major source of 'new' nitrogen to the euphotic zone that supports biological carbon export and sequestration. Since most global biogeochemical models include nitrogen fixation only diagnostically, they are not able to capture its spatial pattern sufficiently. Here we present the incorporation of an explicit, dynamic representation of diazotrophic cyanobacteria and the corresponding nitrogen fixation in the global ocean biogeochemical model HAMOCC (Hamburg Ocean Carbon Cycle model), which is part of the Max Planck Institute for Meteorology Earth system model (MPI-ESM). The parameterization of the diazotrophic growth is thereby based on available knowledge about the cyanobacterium Trichodesmium spp., which is considered as the most significant pelagic nitrogen fixer. Evaluation against observations shows that the model successfully reproduces the main spatial distribution of cyanobacteria and nitrogen fixation, covering large parts of the tropical and subtropical oceans. Besides the role of cyanobacteria in marine biogeochemical cycles, their capacity to form extensive surface blooms induces a number of bio-physical feedback mechanisms in the Earth system. The processes driving these interactions, which are related to the alteration of heat absorption, surface albedo and momentum input by wind, are incorporated in the biogeochemical and physical model of the MPI-ESM in order to investigate their impacts on a global scale. First preliminary results will be shown.

  14. A quantitative coarse-grain model for lipid bilayers.

    PubMed

    Orsi, Mario; Haubertin, David Y; Sanderson, Wendy E; Essex, Jonathan W

    2008-01-24

    A simplified particle-based computer model for hydrated phospholipid bilayers has been developed and applied to quantitatively predict the major physical features of fluid-phase biomembranes. Compared with available coarse-grain methods, three novel aspects are introduced. First, the main electrostatic features of the system are incorporated explicitly via charges and dipoles. Second, water is accurately (yet efficiently) described, on an individual level, by the soft sticky dipole model. Third, hydrocarbon tails are modeled using the anisotropic Gay-Berne potential. Simulations are conducted by rigid-body molecular dynamics. Our technique proves 2 orders of magnitude less demanding of computational resources than traditional atomic-level methodology. Self-assembled bilayers quantitatively reproduce experimental observables such as electron density, compressibility moduli, dipole potential, lipid diffusion, and water permeability. The lateral pressure profile has been calculated, along with the elastic curvature constants of the Helfrich expression for the membrane bending energy; results are consistent with experimental estimates and atomic-level simulation data. Several of the results presented have been obtained for the first time using a coarse-grain method. Our model is also directly compatible with atomic-level force fields, allowing mixed systems to be simulated in a multiscale fashion. PMID:18085766

  15. An exactly solvable coarse-grained model for species diversity

    NASA Astrophysics Data System (ADS)

    Suweis, Samir; Rinaldo, Andrea; Maritan, Amos

    2012-07-01

    We present novel analytical results concerning ecosystem species diversity that stem from a proposed coarse-grained neutral model based on birth-death processes. The relevance of the problem lies in the urgency for understanding and synthesizing both theoretical results from ecological neutral theory and empirical evidence on species diversity preservation. The neutral model of biodiversity deals with ecosystems at the same trophic level, where per capita vital rates are assumed to be species independent. Closed-form analytical solutions for the neutral theory are obtained within a coarse-grained model, where the only input is the species persistence time distribution. Our results pertain to: the probability distribution function of the number of species in the ecosystem, both in transient and in stationary states; the n-point connected time correlation function; and the survival probability, defined as the distribution of time spans to local extinction for a species randomly sampled from the community. Analytical predictions are also tested on empirical data from an estuarine fish ecosystem. We find that emerging properties of the ecosystem are very robust and do not depend on specific details of the model, with implications for biodiversity and conservation biology.

  16. Comparison of model results transporting the odd nitrogen family with results transporting separate odd nitrogen species

    NASA Technical Reports Server (NTRS)

    Douglass, Anne R.; Jackman, Charles H.; Stolarski, Richard S.

    1989-01-01

    A fast two-dimensional residual circulation stratospheric family transport model, designed to minimize computer requirements, is developed. The model was used to calculate the ambient and perturbed atmospheres in which odd nitrogen species are transported as a family, and the results were compared with calculations in which HNO3, N2O5, ClONO2, and HO2NO2 are transported separately. It was found that ozone distributions computed by the two models for a present-day atmosphere are nearly identical. Good agreement was also found between calculated species concentrations and the ozone response, indicating the general applicability of the odd-nitrogen family approximations.

  17. Molecular Dynamics Trajectory Compression with a Coarse-Grained Model

    PubMed Central

    Cheng, Yi-Ming; Gopal, Srinivasa Murthy; Law, Sean M.; Feig, Michael

    2012-01-01

    Molecular dynamics trajectories are very data-intensive thereby limiting sharing and archival of such data. One possible solution is compression of trajectory data. Here, trajectory compression based on conversion to the coarse-grained model PRIMO is proposed. The compressed data is about one third of the original data and fast decompression is possible with an analytical reconstruction procedure from PRIMO to all-atom representations. This protocol largely preserves structural features and to a more limited extent also energetic features of the original trajectory. PMID:22025759

  18. [Effects of postponing nitrogen application on photosynthetic characteristics and grain yield of winter wheat subjected to water stress after heading stage].

    PubMed

    Yang, Ming-da; Ma, Shou-chen; Yang, Shen-jiao; Zhang, Su-yu; Guan, Xiao-kang; Li, Xue-mei; Wang, Tong-chao; Li, Chun-xi

    2015-11-01

    A pot culture experiment was conducted to study the effects of postponing nitrogen (N) application on photosynthetic characteristics and grain yield of winter wheat subjected to water stress after heading stage. Equal in the total N rate in winter wheat growth season, N application was split before sowing, and/or at jointing and /or at anthesis at the ratio of 10:0:0 (N1), 6:4:0 (N2) and 4:3:3 (N3), combined with unfavorable water condition (either waterlogged or drought) with the sufficient water condition as control. The results showed that, under each of the water condition, both N2 and N3 treatments significantly improved the leaf photosynthetic rate and the SPAD value of flag leaf compared with N1 treatment during grain filling stage, and also the crop ear number, grain number per spike and above-ground biomass were increased. Although postponing nitrogen application increased water consumption, both grain yield and water use efficiency were increased. Compared with sufficient water supply, drought stress and waterlogging stress significantly reduced the photosynthetic rate of flag leaves at anthesis and grain filling stages, ear number, 1000-grain mass and yield under all of the N application patterns. The decline of photosynthetic rate under either drought stress or waterlogging stress was much less in N2 and N3 than in N1 treatments, just the same as the grain yield. The results indicated that postponing nitrogen application could regulate winter wheat yield as well as its components to alleviate the damages, caused by unfavorable water stress by increasing flag leaf SPAD and maintaining flag leaf photosynthetic rate after anthesis, and promoting above-ground dry matter accumulation. PMID:26915185

  19. The fate of nitrogen in grain cropping systems: a meta-analysis of 15N field experiments.

    PubMed

    Gardner, Jennifer B; Drinkwater, Laurie E

    2009-12-01

    Intensively managed grain farms are saturated with large inputs of nitrogen (N) fertilizer, leading to N losses and environmental degradation. Despite decades of research directed toward reducing N losses from agroecosystems, progress has been minimal, and the currently promoted best management practices are not necessarily the most effective. We investigated the fate of N additions to temperate grain agroecosystems using a meta-analysis of 217 field-scale studies that followed the stable isotope 15N in crops and soil. We compared management practices that alter inorganic fertilizer additions, such as application timing or reduced N fertilizer rates, to practices that re-couple the biogeochemical cycles of carbon (C) and N, such as organic N sources and diversified crop rotations, and analyzed the following response variables: 15N recovery in crops, total recovery of 15N in crops and soil, and crop yield. More of the literature (94%) emphasized crop recovery of 15N than total 15N recovery in crops and soil (58%), though total recovery is a more ecologically appropriate indicator for assessing N losses. Findings show wide differences in the ability of management practices to improve N use efficiency. Practices that aimed to increase crop uptake of commercial fertilizer had a lower impact on total 15N recovery (3-21% increase) than practices that re-coupled C and N cycling (30-42% increase). A majority of studies (66%) were only one growing season long, which poses a particular problem when organic N sources are used because crops recover N from these sources over several years. These short-term studies neglect significant ecological processes that occur over longer time scales. Field-scale mass balance calculations using the 15N data set show that, on average, 43 kg N x ha(-1) x yr(-1) was unaccounted for at the end of one growing season out of 114 kg N x ha(-1) x yr(-1), representing approximately 38% of the total 15N applied. This comprehensive assessment of

  20. A Coarse-Grained Model for Simulating Chitosan Hydrogels

    NASA Astrophysics Data System (ADS)

    Xu, Hongcheng; Matysiak, Silvina

    Hydrogels are biologically-derived materials composed of water-filled cross-linking polymer chains. It has widely been used as biodegradable material and has many applications in medical devices. The chitosan hydrogel is stimuli-responsive for undergoing pH-sensitive self-assembly process, allowing programmable tuning of the chitosan deposition through electric pulse. To explore the self-assembly mechanism of chitosan hydroge, we have developed an explicit-solvent coarse-grained chitosan model that has roots in the MARTINI force field, and the pH change is modeled by protonating chitosan chains using the Henderson-Hasselbalch equation. The mechanism of hydrogel network formation will be presented. The self-assembled polymer network qualitatively reproduce many experimental observables such as the pH-dependent strain-stress curve, bulk moduli, and structure factor. Our model is also capable of simulating other similar polyelectrolyte polymer systems.

  1. Coarse-Grained Modeling of Mucus Barrier Properties

    PubMed Central

    Gniewek, Pawel; Kolinski, Andrzej

    2012-01-01

    We designed a simple coarse-grained model of the glycocalyx layer, or adhesive mucus layer (AML), covered by mucus gel (luminal mucus layer) using a polymer lattice model and stochastic sampling (replica exchange Monte Carlo) for canonical ensemble simulations. We assumed that mucin MUC16 is responsible for the structural properties of the AML. Other mucins that are much smaller in size and less relevant for layer structure formation were not included. We further assumed that the system was in quasi-equilibrium. For systems with surface coverage and concentrations of model mucins mimicking physiological conditions, we determined the equilibrium distribution of inert nanoparticles within the mucus layers using an efficient replica exchange Monte Carlo sampling procedure. The results show that the two mucus layers penetrate each other only marginally, and the bilayer imposes a strong barrier for nanoparticles, with the AML layer playing a crucial role in the mucus barrier. PMID:22339855

  2. Potential for Optical Sensor-Based Nitrogen Fertilization in Grain Sorghum (Sorghum bicolor L. Moench) in Arkansas

    NASA Astrophysics Data System (ADS)

    Rosales Rodriguez, Kamil

    Ground-based active-optical (GBAO) crop sensors have become an effective tool to improve nitrogen (N) use efficiency and to predict yield early in the growing season, particularly for grass crops. Commercially available canopy sensors calculate the normalized difference vegetative index (NDVI) by emitting light in the red and near infrared range of the electromagnetic spectrum. The NDVI is used to evaluate vigor status and to estimate yield potential. However, few studies have been conducted to compare the performance of commercially available sensors. Therefore, a study was conducted using the most common crop canopy sensors: i) N-Tech's GreenSeeker(TM) (GS), ii) Holland Scientific's Crop Circle(TM) (CC), and iii) Minolta's SPAD-502 chlorophyll content meter (CCM). The objective of this study was to find the optimum time for sensing and compare the relative performance of the sensors in estimating the yield potential of grain sorghum (Sorghum bicolor L. Moench). Treatments included six levels of N fertilization (0, 37, 74, 111, 148, and 185 kg N/ ha), applied in a single split 20 days after planting (DAP). Treatments were arranged in a randomized complete block design with five replications, in four locations in Arkansas, during 2012 and 2013. Sensors readings at vegetative growth stages V3, 4, 5 and 6. Results from simple regression analysis showed that the V3-V4 growth stage correlated better with grain yield than readings collected and any other time. In season estimated yield (INSEY) obtained at V3 captured 41, 57, 78, and 61% of the variation in grain sorghum yield when red NDVI of GS, red NDVI of CC, red edge for CC and CCM, respectively, were used. Results from these studies suggest that the CC sensor has a better potential for in-season site-specific N application in Arkansas than the GS sensor. The GS reflectance values appear to saturate after the V3 stage, in contrast with CC values that allow for discrimination past the V3 Stage. Therefore, the red

  3. Perspective: Coarse-grained models for biomolecular systems

    NASA Astrophysics Data System (ADS)

    Noid, W. G.

    2013-09-01

    By focusing on essential features, while averaging over less important details, coarse-grained (CG) models provide significant computational and conceptual advantages with respect to more detailed models. Consequently, despite dramatic advances in computational methodologies and resources, CG models enjoy surging popularity and are becoming increasingly equal partners to atomically detailed models. This perspective surveys the rapidly developing landscape of CG models for biomolecular systems. In particular, this review seeks to provide a balanced, coherent, and unified presentation of several distinct approaches for developing CG models, including top-down, network-based, native-centric, knowledge-based, and bottom-up modeling strategies. The review summarizes their basic philosophies, theoretical foundations, typical applications, and recent developments. Additionally, the review identifies fundamental inter-relationships among the diverse approaches and discusses outstanding challenges in the field. When carefully applied and assessed, current CG models provide highly efficient means for investigating the biological consequences of basic physicochemical principles. Moreover, rigorous bottom-up approaches hold great promise for further improving the accuracy and scope of CG models for biomolecular systems.

  4. COARSE-GRAINED MODELING OF PROTEIN UNFOLDING DYNAMICS*

    PubMed Central

    DENG, MINGGE

    2014-01-01

    We present a new dynamic elastic network model (DENM) that describes the unfolding process of a force-loaded protein. The protein interaction network and its potentials are constructed based on information of its native-state structure obtained from the Protein Data Bank, with network nodes positioned at the Cα coordinates of the protein backbone. Specifically, to mimic the unfolding process, i.e., to simulate the process of overcoming the local energy barrier on the free energy landscape with force loading, the noncovalent protein network bonds (i.e., hydrogen bonds, salt bridges, hydrophobic contacts, etc.) are broken one-by-one with a certain probability, while the strong covalent bonds along the backbone (i.e., peptide bonds, disulfide bonds, etc.) are kept intact. The jumping event from local energy minima (bonds breaking rate) are chosen according to Kramer’s theory and the Bell model. Moreover, we exploit the self-similar structure of proteins at different scales to design an effective coarse-graining procedure for DENM with optimal parameter selection. The robustness of DENM is validated by coarse-grained molecular dynamics (MD) simulation against atomistic MD simulation of force-extension processes of the Fibrinogen and Titin Immunoglobulin proteins. We observe that the native structure of the proteins determines the total unfolding dynamics (including large deviations) and not just the fluctuations around the native state. PMID:25400515

  5. A diffuse interface model of grain boundary faceting

    NASA Astrophysics Data System (ADS)

    Abdeljawad, Fadi; Medlin, Douglas; Zimmerman, Jonathan; Hattar, Khalid; Foiles, Stephen

    Incorporating anisotropy into thermodynamic treatments of interfaces dates back to over a century ago. For a given orientation of two abutting grains in a pure metal, depressions in the grain boundary (GB) energy may exist as a function of GB inclination, defined by the plane normal. Therefore, an initially flat GB may facet resulting in a hill-and-valley structure. Herein, we present a diffuse interface model of GB faceting that is capable of capturing anisotropic GB energies and mobilities, and accounting for the excess energy due to facet junctions and their non-local interactions. The hallmark of our approach is the ability to independently examine the role of each of the interface properties on the faceting behavior. As a demonstration, we consider the Σ 5 < 001 > tilt GB in iron, where faceting along the { 310 } and { 210 } planes was experimentally observed. Linear stability analysis and numerical examples highlight the role of junction energy and associated non-local interactions on the resulting facet length scales. On the whole, our modeling approach provides a general framework to examine the spatio-temporal evolution of highly anisotropic GBs in polycrystalline metals. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DOE's National Nuclear Security Administration under Contract DE-AC04-94AL85000.

  6. Marine Nitrogen loss in Oxygen minimum zones: a modeling approach

    NASA Astrophysics Data System (ADS)

    Six, Katharina; Hense, Inga; Ilyina, Tatiana

    2015-04-01

    In the oxygen minimum zones (OMZ) of the global ocean fixed nitrogen is lost by two pathways: heterotrophic denitrification and anaerobic ammonium oxidation (anammox). Lab experiments show that denitrification and anammox occur at a ratio of about 70:30 depending on the amount and the C:N ratio of the available organic matter. However, observations in the OMZ are sparse and, thus, the contribution of anammox to the global loss of fixed nitrogen is still under debate. In addition, it is projected that the OMZ expand in the future due to global warming. This compels an urgent need to understand the controlling mechanisms of nitrogen loss in OMZ. Global biogeochemical ocean models assessed in the last IPCC have a rather poor representation of nitrogen related processes, primarily focusing on nitrate. These models do not include the nitrogen loss by anammox as they lack a representation of ammonium and nitrite. Here we present results of a more comprehensive marine nitrogen cycle including interactions between nitrate, nitrite, ammonium and organic matter in the water column and the sediments in the framework of HAMOCC, the global biogeochemical ocean model of the Max Planck Institute for Meteorology. The representation of a stepwise dissimilatory nitrate reduction to nitrite and ammonium captures observed features like the secondary nitrite maximum. We set up a global marine nitrogen budget and discuss changes in the subsurface oxygen distributions.

  7. Comparative analysis of modeled nitrogen removal by shellfish farms.

    PubMed

    Rose, Julie M; Bricker, Suzanne B; Ferreira, Joao G

    2015-02-15

    The use of shellfish aquaculture for nutrient removal and reduction of coastal eutrophication has been proposed. Published literature has indicated that nitrogen contained in harvested shellfish can be accurately estimated from shell length:nitrogen content ratios. The range of nitrogen that could be removed by a typical farm in a specific estuarine or coastal setting is also of interest to regulators and planners. Farm Aquaculture Resource Management (FARM) model outputs of nitrogen removal at the shellfish farm scale have been summarized here, from 14 locations in 9 countries across 4 continents. Modeled nitrogen removal ranged from 105 lbs acre(-1) year(-1) (12 g m(-2) year(-1)) to 1356 lbs acre(-1) year(-1) (152 g m(-2) year(-1)). Mean nitrogen removal was 520 lbs acre(-1) year(-1) (58 g m(-2) year(-1)). These model results are site-specific in nature, but compare favorably to reported nitrogen removal effectiveness of agricultural best management practices and stormwater control measures. PMID:25534625

  8. Coarse-Grained Molecular Models of Water: A Review

    PubMed Central

    Hadley, Kevin R.; McCabe, Clare

    2012-01-01

    Coarse-grained (CG) models have proven to be very effective tools in the study of phenomena or systems that involve large time- and length-scales. By decreasing the degrees of freedom in the system and using softer interactions than seen in atomistic models, larger timesteps can be used and much longer simulation times can be studied. CG simulations are widely used to study systems of biological importance that are beyond the reach of atomistic simulation, necessitating a computationally efficient and accurate CG model for water. In this review, we discuss the methods used for developing CG water models and the relative advantages and disadvantages of the resulting models. In general, CG water models differ with regards to how many waters each CG group or bead represents, whether analytical or tabular potentials have been used to describe the interactions, and how the model incorporates electrostatic interactions. Finally, how the models are parameterized depends on their application, so, while some are fitted to experimental properties such as surface tension and density, others are fitted to radial distribution functions extracted from atomistic simulations. PMID:22904601

  9. Modeling of grain selection during directional solidification of single crystal superalloy turbine blade castings

    NASA Astrophysics Data System (ADS)

    Pan, Dong; Xu, Qingyan; Liu, Baicheng; Li, Jiarong; Yuan, Hailong; Jin, Haipeng

    2010-05-01

    Single crystal superalloy turbine blades are currently widely used as key components in gas turbine engines. The single crystal turbine blade casting’s properties are quite sensitive to the grain orientation determined directly by the grain selector geometry of the casting, A mathematical model was proposed for the grain selection during directional solidification of turbine blade casting. Based on heat transfer modeling of the directional withdrawing process, the competitive grain growth within the starter block and the spiral of the grain selector were simulated by using the cellular automaton method (CA). Validation experiments were carried out, and the measured results were compared quantitatively with the predicted results. The model could be used to predict the grain morphology and the competitive grain evolution during solidification, together with the distribution of grain orientation of primary <001> dendrite growth direction, with respect to the longitudinal axis of the turbine blade casting.

  10. Coarse-grained theory of a realistic tetrahedral liquid model

    NASA Astrophysics Data System (ADS)

    Procaccia, I.; Regev, I.

    2012-02-01

    Tetrahedral liquids such as water and silica-melt show unusual thermodynamic behavior such as a density maximum and an increase in specific heat when cooled to low temperatures. Previous work had shown that Monte Carlo and mean-field solutions of a lattice model can exhibit these anomalous properties with or without a phase transition, depending on the values of the different terms in the Hamiltonian. Here we use a somewhat different approach, where we start from a very popular empirical model of tetrahedral liquids —the Stillinger-Weber model— and construct a coarse-grained theory which directly quantifies the local structure of the liquid as a function of volume and temperature. We compare the theory to molecular-dynamics simulations and show that the theory can rationalize the simulation results and the anomalous behavior.

  11. Coarse-grained, foldable, physical model of the polypeptide chain

    PubMed Central

    Chakraborty, Promita; Zuckermann, Ronald N.

    2013-01-01

    Although nonflexible, scaled molecular models like Pauling–Corey’s and its descendants have made significant contributions in structural biology research and pedagogy, recent technical advances in 3D printing and electronics make it possible to go one step further in designing physical models of biomacromolecules: to make them conformationally dynamic. We report here the design, construction, and validation of a flexible, scaled, physical model of the polypeptide chain, which accurately reproduces the bond rotational degrees of freedom in the peptide backbone. The coarse-grained backbone model consists of repeating amide and α-carbon units, connected by mechanical bonds (corresponding to φ and ψ) that include realistic barriers to rotation that closely approximate those found at the molecular scale. Longer-range hydrogen-bonding interactions are also incorporated, allowing the chain to readily fold into stable secondary structures. The model is easily constructed with readily obtainable parts and promises to be a tremendous educational aid to the intuitive understanding of chain folding as the basis for macromolecular structure. Furthermore, this physical model can serve as the basis for linking tangible biomacromolecular models directly to the vast array of existing computational tools to provide an enhanced and interactive human–computer interface. PMID:23898168

  12. Coarse-Grained Model for Water Involving a Virtual Site.

    PubMed

    Deng, Mingsen; Shen, Hujun

    2016-02-01

    In this work, we propose a new coarse-grained (CG) model for water by combining the features of two popular CG water models (BMW and MARTINI models) as well as by adopting a topology similar to that of the TIP4P water model. In this CG model, a CG unit, representing four real water molecules, consists of a virtual site, two positively charged particles, and a van der Waals (vdW) interaction center. Distance constraint is applied to the bonds formed between the vdW interaction center and the positively charged particles. The virtual site, which carries a negative charge, is determined by the locations of the two positively charged particles and the vdW interaction center. For the new CG model of water, we coined the name "CAVS" (charge is attached to a virtual site) due to the involvment of the virtual site. After being tested in molecular dynamic (MD) simulations of bulk water at various time steps, under different temperatures and in different salt (NaCl) concentrations, the CAVS model offers encouraging predictions for some bulk properties of water (such as density, dielectric constant, etc.) when compared to experimental ones. PMID:26747089

  13. Gas-Grain Models for Interstellar Anion Chemistry

    NASA Technical Reports Server (NTRS)

    Cordiner, M. A.; Charnely, S. B.

    2012-01-01

    Long-chain hydrocarbon anions C(sub n) H(-) (n = 4, 6, 8) have recently been found to be abundant in a variety of interstellar clouds. In order to explain their large abundances in the denser (prestellar/protostellar) environments, new chemical models are constructed that include gas-grain interactions. Models including accretion of gas-phase species onto dust grains and cosmic-ray-induced desorption of atoms are able to reproduce the observed anion-to-neutral ratios, as well as the absolute abundances of anionic and neutral carbon chains, with a reasonable degree of accuracy. Due to their destructive effects, the depletion of oxygen atoms onto dust results in substantially greater polyyne and anion abundances in high-density gas (with n(sub H2) approx > / cubic cm). The large abundances of carbon-chain-bearing species observed in the envelopes of protostars such as L1527 can thus be explained without the need for warm carbon-chain chemistry. The C6H(-) anion-to-neutral ratio is found to be most sensitive to the atomic O and H abundances and the electron density. Therefore, as a core evolves, falling atomic abundances and rising electron densities are found to result in increasing anion-to-neutral ratios. Inclusion of cosmic-ray desorption of atoms in high-density models delays freeze-out, which results in a more temporally stable anion-to-neutral ratio, in better agreement with observations. Our models include reactions between oxygen atoms and carbon-chain anions to produce carbon-chain-oxide species C6O, C7O, HC6O, and HC7O, the abundances of which depend on the assumed branching ratios for associative electron detachment

  14. Modelling grain-scattered ultrasound in austenitic stainless-steel welds: A hybrid model

    SciTech Connect

    Nowers, O.; Duxbury, D. J.; Velichko, A.; Drinkwater, B. W.

    2015-03-31

    The ultrasonic inspection of austenitic stainless steel welds can be challenging due to their coarse grain structure, charaterised by preferentially oriented, elongated grains. The anisotropy of the weld is manifested as both a ‘steering’ of the beam and the back-scatter of energy due to the macroscopic granular structure of the weld. However, the influence of weld properties, such as mean grain size and orientation distribution, on the magnitude of scattered ultrasound is not well understood. A hybrid model has been developed to allow the study of grain-scatter effects in austenitic welds. An efficient 2D Finite Element (FE) method is used to calculate the complete scattering response from a single elliptical austenitic grain of arbitrary length and width as a function of the specific inspection frequency. A grain allocation model of the weld is presented to approximate the characteristic structures observed in austenitic welds and the complete scattering behaviour of each grain calculated. This model is incorporated into a semi-analytical framework for a single-element inspection of a typical weld in immersion. Experimental validation evidence is demonstrated indicating excellent qualitative agreement of SNR as a function of frequency and a minimum SNR difference of 2 dB at a centre frequency of 2.25 MHz. Additionally, an example Monte-Carlo study is presented detailing the variation of SNR as a function of the anisotropy distribution of the weld, and the application of confidence analysis to inform inspection development.

  15. Modelling grain-scattered ultrasound in austenitic stainless-steel welds: A hybrid model

    NASA Astrophysics Data System (ADS)

    Nowers, O.; Duxbury, D. J.; Velichko, A.; Drinkwater, B. W.

    2015-03-01

    The ultrasonic inspection of austenitic stainless steel welds can be challenging due to their coarse grain structure, charaterised by preferentially oriented, elongated grains. The anisotropy of the weld is manifested as both a `steering' of the beam and the back-scatter of energy due to the macroscopic granular structure of the weld. However, the influence of weld properties, such as mean grain size and orientation distribution, on the magnitude of scattered ultrasound is not well understood. A hybrid model has been developed to allow the study of grain-scatter effects in austenitic welds. An efficient 2D Finite Element (FE) method is used to calculate the complete scattering response from a single elliptical austenitic grain of arbitrary length and width as a function of the specific inspection frequency. A grain allocation model of the weld is presented to approximate the characteristic structures observed in austenitic welds and the complete scattering behaviour of each grain calculated. This model is incorporated into a semi-analytical framework for a single-element inspection of a typical weld in immersion. Experimental validation evidence is demonstrated indicating excellent qualitative agreement of SNR as a function of frequency and a minimum SNR difference of 2 dB at a centre frequency of 2.25 MHz. Additionally, an example Monte-Carlo study is presented detailing the variation of SNR as a function of the anisotropy distribution of the weld, and the application of confidence analysis to inform inspection development.

  16. Potts model simulation of grain size distributions during final stage sintering

    SciTech Connect

    Zeng, P.; Tikare, V.

    1998-09-01

    The Potts Monte Carlo model was used to simulate microstructural evolution and characterize grain size distribution during the final stages of sintering. Simultaneous grain growth, pore migration and pore shrinkage were simulated in a system with an initial porosity of 10% with varying ratios of grain boundary mobility to pore shrinkage rates. This investigation shows that the presence of pores changes the grain size distribution and the topological characteristics due to pinning of grains by pores. As pores shrink away, their pinning effect decreases. Once pore shrinkage is complete, normal grain growth is achieved.

  17. A mechanistic nitrogen limitation model for CLM(ED)

    NASA Astrophysics Data System (ADS)

    Ali, A. A.; Xu, C.; McDowell, N. G.; Rogers, A.; Wullschleger, S. D.; Fisher, R.; Vrugt, J. A.

    2014-12-01

    Photosynthetic capacity is a key plant trait that determines the rate of photosynthesis; however, in Earth System Models it is either a fixed value or derived from a linear function of leaf nitrogen content. A mechanistic leaf nitrogen allocation model have been developed for a DOE-sponsored Community Land Model coupled to the Ecosystem Demography model (CLM-ED) to predict the photosynthetic capacity [Vc,max25 (μmol CO2 m-2 s-1)] under different environmental conditions at the global scale. We collected more than 800 data points of photosynthetic capacity (Vc,max25) for 124 species from 57 studies with the corresponding leaf nitrogen content and environmental conditions (temperature, radiation, humidity and day length) from literature and the NGEE arctic site (Barrow). Based on the data, we found that environmental control of Vc,max25 is about 4 times stronger than the leaf nitrogen content. Using the Markov-Chain Monte Carlo simulation approach, we fitted the collected data to our newly developed nitrogen allocation model, which predict the leaf nitrogen investment in different components including structure, storage, respiration, light capture, carboxylation and electron transport at different environmental conditions. Our results showed that our nitrogen allocation model explained 52% of variance in observed Vc,max25 and 65% variance in observed Jmax25 using a single set of fitted model parameters for all species. Across the growing season, we found that the modeled Vc,max25 explained 49% of the variability in measured Vc,max25. In the context of future global warming, our model predicts that a temperature increase by 5oC and the doubling of atmospheric carbon dioxide reduced the Vc,max25 by 5%, 11%, respectively.

  18. Polysaccharide-Protein Complexes in a Coarse-Grained Model.

    PubMed

    Poma, Adolfo B; Chwastyk, Mateusz; Cieplak, Marek

    2015-09-10

    We construct two variants of coarse-grained models of three hexaoses: one based on the centers of mass of the monomers and the other associated with the C4 atoms. The latter is found to be better defined and more suitable for studying interactions with proteins described within α-C based models. We determine the corresponding effective stiffness constants through all-atom simulations and two statistical methods. One method is the Boltzmann inversion (BI) and the other, named energy-based (EB), involves direct monitoring of energies as a function of the variables that define the stiffness potentials. The two methods are generally consistent in their account of the stiffness. We find that the elastic constants differ between the hexaoses and are noticeably different from those determined for the crystalline cellulose Iβ. The nonbonded couplings through hydrogen bonds between different sugar molecules are modeled by the Lennard-Jones potentials and are found to be stronger than the hydrogen bonds in proteins. We observe that the EB method agrees with other theoretical and experimental determinations of the nonbonded parameters much better than BI. We then consider the hexaose-Man5B catalytic complexes and determine the contact energies between their the C4-α-C atoms. These interactions are found to be stronger than the proteinic hydrogen bonds: about four times as strong for cellohexaose and two times for mannohexaose. The fluctuational dynamics of the coarse-grained complexes are found to be compatible with previous all-atom studies by Bernardi et al. PMID:26291477

  19. A course-grained model for polyethylene glycol polymer

    SciTech Connect

    Nicholson, Don M; Wang, Qifei; Keffer, David J

    2011-01-01

    A coarse-grained (CG) model of polyethylene glycol (PEG) was developed and implemented in CG molecular dynamics (MD) simulations of PEG chains with degree of polymerization (DP) 20 and 40. In the model, two repeat units of PEG are grouped as one CG bead. Atomistic MD simulation of PEG chains with DP = 20 was first conducted to obtain the bonded structural probability distribution functions (PDFs) and nonbonded pair correlation function (PCF) of the CG beads. The bonded CG potentials are obtained by simple inversion of the corresponding PDFs. The CG nonbonded potential is parameterized to the PCF using both an inversion procedure based on the Ornstein-Zernike equation with the Percus-Yevick approximation (OZPY{sup -1}) and a combination of OZPY{sup -1} with the iterative Boltzmann inversion (IBI) method (OZPY{sup -1}+IBI). As a simple one step method, the OZPY{sup -1} method possesses an advantage in computational efficiency. Using the potential from OZPY{sup -1} as an initial guess, the IBI method shows fast convergence. The coarse-grained molecular dynamics (CGMD) simulations of PEG chains with DP = 20 using potentials from both methods satisfactorily reproduce the structural properties from atomistic MD simulation of the same systems. The OZPY{sup -1}+IBI method yields better agreement than the OZPY{sup -1} method alone. The new CG model and CG potentials from OZPY{sup -1}+IBI method was further tested through CGMD simulation of PEG with DP = 40 system. No significant changes are observed in the comparison of PCFs from CGMD simulations of PEG with DP = 20 and 40 systems indicating that the potential is independent of chain length.

  20. Modelling soil nitrogen: the MAGIC model with nitrogen retention linked to carbon turnover using decomposer dynamics.

    PubMed

    Oulehle, F; Cosby, B J; Wright, R F; Hruška, J; Kopáček, J; Krám, P; Evans, C D; Moldan, F

    2012-06-01

    We present a new formulation of the acidification model MAGIC that uses decomposer dynamics to link nitrogen (N) cycling to carbon (C) turnover in soils. The new model is evaluated by application to 15-30 years of water chemistry data at three coniferous-forested sites in the Czech Republic where deposition of sulphur (S) and N have decreased by >80% and 40%, respectively. Sulphate concentrations in waters have declined commensurately with S deposition, but nitrate concentrations have shown much larger decreases relative to N deposition. This behaviour is inconsistent with most conceptual models of N saturation, and with earlier versions of MAGIC which assume N retention to be a first-order function of N deposition and/or controlled by the soil C/N ratio. In comparison with earlier versions, the new formulation more correctly simulates observed short-term changes in nitrate leaching, as well as long-term retention of N in soils. The model suggests that, despite recent deposition reductions and recovery, progressive N saturation will lead to increased future nitrate leaching, ecosystem eutrophication and re-acidification. PMID:22459669

  1. Nitrogen

    USGS Publications Warehouse

    Kramer, D.A.

    2006-01-01

    In 2005, ammonia was produced by 15 companies at 26 plants in 16 states in the United States. Of the total ammonia production capacity, 55% was centered in Louisiana, Oklahoma and Texas because of their large reserves of natural gas. US producers operated at 66% of their rated capacity. In descending order, Koch Nitrogen, Terra Industries, CF Industries, Agrium and PCS Nitrogen accounted for 81% of the US ammonia production capacity.

  2. Applications of discrete element method in modeling of grain postharvest operations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Grain kernels are finite and discrete materials. Although flowing grain can behave like a continuum fluid at times, the discontinuous behavior exhibited by grain kernels cannot be simulated solely with conventional continuum-based computer modeling such as finite-element or finite-difference methods...

  3. Coarse grained modeling of transport properties in monoclonal antibody solution

    NASA Astrophysics Data System (ADS)

    Swan, James; Wang, Gang

    Monoclonal antibodies and their derivatives represent the fastest growing segment of the bio pharmaceutical industry. For many applications such as novel cancer therapies, high concentration, sub-cutaneous injections of these protein solutions are desired. However, depending on the peptide sequence within the antibody, such high concentration formulations can be too viscous to inject via human derived force alone. Understanding how heterogenous charge distribution and hydrophobicity within the antibodies leads to high viscosities is crucial to their future application. In this talk, we explore a coarse grained computational model of therapeutically relevant monoclonal antibodies that accounts for electrostatic, dispersion and hydrodynamic interactions between suspended antibodies to predict assembly and transport properties in concentrated antibody solutions. We explain the high viscosities observed in many experimental studies of the same biologics.

  4. Multiscale model of metal alloy oxidation at grain boundaries

    SciTech Connect

    Sushko, Maria L. Alexandrov, Vitaly; Schreiber, Daniel K.; Rosso, Kevin M.; Bruemmer, Stephen M.

    2015-06-07

    High temperature intergranular oxidation and corrosion of metal alloys is one of the primary causes of materials degradation in nuclear systems. In order to gain insights into grain boundary oxidation processes, a mesoscale metal alloy oxidation model is established by combining quantum Density Functional Theory (DFT) and mesoscopic Poisson-Nernst-Planck/classical DFT with predictions focused on Ni alloyed with either Cr or Al. Analysis of species and fluxes at steady-state conditions indicates that the oxidation process involves vacancy-mediated transport of Ni and the minor alloying element to the oxidation front and the formation of stable metal oxides. The simulations further demonstrate that the mechanism of oxidation for Ni-5Cr and Ni-4Al is qualitatively different. Intergranular oxidation of Ni-5Cr involves the selective oxidation of the minor element and not matrix Ni, due to slower diffusion of Ni relative to Cr in the alloy and due to the significantly smaller energy gain upon the formation of nickel oxide compared to that of Cr{sub 2}O{sub 3}. This essentially one-component oxidation process results in continuous oxide formation and a monotonic Cr vacancy distribution ahead of the oxidation front, peaking at alloy/oxide interface. In contrast, Ni and Al are both oxidized in Ni-4Al forming a mixed spinel NiAl{sub 2}O{sub 4}. Different diffusivities of Ni and Al give rise to a complex elemental distribution in the vicinity of the oxidation front. Slower diffusing Ni accumulates in the oxide and metal within 3 nm of the interface, while Al penetrates deeper into the oxide phase. Ni and Al are both depleted from the region 3–10 nm ahead of the oxidation front creating voids. The oxide microstructure is also different. Cr{sub 2}O{sub 3} has a plate-like structure with 1.2–1.7 nm wide pores running along the grain boundary, while NiAl{sub 2}O{sub 4} has 1.5 nm wide pores in the direction parallel to the grain boundary and 0.6 nm pores in the perpendicular

  5. Multiscale model of metal alloy oxidation at grain boundaries.

    PubMed

    Sushko, Maria L; Alexandrov, Vitaly; Schreiber, Daniel K; Rosso, Kevin M; Bruemmer, Stephen M

    2015-06-01

    High temperature intergranular oxidation and corrosion of metal alloys is one of the primary causes of materials degradation in nuclear systems. In order to gain insights into grain boundary oxidation processes, a mesoscale metal alloy oxidation model is established by combining quantum Density Functional Theory (DFT) and mesoscopic Poisson-Nernst-Planck/classical DFT with predictions focused on Ni alloyed with either Cr or Al. Analysis of species and fluxes at steady-state conditions indicates that the oxidation process involves vacancy-mediated transport of Ni and the minor alloying element to the oxidation front and the formation of stable metal oxides. The simulations further demonstrate that the mechanism of oxidation for Ni-5Cr and Ni-4Al is qualitatively different. Intergranular oxidation of Ni-5Cr involves the selective oxidation of the minor element and not matrix Ni, due to slower diffusion of Ni relative to Cr in the alloy and due to the significantly smaller energy gain upon the formation of nickel oxide compared to that of Cr2O3. This essentially one-component oxidation process results in continuous oxide formation and a monotonic Cr vacancy distribution ahead of the oxidation front, peaking at alloy/oxide interface. In contrast, Ni and Al are both oxidized in Ni-4Al forming a mixed spinel NiAl2O4. Different diffusivities of Ni and Al give rise to a complex elemental distribution in the vicinity of the oxidation front. Slower diffusing Ni accumulates in the oxide and metal within 3 nm of the interface, while Al penetrates deeper into the oxide phase. Ni and Al are both depleted from the region 3-10 nm ahead of the oxidation front creating voids. The oxide microstructure is also different. Cr2O3 has a plate-like structure with 1.2-1.7 nm wide pores running along the grain boundary, while NiAl2O4 has 1.5 nm wide pores in the direction parallel to the grain boundary and 0.6 nm pores in the perpendicular direction providing an additional pathway for oxygen

  6. Multiscale model of metal alloy oxidation at grain boundaries

    NASA Astrophysics Data System (ADS)

    Sushko, Maria L.; Alexandrov, Vitaly; Schreiber, Daniel K.; Rosso, Kevin M.; Bruemmer, Stephen M.

    2015-06-01

    High temperature intergranular oxidation and corrosion of metal alloys is one of the primary causes of materials degradation in nuclear systems. In order to gain insights into grain boundary oxidation processes, a mesoscale metal alloy oxidation model is established by combining quantum Density Functional Theory (DFT) and mesoscopic Poisson-Nernst-Planck/classical DFT with predictions focused on Ni alloyed with either Cr or Al. Analysis of species and fluxes at steady-state conditions indicates that the oxidation process involves vacancy-mediated transport of Ni and the minor alloying element to the oxidation front and the formation of stable metal oxides. The simulations further demonstrate that the mechanism of oxidation for Ni-5Cr and Ni-4Al is qualitatively different. Intergranular oxidation of Ni-5Cr involves the selective oxidation of the minor element and not matrix Ni, due to slower diffusion of Ni relative to Cr in the alloy and due to the significantly smaller energy gain upon the formation of nickel oxide compared to that of Cr2O3. This essentially one-component oxidation process results in continuous oxide formation and a monotonic Cr vacancy distribution ahead of the oxidation front, peaking at alloy/oxide interface. In contrast, Ni and Al are both oxidized in Ni-4Al forming a mixed spinel NiAl2O4. Different diffusivities of Ni and Al give rise to a complex elemental distribution in the vicinity of the oxidation front. Slower diffusing Ni accumulates in the oxide and metal within 3 nm of the interface, while Al penetrates deeper into the oxide phase. Ni and Al are both depleted from the region 3-10 nm ahead of the oxidation front creating voids. The oxide microstructure is also different. Cr2O3 has a plate-like structure with 1.2-1.7 nm wide pores running along the grain boundary, while NiAl2O4 has 1.5 nm wide pores in the direction parallel to the grain boundary and 0.6 nm pores in the perpendicular direction providing an additional pathway for oxygen

  7. Testing the responses of four wheat crop models to heat stress at anthesis and grain filling.

    PubMed

    Liu, Bing; Asseng, Senthold; Liu, Leilei; Tang, Liang; Cao, Weixing; Zhu, Yan

    2016-05-01

    Higher temperatures caused by future climate change will bring more frequent heat stress events and pose an increasing risk to global wheat production. Crop models have been widely used to simulate future crop productivity but are rarely tested with observed heat stress experimental datasets. Four wheat models (DSSAT-CERES-Wheat, DSSAT-Nwheat, APSIM-Wheat, and WheatGrow) were evaluated with 4 years of environment-controlled phytotron experimental datasets with two wheat cultivars under heat stress at anthesis and grain filling stages. Heat stress at anthesis reduced observed grain numbers per unit area and individual grain size, while heat stress during grain filling mainly decreased the size of the individual grains. The observed impact of heat stress on grain filling duration, total aboveground biomass, grain yield, and grain protein concentration (GPC) varied depending on cultivar and accumulated heat stress. For every unit increase of heat degree days (HDD, degree days over 30 °C), grain filling duration was reduced by 0.30-0.60%, total aboveground biomass was reduced by 0.37-0.43%, and grain yield was reduced by 1.0-1.6%, but GPC was increased by 0.50% for cv Yangmai16 and 0.80% for cv Xumai30. The tested crop simulation models could reproduce some of the observed reductions in grain filling duration, final total aboveground biomass, and grain yield, as well as the observed increase in GPC due to heat stress. Most of the crop models tended to reproduce heat stress impacts better during grain filling than at anthesis. Some of the tested models require improvements in the response to heat stress during grain filling, but all models need improvements in simulating heat stress effects on grain set during anthesis. The observed significant genetic variability in the response of wheat to heat stress needs to be considered through cultivar parameters in future simulation studies. PMID:26725507

  8. Chemical models of interstellar gas-grain processes. II - The effect of grain-catalysed methane on gas phase evolution

    NASA Technical Reports Server (NTRS)

    Brown, Paul D.; Charnley, S. B.

    1991-01-01

    The effects on gas phase chemistry which result from the continuous desorption of methane molecules from grain surfaces are studied. Significant and sustained enhancements in the abundances of several complex hydrocarbon molecules are found, in good agreement with their observed values in TMC-1. The overall agreement is, however, just as good for the case of zero CH4 desorption efficiency. It is thus impossible to determine from the models whether or not the grain-surface production of methane is responsible for the observed abundances of some hydrocarbon molecules.

  9. Changes in Free Amino Acid Concentration in Rye Grain in Response to Nitrogen and Sulfur Availability, and Expression Analysis of Genes Involved in Asparagine Metabolism.

    PubMed

    Postles, Jennifer; Curtis, Tanya Y; Powers, Stephen J; Elmore, J S; Mottram, Donald S; Halford, Nigel G

    2016-01-01

    Free asparagine plays a central role in nitrogen storage and transport in many plant species due to its relatively high ratio of nitrogen to carbon. However, it is also a precursor for acrylamide, a Class 2a carcinogen that forms during high-temperature processing and cooking. The concentration of free asparagine was shown to increase by approximately 70% in rye grain in response to severe sulfur deficiency (F-test, p = 0.004), while the concentration of both free asparagine and free glutamine increased (by almost threefold and approximately 62%, respectively) in response to nitrogen application (F-test, p < 0.001 for free asparagine; p = 0.004 for free glutamine). There were also effects of nutrient supply on other free amino acids: The concentration of free proline, for example, showed a significant (F-test, p = 0.019) effect of nitrogen interacting with sulfur, with the highest concentration occurring when the plants were deprived of both nitrogen and sulfur. Polymerase chain reaction products for several genes involved in asparagine metabolism and its regulation were amplified from rye grain cDNA. These genes were asparagine synthetase-1 (ScASN1), glutamine synthetase-1 (ScGS1), potassium-dependent asparaginase (ScASP), aspartate kinase (ScASK), and general control non-derepressible-2 (ScGCN2). The expression of these genes and of a previously described sucrose non-fermenting-1-related protein kinase-1 gene (ScSnRK1) was analyzed in flag leaf and developing grain in response to nitrogen and sulfur supply, revealing a significant (F-test, p < 0.05) effect of nitrogen supply on ScGS1 expression in the grain at 21 days post-anthesis. There was also evidence of an effect of sulfur deficiency on ScASN1 gene expression. However, although this effect was large (almost 10-fold) it was only marginally statistically significant (F-test, 0.05 < p < 0.10). The study reinforced the conclusion that nutrient availability can have a profound impact on the concentrations of

  10. Changes in Free Amino Acid Concentration in Rye Grain in Response to Nitrogen and Sulfur Availability, and Expression Analysis of Genes Involved in Asparagine Metabolism

    PubMed Central

    Postles, Jennifer; Curtis, Tanya Y.; Powers, Stephen J.; Elmore, J. S.; Mottram, Donald S.; Halford, Nigel G.

    2016-01-01

    Free asparagine plays a central role in nitrogen storage and transport in many plant species due to its relatively high ratio of nitrogen to carbon. However, it is also a precursor for acrylamide, a Class 2a carcinogen that forms during high-temperature processing and cooking. The concentration of free asparagine was shown to increase by approximately 70% in rye grain in response to severe sulfur deficiency (F-test, p = 0.004), while the concentration of both free asparagine and free glutamine increased (by almost threefold and approximately 62%, respectively) in response to nitrogen application (F-test, p < 0.001 for free asparagine; p = 0.004 for free glutamine). There were also effects of nutrient supply on other free amino acids: The concentration of free proline, for example, showed a significant (F-test, p = 0.019) effect of nitrogen interacting with sulfur, with the highest concentration occurring when the plants were deprived of both nitrogen and sulfur. Polymerase chain reaction products for several genes involved in asparagine metabolism and its regulation were amplified from rye grain cDNA. These genes were asparagine synthetase-1 (ScASN1), glutamine synthetase-1 (ScGS1), potassium-dependent asparaginase (ScASP), aspartate kinase (ScASK), and general control non-derepressible-2 (ScGCN2). The expression of these genes and of a previously described sucrose non-fermenting-1-related protein kinase-1 gene (ScSnRK1) was analyzed in flag leaf and developing grain in response to nitrogen and sulfur supply, revealing a significant (F-test, p < 0.05) effect of nitrogen supply on ScGS1 expression in the grain at 21 days post-anthesis. There was also evidence of an effect of sulfur deficiency on ScASN1 gene expression. However, although this effect was large (almost 10-fold) it was only marginally statistically significant (F-test, 0.05 < p < 0.10). The study reinforced the conclusion that nutrient availability can have a profound impact on the concentrations of

  11. A diffuse interface model of grain boundary faceting

    NASA Astrophysics Data System (ADS)

    Abdeljawad, F.; Medlin, D. L.; Zimmerman, J. A.; Hattar, K.; Foiles, S. M.

    2016-06-01

    Interfaces, free or internal, greatly influence the physical properties and stability of materials microstructures. Of particular interest are the processes that occur due to anisotropic interfacial properties. In the case of grain boundaries (GBs) in metals, several experimental observations revealed that an initially flat GB may facet into hill-and-valley structures with well defined planes and corners/edges connecting them. Herein, we present a diffuse interface model that is capable of accounting for strongly anisotropic GB properties and capturing the formation of hill-and-valley morphologies. The hallmark of our approach is the ability to independently examine the various factors affecting GB faceting and subsequent facet coarsening. More specifically, our formulation incorporates higher order expansions to account for the excess energy due to facet junctions and their non-local interactions. As a demonstration of the modeling capability, we consider the Σ5 <001 > tilt GB in body-centered-cubic iron, where faceting along the {210} and {310} planes was experimentally observed. Atomistic calculations were utilized to determine the inclination-dependent GB energy, which was then used as an input in our model. Linear stability analysis and simulation results highlight the role of junction energy and associated non-local interactions on the resulting facet length scales. Broadly speaking, our modeling approach provides a general framework to examine the microstructural stability of polycrystalline systems with highly anisotropic GBs.

  12. Modelling the interactions between grain, hydraulics, and local topography to understand the impact on incipient motion

    NASA Astrophysics Data System (ADS)

    von Boetticher, Albrecht; Turowski, Jens M.

    2013-04-01

    Sediment transport plays the key role in the forming fluvial systems, and it has become a major issue for the management and operation of hydropower plants and shipping channels as well as for the understanding of flooding hazards. The interactions between grain, hydraulics, and local topography are complicated, and it is difficult to quantify them in the laboratory, in the field, or in simple theoretical models based on two-dimensional force balances. In many theoretical models of incipient motion, grains are assumed to have simple geometrical shapes (usually spheres), despite the fact that in the real world grain shapes can vary from platy to elongated to symmetrical, and from angular to rounded. In addition, grain shape may influence protrusion and angle of repose for a grain sitting in the same pocket, and both local grain environment and grain shape in turn influence the local flow field around the grain, and thus the forces acting on it. In this project a numerical model will be developed that is capable of resolving the interaction between the grain and the flow. The model will be used to study the influence of the grain environment and grain shape on initiation of motion. The aims of the project are three-fold. First, we want to develop a numerical model that is adapted to and can efficiently deal with the specific problems occurring in the study of initiation of bedload sediment motion in streams. Second, we want to identify which of the parameters describing grain shape and local topography (e.g., protrusion, angle of repose, grain angularity) dominantly influence the initiation of motion of an individual grain. Third, we want to clarify when and where simple analytical approximations of the sort that have been used in many previous models are applicable. In three tasks we will develop the model, validate it against laboratory and field data, and perform a number of systematic numerical experiments to better understand incipient motion.

  13. Measurements and modeling of reactive nitrogen deposition in southeast Brazil.

    PubMed

    Allen, A G; Machado, C M D; Cardoso, A A

    2011-05-01

    Increased reactive nitrogen (Nr) deposition due to expansion of agro-industry was investigated considering emission sources, atmospheric transport and chemical reactions. Measurements of the main inorganic nitrogen species (NO2, NH3, HNO3, and aerosol nitrate and ammonium) were made over a period of one year at six sites distributed across an area of ∼130,000 km2 in southeast Brazil. Oxidized species were estimated to account for ∼90% of dry deposited Nr, due to the region's large emissions of nitrogen oxides from biomass burning and road transport. NO2-N was important closer to urban areas, however overall HNO3-N represented the largest component of dry deposited Nr. A simple mathematical modeling procedure was developed to enable estimates of total Nr dry deposition to be made from knowledge of NO2 concentrations. The technique, whose accuracy here ranged from <1% to 29%, provides a useful new tool for the mapping of reactive nitrogen deposition. PMID:21354679

  14. Multiscale model of metal alloy oxidation at grain boundaries

    SciTech Connect

    Sushko, Maria L.; Alexandrov, Vitali Y.; Schreiber, Daniel K.; Rosso, Kevin M.; Bruemmer, Stephen M.

    2015-06-07

    High temperature intergranular oxidation and corrosion of metal alloys is one of the primary causes of materials degradation in nuclear systems. In order to gain insights into grain boundary oxidation processes, a mesoscale metal alloy oxidation model at experimentally relevant length scales is established by combining quantum Density Functional Theory (DFT) and mesoscopic Poisson-Nernst-Planck/classical DFT with predictions focused on Ni alloyed with either Cr or Al. Analysis of species and fluxes at steady-state conditions indicates that the oxidation process involves vacancy-mediated transport of Ni and the minor alloying element to the oxidation front and the formation of stable metal oxides. The simulations further demonstrate that the mechanism of oxidation for Ni-5Cr and Ni-4Al is qualitatively different. Intergranular oxidation of Ni-5Cr involves the selective oxidation of the minor element and not matrix Ni, due to slower diffusion of Ni relative to Cr in the alloy and due to the significantly smaller energy gain upon the formation of nickel oxide compared to that of Cr2O3. This essentially one-component oxidation process results in continuous oxide formation and a monotonic Cr vacancy distribution ahead of the oxidation front, peaking at alloy/oxide interface. In contrast, Ni and Al are both oxidized in Ni-4Al forming a mixed spinel NiAl2O4. Different diffusivities of Ni and Al give rise to a complex elemental distribution in the vicinity of the oxidation front. Slower diffusing Ni accumulates in the oxide and metal within 3 nm of the interface, while Al penetrates deeper into the oxide phase. Ni and Al are both depleted from the region 3–10 nm ahead of the oxidation front creating voids. The oxide microstructure is also different. Cr2O3 has a plate-like structure with 1.2 - 1.7 nm wide pores running along the grain boundary, while NiAl2O4 has 1.5 nm wide pores in the direction parallel to the grain boundary and 0.6 nm pores in the perpendicular

  15. Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli

    PubMed Central

    Resendis-Antonio, Osbaldo; Reed, Jennifer L; Encarnación, Sergio; Collado-Vides, Julio; Palsson, Bernhard Ø

    2007-01-01

    Rhizobiaceas are bacteria that fix nitrogen during symbiosis with plants. This symbiotic relationship is crucial for the nitrogen cycle, and understanding symbiotic mechanisms is a scientific challenge with direct applications in agronomy and plant development. Rhizobium etli is a bacteria which provides legumes with ammonia (among other chemical compounds), thereby stimulating plant growth. A genome-scale approach, integrating the biochemical information available for R. etli, constitutes an important step toward understanding the symbiotic relationship and its possible improvement. In this work we present a genome-scale metabolic reconstruction (iOR363) for R. etli CFN42, which includes 387 metabolic and transport reactions across 26 metabolic pathways. This model was used to analyze the physiological capabilities of R. etli during stages of nitrogen fixation. To study the physiological capacities in silico, an objective function was formulated to simulate symbiotic nitrogen fixation. Flux balance analysis (FBA) was performed, and the predicted active metabolic pathways agreed qualitatively with experimental observations. In addition, predictions for the effects of gene deletions during nitrogen fixation in Rhizobia in silico also agreed with reported experimental data. Overall, we present some evidence supporting that FBA of the reconstructed metabolic network for R. etli provides results that are in agreement with physiological observations. Thus, as for other organisms, the reconstructed genome-scale metabolic network provides an important framework which allows us to compare model predictions with experimental measurements and eventually generate hypotheses on ways to improve nitrogen fixation. PMID:17922569

  16. Coarse-grained DNA modeling: Hybridization and ionic effects

    NASA Astrophysics Data System (ADS)

    Hinckley, Daniel M.

    Deoxyribonucleic acid (DNA) is a biopolymer of enormous significance in living systems. The utility of DNA in such systems is derived from the programmable nature of DNA and its unique mechanical properties. Recently, material scientists have harnessed these properties in order to create systems that spontaneous self-assemble on the nanoscale. Both biologists and material scientists are hindered by an incomplete understanding of the physical interactions that together govern DNA's behavior. Computer simulations, especially those at the coarse-grained (CG) level, can potentially complete this understanding by resolving details indiscernible with current experimental techniques. In this thesis, we advance the state-of-the-art of DNA CG simulations by first reviewing the relevant theory and the evolution of CG DNA models since their inception. Then we present 3SPN.2, an improved CG model for DNA that should provide new insights into biological and nanotechnological systems which incorporate DNA. We perform forward flux sampling simulations in order to examine the effect of sequence, oligomer length, and ionic strength on DNA oligomer hybridization. Due to the limitations inherent in continuum treatments of electrostatic interactions in biological systems, we generate a CG model of biological ions for use with 3SPN.2 and other CG models. Lastly, we illustrate the potential of 3SPN.2 and CG ions by using the models in simulations of viral capsid packaging experiments. The models and results described in this thesis will be useful in future modeling efforts that seek to identify the fundamental physics that govern behavior such as nucleosome positioning, DNA hybridization, and DNA nanoassembly.

  17. Generic Coarse-Grained Model for Protein Folding and Aggregation

    NASA Astrophysics Data System (ADS)

    Bereau, Tristan; Deserno, Markus

    2009-03-01

    The complexity involved in protein structure is not only due to the rich variety of amino acids, but also the inherent weak interactions, comparable to thermal energy, and important cooperative phenomena. This presents a challenge in atomistic simulations, as it is associated with high-dimensionality and ruggedness of the energy landscape as well as long equilibration times. We have recently developed a coarse-grained (CG) implicit solvent peptide model which has been designed to reproduce key consequences of the abovementioned weak interactions. Its intermediate level of resolution, four beads per amino acid, allows for accurate sampling of local conformations by designing a force field that relies on simple interactions. A realistic ratio of α-helix to β-sheet content is achieved by mimicking a nearest-neighbor dipole interaction. We tune the model in order to fold helical proteins while systematically comparing the structure with NMR data. Very good agreement is achieved for proteins that have simple tertiary structures. We further probe the effects of cooperativity between amino acids by looking at peptide aggregation, where hydrophobic peptide fragments cooperatively form large-scale β-sheet structures. The model is able to reproduce features from atomistic simulations on a qualitative basis.

  18. Effect of Nitrogen Content on Grain Refinement and Mechanical Properties of a Reversion-Treated Ni-Free 18Cr-12Mn Austenitic Stainless Steel

    NASA Astrophysics Data System (ADS)

    Behjati, P.; Kermanpur, A.; Najafizadeh, A.; Samaei Baghbadorani, H.; Karjalainen, L. P.; Jung, J.-G.; Lee, Y.-K.

    2014-12-01

    Martensite reversion treatment was utilized to obtain ultrafine grain size in Fe-18Cr-12Mn-N stainless steels containing 0 to 0.44 wt pct N. This was achieved by cold rolling to 80 pct reduction followed by reversion annealing at temperatures between 973 K and 1173 K (700 °C and 900 °C) for 1 to 104 seconds. The microstructural evolution was characterized using both transmission and scanning electron microscopes, and mechanical properties were evaluated using hardness and tensile tests. The steel without nitrogen had a duplex ferritic-austenitic structure and the grain size refinement remained inefficient. The finest austenitic microstructure was achieved in the steels with 0.25 and 0.36 wt pct N following annealing at 1173 K (900 °C) for 100 seconds, resulting in average grain sizes of about 0.240 ± 0.117 and 0.217 ± 0.73 µm, respectively. Nano-size Cr2N precipitates observed in the microstructure were responsible for retarding the grain growth. The reversion mechanism was found to be diffusion controlled in the N-free steel and shear controlled in the N-containing steels. Due to a low fraction of strain-induced martensite in cold rolled condition, the 0.44 wt pct N steel displayed relatively non-uniform, micron-scale grain structure after the same reversion treatment, but it still exhibited superior mechanical properties with a yield strength of 1324 MPa, tensile strength of 1467 MPa, and total elongation of 17 pct. While the high yield strength can be attributed to strengthening by nitrogen alloying, dislocation hardening, and slight grain refinement, the moderate strain-induced martensitic transformation taking place during tensile straining was responsible for enhancement in tensile strength and elongation.

  19. Development and application of coarse-grained models for lipids

    NASA Astrophysics Data System (ADS)

    Cui, Qiang

    2013-03-01

    I'll discuss a number of topics that represent our efforts in developing reliable molecular models for describing chemical and physical processes involving biomembranes. This is an exciting yet challenging research area because of the multiple length and time scales that are present in the relevant problems. Accordingly, we attempt to (1) understand the value and limitation of popular coarse-grained (CG) models for lipid membranes with either a particle or continuum representation; (2) develop new CG models that are appropriate for the particular problem of interest. As specific examples, I'll discuss (1) a comparison of atomistic, MARTINI (a particle based CG model) and continuum descriptions of a membrane fusion pore; (2) the development of a modified MARTINI model (BMW-MARTINI) that features a reliable description of membrane/water interfacial electrostatics and its application to cell-penetration peptides and membrane-bending proteins. Motivated specifically by the recent studies of Wong and co-workers, we compare the self-assembly behaviors of lipids with cationic peptides that include either Arg residues or a combination of Lys and hydrophobic residues; in particular, we attempt to reveal factors that stabilize the cubic ``double diamond'' Pn3m phase over the inverted hexagonal HII phase. For example, to explicitly test the importance of the bidentate hydrogen-bonding capability of Arg to the stabilization of negative Gaussian curvature, we also compare results using variants of the BMW-MARTINI model that treat the side chain of Arg with different levels of details. Collectively, the results suggest that both the bidentate feature of Arg and the overall electrostatic properties of cationic peptides are important to the self-assembly behavior of these peptides with lipids. The results are expected to have general implications to the mechanism of peptides and proteins that stimulate pore formation in biomembranes. Work in collaboration with Zhe Wu, Leili Zhang

  20. Modeling the effect of grain size and dislocation density on hysteretic magnetic properties in steels

    NASA Astrophysics Data System (ADS)

    Sablik, M. J.

    2001-05-01

    In this article, the Jiles-Atherton model is modified to elucidate the variation of magnetic properties with grain size and dislocation density. The modified model predicts generally that coercive field increases with increasing dislocation density and inverse grain size and that remanent flux density and permeability at the coercive field decrease with increasing dislocation density and inverse grain size. Using the same model, it should be possible to model the effects of grain size and dislocation density on other magnetic measurements such as nonlinear harmonics of the flux density or Barkhausen noise.

  1. Complexity and Uncertainty in Soil Nitrogen Modeling

    NASA Astrophysics Data System (ADS)

    Ajami, N. K.; Gu, C.

    2009-12-01

    Model uncertainty is rarely considered in the field of biogeochemical modeling. The standard biogeochemical modeling approach is to proceed based on one selected model with the “right” complexity level based on data availability. However other plausible models can result in dissimilar answer to the scientific question in hand using the same set of data. Relying on a single model can lead to underestimation of uncertainty associated with the results and therefore lead to unreliable conclusions. Multi-model ensemble strategy is a means to exploit the diversity of skillful predictions from different models with multiple levels of complexity. The aim of this study is two fold, first to explore the impact of a model’s complexity level on the accuracy of the end results and second to introduce a probabilistic multi-model strategy in the context of a process-based biogeochemical model. We developed three different versions of a biogeochemical model, TOUGHREACT-N, with various complexity levels. Each one of these models was calibrated against the observed data from a tomato field in Western Sacramento County, California, and considered two different weighting sets on the objective function. This way we created a set of six ensemble members. The Bayesian Model Averaging (BMA) approach was then used to combine these ensemble members by the likelihood that an individual model is correct given the observations. The results clearly indicate the need to consider a multi-model ensemble strategy over a single model selection in biogeochemical modeling.

  2. Nitrogen

    USGS Publications Warehouse

    Kramer, D.A.

    2004-01-01

    Ammonia is the principal source of fixed nitrogen. It was produced by 17 companies at 34 plants in the United States during 2003. Fifty-three percent of U.S. ammonia production capacity was centered in Louisiana, Oklahoma and Texas because of their large reserves of natural gas, the dominant domestic feedstock.

  3. Interactive effects of nitrogen fertilization and irrigation on grain yield, canopy temperature, and nitrogen use efficiency in overhead sprinkler-irrigated Durum Wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nitrogen and irrigation management are crucial in the production of high protein irrigated durum wheat (Triticum durum Desf.) in arid regions. However, as the availability of irrigation water decreases and potential costs and regulation of nitrogen (N) increase, there is a need to understand how ir...

  4. A grain-fluid mixture model to characterize the dynamics of active landslides in fine-grained soils

    NASA Astrophysics Data System (ADS)

    Spickermann, Anke; Toussaint, Renaud; Travelletti, Julien; Malet, Jean-Philippe; van Asch, Theo

    2013-04-01

    Dynamic continuum modeling of slow-moving landslides in fine-grained material is generally performed by means of visco-plastic models applying the approach of one-phase material. Shortcomings of this approach are the uncertainty of using physical realistic material parameters and that solid and fluid stresses are not considered separately. The objective of this work is to overcome the problems of the one-phase material approach by adopting the theory of grain-fluid mixture. Applying a two-phase model approach enables to distinguish explicitly between 25 e.g. solid friction stress, fluid shear stress (viscous stress), buoyancy and momentum exchange between solid and fluid (seepage). The model is implemented in a GIS (Geographic Information System) scripting language, which facilitate the use of complex three-dimensional (3D) topographies. The model is applied to and tested on the well-documented Super-Sauze landslide developed in reworked clay-shales. It is shown that the temporal and spatial varying moving pattern of the landslide can be reproduced. The numerical analysis reveals that viscous stresses produced by the fluid are irrelevant. Movements are mainly controlled by buoyancy, related to the evolution of the ground water level within the landslide that comes from water infiltration, and is introduced as a boundary condition. It is concluded that a two-phase, grain-fluid mixture model is convenient when landslide motion in fine-grained material is mainly controlled by the hydrological conditions (i.e. changes in pore water pressures), as in this example. The material parameters, as viscosity, calibrated to reproduce such landslide motion in models using the one-phase material approach, would take unrealistic values.

  5. Dust grain coagulation modelling : From discrete to continuous

    NASA Astrophysics Data System (ADS)

    Paruta, P.; Hendrix, T.; Keppens, R.

    2016-07-01

    In molecular clouds, stars are formed from a mixture of gas, plasma and dust particles. The dynamics of this formation is still actively investigated and a study of dust coagulation can help to shed light on this process. Starting from a pre-existing discrete coagulation model, this work aims to mathematically explore its properties and its suitability for numerical validation. The crucial step is in our reinterpretation from its original discrete to a well-defined continuous form, which results in the well-known Smoluchowski coagulation equation. This opens up the possibility of exploiting previous results in order to prove the existence and uniqueness of a mass conserving solution for the evolution of dust grain size distribution. Ultimately, to allow for a more flexible numerical implementation, the problem is rewritten as a non-linear hyperbolic integro-differential equation and solved using a finite volume discretisation. It is demonstrated that there is an exact numerical agreement with the initial discrete model, with improved accuracy. This is of interest for further work on dynamically coupled gas with dust simulations.

  6. Modeling of stresses at grain boundaries with respect to occurrence of stress corrosion cracking

    SciTech Connect

    Kozaczek, K.J.; Sinharoy, A.; Ruud, C.O.; McIlree, A.R.

    1995-12-31

    The distributions of elastic stresses/strains in the grain boundary regions were studied by the analytical and the finite element models. The grain boundaries represent the sites where stress concentration occurs as a result of discontinuity of elastic properties across the grain boundary and the presence of second phase particles elastically different from the surrounding matrix grains. A quantitative analysis of those stresses for steels and nickel based alloys showed that the stress concentrations in the grain boundary regions are high enough to cause a local microplastic deformation even when the material is in the macroscopic elastic regime. The stress redistribution as a result of such a plastic deformation was discussed.

  7. An integrated soil-crop system model for water and nitrogen management in North China

    PubMed Central

    Liang, Hao; Hu, Kelin; Batchelor, William D.; Qi, Zhiming; Li, Baoguo

    2016-01-01

    An integrated model WHCNS (soil Water Heat Carbon Nitrogen Simulator) was developed to assess water and nitrogen (N) management in North China. It included five main modules: soil water, soil temperature, soil carbon (C), soil N, and crop growth. The model integrated some features of several widely used crop and soil models, and some modifications were made in order to apply the WHCNS model under the complex conditions of intensive cropping systems in North China. The WHCNS model was evaluated using an open access dataset from the European International Conference on Modeling Soil Water and N Dynamics. WHCNS gave better estimations of soil water and N dynamics, dry matter accumulation and N uptake than 14 other models. The model was tested against data from four experimental sites in North China under various soil, crop, climate, and management practices. Simulated soil water content, soil nitrate concentrations, crop dry matter, leaf area index and grain yields all agreed well with measured values. This study indicates that the WHCNS model can be used to analyze and evaluate the effects of various field management practices on crop yield, fate of N, and water and N use efficiencies in North China. PMID:27181364

  8. An integrated soil-crop system model for water and nitrogen management in North China.

    PubMed

    Liang, Hao; Hu, Kelin; Batchelor, William D; Qi, Zhiming; Li, Baoguo

    2016-01-01

    An integrated model WHCNS (soil Water Heat Carbon Nitrogen Simulator) was developed to assess water and nitrogen (N) management in North China. It included five main modules: soil water, soil temperature, soil carbon (C), soil N, and crop growth. The model integrated some features of several widely used crop and soil models, and some modifications were made in order to apply the WHCNS model under the complex conditions of intensive cropping systems in North China. The WHCNS model was evaluated using an open access dataset from the European International Conference on Modeling Soil Water and N Dynamics. WHCNS gave better estimations of soil water and N dynamics, dry matter accumulation and N uptake than 14 other models. The model was tested against data from four experimental sites in North China under various soil, crop, climate, and management practices. Simulated soil water content, soil nitrate concentrations, crop dry matter, leaf area index and grain yields all agreed well with measured values. This study indicates that the WHCNS model can be used to analyze and evaluate the effects of various field management practices on crop yield, fate of N, and water and N use efficiencies in North China. PMID:27181364

  9. A model for nitrogen chemisorption in ion thrusters

    NASA Technical Reports Server (NTRS)

    Wilbur, P. J.

    1979-01-01

    A theoretical model describing the formation of nitrogen species subject to chemisorption on ion thruster discharge chamber surfaces is presented. Molecules, atoms, atomic ions and molecular ions are identified as the important species in the analysis. Current densities of the atomic and molecular ions predicted by the model are compared to current densities measured in the beam of a SERT II thruster. The predicted and measured values of these two current densities are shown to agree within about + or - 100%. The mechanisms involved in the erosion of a surface subjected to simultaneous nitrogen chemisorption and sputter erosion by high energy ions are also discussed.

  10. Managing grain protein content by remote sensing in winter wheat

    NASA Astrophysics Data System (ADS)

    Huang, Wenjiang; Wang, Jihua; Song, Xiaoyu; Zhao, Chunjiang; Liu, Liangyun

    2007-10-01

    Advanced site-specific determination of grain protein content by remote sensing can provide opportunities to optimize the strategies for purchasing and pricing grain, and to maximize the grain output by adjusting field inputs. Field experiments were performed to study the relationship between grain quality indicators and foliar nitrogen concentration. Foliar nitrogen concentration at the anthesis stage is suggested to be significantly correlated with grain protein content, while spectral vegetation index is significantly correlated to foliar nitrogen concentration around the anthesis stage. Based on the relationships among nitrogen reflectance index (NRI), foliar nitrogen concentration, and grain protein content, a statistical evaluation model of grain protein content was developed. NRI proved to be able to evaluate foliar nitrogen concentration with a coefficient of determination of R2= 0.7302 in year 2002. The relationship between measured and remote sensing derived foliar nitrogen concentration had a coefficient of determination of R2=0.7279 in year 2003. The results mentioned above indicate that the inversion of foliar nitrogen concentration and the evaluation of grain protein content by NRI are surprisingly good.

  11. A wheat grazing model for simulating grain and beef production: Part II - model validation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Model evaluation is a prerequisite to its adoption and successful application. The objective of this paper is to evaluate the ability of a newly developed wheat grazing model to predict fall-winter forage and grain yields of winter wheat (Triticum aestivum L.) as well as daily weight gains per steer...

  12. Modeling inorganic nitrogen deposition in Guangdong province, China

    NASA Astrophysics Data System (ADS)

    Huang, Zhijiong; Wang, Shuisheng; Zheng, Junyu; Yuan, Zibing; Ye, Siqi; Kang, Daiwen

    2015-05-01

    Atmospheric nitrogen deposition is an essential component of acid deposition and serves as one of main sources of nitrogen of the ecosystem. Along with rapidly developed economy, it is expected that the nitrogen deposition in Guangdong province is considerably large, due to substantial anthropogenic reactive nitrogen lost to the Pearl River Delta (PRD) region, one of the most developed region in China. However, characterization of chemical compositions of inorganic nitrogen (IN) deposition and quantification of nitrogen deposition fluxes in time and space in Guangdong province were seldom conducted, especially using a numerical modeling approach. In this study, we established a WRF/SMOKE-PRD/CMAQ model system and expanded 2006-based PRD regional emission inventories to Guangdong provincial ones, including SO2, NOx, VOC, PM10, PM2.5, and NH3 emissions for modeling nitrogen deposition in Guangdong province. Observations, including meteorological observed data, rainfall data, ground-level criteria pollutant measurements, satellite-derived data, and nitrogen deposition fluxes from field measurements were employed in the evaluation of model performance. Results showed that annual nitrogen deposition fluxes in the PRD region and Guangdong province were 31.01 kg N hm-1 a-1 and 26.03 kg N hm-1 a-1, dominated by NHx (including NH3 and NH,SUB>4,/SUB>+), with a percentage of 63% and 71% of the total deposition flux of IN, respectively. The ratio of dry deposition to wet deposition was approximately 2:1 in the PRD region and about 3:2 in the whole Guangdong province. IN deposition was mainly distributed in the PRD region, Chaozhou, and Maoming, which was similar to the spatial distributions of NOx and NH3 emissions. The spatial distributions of chemical compositions of IN deposition implied that NH3-N and NOx-N tended to deposit in places close to emission sources, while spatial distributions of aerosol NH4+ -N and NO3- -N usually exhibited broader deposition areas, along with

  13. Controlled release urea as a nitrogen source for spring wheat in Western Canada: yield, grain N content, and N use efficiency.

    PubMed

    Haderlein, L; Jensen, T L; Dowbenko, R E; Blaylock, A D

    2001-10-30

    Controlled release nitrogen (N) fertilizers have been commonly used in horticultural applications such as turf grasses and container-grown woody perennials. Agrium, a major N manufacturer in North and South America, is developing a low-cost controlled release urea (CRU) product for use in field crops such as grain corn, canola, wheat, and other small grain cereals. From 1998 to 2000, 11 field trials were conducted across western Canada to determine if seed-placed CRU could maintain crop yields and increase grain N and N use efficiency when compared to the practice of side-banding of urea N fertilizer. CRU was designed to release timely and adequate, but not excessive, amounts of N to the crop. Crop uptake of N from seed-placed CRU was sufficient to provide yields similar to those of side-banded urea N. Grain N concentrations of the CRU treatments were higher, on average, than those from side-banded urea, resulting in 4.2% higher N use efficiency across the entire N application range from 25 to 100 kg ha(-1). Higher levels of removal of N in grain from CRU compared to side-banded urea can result in less residual N remaining in the soil, and limit the possibility of N losses due to denitrification and leaching. PMID:12805867

  14. Nitrogen

    USGS Publications Warehouse

    Kramer, D.A.

    2007-01-01

    Ammonia was produced by 15 companies at 25 plants in 16 states in the United States during 2006. Fifty-seven percent of U.S. ammonia production capacity was centered in Louisiana, Oklahoma and Texas because of their large reserves of natural gas, the dominant domestic feedstock. In 2006, U.S. producers operated at about 72 percent of their rated capacity (excluding plants that were idle for the entire year). Five companies, Koch Nitrogen, Terra Industries, CF Industries, PCS Nitro-gen, and Agrium, in descending order, accounted for 79 percent U.S. ammonia production capacity. The United States was the world's fourth-ranked ammonia producer and consumer following China, India and Russia. Urea, ammonium nitrate, ammonium phosphates, nitric acid and ammonium sulfate were the major derivatives of ammonia in the United States, in descending order of importance.

  15. The effects of free-air CO2 enrichment (FACE) on carbon and nitrogen accumulation in grains of rice (Oryza sativa L.)

    PubMed Central

    Zhu, Chunwu; Hasegawa, Toshihiro

    2013-01-01

    Rising atmospheric CO2 concentrations will probably increase rice (Oryza sativa L.) yield but decrease grain nitrogen (GN) concentration. Grains attached to different positions in the panicles differ greatly in weight and quality, but their responses to elevated CO2 (e[CO2]) are poorly understood, which limits our understanding of the mechanisms of yield enhancement and quality degradation. Thus a free-air CO2 enrichment experiment was conducted to examine the effects of e[CO2] on grain mass (GM), grain carbon (GC), and GN accumulation in the spikelets attached to the upper primary rachis branch (superior spikelets; SS) and those attached to the lower secondary rachis (inferior spikelets; IS). e[CO2] stimulated the rice yield by 13% but decreased the N concentration in the panicle by 7% when averaged over two levels of N fertilizations (P < 0.01). The responses of SS and IS to e[CO2] were different particularly under higher N supply. For SS, e[CO2] decreased GN by 24% (P < 0.01) but did not affect GM. For IS, e[CO2] increased GM by 13% (P < 0.05) but GN was not affected. The reduction of GN due to e[CO2] started to appear at the beginning of grain filling. These results suggest that future [CO2] levels probably stimulate the grain growth of IS, most of which are not marketable due to limited size, at the expense of GN reduction in SS. Translocation of N from SS to IS may be a possible mechanism for reduction in GN of SS. This may degrade the grain quality of marketable rice under e[CO2]. PMID:23918962

  16. An improved model for interplanetary dust grain fluxes to the outer planets

    NASA Astrophysics Data System (ADS)

    Poppe, A. R.

    2015-12-01

    We present an improved model for interplanetary dust grain fluxes in the outer solar system constrained by in-situ dust density observations. A dynamical dust grain tracing code is used to establish relative dust grain densities and three-dimensional velocity distributions in the outer solar system for four main sources of dust grains: Jupiter-family comets, Halley-type comets, Oort-Cloud comets, and Edgeworth-Kuiper Belt objects. Model densities are constrained by in-situ dust measurements by the New Horizons Student Dust Counter, the Pioneer 10 meteoroid detector, and the Galileo Dust Detection System (DDS). The model predicts that Jupiter-family comet grains dominate the interplanetary dust grain mass flux inside approximately 10 AU, Oort-Cloud cometary grains may dominate between 10 and 25 AU, and Edgeworth-Kuiper Belt grains are dominant outside 25 AU. The model also predicts that while the total interplanetary mass flux at Jupiter roughly matches that inferred by the analysis of the Galileo DDS measurements, mass fluxes to Saturn, Uranus, and Neptune are at least one order-of-magnitude lower than that predicted by extrapolations of dust grain flux models from 1 AU. We present modeled mass fluxes to various moons, atmospheres, and ring systems of the outer planets.

  17. Modeling of grain boundary stresses in Alloy 600

    SciTech Connect

    Kozaczek, K.J.; Sinharoy, A.; Ruud, C.O.; Mcllree, A.R.

    1995-04-01

    Corrosive environments combined with high stress levels and susceptible microstructures can cause intergranular stress corrosion cracking (IGSCC) of Alloy 600 components on both primary and secondary sides of pressurized water reactors. One factor affecting the IGSCC is intergranular carbide precipitation controlled by heat treatment of Alloy 600. This study is concerned with analysis of elastic stress fields in vicinity of M{sub 7}C{sub 3} and M{sub 23}C{sub 6} carbides precipitated in the matrix and at a grain boundary triple point. The local stress concentration which can lead to IGSCC initiation was studied using a two-dimensional finite element model. The intergranular precipitates are more effective stress raisers than the intragranular precipitates. The combination of the elastic property mismatch and the precipitate shape can result in a local stress field substantially different than the macroscopic stress. The maximum local stresses in the vicinity of the intergranular precipitate were almost twice as high as the applied stress.

  18. Models for grains and gas ejection dynamics from a silo

    NASA Astrophysics Data System (ADS)

    Zhou, Yixian; Aussillous, Pascale; Ruyer, Pierre; Iusti/Gep Team; Semia/Limar Team

    2015-11-01

    In the hypothetical conditions of a reactivity initiated accident in a nuclear power plant, some of the fuel rods could break. If fuel fragmentation occurs, hot fuel particles and pressurized gas could interact with the surrounding fluid. The violence of this interaction depends on the discharge rate toward the fluid. In the present work, we study the discharge dynamics and identify the parameters governing this flow. In this paper, we focus on the experimental study of the discharge of a silo composed of spherical glass beads, with an orifice either lateral or at the bottom, with or without air flow. The measured parameters are the mass flow rate and the pressure along the silo, whereas the controlled parameters are the size of particles, the size of orifices, and the flow rate of air. For the case without air flow we found that the flow rate of particles ejected from the bottom orifice is 3 times greater than from the lateral orifice. For the case of a lateral orifice, when the form of the orifice is rectangular with width W and height D, we identify two regimes which depend on the ratio of width to height W / D . For the case with air flow, we found that the flow rate increases with the air flow. A simple physical model is proposed to describe the grains and gas ejection.

  19. Unraveling irradiation induced grain growth with in situ transmission electron microscopy and coordinated modeling

    SciTech Connect

    Bufford, D. C.; Abdeljawad, F. F.; Foiles, S. M.; Hattar, K.

    2015-11-09

    Nanostructuring has been proposed as a method to enhance radiation tolerance, but many metallic systems are rejected due to significant concerns regarding long term grain boundary and interface stability. This work utilized recent advancements in transmission electron microscopy (TEM) to quantitatively characterize the grain size, texture, and individual grain boundary character in a nanocrystalline gold model system before and after in situ TEM ion irradiation with 10 MeV Si. The initial experimental measurements were fed into a mesoscale phase field model, which incorporates the role of irradiation-induced thermal events on boundary properties, to directly compare the observed and simulated grain growth with varied parameters. The observed microstructure evolution deviated subtly from previously reported normal grain growth in which some boundaries remained essentially static. In broader terms, the combined experimental and modeling techniques presented herein provide future avenues to enhance quantification and prediction of the thermal, mechanical, or radiation stability of grain boundaries in nanostructured crystalline systems.

  20. Unraveling irradiation induced grain growth with in situ transmission electron microscopy and coordinated modeling

    NASA Astrophysics Data System (ADS)

    Bufford, D. C.; Abdeljawad, F. F.; Foiles, S. M.; Hattar, K.

    2015-11-01

    Nanostructuring has been proposed as a method to enhance radiation tolerance, but many metallic systems are rejected due to significant concerns regarding long term grain boundary and interface stability. This work utilized recent advancements in transmission electron microscopy (TEM) to quantitatively characterize the grain size, texture, and individual grain boundary character in a nanocrystalline gold model system before and after in situ TEM ion irradiation with 10 MeV Si. The initial experimental measurements were fed into a mesoscale phase field model, which incorporates the role of irradiation-induced thermal events on boundary properties, to directly compare the observed and simulated grain growth with varied parameters. The observed microstructure evolution deviated subtly from previously reported normal grain growth in which some boundaries remained essentially static. In broader terms, the combined experimental and modeling techniques presented herein provide future avenues to enhance quantification and prediction of the thermal, mechanical, or radiation stability of grain boundaries in nanostructured crystalline systems.

  1. Mean-field model for the growth and coarsening of stoichiometric precipitates at grain boundaries

    NASA Astrophysics Data System (ADS)

    Kozeschnik, E.; Svoboda, J.; Radis, R.; Fischer, F. D.

    2010-01-01

    In this paper, a model for growth and coarsening of precipitates at grain boundaries is developed. The concept takes into account that the evolution of grain boundary precipitates involves fast short-circuit diffusion along grain boundaries as well as slow bulk diffusion of atoms from the grain interior to the grain boundaries. The mathematical formalism is based on a mean-field approximation, utilizing the thermodynamic extremal principle. The model is applied to the precipitation of aluminum nitrides in microalloyed steel in austenite, where precipitation occurs predominately at the austenite grain boundaries. It is shown that the kinetics of precipitation predicted by the proposed model differs significantly from that calculated for randomly distributed precipitates with spherical diffusion fields. Good agreement of the numerical solution is found with experimental observations as well as theoretical treatment of precipitate coarsening.

  2. [Effects of application time and basal/topdressing ratio of nitrogen fertilizer on the spatiotemporal variation of soil NO3- -N and NH4+ -N contents and the grain yield and its quality of wheat].

    PubMed

    Wu, Ji; Guo, Xi-sheng; Yang, Xiao-hu; Huang, Xiao-rong

    2008-11-01

    Field trials were conducted to study the effects of different application time and basal/topdressing ratio of nitrogen fertilizer on the spatiotemporal variation of soil NO3- -N and NH4+ -N contents and the grain yield and its quality of wheat. The results showed that soil NO3- -N and NH4+ -N contents decreased with increasing soil depth. Both the application time and the basal/topdressing ratio of nitrogen fertilizer had significant effects on the NO3- -N and NH4+ -N contents in 0-20 cm soil layer. Compared with basal application, later fertilization and higher topdressing ratio could promote the nitrogen uptake by wheat plant and increase the plant nitrogen recovery significantly, decrease the soil nitrogen recovery during wheat growth, and improve the grain quality significantly, while had less effects on the grain yield. Topdressing too much nitrogen fertilizer at booting stage could result in a significant decrease of grain yield. Under the condition of this experiment, the optimal nitrogen fertilization mode for good wheat grain yield and its quality and good ecological benefits was 5:3:2 of basal application: topdressing at jointing stage: topdressing at booting stage. PMID:19238836

  3. Modeling proximity-coupling in multifilamentary wires by grained Bean model

    NASA Astrophysics Data System (ADS)

    Akune, T.; Yumoto, W.; Sakamoto, N.

    2008-09-01

    Proximity-currents between filaments in a multifilamentary wire show a close resemblance with the inter-grain current in a high- Tc superconductor. The critical current densities of the proximity-induced superconducting matrix Jcm can be estimated from measured twist-pitch dependence of magnetization and have been shown to follow the well-known scaling law of the pinning strength. In the grained Bean model, the filaments are immersed in the proximity-induced superconducting matrix. Difference of the superconducting characteristics of the filament, the matrix and the filament content factor give a variety of deformation on the AC susceptibility curves. The computed AC susceptibility curves of multifilamentary wires using the grained Bean model are favorably compared with the experimental results.

  4. Langrangian model of nitrogen kinetics in the Chattahoochee river

    USGS Publications Warehouse

    Jobson, H.E.

    1987-01-01

    A Lagrangian reference frame is used to solve the convection-dispersion equation and interpret water-quality obtained from the Chattahoochee River. The model was calibrated using unsteady concentrations of organic nitrogen, ammonia, and nitrite plus nitrate obtained during June 1977 and verified using data obtained during August 1976. Reaction kinetics of the cascade type are shown to provide a reasonable description of the nitrogen-species processes in the Chattahoochee River. The conceptual model is easy to visualize in the physical sense and the output includes information that is not easily determined from an Eulerian approach, but which is very helpful in model calibration and data interpretation. For example, the model output allows one to determine which data are of most value in model calibration or verification.

  5. Effects of grain size and shape in modeling reflectance spectra of mineral mixtures

    NASA Technical Reports Server (NTRS)

    Hiroi, T.; Pieters, Carle M.

    1991-01-01

    The effects of grain size and shape on the reflectance spectra of mineral mixtures are investigated to improve a reflectance model called the isograin model, whose prototype was proposed by M. Kinoshita in 1985. The sample powder was assumed to consist of an infinite number of layers, each of which has the same thickness with the grain size d.

  6. Wheat (Triticum aestivum) NAM proteins regulate the translocation of iron, zinc, and nitrogen compounds from vegetative tissues to grain

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The NAM-B1 gene is a NAC transcription factor that affects grain nutrient concentrations in wheat (Triticum aestivum). An RNAi line with reduced expression of NAM genes has lower grain protein, iron (Fe), and zinc (Zn) concentrations. To determine whether decreased remobilization, lower plant uptak...

  7. Probing model interstellar grain surfaces with small molecules

    NASA Astrophysics Data System (ADS)

    Collings, M. P.; Frankland, V. L.; Lasne, J.; Marchione, D.; Rosu-Finsen, A.; McCoustra, M. R. S.

    2015-05-01

    Temperature-programmed desorption and reflection-absorption infrared spectroscopy have been used to explore the interaction of oxygen (O2), nitrogen (N2), carbon monoxide (CO) and water (H2O) with an amorphous silica film as a demonstration of the detailed characterization of the silicate surfaces that might be present in the interstellar medium. The simple diatomic adsorbates are found to wet the silica surface and exhibit first-order desorption kinetics in the regime up to monolayer coverage. Beyond that, they exhibit zero-order kinetics as might be expected for sublimation of bulk solids. Water, in contrast, does not wet the silica surface and exhibits zero-order desorption kinetics at all coverages consistent with the formation of an islanded structure. Kinetic parameters for use in astrophysical modelling were obtained by inversion of the experimental data at sub-monolayer coverages and by comparison with models in the multilayer regime. Spectroscopic studies in the sub-monolayer regime show that the C-O stretching mode is at around 2137 cm-1 (5.43 μm), a position consistent with a linear surface-CO interaction, and is inhomogenously broadened as resulting from the heterogeneity of the surface. These studies also reveal, for the first time, direct evidence for the thermal activation of diffusion, and hence de-wetting, of H2O on the silica surface. Astrophysical implications of these findings could account for a part of the missing oxygen budget in dense interstellar clouds, and suggest that studies of the sub-monolayer adsorption of these simple molecules might be a useful probe of surface chemistry on more complex silicate materials.

  8. Whole-Plant Dynamic System of Nitrogen Use for Vegetative Growth and Grain Filling in Rice Plants (Oryza sativa L.) as Revealed through the Production of 350 Grains from a Germinated Seed Over 150 Days: A Review and Synthesis

    PubMed Central

    Yoneyama, Tadakatsu; Tanno, Fumio; Tatsumi, Jiro; Mae, Tadahiko

    2016-01-01

    A single germinated rice (Oryza sativa L) seed can produce 350 grains with the sequential development of 15 leaves on the main stem and 7–10 leaves on four productive tillers (forming five panicles in total), using nitrogen (N) taken up from the environment over a 150-day growing season. Nitrogen travels from uptake sites to the grain through growing organ-directed cycling among sequentially developed organs. Over the past 40 years, the dynamic system for N allocation during vegetative growth and grain filling has been elucidated through studies on N and 15N transport as well as enzymes and transporters involved. In this review, we synthesize the information obtained in these studies along the following main points: (1) During vegetative growth before grain-filling, about half of the total N in the growing organs, including young leaves, tillers, root tips and differentiating panicles is supplied via phloem from mature source organs such as leaves and roots, after turnover and remobilization of proteins, whereas the other half is newly taken up and supplied via xylem, with an efficient xylem-to-phloem transfer at stem nodes. Thus, the growth of new organs depends equally on both N sources. (2) A large fraction (as much as 80%) of the grain N is derived largely from mature organs such as leaves and stems by degradation, including the autophagy pathway of chloroplast proteins (e.g., Rubisco). (3) Mobilized proteinogenic amino acids (AA), including arginine, lysine, proline and valine, are derived mainly from protein degradation, with AA transporters playing a role in transferring these AAs across cell membranes of source and sink organs, and enabling their efficient reutilization in the latter. On the other hand, AAs such as glutamine, glutamic acid, γ-amino butyric acid, aspartic acid, and alanine are produced by assimilation of newly taken up N by roots and and transported via xylem and phloem. The formation of 350 filled grains over 50 days during the

  9. Whole-Plant Dynamic System of Nitrogen Use for Vegetative Growth and Grain Filling in Rice Plants (Oryza sativa L.) as Revealed through the Production of 350 Grains from a Germinated Seed Over 150 Days: A Review and Synthesis.

    PubMed

    Yoneyama, Tadakatsu; Tanno, Fumio; Tatsumi, Jiro; Mae, Tadahiko

    2016-01-01

    A single germinated rice (Oryza sativa L) seed can produce 350 grains with the sequential development of 15 leaves on the main stem and 7-10 leaves on four productive tillers (forming five panicles in total), using nitrogen (N) taken up from the environment over a 150-day growing season. Nitrogen travels from uptake sites to the grain through growing organ-directed cycling among sequentially developed organs. Over the past 40 years, the dynamic system for N allocation during vegetative growth and grain filling has been elucidated through studies on N and (15)N transport as well as enzymes and transporters involved. In this review, we synthesize the information obtained in these studies along the following main points: (1) During vegetative growth before grain-filling, about half of the total N in the growing organs, including young leaves, tillers, root tips and differentiating panicles is supplied via phloem from mature source organs such as leaves and roots, after turnover and remobilization of proteins, whereas the other half is newly taken up and supplied via xylem, with an efficient xylem-to-phloem transfer at stem nodes. Thus, the growth of new organs depends equally on both N sources. (2) A large fraction (as much as 80%) of the grain N is derived largely from mature organs such as leaves and stems by degradation, including the autophagy pathway of chloroplast proteins (e.g., Rubisco). (3) Mobilized proteinogenic amino acids (AA), including arginine, lysine, proline and valine, are derived mainly from protein degradation, with AA transporters playing a role in transferring these AAs across cell membranes of source and sink organs, and enabling their efficient reutilization in the latter. On the other hand, AAs such as glutamine, glutamic acid, γ-amino butyric acid, aspartic acid, and alanine are produced by assimilation of newly taken up N by roots and and transported via xylem and phloem. The formation of 350 filled grains over 50 days during the

  10. Uncertainties of Nitrogen Fixation in a Dynamic Global Vegetation Model

    NASA Astrophysics Data System (ADS)

    Steinkamp, Joerg; Werner, Christian; Weber, Bettina; Hickler, Thomas

    2015-04-01

    Nitrogen is an essential nutrient for life on earth. However, most of it is in the form of dinitrogen (N2) unutilizable to life and only few organisms are able to break the triple bond, fix the nitrogen and thus make it available for cycling in the biosphere through "fixation". In most state-of-the-art dynamic global vegetation models (DGVMs) including a nitrogen cycle, N fixation is simulated by the Cleveland et al. (1999) algorithm (O-CN, LPJ-GUESS, CLM), that correlates annual N fixation to evapotranspiration rates or net primary production. Nevertheless, this algorithm has two major uncertainties, which are investigated by us: 1. The algorithm is based on annual fixation rates that are then applied uniformly throughout the year. However, in nature nitrogen fixation is an expensive process, which occurs only under favorable conditions. Here we compare the annual fixation values evenly distributed over the year with daily-derived fixation values based on a modified version of the Cleveland algorithm. We postulate that in higher latitudinal regions with seasonal climate as well as in regions with a distinct dry/wet season, modeled growth is enhanced by daily derived values compared to evenly distributed values, whereas in tropical regions hardly any difference will be visible. 2. One distinguishes between symbiotic and unsymbiotic nitrogen fixation, where the first one is associated with higher plants as symbionts supplying the fixers with carbohydrates, whereas the second, unsymbiotic is performed by so-called cryptogamic covers (CC). We found that the fixation by CC is underrepresented by the Cleveland algorithm, and a correction thus leads to enhanced growth in forested regions of higher latitudes that feature substantial CC fractions. Overall, the improvements of the algorithm proposed by us are expected to better reflect the reality of nitrogen fixation and cause an increased growth of vegetation, especially in higher northern latitudes.

  11. Modeling nitrogen removal for a denitrification biofilter.

    PubMed

    Samie, Guillaume; Bernier, Jean; Rocher, Vincent; Lessard, Paul

    2011-08-01

    Nitrous oxide (N2O) is a major greenhouse gas, heavily contributing to global warming. N2O is emitted from various sources such as wastewater treatment plants, during the nitrification and denitrification steps. ASM models, which are commonly used in wastewater treatment, usually consider denitrification as a one-step process (NO3- directly reduced to N2) and are as such unable to provide values for intermediate products of the reaction like N2O. In this study, a slightly modified ASM1 model was implemented in the GPS-X software to simulate the concentration of such intermediate products (NO2-, NO and N2O) and to estimate the amounts of gaseous N2O emitted by the denitrification stage (12 biofilters) of the Seine-Centre WWTP (SIAAP, Paris). Simulations running on a 1-year period have shown good agreements with measured effluent data for nitrate and nitrite. The calculated mean value for emitted N2O is 4.95 kgN-N2O/day, which stands in the typical range of estimated experimental values of 4-31 kgN-N2O/day. Nitrous oxide emissions are usually not measured on WWTPs and so, as obtained results show, there is a certain potential for using models that quantify those emissions using traditionally measured influent data. PMID:21340676

  12. Idealized model of nitrogen recycling in marine sediments

    SciTech Connect

    Billen, G.

    1982-04-01

    A model of the interdependent processes involved in nitrogen mineralization in marine sediments is presented, based on data collected in the sandy sediments of the North Sea. It relates the flux of organic material deposited in the sediments to the release of dissolved nitrogen to the overlying water, given the mixing conditions undergone by the solid and interstitial phases of the sediment under the action of physical or biological processes. Although idealized, the model can be useful in predicting the trends of variation in the relative importance of ammonification, nitrification, and denitrification, as a result of variations in the organic matter input to the bottom. It shows that, at low input of organic matter, most nitrogen release occurs as nitrate, whereas, at higher input, ammonium release prevails. Denitrification reaches a plateau above a certain input of organic material. It can involve an appreciable proportion (more than about 30 percent of the flux) of remineralized nitrogen only at high organic input and when a high nitrate concentration exists in the overlying water.

  13. Snow grain size and albedo in Dronning Maud Land, Antarctica: measurements and modeling

    NASA Astrophysics Data System (ADS)

    Pirazzini, Roberta; Räisänen, Petri; Vihma, Timo; Johansson, Milla; Tastula, Esa-Matti

    2014-05-01

    Snow grain macro-photos collected near the Finnish Antarctic Station Aboa during summer 2009-2010 were analyzed, and the link between snow grain metamorphism and surface albedo was investigated. Snow grain macro-photos were taken twice a day for a one-month period from four snowpack layers (at the surface and at the depths of 5, 10, and 20 cm). A cave inside the snowpack was used as a cold and dark "laboratory". The dataset also includes vertical profiles of snow temperature and density (twice a day), surface broadband albedo, surface spectral reflectance during clear and overcast days, and ancillary meteorological data. With such an extensive and complete dataset, we studied the snow grain metric that best represents the grain scattering properties at various wavelengths, establishing a direct relationship between measured grain dimensions and optically-equivalent grain size. For this purpose, we analyzed the 2D macro-photos with an image processing software (based on Matlab) that allows the determination of the size distribution of many dimensional quantities. A statistical approach was applied to estimate the representativeness error in the snow grain observations. The distributions of the obtained grain size metrics and the snow density profiles were utilized in the radiative transfer model DISORT to simulate the surface spectral albedo. The comparison of the model results with the observed spectral albedo allowed the identification of the snow grain dimensions that best explain the albedo at each wavelength. The impact of the snow grain shape in the model simulations was addressed utilizing spherical and droxtal grain representations.

  14. [Establishment of The Crop Growth and Nitrogen Nutrition State Model Using Spectral Parameters Canopy Cover].

    PubMed

    Tao, Zhi-Qiang; Bagum, Shamim Ara; Ma, Wei; Zhou, Bao-yuan; Fu, Jin-dong; Cui, Ri-xian; Sun, Xue-fang; Zhao, Ming

    2016-01-01

    In order to explore a non-destructive monitoring technique, the use of digital photo pixels canopy cover (CC) diagnosis and prediction on maize growth and its nitrogen nutrition status. This study through maize canopy digital photo images on relationship between color index in the photo and the leaf area index (LAI), shoot dry matter weight (DM), leaf nitrogen content percentage (N%). The test conducted in the Chinese Academy of Agricultural Science from 2012 to 2013, based on Maize canopy Visual Image Analysis System developed by Visual Basic Version 6.0, analyzed the correlation of CC, color indices, LAI, DM, N% on maize varieties (Zhongdan909, ZD 909) under three nitrogen levels treatments, furthermore the indicators significantly correlated were fitted with modeling, The results showed that CC had a highly significant correlation with LAI (r = 0.93, p < 0.01), DM (r = 0. 94, p < 0.01), N% (r = 0.82, p < 0.01). Estimating the model of LAI, DM and N% by CC were all power function, and the equation respectively were y = 3.281 2x(0.763 9), y = 283.658 1x(0.553 6) and y = 3.064 5x(0.932 9); using independent data from modeling for model validation indicated that R2, RMSE and RE based on 1 : 1 line relationship between measured values and simulated values in the model of CC estimating LAI were 0.996, 0.035 and 1.46%; R2, RMSE and RE in the model of CC estimating DM were 0.978, 5.408 g and 2.43%; R2, RMSE and RE in the model of CC estimating N% were 0.990, 0.054 and 2.62%. In summary, the model can comparatively accurately estimate the LAI, DM and N% by CC under different nitrogen levels at maize grain filling stage, indicating that it is feasible to apply digital camera on real-time undamaged rapid monitoring and prediction for maize growth conditions and its nitrogen nutrition status. This research finding is to be verified in the field experiment, and further analyze the applicability throughout the growing period in other maize varieties and different planting

  15. Pore and grain boundary migration under a temperature gradient: a phase-field model study

    NASA Astrophysics Data System (ADS)

    Biner, S. B.

    2016-03-01

    The collective migration behavior of pores and grain boundaries under a temperature gradient is studied for simple single crystal, bi-crystal and polycrystal configurations with a phase-field model formulism. For simulation of the microstructure of solids, composed of pores and grain boundaries, the results indicate that not only the volume fraction of pores, but also its spatial partitioning between the grain boundary junctions and the grain boundary segments appears to be important. In addition to various physical properties, the evolution kinetics, under given temperature gradients, will be strongly influenced with the initial morphology of a poly-crystalline microstructure.

  16. Pore and grain boundary migration under a temperature gradient: A phase-field model study

    DOE PAGESBeta

    Biner, S. B.

    2016-03-16

    In this study, the collective migration behavior of pores and grain boundaries under a temperature gradient is studied for simple single crystal, bi-crystal and polycrystal configurations with a phase-field model formulism. For simulation of the microstructure of solids, composed of pores and grain boundaries, the results indicate that not only the volume fraction of pores, but also its spatial partitioning between the grain boundary junctions and the grain boundary segments appears to be important. In addition to various physical properties, the evolution kinetics, under given temperature gradients, will be strongly influenced with the initial morphology of a poly-crystalline microstructure.

  17. Migration mechanism of a GaN bicrystalline grain boundary as a model system

    PubMed Central

    Lee, Sung Bo; Yoo, Seung Jo; Kim, Young-Min; Kim, Jin-Gyu; Han, Heung Nam

    2016-01-01

    Using in situ high-resolution transmission electron microscopy, we have explored migration mechanism of a grain boundary in a GaN bicrystal as a model system. During annealing at 500 °C, the grain-boundary region underwent a decrease in thickness, which occurred by decomposition or sublimation of GaN during annealing at 500 °C coupled with electron-beam sputtering. The decrease in thickness corresponds to an increase in the driving force for migration, because the migration of the grain boundary was driven by the surface energy difference. As the driving force increased with annealing time, the grain-boundary morphology turned from atomically smooth to rough, which is characterized by kinetic roughening. The observations indicate that a grain boundary exhibits a nonlinear relationship between driving force for migration and migration velocity, in discord with the general presumption that a grain boundary follows a linear relationship. PMID:27210538

  18. Migration mechanism of a GaN bicrystalline grain boundary as a model system.

    PubMed

    Lee, Sung Bo; Yoo, Seung Jo; Kim, Young-Min; Kim, Jin-Gyu; Han, Heung Nam

    2016-01-01

    Using in situ high-resolution transmission electron microscopy, we have explored migration mechanism of a grain boundary in a GaN bicrystal as a model system. During annealing at 500 °C, the grain-boundary region underwent a decrease in thickness, which occurred by decomposition or sublimation of GaN during annealing at 500 °C coupled with electron-beam sputtering. The decrease in thickness corresponds to an increase in the driving force for migration, because the migration of the grain boundary was driven by the surface energy difference. As the driving force increased with annealing time, the grain-boundary morphology turned from atomically smooth to rough, which is characterized by kinetic roughening. The observations indicate that a grain boundary exhibits a nonlinear relationship between driving force for migration and migration velocity, in discord with the general presumption that a grain boundary follows a linear relationship. PMID:27210538

  19. Migration mechanism of a GaN bicrystalline grain boundary as a model system

    NASA Astrophysics Data System (ADS)

    Lee, Sung Bo; Yoo, Seung Jo; Kim, Young-Min; Kim, Jin-Gyu; Han, Heung Nam

    2016-05-01

    Using in situ high-resolution transmission electron microscopy, we have explored migration mechanism of a grain boundary in a GaN bicrystal as a model system. During annealing at 500 °C, the grain-boundary region underwent a decrease in thickness, which occurred by decomposition or sublimation of GaN during annealing at 500 °C coupled with electron-beam sputtering. The decrease in thickness corresponds to an increase in the driving force for migration, because the migration of the grain boundary was driven by the surface energy difference. As the driving force increased with annealing time, the grain-boundary morphology turned from atomically smooth to rough, which is characterized by kinetic roughening. The observations indicate that a grain boundary exhibits a nonlinear relationship between driving force for migration and migration velocity, in discord with the general presumption that a grain boundary follows a linear relationship.

  20. Modeling Winter Cereal Grain Canopies for Legume Intercrop Establishment

    Technology Transfer Automated Retrieval System (TEKTRAN)

    As energy demands continue to increase and wheat (Triticum aestivum L.) prices remain high, more North Central U.S. corn (Zea mays L.) and soybean [Glycine max (L.) Merr.] producers may convert some production acres to wheat. Including a winter cereal grain in the rotation increases the opportunity ...

  1. Accurate Modeling of X-ray Extinction by Interstellar Grains

    NASA Astrophysics Data System (ADS)

    Hoffman, John; Draine, B. T.

    2016-02-01

    Interstellar abundance determinations from fits to X-ray absorption edges often rely on the incorrect assumption that scattering is insignificant and can be ignored. We show instead that scattering contributes significantly to the attenuation of X-rays for realistic dust grain size distributions and substantially modifies the spectrum near absorption edges of elements present in grains. The dust attenuation modules used in major X-ray spectral fitting programs do not take this into account. We show that the consequences of neglecting scattering on the determination of interstellar elemental abundances are modest; however, scattering (along with uncertainties in the grain size distribution) must be taken into account when near-edge extinction fine structure is used to infer dust mineralogy. We advertise the benefits and accuracy of anomalous diffraction theory for both X-ray halo analysis and near edge absorption studies. We present an open source Fortran suite, General Geometry Anomalous Diffraction Theory (GGADT), that calculates X-ray absorption, scattering, and differential scattering cross sections for grains of arbitrary geometry and composition.

  2. MODELING EXTRUSION PROCESSING OF AQUACULTURE FEED INCORPORATING DISTILLERS GRAINS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Three ingredient blends containing 20, 30, and 40% Distillers Dried Grains with Solubles (DDGS), with a net protein adjusted to 28% were prepared. Extrusion studies were conducted at 3 levels of moisture content, 3 levels of barrel temperature profile, and 5 levels of screw speed in a single screw e...

  3. Modeling of Austenite Grain Growth During Austenitization in a Low Alloy Steel

    NASA Astrophysics Data System (ADS)

    Dong, Dingqian; Chen, Fei; Cui, Zhenshan

    2016-01-01

    The main purpose of this work is to develop a pragmatic model to predict austenite grain growth in a nuclear reactor pressure vessel steel. Austenite grain growth kinetics has been investigated under different heating conditions, involving heating temperature, holding time, as well as heating rate. Based on the experimental results, the mathematical model was established by regression analysis. The model predictions present a good agreement with the experimental data. Meanwhile, grain boundary precipitates and pinning effects on grain growth were studied by transmission electron microscopy. It is found that with the increasing of the temperature, the second-phase particles tend to be dissolved and the pinning effects become smaller, which results in a rapid growth of certain large grains with favorable orientation. The results from this study provide the basis for the establishment of large-sized ingot heating specification for SA508-III steel.

  4. Brachypodium seed - a potential model for studying grain development of cereal crops

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Seeds of small grains are important resources for human and animal food. The understanding of seed biology is essential for crop improvement by increasing grain yields and nutritional value. In the last decade, Brachypodium distachyon has been developed as a model plant for temperate cereal grasses...

  5. Mathematical modeling of wastewater-derived biodegradable dissolved organic nitrogen.

    PubMed

    Simsek, Halis

    2016-11-01

    Wastewater-derived dissolved organic nitrogen (DON) typically constitutes the majority of total dissolved nitrogen (TDN) discharged to surface waters from advanced wastewater treatment plants (WWTPs). When considering the stringent regulations on nitrogen discharge limits in sensitive receiving waters, DON becomes problematic and needs to be reduced. Biodegradable DON (BDON) is a portion of DON that is biologically degradable by bacteria when the optimum environmental conditions are met. BDON in a two-stage trickling filter WWTP was estimated using artificial intelligence techniques, such as adaptive neuro-fuzzy inference systems, multilayer perceptron, radial basis neural networks (RBNN), and generalized regression neural networks. Nitrite, nitrate, ammonium, TDN, and DON data were used as input neurons. Wastewater samples were collected from four different locations in the plant. Model performances were evaluated using root mean square error, mean absolute error, mean bias error, and coefficient of determination statistics. Modeling results showed that the R(2) values were higher than 0.85 in all four models for all wastewater samples, except only R(2) in the final effluent sample for RBNN modeling was low (0.52). Overall, it was found that all four computing techniques could be employed successfully to predict BDON. PMID:27019968

  6. Yield, nutrient removal, and quality of sorghum grain and biomass as influenced by nitrogen and phosphorus fertilization

    SciTech Connect

    Moresco, R.F.

    1985-01-01

    Field experiments were conducted during 1983 and 1984 at two locations using one conventional (ATx399xRTx430) and two high energy sorghum hybrids (Sorghum bicolor L., Moench) to evaluate the effects of N and P applications on grain, biomass, and fermentable carbohydrate production. Genotype and N most influenced grain and biomass yields at both locations. Cultivars ATx399xRTx430 and ATx623xRTx430 produced more grain, but less biomass than ATx623xRio. Applied N increased grain yields at College Station more in 1984 than in 1983, indicating a decrease in soil N after one year of total dry matter removal. Less yield response to N was observed at Weslaco. Applied P had little effect on grain or biomass production at either location. Applied N increased grain and biomass concentrations and uptake of most nutrients. Increased nutrient removals generally resulted more from increases in dry matter production than from changes in nutrient concentrations. Apparent N uptake efficiency was higher at College Station (41 to 53%) than at Weslaco (24 to 37%). Complete aboveground dry matter removal of high energy sorghums resulted in an additional removal of 100 to 180 kg K and 40 to 50 kg N/ha when compared with conventional sorghum produced for grain only. Genotype influenced stalk fermentable carbohydrate yields, with ATx623xRio producing substantially greater amounts than the other hybrids. Applied N decreased structural carbohydrates, while nonstructural carbohydrates remained unchanged. Stalk fermentable carbohydrate fuels, however, increased linearly with N application because of higher biomass yields with applied N.

  7. Empirical model of atomic nitrogen in the upper thermosphere

    NASA Technical Reports Server (NTRS)

    Engebretson, M. J.; Mauersberger, K.; Kayser, D. C.; Potter, W. E.; Nier, A. O.

    1977-01-01

    Atomic nitrogen number densities in the upper thermosphere measured by the open source neutral mass spectrometer (OSS) on Atmosphere Explorer-C during 1974 and part of 1975 have been used to construct a global empirical model at an altitude of 375 km based on a spherical harmonic expansion. The most evident features of the model are large diurnal and seasonal variations of atomic nitrogen and only a moderate and latitude-dependent density increase during periods of geomagnetic activity. Maximum and minimum N number densities at 375 km for periods of low solar activity are 3.6 x 10 to the 6th/cu cm at 1500 LST (local solar time) and low latitude in the summer hemisphere and 1.5 x 10 to the 5th/cu cm at 0200 LST at mid-latitudes in the winter hemisphere.

  8. Burkholderia ambifaria and B. caribensis Promote Growth and Increase Yield in Grain Amaranth (Amaranthus cruentus and A. hypochondriacus) by Improving Plant Nitrogen Uptake

    PubMed Central

    Parra-Cota, Fannie I.; Peña-Cabriales, Juan J.; de los Santos-Villalobos, Sergio; Martínez-Gallardo, Norma A.; Délano-Frier, John P.

    2014-01-01

    Grain amaranth is an emerging crop that produces seeds having high quality protein with balanced amino-acid content. However, production is restricted by agronomic limitations that result in yields that are lower than those normally produced by cereals. In this work, the use of five different rhizobacteria were explored as a strategy to promote growth and yields in Amaranthus hypochondriacus cv. Nutrisol and A. cruentus cv. Candil, two commercially important grain amaranth cultivars. The plants were grown in a rich substrate, high in organic matter, nitrogen (N), and phosphorus (P) and under greenhouse conditions. Burkholderia ambifaria Mex-5 and B. caribensis XV proved to be the most efficient strains and significantly promoted growth in both grain amaranth species tested. Increased grain yield and harvest index occurred in combination with chemical fertilization when tested in A. cruentus. Growth-promotion and improved yields correlated with increased N content in all tissues examined. Positive effects on growth also occurred in A. cruentus plants grown in a poor soil, even after N and P fertilization. No correlation between non-structural carbohydrate levels in roots of inoculated plants and growth promotion was observed. Conversely, gene expression assays performed at 3-, 5- and 7-weeks after seed inoculation in plants inoculated with B. caribensis XV identified a tissue-specific induction of several genes involved in photosynthesis, sugar- and N- metabolism and transport. It is concluded that strains of Burkholderia effectively promote growth and increase seed yields in grain amaranth. Growth promotion was particularly noticeable in plants grown in an infertile soil but also occurred in a well fertilized rich substrate. The positive effects observed may be attributed to a bio-fertilization effect that led to increased N levels in roots and shoots. The latter effect correlated with the differential induction of several genes involved in carbon and N metabolism

  9. Burkholderia ambifaria and B. caribensis promote growth and increase yield in grain amaranth (Amaranthus cruentus and A. hypochondriacus) by improving plant nitrogen uptake.

    PubMed

    Parra-Cota, Fannie I; Peña-Cabriales, Juan J; de Los Santos-Villalobos, Sergio; Martínez-Gallardo, Norma A; Délano-Frier, John P

    2014-01-01

    Grain amaranth is an emerging crop that produces seeds having high quality protein with balanced amino-acid content. However, production is restricted by agronomic limitations that result in yields that are lower than those normally produced by cereals. In this work, the use of five different rhizobacteria were explored as a strategy to promote growth and yields in Amaranthus hypochondriacus cv. Nutrisol and A. cruentus cv. Candil, two commercially important grain amaranth cultivars. The plants were grown in a rich substrate, high in organic matter, nitrogen (N), and phosphorus (P) and under greenhouse conditions. Burkholderia ambifaria Mex-5 and B. caribensis XV proved to be the most efficient strains and significantly promoted growth in both grain amaranth species tested. Increased grain yield and harvest index occurred in combination with chemical fertilization when tested in A. cruentus. Growth-promotion and improved yields correlated with increased N content in all tissues examined. Positive effects on growth also occurred in A. cruentus plants grown in a poor soil, even after N and P fertilization. No correlation between non-structural carbohydrate levels in roots of inoculated plants and growth promotion was observed. Conversely, gene expression assays performed at 3-, 5- and 7-weeks after seed inoculation in plants inoculated with B. caribensis XV identified a tissue-specific induction of several genes involved in photosynthesis, sugar- and N- metabolism and transport. It is concluded that strains of Burkholderia effectively promote growth and increase seed yields in grain amaranth. Growth promotion was particularly noticeable in plants grown in an infertile soil but also occurred in a well fertilized rich substrate. The positive effects observed may be attributed to a bio-fertilization effect that led to increased N levels in roots and shoots. The latter effect correlated with the differential induction of several genes involved in carbon and N metabolism

  10. YUP: A Molecular Simulation Program for Coarse-Grained and Multi-Scaled Models.

    PubMed

    Tan, Robert K Z; Petrov, Anton S; Harvey, Stephen C

    2006-05-01

    Coarse-grained models can be very different from all-atom models and are highly varied. Each class of model is assembled very differently and some models need customized versions of the standard molecular mechanics methods. The most flexible way to meet these diverse needs is to provide access to internal data structures and a programming language to manipulate these structures. We have created YUP, a general-purpose program for coarse-grained and multi-scaled models. YUP extends the Python programming language by adding new data types. We have then used the extended language to implement three classes of coarse-grained models. The coarse-grained RNA model type is an unusual non-linear polymer and the assembly was easily handled with a simple program. The molecular dynamics algorithm had to be extended for a coarse-grained DNA model so that it could detect a failure that is invisible to a standard implementation. A third model type took advantage of access to the force field to simulate the packing of DNA in viral capsid. We find that objects are easy to modify, extend and redeploy. Thus, new classes of coarse-grained models can be implemented easily. PMID:22844233

  11. Modeling Nitrogen Cycle at the Surface-Subsurface Water Interface

    NASA Astrophysics Data System (ADS)

    Marzadri, A.; Tonina, D.; Bellin, A.

    2011-12-01

    Anthropogenic activities, primarily food and energy production, have altered the global nitrogen cycle, increasing reactive dissolved inorganic nitrogen, Nr, chiefly ammonium NH4+ and nitrate NO3-, availability in many streams worldwide. Increased Nr promotes biological activity often with negative consequences such as water body eutrophication and emission of nitrous oxide gas, N2O, an important greenhouse gas as a by-product of denitrification. The hyporheic zone may play an important role in processing Nr and returning it to the atmosphere. Here, we present a process-based three-dimensional semi-analytical model, which couples hyporheic hydraulics with biogeochemical reactions and transport equations. Transport is solved by means of particle tracking with negligible local dispersion and biogeochemical reactions modeled by linearized Monod's kinetics with temperature dependant reaction rate coefficients. Comparison of measured and predicted N2O emissions from 7 natural stream shows a good match. We apply our model to gravel bed rivers with alternate bar morphology to investigate the role of hyporheic hydraulic, depth of alluvium, relative availability of stream concentration of NO3- and NH4+ and water temperature on nitrogen gradients within the sediment. Our model shows complex concentration dynamics, which depend on hyporheic residence time distribution and consequently on streambed morphology, within the hyporheic zone. Nitrogen gas emissions from the hyporheic zone increase with alluvium depth in large low-gradient streams but not in small steep streams. On the other hand, hyporheic water temperature influences nitrification/denitrification processes mainly in small-steep than large low-gradient streams, because of the long residence times, which offset the slow reaction rates induced by low temperatures in the latter stream. The overall conclusion of our analysis is that river morphology has a major impact on biogeochemical processes such as nitrification

  12. NITROGEN ISOTOPES IN ASYMPTOTIC GIANT BRANCH CARBON STARS AND PRESOLAR SiC GRAINS: A CHALLENGE FOR STELLAR NUCLEOSYNTHESIS

    SciTech Connect

    Hedrosa, R. P.; Abia, C.; Dominguez, I.; Palmerini, S.; Busso, M.; Cristallo, S.; Straniero, O.; Plez, B.

    2013-05-01

    Isotopic ratios of C, N, Si, and trace heavy elements in presolar SiC grains from meteorites provide crucial constraints to nucleosynthesis. A long-debated issue is the origin of the so-called A+B grains, as of yet no stellar progenitor thus far has been clearly identified on observational grounds. We report the first spectroscopic measurements of {sup 14}N/{sup 15}N ratios in Galactic carbon stars of different spectral types and show that J- and some SC-type stars might produce A+B grains, even for {sup 15}N enrichments previously attributed to novae. We also show that most mainstream grains are compatible with the composition of N-type stars, but in some cases might also descend from SC stars. From a theoretical point of view, no astrophysical scenario can explain the C and N isotopic ratios of SC-, J-, and N-type carbon stars together, as well as those of many grains produced by them. This poses urgent questions to stellar physics.

  13. Further contributions to nitrogen removal modelling in waste stabilization ponds.

    PubMed

    Bastos, R K X; Cabral, V A L; Rios, E N; Combatt, M P M

    2014-01-01

    A large database from an experimental maturation pond system in Brazil was used to verify the agreement of field results with values predicted by some of the most widely accepted models to describe ammonium and total nitrogen (TN) removal in facultative and maturation ponds. The same database was used to derive a pH-independent linear model to predict ammonium removal in ponds, which was proved to be, essentially, a function of ammonium surface loading rate. In general, all these models made reasonable predictions of ammonium or TN removal but tended to overestimate low ammonium effluent concentrations while underestimating higher values of field data. PMID:25521122

  14. Modeling grain size during hot deformation of IN 718

    SciTech Connect

    Medeiros, S.C.; Prasad, Y.V.R.K.; Frazier, W.G.; Srinivasan, R.

    1999-12-17

    Aerospace gas turbine disks operate in an environment of relatively high stresses caused by centrifugal forces and elevated temperatures. These severe conditions necessitate the need for materials with high temperature strength and good low cycle fatigue resistance. One class of alloys used for this task is the nickel base superalloys, out of which, IN 718 is the most widely used in the aerospace industry. The properties of IN 718 are attributed to the combined effects of the chemistry, heat treatment, and microstructure. The chemistry is tailored not only for solid solution strengthening but also for precipitation hardening developed during heat treatment, which combined with a fine grained microstructure lead to excellent mechanical properties such as low cycle fatigue resistance and elevated temperature strength. The properties of a gas turbine disk are sensitive to the microstructure, in particular the grain size, which is dependent on the processing history. The ability to precisely control the microstructural development during forging is dependent on controlling the process so that the workpiece is deformed within a safe region where no microstructural damage or flow instabilities occur. The microstructural mechanisms during deformation may themselves vary within the age region and it is desirable to determine them within the range of parameters that are commonly used in industrial processing. The objective of this work is to establish a relationship between the grain size and the process control parameters i.e., temperature and strain rate, in the hot working of IN 178.

  15. Model reduction for agent-based social simulation: coarse-graining a civil violence model.

    PubMed

    Zou, Yu; Fonoberov, Vladimir A; Fonoberova, Maria; Mezic, Igor; Kevrekidis, Ioannis G

    2012-06-01

    Agent-based modeling (ABM) constitutes a powerful computational tool for the exploration of phenomena involving emergent dynamic behavior in the social sciences. This paper demonstrates a computer-assisted approach that bridges the significant gap between the single-agent microscopic level and the macroscopic (coarse-grained population) level, where fundamental questions must be rationally answered and policies guiding the emergent dynamics devised. Our approach will be illustrated through an agent-based model of civil violence. This spatiotemporally varying ABM incorporates interactions between a heterogeneous population of citizens [active (insurgent), inactive, or jailed] and a population of police officers. Detailed simulations exhibit an equilibrium punctuated by periods of social upheavals. We show how to effectively reduce the agent-based dynamics to a stochastic model with only two coarse-grained degrees of freedom: the number of jailed citizens and the number of active ones. The coarse-grained model captures the ABM dynamics while drastically reducing the computation time (by a factor of approximately 20). PMID:23005161

  16. Model reduction for agent-based social simulation: Coarse-graining a civil violence model

    NASA Astrophysics Data System (ADS)

    Zou, Yu; Fonoberov, Vladimir A.; Fonoberova, Maria; Mezic, Igor; Kevrekidis, Ioannis G.

    2012-06-01

    Agent-based modeling (ABM) constitutes a powerful computational tool for the exploration of phenomena involving emergent dynamic behavior in the social sciences. This paper demonstrates a computer-assisted approach that bridges the significant gap between the single-agent microscopic level and the macroscopic (coarse-grained population) level, where fundamental questions must be rationally answered and policies guiding the emergent dynamics devised. Our approach will be illustrated through an agent-based model of civil violence. This spatiotemporally varying ABM incorporates interactions between a heterogeneous population of citizens [active (insurgent), inactive, or jailed] and a population of police officers. Detailed simulations exhibit an equilibrium punctuated by periods of social upheavals. We show how to effectively reduce the agent-based dynamics to a stochastic model with only two coarse-grained degrees of freedom: the number of jailed citizens and the number of active ones. The coarse-grained model captures the ABM dynamics while drastically reducing the computation time (by a factor of approximately 20).

  17. Calibration and validation of coarse-grained models of atomic systems: application to semiconductor manufacturing

    NASA Astrophysics Data System (ADS)

    Farrell, Kathryn; Oden, J. Tinsley

    2014-07-01

    Coarse-grained models of atomic systems, created by aggregating groups of atoms into molecules to reduce the number of degrees of freedom, have been used for decades in important scientific and technological applications. In recent years, interest in developing a more rigorous theory for coarse graining and in assessing the predictivity of coarse-grained models has arisen. In this work, Bayesian methods for the calibration and validation of coarse-grained models of atomistic systems in thermodynamic equilibrium are developed. For specificity, only configurational models of systems in canonical ensembles are considered. Among major challenges in validating coarse-grained models are (1) the development of validation processes that lead to information essential in establishing confidence in the model's ability predict key quantities of interest and (2), above all, the determination of the coarse-grained model itself; that is, the characterization of the molecular architecture, the choice of interaction potentials and thus parameters, which best fit available data. The all-atom model is treated as the "ground truth," and it provides the basis with respect to which properties of the coarse-grained model are compared. This base all-atom model is characterized by an appropriate statistical mechanics framework in this work by canonical ensembles involving only configurational energies. The all-atom model thus supplies data for Bayesian calibration and validation methods for the molecular model. To address the first challenge, we develop priors based on the maximum entropy principle and likelihood functions based on Gaussian approximations of the uncertainties in the parameter-to-observation error. To address challenge (2), we introduce the notion of model plausibilities as a means for model selection. This methodology provides a powerful approach toward constructing coarse-grained models which are most plausible for given all-atom data. We demonstrate the theory and

  18. Photostability of glycine and nitrogen basis in cometary grains : application to the transport of organic matter within the primitive Earth

    NASA Astrophysics Data System (ADS)

    Saiagh, K.; Belilla, J.; Fray, N.; Valorso, R.; Cottin, H.

    2015-10-01

    The study of photochemistry in the solar system is of prime importance to assess complex organic chemistry in any extraterrestrial environment. Among those environments, comets and grains ejected from their nuclei are of particular interest in the context of astrobiology as they could have brought organic matter on the primitive Earth, and hence contribute to the emergence of life. Furthermore, they can provide precious information on the physico-chemical parameters prevailing in the primitive solar nebula during its formation. In this context, we are studying the extent to which organic matter within grains may survive to solar radiation and the fraction of these organic molecules destroyed when it is subjected to sunlight.

  19. Synthesis of a control model for a liquid nitrogen cooled, closed circuit, cryogenic nitrogen wind tunnel and its validation

    NASA Technical Reports Server (NTRS)

    Balakrishna, S.; Goglia, G. L.

    1979-01-01

    The details of the efforts to synthesize a control-compatible multivariable model of a liquid nitrogen cooled, gaseous nitrogen operated, closed circuit, cryogenic pressure tunnel are presented. The synthesized model was transformed into a real-time cryogenic tunnel simulator, and this model is validated by comparing the model responses to the actual tunnel responses of the 0.3 m transonic cryogenic tunnel, using the quasi-steady-state and the transient responses of the model and the tunnel. The global nature of the simple, explicit, lumped multivariable model of a closed circuit cryogenic tunnel is demonstrated.

  20. Evolutionary models of the Earth with a grain size-dependent rheology: diffusion versus dislocation creep

    NASA Astrophysics Data System (ADS)

    Rozel, Antoine; Golabek, Gregor; Thielmann, Marcel; Schierjott, Jana; Tackley, Paul

    2016-04-01

    We present a set of 2D numerical simulations of mantle convection considering grain size evolution and a composite visco-plastic rheology including diffusion and dislocation creep. A 1D parameterization allows us to anticipate the stress conditions for the present-day temperature profile in a convection cell. We are therefore able to obtain self-consistent 2D convecion models together with non-equilibrium grain size for present-day conditions, controlling the partitioning between diffusion and dislocation creep. However, the internal temperature of the mantle is thought to have significantly evolved throughout the history of the Earth. Using a higher internal temperature is usually believed to decrease both viscosity and internal stresses. In our case, a high temperature potentially increases the grain size, which tends to increase the viscosity: the temperature and grain size-dependence of the viscosity are in competition. We study the evolution of the diffusion-dislocation partitioning throughout the history of the Earth. We report the evolution of grain size and stress over time in our simulations. Several complex processes are included in our models. Grain size evolution is a sum of grain growth and dynamic recrystallization. All our simulations consider thermochemical convection in a compressible mantle with melting producting basaltic crust and depleted mantle. Close to the surface, melting produces basaltic material which is erupted or intruded at the base of the crust. Phase transitions reset the grain size to a low value, which influences the whole dynamics of the mantle.

  1. Systematic coarse-graining of the wormlike chain model for dynamic simulations

    NASA Astrophysics Data System (ADS)

    Koslover, Elena; Spakowitz, Andrew

    2014-03-01

    One of the key goals of macromolecular modeling is to elucidate how macroscale physical properties arise from the microscale behavior of the polymer constituents. For many biological and industrial applications, a direct simulation approach is impractical due to to the wide range of length and time scales that must be spanned by the model, necessitating physically sound and practically relevant procedures for coarse-graining polymer systems. We present a highly general systematic coarse-graining procedure that maps any detailed polymer model onto effective elastic-chain models at intermediate and large length scales, and we specifically focus on the wormlike chain model of semiflexible polymers. Our approach defines a continuous flow of coarse-grained models starting from the wormlike chain model, proceeding through an intermediate-scale stretchable, shearable wormlike chain, and finally resolving to a Gaussian chain at the longest lengths. Using Brownian dynamic simulations of our coarse grained polymer, we show that this approach to coarse graining the wormlike chain model captures analytical predictions for stress relaxation in a semiflexible polymer. Since we can arbitrarily coarse grain the polymer in these dynamic simulations, our approach greatly accelerates simulations.

  2. Modelling the Complex Conductivity of Charged Porous Media using The Grain Polarization Model

    NASA Astrophysics Data System (ADS)

    Leroy, P.; Revil, A.; Jougnot, D.; Li, S.

    2015-12-01

    The low-frequency complex conductivity response of charged porous media reflects a combination of three polarization processes occuring at different frequency ranges. One polarization process corresponds to the membrane polarization phenomenon, which is the polarization mechanism associated with the back-diffusion of salt ions through different pore spaces of the porous material (ions-selective zones and zones with no selectivity). This polarization process generally occurs at the lowest frequency range, typically in the frequency range [mHz Hz] because it involves polarization mechanism occurring over different pore spaces (the relaxation frequency is inversely proportional to the length of the polarization process). Another polarization process corresponds to the electrochemical polarization of the electrical double layer coating the surface of the grains. In the grain polarization model, the diffuse layer is assumed to not polarize because it is assumed to form a continuum in the porous medium. The compact Stern layer is assumed to polarize because the Stern layer is assumed to be discontinuous over multiple grains. The electrochemical polarization of the Stern layer typically occurs in the frequency range [Hz kHz]. The last polarization process corresponds to the Maxwell-Wagner polarization mechanism, which is caused by the formation of field-induced free charge distributions near the interface between the phases of the medium. In this presentation, the grain polarization model based on the O'Konski, Schwarz, Schurr and Sen theories and developed later by Revil and co-workers is showed. This spectral induced polarization model was successfully applied to describe the complex conductivity responses of glass beads, sands, clays, clay-sand mixtures and other minerals. The limits of this model and future developments will also be presented.

  3. Theory and modeling of microstructural evolution in polycrystalline materials: Solute segregation, grain growth and phase transformations

    NASA Astrophysics Data System (ADS)

    Ma, Ning

    2005-11-01

    To accurately predict microstructure evolution and, hence, to synthesis metal and ceramic alloys with desirable properties involves many fundamental as well as practical issues. In the present study, novel theoretical and phase field approaches have been developed to address some of these issues including solute drag and segregation transition at grain boundaries and dislocations, grain growth in systems of anisotropic boundary properties, and precipitate microstructure development in polycrystalline materials. The segregation model has allowed for the prediction of a first-order segregation transition, which could be related to the sharp transition of solute concentration of grain boundary as a function of temperature. The incorporating of interfacial energy and mobility as functions of misorientation and inclination in the phase field model has allowed for the study of concurrent grain growth and texture evolution. The simulation results were analyzed using the concept of local grain boundary energy density, which simplified significantly the development of governing equations for texture controlled grain growth in Ti-6Al-4V. Quantitative phase field modeling techniques have been developed by incorporating thermodynamic and diffusivity databases. The models have been validated against DICTRA simulations in simple 1D problems and applied to simulate realistic microstructural evolutions in Ti-6Al-4V, including grain boundary a and globular a growth and sideplate development under both isothermal aging and continuous cooling conditions. The simulation predictions agree well with experimental observations.

  4. Coarse-Grained Models Reveal Functional Dynamics - I. Elastic Network Models – Theories, Comparisons and Perspectives

    PubMed Central

    Yang, Lee-Wei; Chng, Choon-Peng

    2008-01-01

    In this review, we summarize the progress on coarse-grained elastic network models (CG-ENMs) in the past decade. Theories were formulated to allow study of conformational dynamics in time/space frames of biological interest. Several highlighted models and their underlined hypotheses are introduced in physical depth. Important ENM offshoots, motivated to reproduce experimental data as well as to address the slow-mode-encoded configurational transitions, are also introduced. With the theoretical developments, computational cost is significantly reduced due to simplified potentials and coarse-grained schemes. Accumulating wealth of data suggest that ENMs agree equally well with experiment in describing equilibrium dynamics despite their distinct potentials and levels of coarse-graining. They however do differ in the slowest motional components that are essential to address large conformational changes of functional significance. The difference stems from the dissimilar curvatures of the harmonic energy wells described for each model. We also provide our views on the predictability of ‘open to close’ (open→close) transitions of biomolecules on the basis of conformational selection theory. Lastly, we address the limitations of the ENM formalism which are partially alleviated by the complementary CG-MD approach, to be introduced in the second paper of this two-part series. PMID:19812764

  5. The influence of inorganic nitrogen fertilizer forms on micronutrient retranslocation and accumulation in grains of winter wheat

    PubMed Central

    Barunawati, Nunun; Giehl, Ricardo F. Hettwer; Bauer, Bernhard; von Wirén, Nicolaus

    2013-01-01

    The fortification of cereal grains with metal micronutrients is a major target to combat human malnutrition of Fe and Zn. Based on recent studies showing that N fertilization can promote Fe and Zn accumulation in cereal grains, we investigated here the influence of nitrate- or ammonium-based N fertilization on the accumulation of Fe, Zn, and Cu as well as metal chelator pools in flag leaves and grains of winter wheat. Fertilization with either N form increased the concentrations of N and of the metal chelator nicotianamine (NA) in green leaves, while 2'-deoxymugineic acid (DMA) remained unaffected. Despite the differential response to N fertilization of NA and DMA levels in flag leaves, N fertilization remained without any significant effect on the net export of these metals during flag leaf senescence, which accounted for approximately one third of the total Fe, Zn, or Cu content in leaves. The significant increase in the accumulation of Fe, Zn, and Cu found in the grains of primarily ammonium-fertilized plants was unrelated to the extent of metal retranslocation from flag leaves. These results indicate that an increased N nutritional status of flag leaves promotes the accumulation of Fe, Zn, and Cu in flag leaves, which is accompanied by an increased pool of NA but not of DMA. With regard to the far higher concentrations of DMA relative to NA in leaves and leaf exudates, DMA may be more relevant for the mobilization and retranslocation of these metals in high-yielding wheat production. PMID:23967006

  6. Modelling fungal sink competitiveness with grains for assimilates in wheat infected by a biotrophic pathogen

    PubMed Central

    Bancal, Marie-Odile; Hansart, Amandine; Sache, Ivan; Bancal, Pierre

    2012-01-01

    Background and Aims Experiments have shown that biotrophic fungi divert assimilates for their growth. However, no attempt has been made either to account for this additional sink or to predict to what extent it competes with both grain filling and plant reserve metabolism for carbon. Fungal sink competitiveness with grains was quantified by a mixed experimental–modelling approach based on winter wheat infected by Puccinia triticina. Methods One week after anthesis, plants grown under controlled conditions were inoculated with varying loads. Sporulation was recorded while plants underwent varying degrees of shading, ensuring a range of both fungal sink and host source levels. Inoculation load significantly increased both sporulating area and rate. Shading significantly affected net assimilation, reserve mobilization and sporulating area, but not grain filling or sporulation rates. An existing carbon partitioning (source–sink) model for wheat during the grain filling period was then enhanced, in which two parameters characterize every sink: carriage capacity and substrate affinity. Fungal sink competitiveness with host sources and sinks was modelled by representing spore production as another sink in diseased wheat during grain filling. Key Results Data from the experiment were fitted to the model to provide the fungal sink parameters. Fungal carriage capacity was 0·56 ± 0·01 µg dry matter °Cd−1 per lesion, much less than grain filling capacity, even in highly infected plants; however, fungal sporulation had a competitive priority for assimilates over grain filling. Simulation with virtual crops accounted for the importance of the relative contribution of photosynthesis loss, anticipated reserve depletion and spore production when light level and disease severity vary. The grain filling rate was less reduced than photosynthesis; however, over the long term, yield loss could double because the earlier reserve depletion observed here would shorten the

  7. The Lightning Nitrogen Oxides Model (LNOM): Status and Recent Applications

    NASA Technical Reports Server (NTRS)

    Koshak, William; Khan, Maudood; Peterson, Harold

    2011-01-01

    Improvements to the NASA Marshall Space Flight Center Lightning Nitrogen Oxides Model (LNOM) are discussed. Recent results from an August 2006 run of the Community Multiscale Air Quality (CMAQ) modeling system that employs LNOM lightning NOx (= NO + NO2) estimates are provided. The LNOM analyzes Lightning Mapping Array (LMA) data to estimate the raw (i.e., unmixed and otherwise environmentally unmodified) vertical profile of lightning NOx. The latest LNOM estimates of (a) lightning channel length distributions, (b) lightning 1-m segment altitude distributions, and (c) the vertical profile of NOx are presented. The impact of including LNOM-estimates of lightning NOx on CMAQ output is discussed.

  8. A fate model for nitrogen dynamics in the Scheldt basin

    NASA Astrophysics Data System (ADS)

    Haest, Pieter Jan; van der Kwast, Johannes; Broekx, Steven; Seuntjens, Piet

    2010-05-01

    The European Union (EU) adopted the Water Framework Directive (WFD) in 2000 ensuring that all aquatic ecosystems meet ‘good ecological status' by 2015. However, the large population density in combination with agricultural and industrial activities in some European river basins pose challenges for river basin managers in meeting this status. The EU financed AQUAREHAB project (FP7) specifically examines the ecological and economic impact of innovative rehabilitation technologies for multi-pressured degraded waters. For this purpose, a numerical spatio-temporal model is developed to evaluate innovative technologies versus conventional measures at the river basin scale. The numerical model describes the nitrogen dynamics in the Scheldt river basin. Nitrogen is examined since nitrate is of specific concern in Belgium, the country comprising the largest area of the Scheldt basin. The Scheldt basin encompasses 20000 km2 and houses over 10 million people. The governing factors describing nitrogen fluxes at this large scale differ from the field scale with a larger uncertainty on input data. As such, the environmental modeling language PCRaster was selected since it was found to provide a balance between process descriptions and necessary input data. The resulting GIS-based model simulates the nitrogen dynamics in the Scheldt basin with a yearly time step and a spatial resolution of 1 square kilometer. A smaller time step is being evaluated depending on the description of the hydrology. The model discerns 4 compartments in the Scheldt basin: the soil, shallow groundwater, deep groundwater and the river network. Runoff and water flow occurs along the steepest slope in all model compartments. Diffuse emissions and direct inputs are calculated from administrative and statistical data. These emissions are geographically defined or are distributed over the domain according to land use and connectivity to the sewer system. The reactive mass transport is described using

  9. An Overview of Modeling Middle Atmospheric Odd Nitrogen

    NASA Technical Reports Server (NTRS)

    Jackman, Charles H.; Kawa, S. Randolph; Einaudi, Franco (Technical Monitor)

    2001-01-01

    Odd nitrogen (N, NO, NO2, NO3, N2O5, HNO3, HO2NO2, ClONO2, and BrONO2) constituents are important components in the control of middle atmospheric ozone. Several processes lead to the production of odd nitrogen (NO(sub y)) in the middle atmosphere (stratosphere and mesosphere) including the oxidation of nitrous oxide (N2O), lightning, downflux from the thermosphere, and energetic charged particles (e.g., galactic cosmic rays, solar proton events, and energetic electron precipitation). The dominant production mechanism of NO(sub y) in the stratosphere is N2O oxidation, although other processes contribute. Mesospheric NO(sub y) is influenced by N2O oxidation, downflux from the thermosphere, and energetic charged particles. NO(sub y) is destroyed in the middle atmosphere primarily via two processes: 1) dissociation of NO to form N and O followed by N + NO yielding N2 + O to reform even nitrogen; and 2) transport to the troposphere where HNO3 can be rapidly scavenged in water droplets and rained out of the atmosphere. There are fairly significant differences among global models that predict NO(sub y). NO(sub y) has a fairly long lifetime in the stratosphere (months to years), thus disparate transport in the models probably contributes to many of these differences. Satellite and aircraft measurement provide modeling tests of the various components of NO(sub y). Although some recent reaction rate measurements have led to improvements in model/measurement agreement, significant differences do remain. This presentation will provide an overview of several proposed sources and sinks of NO(sub y) and their regions of importance. Multi-dimensional modeling results for NO(sub y) and its components with comparisons to observations will also be presented.

  10. A comparison of models for estimating the riverine export of nitrogen from large watersheds

    USGS Publications Warehouse

    Alexander, R.B.; Johnes, P.J.; Boyer, E.W.; Smith, R.A.

    2002-01-01

    We evaluated the accuracy of six watershed models of nitrogen export in streams (kg km2 yr-1) developed for use in large watersheds and representing various empirical and quasi-empirical approaches described in the literature. These models differ in their methods of calibration and have varying levels of spatial resolution and process complexity, which potentially affect the accuracy (bias and precision) of the model predictions of nitrogen export and source contributions to export. Using stream monitoring data and detailed estimates of the natural and cultural sources of nitrogen for 16 watersheds in the northeastern United States (drainage sizes = 475 to 70,000 km2), we assessed the accuracy of the model predictions of total nitrogen and nitrate-nitrogen export. The model validation included the use of an error modeling technique to identify biases caused by model deficiencies in quantifying nitrogen sources and biogeochemical processes affecting the transport of nitrogen in watersheds. Most models predicted stream nitrogen export to within 50% of the measured export in a majority of the watersheds. Prediction errors were negatively correlated with cultivated land area, indicating that the watershed models tended to over predict export in less agricultural and more forested watersheds and under predict in more agricultural basins. The magnitude of these biases differed appreciably among the models. Those models having more detailed descriptions of nitrogen sources, land and water attenuation of nitrogen, and water flow paths were found to have considerably lower bias and higher precision in their predictions of nitrogen export.

  11. Modeling of Ultrasonic Propagation in a Coarse Grain Structure

    NASA Astrophysics Data System (ADS)

    Jenson, F.; Fortuna, T.; Doudet, L.

    2009-03-01

    The metallurgical structure of centrifugally cast stainless steel components makes it difficult to ultrasonically inspect them. The centimeter-size grains forming the macrostructure strongly affect the transmitted field and thus limit inspection capabilities. Such macrostructures can be computed using an algorithm based on the Voronoi diagrams. This mathematical tool provides good qualitative representations of equiaxed and columnar structures. By combining the Voronoi diagrams with existing CIVA functionalities such as the transmitted field computation in a heterogeneous medium using the so-called pencil method, it is shown that some important physical phenomena responsible for inspection difficulties may be reproduced. For instance, the field distortions in phase and amplitude due to the velocity fluctuations that are caused by the large grain structures of these materials are properly described thanks to this approach. These distortions represent deviations from quantities that are usually described by existing theories, such as the mean field attenuation. Comparisons of simulated results with experimental data are also presented and discussed in this paper.

  12. Solar Ion Processing of Itokawa Grains: Reconciling Model Predictions with Sample Observations

    NASA Technical Reports Server (NTRS)

    Christoffersen, Roy; Keller, L. P.

    2014-01-01

    Analytical TEM observations of Itokawa grains reported to date show complex solar wind ion processing effects in the outer 30-100 nm of pyroxene and olivine grains. The effects include loss of long-range structural order, formation of isolated interval cavities or "bubbles", and other nanoscale compositional/microstructural variations. None of the effects so far described have, however, included complete ion-induced amorphization. To link the array of observed relationships to grain surface exposure times, we have adapted our previous numerical model for progressive solar ion processing effects in lunar regolith grains to the Itokawa samples. The model uses SRIM ion collision damage and implantation calculations within a framework of a constant-deposited-energy model for amorphization. Inputs include experimentally-measured amorphization fluences, a Pi steradian variable ion incidence geometry required for a rotating asteroid, and a numerical flux-versus-velocity solar wind spectrum.

  13. Phase-field model of strain-induced grain-boundary premelting

    NASA Astrophysics Data System (ADS)

    Wang, Nan; Spatschek, Robert; Karma, Alain

    2008-03-01

    Grain-boundary premelting depends in a complex way on the relative magnitude of the solid-liquid interfacial free-energy and grain boundary energy as well as temperature and strain. We study this dependence in a bicrystal geometry using a phenomenological three-order parameter phase-field model. This model describes the short scale attractive or repulsive interaction between crystal-melt interfaces and macroscopic linear elasticity including the important effect of the density contrast between solid and liquid. The model exhibits a rich behavior characterized by single or multiple premelting transitions between dry or wet grain boundaries with different liquid layer thicknesses as a function of applied tensile stress. The results have important implications for the phenomenon of liquid metal embrittlement associated with the stress-driven penetration of nanometric liquid films along grain boundaries.

  14. Phase field modelling of stressed grain growth: Analytical study and the effect of microstructural length scale

    SciTech Connect

    Jamshidian, M.; Rabczuk, T.

    2014-03-15

    We establish the correlation between the diffuse interface and sharp interface descriptions for stressed grain boundary migration by presenting analytical solutions for stressed migration of a circular grain boundary in a bicrystalline phase field domain. The validity and accuracy of the phase field model is investigated by comparing the phase field simulation results against analytical solutions. The phase field model can reproduce precise boundary kinetics and stress evolution provided that a thermodynamically consistent theory and proper expressions for model parameters in terms of physical material properties are employed. Quantitative phase field simulations are then employed to investigate the effect of microstructural length scale on microstructure and texture evolution by stressed grain growth in an elastically deformed polycrystalline aggregate. The simulation results reveal a transitional behaviour from normal to abnormal grain growth by increasing the microstructural length scale.

  15. Terrestrial nitrogen cycling in Earth system models revisited

    USGS Publications Warehouse

    Stocker, Benjamin D; Prentice, I Colin; Cornell, Sarah; Davies-Barnard, T; Finzi, Adrien; Franklin, Oskar; Janssens, Ivan; Larmola, Tuula; Manzoni, Stefano; Näsholm, Torgny; Raven, John; Rebel, Karin; Reed, Sasha C.; Vicca, Sara; Wiltshire, Andy; Zaehle, Sönke

    2016-01-01

    Understanding the degree to which nitrogen (N) availability limits land carbon (C) uptake under global environmental change represents an unresolved challenge. First-generation ‘C-only’vegetation models, lacking explicit representations of N cycling,projected a substantial and increasing land C sink under rising atmospheric CO2 concentrations. This prediction was questioned for not taking into account the potentially limiting effect of N availability, which is necessary for plant growth (Hungate et al.,2003). More recent global models include coupled C and N cycles in land ecosystems (C–N models) and are widely assumed to be more realistic. However, inclusion of more processes has not consistently improved their performance in capturing observed responses of the global C cycle (e.g. Wenzel et al., 2014). With the advent of a new generation of global models, including coupled C, N, and phosphorus (P) cycling, model complexity is sure to increase; but model reliability may not, unless greater attention is paid to the correspondence of model process representations ande mpirical evidence. It was in this context that the ‘Nitrogen Cycle Workshop’ at Dartington Hall, Devon, UK was held on 1–5 February 2016. Organized by I. Colin Prentice and Benjamin D. Stocker (Imperial College London, UK), the workshop was funded by the European Research Council,project ‘Earth system Model Bias Reduction and assessing Abrupt Climate change’ (EMBRACE). We gathered empirical ecologists and ecosystem modellers to identify key uncertainties in terrestrial C–N cycling, and to discuss processes that are missing or poorly represented in current models.

  16. Modelling mortality of a stored grain insect pest with fumigation: probit, logistic or Cauchy model?

    PubMed

    Shi, Mingren; Renton, Michael

    2013-06-01

    Computer simulation models can provide a relatively fast, safe and inexpensive means to judge and weigh the merits of various pest control management options. However, the usefulness of such simulation models relies on the accurate estimation of important model parameters, such as the pest mortality under different treatments and conditions. Recently, an individual-based simulation model of population dynamics and resistance evolution has been developed for the stored grain insect pest Rhyzopertha dominica, based on experimental results showing that alleles at two different loci are involved in resistance to the grain fumigant phosphine. In this paper, we describe how we used three generalized linear models, probit, logistic and Cauchy models, each employing two- and four-parameter sub-models, to fit experimental data sets for five genotypes for which detailed mortality data was already available. Instead of the usual statistical iterative maximum likelihood estimation, a direct algebraic approach, generalized inverse matrix technique, was used to estimate the mortality model parameters. As this technique needs to perturb the observed mortality proportions if the proportions include 0 or 1, a golden section search approach was used to find the optimal perturbation in terms of minimum least squares (L2) error. The results show that the estimates using the probit model were the most accurate in terms of L2 errors between observed and predicted mortality values. These errors with the probit model ranged from 0.049% to 5.3%, from 0.381% to 8.1% with the logistic model and from 8.3% to 48.2% with the Cauchy model. Meanwhile, the generalized inverse matrix technique achieved similar results to the maximum likelihood estimation ones, but is less time consuming and computationally demanding. We also describe how we constructed a two-parameter model to estimate the mortalities for each of the remaining four genotypes based on realistic genetic assumptions. PMID:23473941

  17. Modelling of adaptation processes of crops to water and nitrogen stress

    NASA Astrophysics Data System (ADS)

    Kovács, Géza J.

    In the early 1980s the author published interpretations of his observations on special adaptation processes of crops (“Zichy” experiment). Those days it was not yet possible to include these details into a crop model. The knowledge has grown about the systems of crops and their environment, now it is appropriate to test those hypothesis by systems models. The 4M system model used in this study was developed by RISSAC modelling team lead by the author. 4M is based on CERES model family and the advices of the “father” of CERES, J.T. Ritchie. 4M aims to include a lot of results from Hungarian agricultural research. Some observations of “Zichy” experiment needed explanations but there were shortages of information on some parts of the system in order to test the hypothesis. Observations were as it follows: (1) The growth of above ground maize biomass slowed down in both years after a heavy rainy period. (2) Following the rainy period there was a fast drop of nitrate content in the soil and (3) following this time the water content of soil decreased with a fast rate approaching the wilting point. (4) When maize reacted on the emerging water stress there was a second (and even deeper) slow down of growth of above ground biomass. (5) The consequences of the stormy period was more dramatic in the second year of the experiment (1979), there was 3 t ha -1 loss of biomass and 2.5 t ha -1 loss of grain yield relative to 1978. (6) There was a significant difference in the time of stormy rain: in 1978 it occurred post-anthesis while in 1979 it occurred just prior to anthesis. Hypothesis tested here were as it follows: (1) The cause of observed growth stress reaction was a fast nitrate leaching from the rooted zone. (2) The crops cannot take up all the mineral nitrogen measured in a soil probe, the major limit is the mass flow to the roots controlled by transpiration and nitrogen concentration of soil solution. (3) “Leaching of soil by a flush of rain leads to

  18. Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models

    PubMed Central

    Na, Hyuntae; Jernigan, Robert L.; Song, Guang

    2015-01-01

    Dynamics can provide deep insights into the functional mechanisms of proteins and protein complexes. For large protein complexes such as GroEL/GroES with more than 8,000 residues, obtaining a fine-grained all-atom description of its normal mode motions can be computationally prohibitive and is often unnecessary. For this reason, coarse-grained models have been used successfully. However, most existing coarse-grained models use extremely simple potentials to represent the interactions within the coarse-grained structures and as a result, the dynamics obtained for the coarse-grained structures may not always be fully realistic. There is a gap between the quality of the dynamics of the coarse-grained structures given by all-atom models and that by coarse-grained models. In this work, we resolve an important question in protein dynamics computations—how can we efficiently construct coarse-grained models whose description of the dynamics of the coarse-grained structures remains as accurate as that given by all-atom models? Our method takes advantage of the sparseness of the Hessian matrix and achieves a high efficiency with a novel iterative matrix projection approach. The result is highly significant since it can provide descriptions of normal mode motions at an all-atom level of accuracy even for the largest biomolecular complexes. The application of our method to GroEL/GroES offers new insights into the mechanism of this biologically important chaperonin, such as that the conformational transitions of this protein complex in its functional cycle are even more strongly connected to the first few lowest frequency modes than with other coarse-grained models. PMID:26473491

  19. Solid-state phase transformations involving solute partitioning: modeling and measuring on the level of individual grains

    SciTech Connect

    Offerman, S.E.; Dijk, N.H. van; Sietsma, J.; Lauridsen, E.M.; Margulies, L.; Grigull, S.; Poulsen, H.F.; Zwaag, S. van der

    2004-09-20

    A simplified grain growth model is presented for the transition from non-overlapping to overlapping diffusion fields of growing neighboring grains during partitioning solid-state transformations in polycrystalline materials. The model is based on unique observations on the austenite decomposition into ferrite and pearlite in medium-carbon steel with the three-dimensional X-ray diffraction microscope. The model explains three types of observed pro-eutectoid ferrite grain growth and austenite grain decomposition, and the indirectly observed carbon exchange between decomposing austenite grains. A direct comparison of the model and the experiment at the level of individual grains shows that the growth of ferrite grains is strongly related to the local carbon concentration and the local density of nuclei. Unusual observations of a non-stationary austenite grain size prior to the transformation, and oscillatory ferrite growth are reported.

  20. Modeling of dissociation and energy transfer in shock-heated nitrogen flows

    SciTech Connect

    Munafò, A.; Liu, Y.; Panesi, M.

    2015-12-15

    This work addresses the modeling of dissociation and energy transfer processes in shock heated nitrogen flows by means of the maximum entropy linear model and a newly proposed hybrid bin vibrational collisional model. Both models aim at overcoming two of the main limitations of the state of the art non-equilibrium models: (i) the assumption of equilibrium between rotational and translational energy modes of the molecules and (ii) the reliance on the quasi-steady-state distribution for the description of the population of the internal levels. The formulation of the coarse-grained models is based on grouping the energy levels into bins, where the population is assumed to follow a Maxwell-Boltzmann distribution at its own temperature. Different grouping strategies are investigated. Following the maximum entropy principle, the governing equations are obtained by taking the zeroth and first-order moments of the rovibrational master equations. The accuracy of the proposed models is tested against the rovibrational master equation solution for both flow quantities and population distributions. Calculations performed for free-stream velocities ranging from 5 km/s to 10 km/s demonstrate that dissociation can be accurately predicted by using only 2-3 bins. It is also shown that a multi-temperature approach leads to an under-prediction of dissociation, due to the inability of the former to account for the faster excitation of high-lying vibrational states.

  1. Modeling of dissociation and energy transfer in shock-heated nitrogen flows

    NASA Astrophysics Data System (ADS)

    Munafò, A.; Liu, Y.; Panesi, M.

    2015-12-01

    This work addresses the modeling of dissociation and energy transfer processes in shock heated nitrogen flows by means of the maximum entropy linear model and a newly proposed hybrid bin vibrational collisional model. Both models aim at overcoming two of the main limitations of the state of the art non-equilibrium models: (i) the assumption of equilibrium between rotational and translational energy modes of the molecules and (ii) the reliance on the quasi-steady-state distribution for the description of the population of the internal levels. The formulation of the coarse-grained models is based on grouping the energy levels into bins, where the population is assumed to follow a Maxwell-Boltzmann distribution at its own temperature. Different grouping strategies are investigated. Following the maximum entropy principle, the governing equations are obtained by taking the zeroth and first-order moments of the rovibrational master equations. The accuracy of the proposed models is tested against the rovibrational master equation solution for both flow quantities and population distributions. Calculations performed for free-stream velocities ranging from 5 km/s to 10 km/s demonstrate that dissociation can be accurately predicted by using only 2-3 bins. It is also shown that a multi-temperature approach leads to an under-prediction of dissociation, due to the inability of the former to account for the faster excitation of high-lying vibrational states.

  2. A novel family of γ-gliadin genes are highly regulated by nitrogen supply in developing wheat grain

    PubMed Central

    Shewry, Peter R.

    2013-01-01

    Six wheat cultivars were grown at Rothamsted (UK) with three levels of nitrogen fertilizer (100, 200 and 350kg N/ha) in 2009 and 2010. Gene expression in developing caryopses at 21 days post-anthesis (DPA) was profiled using the Affymetrix Wheat GeneChip®. Four of 105 transcripts which were significantly upregulated by nitrogen level were annotated as γ-3 hordein and the identification of corresponding expressed sequence tags showed that they differed in sequence from previously described (typical) γ-gliadins and represented a novel form of γ-gliadin. Real-time reverse transcriptase PCR at 14, 21, 28 and 35 DPA revealed that this transcript was most abundant and most responsive to nitrogen at 21 DPA. Four novel γ-gliadin genes were isolated by PCR amplification from wheat cv. Hereward and the related species Aegilops tauschii and Triticum monococcum while three were assembled from the genomic sequence database of wheat cv. Chinese Spring (www.cerealsdb.uk.net). Comparison of the deduced amino acid sequences of the seven genes showed that they shared only 44.4–46.0% identity with the sequence of a typical γ-gliadin (accession number EF15018), but 61.8–68.3% identity with the sequence of γ-3 hordein from the wild barley species Hordeum chilense (AY338065). The novel γ-gliadin genes were localized to the group 1 chromosomes (1A, 1B, 1D). PMID:23162123

  3. A Model for SiC Grain Coagulation in Supernova Ejecta

    NASA Astrophysics Data System (ADS)

    Deneault, Ethan

    2009-12-01

    We present a model for the formation of silicon carbide grains within the expanding and cooling supernova ejecta. Supernova SiC grains (SiC-X grains) have been found to be aggregates of smaller subgrains. We propose that the subgrains initially condensed in interior dense shell, were moved out of that region through velocity differentiation due to reverse shocks, and coagulated via impacts with other subgrains. The size distribution as well as the isotopic homogeneity of the subgrains places a limit on the initial location and conditions of their formation.

  4. Boltzmann rovibrational collisional coarse-grained model for internal energy excitation and dissociation in hypersonic flows.

    PubMed

    Munafò, A; Panesi, M; Magin, T E

    2014-02-01

    A Boltzmann rovibrational collisional coarse-grained model is proposed to reduce a detailed kinetic mechanism database developed at NASA Ames Research Center for internal energy transfer and dissociation in N(2)-N interactions. The coarse-grained model is constructed by lumping the rovibrational energy levels of the N(2) molecule into energy bins. The population of the levels within each bin is assumed to follow a Boltzmann distribution at the local translational temperature. Excitation and dissociation rate coefficients for the energy bins are obtained by averaging the elementary rate coefficients. The energy bins are treated as separate species, thus allowing for non-Boltzmann distributions of their populations. The proposed coarse-grained model is applied to the study of nonequilibrium flows behind normal shock waves and within converging-diverging nozzles. In both cases, the flow is assumed inviscid and steady. Computational results are compared with those obtained by direct solution of the master equation for the rovibrational collisional model and a more conventional multitemperature model. It is found that the proposed coarse-grained model is able to accurately resolve the nonequilibrium dynamics of internal energy excitation and dissociation-recombination processes with only 20 energy bins. Furthermore, the proposed coarse-grained model provides a superior description of the nonequilibrium phenomena occurring in shock heated and nozzle flows when compared with the conventional multitemperature models. PMID:25353565

  5. Boltzmann rovibrational collisional coarse-grained model for internal energy excitation and dissociation in hypersonic flows

    NASA Astrophysics Data System (ADS)

    Munafò, A.; Panesi, M.; Magin, T. E.

    2014-02-01

    A Boltzmann rovibrational collisional coarse-grained model is proposed to reduce a detailed kinetic mechanism database developed at NASA Ames Research Center for internal energy transfer and dissociation in N2-N interactions. The coarse-grained model is constructed by lumping the rovibrational energy levels of the N2 molecule into energy bins. The population of the levels within each bin is assumed to follow a Boltzmann distribution at the local translational temperature. Excitation and dissociation rate coefficients for the energy bins are obtained by averaging the elementary rate coefficients. The energy bins are treated as separate species, thus allowing for non-Boltzmann distributions of their populations. The proposed coarse-grained model is applied to the study of nonequilibrium flows behind normal shock waves and within converging-diverging nozzles. In both cases, the flow is assumed inviscid and steady. Computational results are compared with those obtained by direct solution of the master equation for the rovibrational collisional model and a more conventional multitemperature model. It is found that the proposed coarse-grained model is able to accurately resolve the nonequilibrium dynamics of internal energy excitation and dissociation-recombination processes with only 20 energy bins. Furthermore, the proposed coarse-grained model provides a superior description of the nonequilibrium phenomena occurring in shock heated and nozzle flows when compared with the conventional multitemperature models.

  6. Anisotropic Coarse-Grained Model for Proteins Based On Gay–Berne and Electric Multipole Potentials

    PubMed Central

    2015-01-01

    Gay–Berne anisotropic potential has been widely used to evaluate the nonbonded interactions between coarse-grained particles being described as elliptical rigid bodies. In this paper, we are presenting a coarse-grained model for twenty kinds of amino acids and proteins, based on the anisotropic Gay–Berne and point electric multipole (EMP) potentials. We demonstrate that the anisotropic coarse-grained model, namely GBEMP model, is able to reproduce many key features observed from experimental protein structures (Dunbrack Library), as well as from atomistic force field simulations (using AMOEBA, AMBER, and CHARMM force fields), while saving the computational cost by a factor of about 10–200 depending on specific cases and atomistic models. More importantly, unlike other coarse-grained approaches, our framework is based on the fundamental intermolecular forces with explicit treatment of electrostatic and repulsion-dispersion forces. As a result, the coarse-grained protein model presented an accurate description of nonbonded interactions (particularly electrostatic component) between hetero/homodimers (such as peptide–peptide, peptide–water). In addition, the encouraging performance of the model was reflected by the excellent correlation between GBEMP and AMOEBA models in the calculations of the dipole moment of peptides. In brief, the GBEMP model given here is general and transferable, suitable for simulating complex biomolecular systems. PMID:24659927

  7. Toward an Improved Single-Particle Model for Large Irregular Grains

    NASA Technical Reports Server (NTRS)

    Grundy, W. M.; Schmitt, B.; Doute, S.

    2002-01-01

    To interpret remote spectral observations, scattering and absorption in a particulate surface are simulated via radiative transfer models. The standard model for this purpose among the planetary science community is the Hapke model. This model (like many others) uses two parameters to characterize the optical behavior of individual grains in a particulate surface, the single-scattering albedo omega and phase function p(g). These terms describe, respectively, the quantity and the angular distribution of light scattered by an individual grain. Unfortunately, these parameters are strictly optical. They can be rather difficult to interpret in terms of more interesting particle properties such as grain sizes, shapes, and compositions, that a remote sensing experiment might seek to discover. An equivalent slab approximation is typically used to relate omega to the grain size and optical constants of the material. This approach can mimic the wavelength-dependent absorption behavior of irregular grains, as long as the imaginary index kappa is much less than 1, the shape is equant, and the grain size D is much larger than the wavelength lambda. Unfortunately, the equivalent slab approach provides no information about p(g), which also has a strong dependence on optical constants and particle form.

  8. The role of the stagnant-film thickness in mesoscopic modeling of equiaxed grain envelopes

    NASA Astrophysics Data System (ADS)

    Souhar, Youssef; De Felice, Valerio F.; Založnik, Miha; Combeau, Hervé; Beckermann, Christoph

    2016-03-01

    The mesoscopic envelope model overcomes the limitations of phase-field methods. It can be applied at larger scales and can include fluid flow at reasonable computing cost. It consists of the description of a dendritic grain by an envelope that links the active dendrite branches. The grain is modelled as an evolving porous medium and the liquid-solid phase change and solute transport are modelled by volume-averaged equations. The velocities of the dendrite tips are determined by the local solute-concentration field in the proximity of the envelope through an analytical stagnant-film model. In this publication, we present our implementation of the model for a binary alloy and we discuss the influence of the stagnant-film thickness, the principal model parameter, on the predicted 3D equiaxed grains by comparisons with the scaling laws for binary-alloy dendrites obtained in recent experiments by Melendez and Beckermann.

  9. Effects of reduced terrestrial LiDAR point density on high-resolution grain crop surface models in precision agriculture.

    PubMed

    Hämmerle, Martin; Höfle, Bernhard

    2014-01-01

    3D geodata play an increasingly important role in precision agriculture, e.g., for modeling in-field variations of grain crop features such as height or biomass. A common data capturing method is LiDAR, which often requires expensive equipment and produces large datasets. This study contributes to the improvement of 3D geodata capturing efficiency by assessing the effect of reduced scanning resolution on crop surface models (CSMs). The analysis is based on high-end LiDAR point clouds of grain crop fields of different varieties (rye and wheat) and nitrogen fertilization stages (100%, 50%, 10%). Lower scanning resolutions are simulated by keeping every n-th laser beam with increasing step widths n. For each iteration step, high-resolution CSMs (0.01 m2 cells) are derived and assessed regarding their coverage relative to a seamless CSM derived from the original point cloud, standard deviation of elevation and mean elevation. Reducing the resolution to, e.g., 25% still leads to a coverage of >90% and a mean CSM elevation of >96% of measured crop height. CSM types (maximum elevation or 90th-percentile elevation) react differently to reduced scanning resolutions in different crops (variety, density). The results can help to assess the trade-off between CSM quality and minimum requirements regarding equipment and capturing set-up. PMID:25521383

  10. Effects of Reduced Terrestrial LiDAR Point Density on High-Resolution Grain Crop Surface Models in Precision Agriculture

    PubMed Central

    Hämmerle, Martin; Höfle, Bernhard

    2014-01-01

    3D geodata play an increasingly important role in precision agriculture, e.g., for modeling in-field variations of grain crop features such as height or biomass. A common data capturing method is LiDAR, which often requires expensive equipment and produces large datasets. This study contributes to the improvement of 3D geodata capturing efficiency by assessing the effect of reduced scanning resolution on crop surface models (CSMs). The analysis is based on high-end LiDAR point clouds of grain crop fields of different varieties (rye and wheat) and nitrogen fertilization stages (100%, 50%, 10%). Lower scanning resolutions are simulated by keeping every n-th laser beam with increasing step widths n. For each iteration step, high-resolution CSMs (0.01 m2 cells) are derived and assessed regarding their coverage relative to a seamless CSM derived from the original point cloud, standard deviation of elevation and mean elevation. Reducing the resolution to, e.g., 25% still leads to a coverage of >90% and a mean CSM elevation of >96% of measured crop height. CSM types (maximum elevation or 90th-percentile elevation) react differently to reduced scanning resolutions in different crops (variety, density). The results can help to assess the trade-off between CSM quality and minimum requirements regarding equipment and capturing set-up. PMID:25521383

  11. Covalent adduction of nitrogen mustards to model protein nucleophiles.

    PubMed

    Thompson, Vanessa R; DeCaprio, Anthony P

    2013-08-19

    Protein adducts have the potential to serve as unique biomarkers of exposure to compounds of interest. Many xenobiotics (or their metabolites) are electrophilic and therefore reactive with nucleophilic amino acid residues on proteins. Nitrogen mustards are reactive xenobiotics with potential use as chemical warfare agents (CWA) or agents of terrorist attack, in addition to being employed as chemotherapeutic agents. The present study utilized cysteine-, lysine-, and histidine-containing model peptides to characterize in vitro adduction of the nitrogen mustards mechloroethamine (HN-2) and tris-(2-chlorethyl)amine (HN-3) to these nucleophilic amino acid residues by means of liquid chromatography-tandem mass spectrometry. The study assessed the structure of adducts formed, the time course of adduct formation, concentration-response relationships, and temporal stability of adducts. Adduction was hypothesized to occur on all three model peptides via initial formation of a reactive aziridinium intermediate for both mechloroethamine and tris-(2-chlorethyl)amine, followed by covalent adduction to nucleophilic residues. While adduction was found to occur most readily with cysteine, it was also observed at lysine and histidine, demonstrating that adduction by mechloroethamine and tris-(2-chlorethyl)amine is possible at multiple nucleophilic sites. Following solid phase extraction cleanup, adducts formed with mechloroethamine were stable for up to three weeks. Adducts formed with tris-(2-chlorethyl)amine were less stable; however, hydrolyzed secondary adducts were observed throughout the three week period. This study demonstrates that the nitrogen mustards mechloroethamine and tris-(2-chlorethyl)amine form stable adducts with reactive protein nucleophiles other than cysteine. PMID:23859065

  12. Model for evolution of grain size in the rim region of high burnup UO2 fuel

    NASA Astrophysics Data System (ADS)

    Xiao, Hongxing; Long, Chongsheng; Chen, Hongsheng

    2016-04-01

    The restructuring process of the high burnup structure (HBS) formation in UO2 fuel results in sub-micron size grains that accelerate the fission gas swelling, which will raise some concern over the safety of extended the nuclear fuel operation life in the reactor. A mechanistic and engineering model for evolution of grain size in the rim region of high burnup UO2 fuel based on the experimental observations of the HBS in the literature is presented. The model takes into account dislocations evolution under irradiation and the grain subdivision occur successively at increasing local burnup. It is assumed that the original driving force for subdivision of grain in the HBS of UO2 fuel is the production and accumulation of dislocation loops during irradiation. The dislocation loops can also be annealed through thermal diffusion when the temperature is high enough. The capability of this model is validated by the comparison with the experimental data of temperature threshold of subdivision, dislocation density and sub-grain size as a function of local burnup. It is shown that the calculated results of the dislocation density and subdivided grain size as a function of local burnup are in good agreement with the experimental results.

  13. Evolution of isotopic signatures in lunar-regolith nitrogen - Noble gases and nitrogen in grain-size fractions from regolith breccia 79035

    NASA Technical Reports Server (NTRS)

    Kerridge, J. F.; Kim, J. S.; Kim, Y.; Marti, K.

    1992-01-01

    Ilmenite and pyroxene grain-size separates from 79035 were analyzed for trapped N; the ilmenite was also analyzed for trapped Xe. Ilmenite N contains two or more isotopically distinct trapped components differing in release temperature and therefore plausibly in implantation energy. The isotopically light, higher-temperature (higher-energy?) component has a delta N-15 value equal to -180 percent, significantly above the minimum value observed in bulk 79035, suggesting that parts of 79035 were exposed on the lunar surface earlier than the ilmenite. Using trapped Ar-40/Ar-36 and cosmogenic Ne-21 (Benkert, 1989) a compaction age of about 1 Ga was derived for the ilmenite. This implies a considerably more recent exposure than previously thought, and suggests that the long-term change in delta N-15 of regolith N was more rapid than generally believed. Comparison of these results with those for black/orange glass from 74001/74002 (compaction age 3.7 Ga; delta N-15 in the range -36 to +18 percent (Kerridge et al., 1991) indicates that the long-term trend may have followed a complex evolutionary path. Data for 79035 pyroxenes are consistent with the ilmenite compaction age but suggest a more complex exposure history.

  14. Symmetry-adapted digital modeling III. Coarse-grained icosahedral viruses.

    PubMed

    Janner, A

    2016-05-01

    Considered is the coarse-grained modeling of icosahedral viruses in terms of a three-dimensional lattice (the digital modeling lattice) selected among the projected points in space of a six-dimensional icosahedral lattice. Backbone atomic positions (Cα's for the residues of the capsid and phosphorus atoms P for the genome nucleotides) are then indexed by their nearest lattice point. This leads to a fine-grained lattice point characterization of the full viral chains in the backbone approximation (denoted as digital modeling). Coarse-grained models then follow by a proper selection of the indexed backbone positions, where for each chain one can choose the desired coarseness. This approach is applied to three viruses, the Satellite tobacco mosaic virus, the bacteriophage MS2 and the Pariacoto virus, on the basis of structural data from the Brookhaven Protein Data Bank. In each case the various stages of the procedure are illustrated for a given coarse-grained model and the corresponding indexed positions are listed. Alternative coarse-grained models have been derived and compared. Comments on related results and approaches, found among the very large set of publications in this field, conclude this article. PMID:27126109

  15. Monte Carlo Simulations of inter- and intra-grain spin structure of Ising and Heisenberg models

    NASA Astrophysics Data System (ADS)

    Leblanc, Martin

    In order to keep supplying computer hard disk drives with more and more storage space, it is essential to have smaller bits. With smaller bits, superparamagnetism, the spontaneous flipping of the magnetic moments in a bit caused by thermal fluctuations, becomes increasingly important and impacts the stability of stored data. Recording media is composed of magnetic grains (usually made of CoCrPt alloys) roughly 10 nm in size from which bits are composed. Most modeling efforts that study magnetic recording media treat the grains as weakly interacting uniformly magnetized objects. In this work, the spin structure internal to a grain is examined along with the impact of varying the relative strengths of intrar-grain and inter-grain exchange interactions. The interplay between these two effects needs to be examined for a greater understanding of superparamagnetism as well as for the applications of the proposed Heat Assisted Magnetic Recording (HAMR) technology where thermal fluctuations facilitate head-field induced bit reversal in high anisotropy media. Simulations using the Monte Carlo method (with cluster-flipping algorithms) are performed on a 2D single-layer and multilayer Ising model with a strong intrar-grain exchange interaction J as well as a weak inter-grain exchange J'. A strong deviation from traditional behavior is found when J'/J is significant. M-H hysteresis loops are also calculated and the coercivity, H c is estimated. A large value represents a strong resilience to the superparamagnetic effect. It is found that taking into account the internal degrees of freedom has a significant effect on Hce. As the Ising model serves only as an approximation, preliminary simulations are also reported on a more realistic Heisenberg model with uniaxial anisotropy. Key Words: Ising model, Heisenberg model, Monte Carlo Simulation

  16. Modeling and Measurement of 39Ar Recoil Loss From Biotite as a Function of Grain Dimensions

    NASA Astrophysics Data System (ADS)

    Paine, J. H.; Nomade, S.; Renne, P. R.

    2004-12-01

    The call for age measurements with less than 1 per mil error puts a demand upon geochronologists to be aware of and quantify a number of problems which were previously negligible. One such factor is 39Ar recoil loss during sample irradiation, a phenomenon which is widely assumed to affect only unusually small crystals having exceptionally high surface/volume ratios. This phenomenon has important implications for thermochronologic studies seeking to exploit a range of closure temperatures arising from variable diffusion radii. Our study focuses on biotite, in which spatial isotope distributions cannot be reliably recovered by stepwise heating and which therefore lack recoil-diagnostic age spectrum behavior. Previous work by Renne et al. [Application of a deuteron-deuteron (D-D) neutron generator to 40Ar/39Ar geochronology, Applied Radiation and Isotopes, in press] used the SRIM code to calculate a ˜20% 39Ar recoil loss from the outermost 0.25 μ m of an infinite slab of phyllosillicate. This result is applied to measured grains of the biotite standard GA1550, a hypabyssal granite from the Mount Dromedary Complex, Australia. We measure the thickness and surface area of 166 grains and approximate the shape of each grain as a cylinder. Grain thickness ranges from 3 to 210 μ m, with an average grain radius of 350 μ m. We predict the amount of 39Ar recoil loss from each grain, finding an expected age error >0.1 % for grains thinner than 150 μ m, a >1% error for grain less than 10 μ m thick, and up to a 3% error for grains less than 3 μ m thick. These modeling results will be tested by analysis of the measured grains after irradiation in the Oregon State University TRIGA reactor. It is important to either account for 39Ar loss in thin biotite grains, or use sufficiently thick ones so that recoil loss is negligible. Our results indicate that only biotite grains thicker than 150 μ m should be used for neutron fluence monitoring in order to avoid bias greater than the

  17. Effect of quenching conditions on the formation of the grain structure and the mechanical properties of high-nitrogen austenitic 02Kh20AG14N8MF and 02Kh20AG12N4 steels

    NASA Astrophysics Data System (ADS)

    Bannykh, I. O.

    2015-11-01

    The formation of the grain structure of high-nitrogen 02Kh20AG14N8MF and 02Kh20AG12N4 steels in forging and quenching and their mechanical properties in this state have been studied. It is found that both steels have close mechanical properties under the same quenching conditions. In 02Kh20AG14N8MF steel, a homogeneous structure of primarily recrystallized austenite grains forms under the quenching conditions under study. In 02Kh20AG12N4 steel, the processes of secondary recrystallization and normal grain growth take place.

  18. Modeling the chemical evolution of nitrogen oxides near roadways

    NASA Astrophysics Data System (ADS)

    Wang, Yan Jason; DenBleyker, Allison; McDonald-Buller, Elena; Allen, David; Zhang, K. Max

    2011-01-01

    The chemical evolution of nitrogen dioxide (NO 2) and nitrogen monoxide (NO) in the vicinity of roadways is numerically investigated using a computational fluid dynamics model, CFD-VIT-RIT and a Gaussian-based model, CALINE4. CFD-VIT-RIT couples a standard k- ɛ turbulence model for turbulent mixing and the Finite-Rate model for chemical reactions. CALINE4 employs a discrete parcel method, assuming that chemical reactions are independent of the dilution process. The modeling results are compared to the field measurement data collected near two roadways in Austin, Texas, State Highway 71 (SH-71) and Farm to Market Road 973 (FM-973), under parallel and perpendicular wind conditions during the summer of 2007. In addition to ozone (O 3), other oxidants and reactive species including hydroperoxyl radical (HO 2), organic peroxyl radical (RO 2), formaldehyde (HCHO) and acetaldehyde (CH 3CHO) are considered in the transformation from NO to NO 2. CFD-VIT-RIT is shown to be capable of predicting both NO x and NO 2 profiles downwind. CALINE4 is able to capture the NO x profiles, but underpredicts NO 2 concentrations under high wind velocity. Our study suggests that the initial NO 2/NO x ratios have to be carefully selected based on traffic conditions in order to assess NO 2 concentrations near roadways. The commonly assumed NO 2/NO x ratio by volume of 5% may not be suitable for most roadways, especially those with a high fraction of heavy-duty truck traffic. In addition, high O 3 concentrations and high traffic volumes would lead to the peak NO 2 concentration occurring near roadways with elevated concentrations persistent over a long distance downwind.

  19. Modeling Nitrogen Processing in Northeast US River Networks

    NASA Astrophysics Data System (ADS)

    Whittinghill, K. A.; Stewart, R.; Mineau, M.; Wollheim, W. M.; Lammers, R. B.

    2013-12-01

    Due to increased nitrogen (N) pollution from anthropogenic sources, the need for aquatic ecosystem services such as N removal has also increased. River networks provide a buffering mechanism that retains or removes anthropogenic N inputs. However, the effectiveness of N removal in rivers may decline with increased loading and, consequently, excess N is eventually delivered to estuaries. We used a spatially distributed river network N removal model developed within the Framework for Aquatic Modeling in the Earth System (FrAMES) to examine the geography of N removal capacity of Northeast river systems under various land use and climate conditions. FrAMES accounts for accumulation and routing of runoff, water temperatures, and serial biogeochemical processing using reactivity derived from the Lotic Intersite Nitrogen Experiment (LINX2). Nonpoint N loading is driven by empirical relationships with land cover developed from previous research in Northeast watersheds. Point source N loading from wastewater treatment plants is estimated as a function of the population served and the volume of water discharged. We tested model results using historical USGS discharge data and N data from historical grab samples and recently initiated continuous measurements from in-situ aquatic sensors. Model results for major Northeast watersheds illustrate hot spots of ecosystem service activity (i.e. N removal) using high-resolution maps and basin profiles. As expected, N loading increases with increasing suburban or agricultural land use area. Network scale N removal is highest during summer and autumn when discharge is low and river temperatures are high. N removal as the % of N loading increases with catchment size and decreases with increasing N loading, suburban land use, or agricultural land use. Catchments experiencing the highest network scale N removal generally have N inputs (both point and non-point sources) located in lower order streams. Model results can be used to better

  20. Grain sorting in the morphological active layer of a braided river physical model

    NASA Astrophysics Data System (ADS)

    Leduc, P.; Ashmore, P.; Gardner, J. T.

    2015-12-01

    A physical scale model of a gravel-bed braided river was used to measure vertical grain size sorting in the morphological active layer aggregated over the width of the river. This vertical sorting is important for analyzing braided river sedimentology, for numerical modeling of braided river morphodynamics, and for measuring and predicting bedload transport rate. We define the morphological active layer as the bed material between the maximum and minimum bed elevations at a point over extended time periods sufficient for braiding processes to rework the river bed. The vertical extent of the active layer was measured using 40 hourly high-resolution DEMs (digital elevation models) of the model river bed. An image texture algorithm was used to map bed material grain size of each DEM. Analysis of the 40 DEMs and texture maps provides data on the geometry of the morphological active layer and variation in grain size in three dimensions. By normalizing active layer thickness and dividing into 10 sublayers, we show that all grain sizes occur with almost equal frequency in all sublayers. Occurrence of patches and strings of coarser (or finer) material relates to preservation of particular morpho-textural features within the active layer. For numerical modeling and bedload prediction, a morphological active layer that is fully mixed with respect to grain size is a reliable approximation.

  1. A double species model for study of relaxation of impure Ni 3Al grain boundaries

    NASA Astrophysics Data System (ADS)

    Zheng, Li-Ping; Ma, Yu-Gang; Han, Jia-Guang; Li, D. X.; Zhang, Xiu-Rong

    2004-04-01

    Based on the Monte Carlo simulation conjoined with the embedded atom method (EAM) potentials, the double species model is established to study relaxation of impure Ni 3Al grain boundaries. The present double species model suggests that the impure atoms are not only segregating species but also inducing species. The present model also suggests that study of combination of the positive (the impure atoms induce Ni atoms to substitute into Al sites) and the negative (the impure atoms substitute into Ni sites) bulk effects of impure atoms is available, in order to understand dependence of the cohesion of the impure Ni 3Al grain boundary (or the Ni enrichment at the impure Ni 3Al grain boundary) on the bulk concentration of impure atoms. The double species model is clarified in comparison between the Ni 3AlB and the Ni 3AlMg systems.

  2. Bottom-up coarse-graining of a simple graphene model: the blob picture.

    PubMed

    Kauzlarić, David; Meier, Julia T; Español, Pep; Succi, Sauro; Greiner, Andreas; Korvink, Jan G

    2011-02-14

    The coarse-graining of a simple all-atom 2D microscopic model of graphene, in terms of "blobs" described by center of mass variables, is presented. The equations of motion of the coarse-grained variables take the form of dissipative particle dynamics (DPD). The coarse-grained conservative forces and the friction of the DPD model are obtained via a bottom-up procedure from molecular dynamics (MD) simulations. The separation of timescales for blobs of 24 and 96 carbon atoms is sufficiently pronounced for the Markovian assumption, inherent to the DPD model, to provide satisfactory results. In particular, the MD velocity autocorrelation function of the blobs is well reproduced by the DPD model, provided that the effect of friction and noise is taken into account. However, DPD cross-correlations between neighbor blobs show appreciable discrepancies with respect to the MD results. Possible extensions to mend these discrepancies are briefly outlined. PMID:21322660

  3. Modeling grain size and dislocation density effects on harmonics of the magnetic induction

    SciTech Connect

    Sablik, M. J.; Stegemann, D.; Krys, A.

    2001-06-01

    Microstructural attributes of steels affect hysteretic magnetic properties because the microstructure affects domain wall movement and pinning. Two important features are grain size and dislocation density. The consensus experimentally is that the coercivity tends to be linearly related to the inverse of the average grain diameter and to the square root of the dislocation density. In this article, these experimental tendencies are utilized in formulating the dependence of the hysteresis parameters of the Jiles{endash}Atherton model as a function of grain size and dislocation density. The results are then used in computing the first and third harmonics of the magnetic induction as a function of grain size and dislocation density. This is done via an adaptation of a hysteresis model formulated by Jiles for higher excitation frequencies. The results indicate that the harmonic amplitudes decrease monotonically with inverse grain size and the square root of dislocation density. Since increasing inverse grain size and dislocation density are correlated with increasing tensile strength, the results are consistent with experimental results for the decrease of the harmonic amplitudes with increasing tensile strength in automotive steels. Also, the harmonic amplitudes decrease with increasing excitation frequency, consistent with experiment. {copyright} 2001 American Institute of Physics.

  4. Modeling grain size and dislocation density effects on harmonics of the magnetic induction

    NASA Astrophysics Data System (ADS)

    Sablik, M. J.; Stegemann, D.; Krys, A.

    2001-06-01

    Microstructural attributes of steels affect hysteretic magnetic properties because the microstructure affects domain wall movement and pinning. Two important features are grain size and dislocation density. The consensus experimentally is that the coercivity tends to be linearly related to the inverse of the average grain diameter and to the square root of the dislocation density. In this article, these experimental tendencies are utilized in formulating the dependence of the hysteresis parameters of the Jiles-Atherton model as a function of grain size and dislocation density. The results are then used in computing the first and third harmonics of the magnetic induction as a function of grain size and dislocation density. This is done via an adaptation of a hysteresis model formulated by Jiles for higher excitation frequencies. The results indicate that the harmonic amplitudes decrease monotonically with inverse grain size and the square root of dislocation density. Since increasing inverse grain size and dislocation density are correlated with increasing tensile strength, the results are consistent with experimental results for the decrease of the harmonic amplitudes with increasing tensile strength in automotive steels. Also, the harmonic amplitudes decrease with increasing excitation frequency, consistent with experiment.

  5. 3-D and quasi-2-D discrete element modeling of grain commingling in a bucket elevator boot system

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Unwanted grain commingling impedes new quality-based grain handling systems and has proven to be an expensive and time consuming issue to study experimentally. Experimentally validated models may reduce the time and expense of studying grain commingling while providing additional insight into detail...

  6. Use of the USEPA Estuary Nitrogen Model to Estimate Concentrations of Total Nitrogen in Estuaries Using Loads Calculated by Watershed Models and Monitoring Data

    EPA Science Inventory

    We use USEPA’s Estuary Nitrogen Model (ENM) to calculate annual average concentrations of total nitrogen (TN) in ten estuaries or sub-estuaries along the Atlantic coast from New Hampshire to Florida. These include a variety of systems, ranging from strongly-flushed bays to weakly...

  7. Effect of dried distillers grains plus solubles on enteric methane emissions and nitrogen excretion from growing beef cattle.

    PubMed

    Hünerberg, M; McGinn, S M; Beauchemin, K A; Okine, E K; Harstad, O M; McAllister, T A

    2013-06-01

    The objectives of this study were to examine the impact of corn- or wheat-based dried distillers grains with solubles (CDDGS or WDDGS) on enteric methane (CH4) emissions from growing beef cattle and determine if the oil in CDDGS was responsible for any response observed. Effects of CDDGS or WDDGS on total N excretion and partitioning between urine and fecal N were also examined in this replicated 4 × 4 Latin square using 16 ruminally cannulated crossbreed heifers (388.5 ± 34.9 kg of initial BW). The control diet contained (DM basis) 55% whole crop barley silage, 35% barley grain, 5% canola meal, and 5% vitamin and mineral supplement. Three dried distillers grains with solubles (DDGS) diets were formulated by replacing barley grain and canola meal (40% of dietary DM) with CDDGS, WDDGS, or WDDGS plus corn oil (WDDGS+oil). For WDDGS+oil, corn oil was added to WDDGS (4.11% fat DM basis) to achieve the same fat level as in CDDGS (9.95% fat DM basis). All total mixed diets were fed once daily ad libitum. Total collection of urine and feces was conducted between d 11 and 14. Enteric CH4 was measured between d 18 and 21 using 4 environmental chambers (2 animals fed the same diet per chamber). Methane emissions per kilogram of DM intake (DMI) and as percent of GE intake (GEI) among heifers fed WDDGS (23.9 g/kg DMI and 7.3% of GEI) and the control (25.3 g/kg DMI and 7.8% of GEI) were similar (P = 0.21 and P = 0.19) whereas heifers fed CDDGS (21.5 g/kg DMI and 6.6% of GEI) and WDDGS+oil (21.1 g/kg DMI and 6.3% of GEI) produced less (P < 0.05) CH4. Total N excretion (g/d) differed (P < 0.001) among treatments with WDDGS resulting in the greatest total N excretion (303 g/d) followed by WDDGS+oil (259 g/d), CDDGS (206 g/d), and the control diet (170 g/d), respectively. Compared with the control diet, heifers offered WDDGS, CDDGS, and WDDGS+oil excreted less fecal N (P < 0.001) but more (P < 0.001) urinary N. Results suggest that high-fat CDDGS or WDDGS+oil can mitigate enteric

  8. Mesoscale modeling of grain fracturing in high porosity rocks using the strong discontinuity approach

    NASA Astrophysics Data System (ADS)

    Tjioe, M.; Choo, J.; Borja, R. I.

    2013-12-01

    In previous studies, it has been found that two dominant micro-mechanisms play important roles in the deformation of high-porosity rocks. They are grain fracturing and crystal plasticity. Grain fracturing is a phenomenon where larger grains cleave to their smaller constituents as they respond to the stress concentration exerted on them close to the open pore spaces. Specimen-scale modeling cannot reflect such mechanism so our investigation is carried out in the next smaller scale, namely the mesoscopic scale. We model a solid matrix microstructure using finite element in which displacement discontinuity is introduced in each element where the slip condition has been exceeded. Such discontinuity is termed strong discontinuity and is characterized by zero band thickness and localized strain in the band that reaches infinity. For grains under compression, this slip condition is the cohesive-frictional law governing the behavior on the surface of discontinuity. The strong discontinuity in the grain scale is modeled via an Assumed Enhanced Strain (AES) method formulated within the context of nonlinear finite elements. Through this method, we can model grain-splitting as well as halos of cataclastic damage that are usually observed before a macropore collapses. The overall stress-strain curve and plastic slip of the mesoscopic element are then obtained and comparison to the crystal plasticity behavior is made to show the differences between the two mechanisms. We demonstrate that the incorporation of grain-fracturing and crystal plasticity can shed light onto the pore-scale deformation of high-porosity rocks.

  9. Modeling grain size variations of aeolian gypsum deposits at White Sands, New Mexico, using AVIRIS imagery

    USGS Publications Warehouse

    Ghrefat, H.A.; Goodell, P.C.; Hubbard, B.E.; Langford, R.P.; Aldouri, R.E.

    2007-01-01

    also show that there are no significant differences between modeled and laboratory-measured grain size values. Hyperspectral grain size modeling can help to determine dynamic processes shaping the formation of the dunes such as wind directions, and the relative strengths of winds through time. This has implications for studying such processes on other planetary landforms that have mineralogy with unique absorption bands in VNIR-SWIR hyperspectral data. ?? 2006 Elsevier B.V. All rights reserved.

  10. Modeling of grain growth behavior of S34MnV steel at elevated temperatures

    NASA Astrophysics Data System (ADS)

    Sun, Mingyue; Xu, Bin; Li, Dianzhong; Li, Yiyi

    2013-05-01

    S34MnV steel is widely used as a fundamental material in manufacturing crankshaft in diesel engine. However, due to amount of addition of Manganese element in the steel, coarse grain and mixed grain are commonly observed after long time heating during the forging passes in industrial practice, which may seriously reduce the impact toughness of the material. In current study, based on the observed microstructure of S34MnV steel at different temperatures and heating times, an empirical model has been established which reflects the relationship between the final grain size and the initial grain size, as well as heating temperature and holding time. This model has been validated by a scaled sample, and we further represented a successful industrial application of this model to simulate the grain size distribution and evolution during a large crankthrow heating and forging process, which evidences its practical and promising perspective of our model with an aim of widely promoting the mechanical properties heavy marine components.

  11. Grain sorting in the morphological active layer of a braided river physical model

    NASA Astrophysics Data System (ADS)

    Leduc, P.; Ashmore, P.; Gardner, J. T.

    2015-07-01

    A physical scale model of a gravel-bed braided river was used to measure vertical grain size sorting in the morphological active layer aggregated over the width of the river. This vertical sorting is important for analyzing braided river sedimentology, for numerical modeling of braided river morpho-dynamics and for measuring and predicting bed load transport rate. We define the morphological active layer as the bed material between the maximum and minimum bed elevations at a point over extended time periods sufficient for braiding processes to re-work the river bed. The vertical extent of the active layer was measured using 40 hourly high-resolution DEMs of the model river bed. An image texture algorithm was used to map bed material grain size of each DEM. Analysis of the 40 DEMs and texture maps provides data on the geometry of the morphological active layer and variation in grain size in three-dimensions. Normalizing active layer thickness and dividing into 10 sub-layers we show that all grain sizes occur with almost equal frequency in all sub-layers. Occurrence of patches and strings of coarser (or finer) material relates to preservation of particular morpho-textural features within the active layer. For numerical modeling and bed load prediction a morphological active layer that is fully mixed with respect to grain size is a reliable approximation.

  12. Evaluating a wheat grazing model for managing wheat grain and beef production

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Model evaluation and validation are prerequisite to its successful application. The objective of this paper is to evaluate the ability of the newly developed wheat grazing model to predict fall-winter forage and grain yields of winter wheat (Triticum aestivum L.) as well as daily weight gains per st...

  13. Description of the FORTRAN implementation of the spring small grains planting date distribution model

    NASA Technical Reports Server (NTRS)

    Artley, J. A. (Principal Investigator)

    1981-01-01

    The Hodges-Artley spring small grains planting date distribution model was coded in FORTRAN. The PLDRVR program, which implements the model, is described and a copy of the code is provided. The purpose, calling procedure, local variables, and input/output devices for each subroutine are explained to supplement the user's guide.

  14. Strain mapping in nanocrystalline grains simulated by phase field crystal model

    NASA Astrophysics Data System (ADS)

    Guo, Yaolin; Wang, Jincheng; Wang, Zhijun; Li, Junjie; Tang, Sai; Liu, Feng; Zhou, Yaohe

    2015-03-01

    In recent years, the phase field crystal (PFC) model has been confirmed as a good candidate to describe grain boundary (GB) structures and their nearby atomic arrangement. To further understand the mechanical behaviours of nanocrystalline materials, strain fields near GBs need to be quantitatively characterized. Using the strain mapping technique of geometric phase approach (GPA), we have conducted strain mapping across the GBs in nanocrystalline grains simulated by the PFC model. The results demonstrate that the application of GPA in strain mapping of low and high angles GBs as well as polycrystalline grains simulated by the PFC model is very successful. The results also show that the strain field around the dislocation in a very low angle GB is quantitatively consistent with the anisotropic elastic theory of dislocations. Moreover, the difference between low angle GBs and high angle GBs is revealed by the strain analysis in terms of the strain contour shape and the structural GB width.

  15. Studying the Enhanced Ductility of Bimodal Nanocrystalline Copper Using a Coarse-Grained Model

    NASA Astrophysics Data System (ADS)

    Gao, Guo-Jie Jason; Wang, Yun-Jiang; Ogata, Shigenobu

    Viewing a bimodal configuration of nanocrystalline copper as composed of soft grains containing stiff cores, we proposed a coarse-grained model with systematically tunable stiffness of grains to study the enhanced ductility of bimodal nanocrystalline copper [Y. Wang, M. Chen, F. Zhou, and E. Ma, Nature 419 (2002) 912]. Using molecular dynamics simulations, we shear our model quasistatically. Our results not only qualitatively confirms that a bimodal configuration could behave more ductile than a monomodal one but also predicts there exists a range of ratio of soft/stiff domains that best minimizes shear localization. Moreover, our model indicates that a bimodal configuration could sometimes exacerbate shear localization and therefore jeopardize ductility if the ratio of soft/stiff domains is not properly chosen. This may explain why some experimental results are hard to be reproduced.

  16. NEAMS FPL M2 Milestone Report: Development of a UO₂ Grain Size Model using Multicale Modeling and Simulation

    SciTech Connect

    Michael R Tonks; Yongfeng Zhang; Xianming Bai

    2014-06-01

    This report summarizes development work funded by the Nuclear Energy Advanced Modeling Simulation program's Fuels Product Line (FPL) to develop a mechanistic model for the average grain size in UO₂ fuel. The model is developed using a multiscale modeling and simulation approach involving atomistic simulations, as well as mesoscale simulations using INL's MARMOT code.

  17. Movement and Orientation Decision Modeling of Rhyzopertha dominica (Coleoptera: Bostrichidae) in the Grain Mass.

    PubMed

    Cordeiro, Erick M G; Campbell, James F; Phillips, Thomas W

    2016-04-01

    Grain stored in bins is initially a relatively homogenous resource patch for stored-product insects, but over time, spatial pattern in insect distribution can form, due in part to insect movement patterns. However, the factors that influence stored-product insect movement patterns in grain are not well-understood. This research focused on the movement of the lesser grain borer, Rhyzopertha dominica (F.), within a simulated wheat grain mass (vertical monolayer of wheat) and the identification of factors that contribute to overall and upward movement (age since adult emergence from an infested kernel [1, 7, and 14 d], sex, strain, and different levels of environment quality). We also used the model selection approach to select the most relevant factors and determine the relationships among them. Three-week-old adults tended to stay closer to the surface compared with 1- or 2-wk-old insects. Also, females tended to be more active and to explore a larger area compared with males. Explored area and daily displacement were also significantly strain-dependent, and increasing grain infestation level decreased daily displacement and explored area. Variation in movement pattern is likely to influence the formation of spatial pattern and affect probability to disperse. Understanding movement behavior within a grain bin is crucial to designing better strategies to implement and interpret monitoring programs and to target control tactics. PMID:26837621

  18. A transferable coarse-grained model for hydrogen-bonding liquids.

    PubMed

    Golubkov, Pavel A; Wu, Johnny C; Ren, Pengyu

    2008-04-21

    We present here a recent development of a generalized coarse-grained model for use in molecular simulations. In this model, interactions between coarse-grained particles consist of both van der Waals and explicit electrostatic components. As a result, the coarse-grained model offers the transferability that is lacked by most current effective-potential based approaches. The previous center-of-mass framework (P. A. Golubkov and P. Ren, J. Chem. Phys., 2006, 125, 64103) is generalized here to include arbitrary off-center interaction sites for both Gay-Berne and multipoles. The new model has been applied to molecular dynamic simulations of neat methanol liquid. By placing a single point multipole at the oxygen atom rather than at the center of mass of methanol, there is a significant improvement in the ability to capture hydrogen-bonding. The critical issue of transferability of the coarse-grained model is verified on methanol-water mixtures, using parameters derived from neat liquids without any modification. The mixture density and internal energy from coarse-grained molecular dynamics simulations show good agreement with experimental measurements, on a par with what has been obtained from more detailed atomic models. By mapping the dynamics trajectory from the coarse-grained simulation into the all-atom counterpart, we are able to investigate atomic-level structure and interaction. Atomic radial distribution functions of neat methanol, neat water and mixtures compare favorably to experimental measurements. Furthermore, hydrogen-bonded 6- and 7-molecule chains of water and methanol observed in the mixture are in agreement with previous atomic simulations. PMID:18688358

  19. Observation and modeling of polycrystalline grain formation in Ge2Sb2Te5

    NASA Astrophysics Data System (ADS)

    Burr, Geoffrey W.; Tchoulfian, Pierre; Topuria, Teya; Nyffeler, Clemens; Virwani, Kumar; Padilla, Alvaro; Shelby, Robert M.; Eskandari, Mona; Jackson, Bryan; Lee, Bong-Sub

    2012-05-01

    The relationship between the polycrystalline nature of phase change materials (such as Ge2Sb2Te5) and the intermediate resistance states of phase change memory (PCM) devices has not been widely studied. A full understanding of such states will require knowledge of how polycrystalline grains form, how they interact with each other at various temperatures, and how the differing electrical (and thermal) characteristics within the grains and at their boundaries combine through percolation to produce the externally observed electrical (and thermal) characteristics of a PCM device. We address the first of these tasks (and introduce a vehicle for the second) by studying the formation of fcc polycrystalline grains from the as-deposited amorphous state in undoped Ge2Sb2Te5. We perform ex situ transmission electron microscopy membrane experiments and then match these observations against numerical simulation. Ramped-anneal experiments show that the temperature ramp-rate strongly influences the median grain size. By truncating such ramped-anneal experiments at various peak temperatures, we convincingly demonstrate that the temperature range over which these grains are established is quite narrow. Subsequent annealing at elevated temperature appears to change these established distributions of grain sizes only slightly. Our numerical simulator—which models nuclei formation through classical nucleation theory and then tracks the subsequent time- and temperature-dependent growth of these grains—can match these experimental observations of initial grain distributions and crystallization temperature both qualitatively and quantitatively. These simulations show that the particular narrow temperature range over which crystallization occurs shifts as a function of temperature ramp-rate, which allows us to quantify the lower portions of the time-temperature-transformation map for Ge2Sb2Te5. Future experiments and extensions of the simulator to investigate temperature

  20. Prediction models for transfer of arsenic from soil to corn grain (Zea mays L.).

    PubMed

    Yang, Hua; Li, Zhaojun; Long, Jian; Liang, Yongchao; Xue, Jianming; Davis, Murray; He, Wenxiang

    2016-04-01

    In this study, the transfer of arsenic (As) from soil to corn grain was investigated in 18 soils collected from throughout China. The soils were treated with three concentrations of As and the transfer characteristics were investigated in the corn grain cultivar Zhengdan 958 in a greenhouse experiment. Through stepwise multiple-linear regression analysis, prediction models were developed combining the As bioconcentration factor (BCF) of Zhengdan 958 and soil pH, organic matter (OM) content, and cation exchange capacity (CEC). The possibility of applying the Zhengdan 958 model to other cultivars was tested through a cross-cultivar extrapolation approach. The results showed that the As concentration in corn grain was positively correlated with soil pH. When the prediction model was applied to non-model cultivars, the ratio ranges between the predicted and measured BCF values were within a twofold interval between predicted and measured values. The ratios were close to a 1:1 relationship between predicted and measured values. It was also found that the prediction model (Log [BCF]=0.064 pH-2.297) could effectively reduce the measured BCF variability for all non-model corn cultivars. The novel model is firstly developed for As concentration in crop grain from soil, which will be very useful for understanding the As risk in soil environment. PMID:26611632

  1. A Grain Boundary Fracture Model for Predicting Dynamic Embrittlement and Oxidation-Induced Cracking in Superalloys

    NASA Astrophysics Data System (ADS)

    Chan, Kwai S.

    2015-06-01

    Nickel-based superalloys are sometimes susceptible to oxygen embrittlement in the form of dynamic embrittlement or oxidation-induced grain boundary cracking during services at elevated temperatures. Dynamic embrittlement is a fracture process that involves the ingress and diffusion of atomic oxygen to induce time-dependent decohesion of grain boundaries. A related fracture process, also a time-dependent process, is stress-accelerated grain boundary oxidation and oxide-induced cracking along grain boundaries. In this paper, a micromechanical model is developed to treat both dynamic embrittlement and oxidation-induced crack growth in Ni-based superalloys. The model is utilized to assess: (1) the conditions where dynamic embrittlement are dominant, (2) the conditions where oxidation-induced crack growth are dominant, and (3) the role of oxidation in suppressing dynamic embrittlement in Ni-based superalloys. For illustration, the grain boundary fracture model is applied to predict the onset of dynamic embrittlement and oxidation-induced crack growth in superalloys such as IN 718.

  2. Effective rates from thermodynamically consistent coarse-graining of models for molecular motors with probe particles

    NASA Astrophysics Data System (ADS)

    Zimmermann, Eva; Seifert, Udo

    2015-02-01

    Many single-molecule experiments for molecular motors comprise not only the motor but also large probe particles coupled to it. The theoretical analysis of these assays, however, often takes into account only the degrees of freedom representing the motor. We present a coarse-graining method that maps a model comprising two coupled degrees of freedom which represent motor and probe particle to such an effective one-particle model by eliminating the dynamics of the probe particle in a thermodynamically and dynamically consistent way. The coarse-grained rates obey a local detailed balance condition and reproduce the net currents. Moreover, the average entropy production as well as the thermodynamic efficiency is invariant under this coarse-graining procedure. Our analysis reveals that only by assuming unrealistically fast probe particles, the coarse-grained transition rates coincide with the transition rates of the traditionally used one-particle motor models. Additionally, we find that for multicyclic motors the stall force can depend on the probe size. We apply this coarse-graining method to specific case studies of the F1-ATPase and the kinesin motor.

  3. A model for estimating the hydraulic conductivity of granular material based on grain shape, grain size, and porosity

    SciTech Connect

    Sperry, J.M.; Peirce, J.J.

    1995-11-01

    Particle shape is an important parameter in numerous civil, environmental, and petroleum engineering applications. In ground-water flow, the shape of individual particles comprising the soil affects the soil`s pore size distribution and, hence, the important flow characteristics such as hydraulic conductivity and headloss. A model for delineating the relative importance of particle size, particle shape, and porosity, (and their interactions), in explaining the variability of hydraulic conductivity of a granular porous medium is developed and tested. Three types of porous media are considered in this work: spherical glass beads; granular sand; and irregularly shaped, shredded glass particles. A reliable method for quantifying the three-dimensional shape and packing of large samples of irregular particles based on their angle of repose is presented. The results of column experiments indicate that in the size range examined (i.e., 149 {micro}m to 2,380 {micro}m), the single most important predictor of hydraulic conductivity is seen to be particle size, explaining 69% of the variability. Porous media comprising irregular particles exhibit lower hydraulic conductivity only for the larger (707 to 841 {micro}m) particles. For the smaller (149 to 177 {micro}m) particles, particle shape has no observable influence on hydraulic conductivity. The results of the regression analysis reveal the importance off the interaction between particle size and porosity, indicating that similar pore configurations for a given type of particle are not achieved at different sizes. This empirical model seems to provide better estimates of the hydraulic conductivity of granular porous media comprising irregular particles than selected models based solely on grain size, including Hazen, Kozeny-Carman, and more recently Alyamani and Sen.

  4. Numerical modelling and in-situ radiographic study of the grain nucleation and growth of inoculated aluminum alloys

    NASA Astrophysics Data System (ADS)

    Li, Yanjun; Xu, Yijiang; Du, Qiang; Arnberg, Lars; Mathiesen, Ragnvald

    2015-06-01

    To precisely predict the grain size of inoculated aluminium alloy castings has been a big challenge for the researchers in the field of solidification and casting. Up to date, most of grain size prediction models are based on the Free Growth Model, in which the nucleation process is stopped by recalescence. In a previous work [1], we have proposed a new grain size prediction model applicable for solidification of castings without recalescence. In the present work, an in-situ X-ray radiographic study on the grain nucleation and grain growth of inoculated Al-Cu alloys during isothermal melt solidification has been carried out, where the effect of melt convection is minimized. The influences of inoculant particles and cooling rate on the nucleation rate, grain growth rate and final grain size have been quantitatively studied. A comparison between the prediction results and the experimental results is presented.

  5. A new constitutive model for nitrogen austenitic stainless steel

    NASA Astrophysics Data System (ADS)

    Fréchard, S.; Lichtenberger, A.; Rondot, F.; Faderl, N.; Redjaïmia, A.; Adoum, M.

    2003-09-01

    Quasi-static, quasi-dynamic and dynamic compression tests have been performed on a nitrogen alloyed austenitic stainless steel. For all strain rates, a high strain hardening rate and a good ductility have been achieved. In addition, this steel owns a great strain rate sensitivity. The temperature sensitivity bas been determined between 20°C and 400°C. Microstructural analysis has been performed after different loading conditions in relation to the behaviour of the material. Johnson-Cook and Zerilli-Armstrong models have been selected to fit the experimental data into constitutive equations. These models do not reproduce properly the behaviour of this type of steel over the complete range. A new constitutive model that fits very well all the experimental data at different strain, strain rate and temperature has been determined. The model is based on empirical considerations on the separated influence of the main parameters. Single Taylor tests have been realized to validate the models. Live observations of the specimen during impact have been achieved using a special CCD camera set-up. The overall profile at different times are compared to numerical predictions using LS-DYNA code.

  6. Robust biological nitrogen fixation in a model grass-bacterial association.

    PubMed

    Pankievicz, Vânia C S; do Amaral, Fernanda P; Santos, Karina F D N; Agtuca, Beverly; Xu, Youwen; Schueller, Michael J; Arisi, Ana Carolina M; Steffens, Maria B R; de Souza, Emanuel M; Pedrosa, Fábio O; Stacey, Gary; Ferrieri, Richard A

    2015-03-01

    Nitrogen-fixing rhizobacteria can promote plant growth; however, it is controversial whether biological nitrogen fixation (BNF) from associative interaction contributes to growth promotion. The roots of Setaria viridis, a model C4 grass, were effectively colonized by bacterial inoculants resulting in a significant enhancement of growth. Nitrogen-13 tracer studies provided direct evidence for tracer uptake by the host plant and incorporation into protein. Indeed, plants showed robust growth under nitrogen-limiting conditions when inoculated with an ammonium-excreting strain of Azospirillum brasilense. (11)C-labeling experiments showed that patterns in central carbon metabolism and resource allocation exhibited by nitrogen-starved plants were largely reversed by bacterial inoculation, such that they resembled plants grown under nitrogen-sufficient conditions. Adoption of S. viridis as a model should promote research into the mechanisms of associative nitrogen fixation with the ultimate goal of greater adoption of BNF for sustainable crop production. PMID:25645593

  7. Mathematical modeling of moisture extraction from rice grains

    NASA Astrophysics Data System (ADS)

    Fedorov, A. V.; Zhilin, A. A.

    2014-11-01

    The process of moisture extraction from unhusked Korean rice is modeled with the use of a diffusion model. The diffusion coefficient is determined, which makes it possible to reconstruct the dynamics of the moisture distribution in a cylindrical sack filled by rice. It is demonstrated that the results of calculations performed for different values of the initial humidity are in reasonable agreement with experimental data obtained in the case of drying of unhusked rice in an acousto-convective drier. Results testifying to significant intensification of acousto-convective drying as compared to natural drying are obtained.

  8. Two key processes in dust/gas chemical modelling: photoprocessing of grain mantles and explosive desorption.

    NASA Astrophysics Data System (ADS)

    Shalabiea, O. M.; Greenberg, J. M.

    1994-10-01

    Two models of the time dependent chemical evolution of stable dense and translucent clouds are presented: one for pure gas phase chemistry and the other in which solid grain chemistry is included along with the gas. Comparing the results using these two schemes for the theoretical abundances of certain key molecules shows that including the dust provides a significantly (often by orders of magnitude) better agreement with the observations than those derived by pure gas phase chemistry models. The initial atomic abundances are those given by observations and are not modified to suit the model. Moreover, the inclusion of grain chemistry appears to minimize the effects of uncertainties in some important gas phase reaction rates, which would otherwise strongly affect the results of pure gas phase models. The grain mantle composition and gas phase abundances have been investigated using a number of different physical assumptions for both dense and translucent cloud models, taking into consideration the accretion, photochemical processing and desorption mechanisms involving the dust grains. The use of triggered explosive desorption is critical to providing reasonable steady state abundances. The abundances of H_2_O, H_2_CO, CH_3_OH and NH_3_ have a particular relevance because they are more abundantly produced in dust than in the gas. The most abundant observed molecules in grain mantles are H_2_O and CO which, under irradiation by ultraviolet light, not only produce H_2_CO but the latter can in turn react with water ice producing CH_3_OH. The reversible transformation between formaldehyde and methanol in the dust affects their gas phase abundances in both translucent and dense clouds. Depth dependent calculations have been performed and it is found that the effects of solid state photochemical molecular production in the inner part of a dense cloud are much larger than in the outer part or in a translucent cloud. In addition to matching observed gas phase abundances

  9. Application of image texture analysis to grain sorting in a braided river physical model

    NASA Astrophysics Data System (ADS)

    Leduc, P.; Ashmore, P.; Gardner, T.

    2014-12-01

    Gravel braided rivers have complex lateral and vertical patterns of grain size sorting characterizing the river deposit and patchiness within the channel. Sorting has direct interactions with bed material transport processes for which it is important to know both the surface grain size relative to morphology and also the distribution of sizes in the morphological active layer involved in sediment transport over longer time periods. In the field, analysis of vertical sorting from direct sampling is either extremely laborious or requires long-term tracer studies of burial and mixing. We approached the problem from a new direction using a small-scale physical model of a braided channel to map bed elevation changes and grain size over time. The braided channel was developed at a slope of 1.5% and discharge of 2.1 l/s. The grain size distribution in the model is an approximately 1:30 scaled distribution of medium fluvial gravel with median size 1.3mm (D10 0.3 mm, D90 4mm). Vertical stereo images (with pixel resolution of approximately 1mm) of the dry bed were taken at one hour intervals over 40 hours of flume running time during which a large area of the river was re-worked. DEMs were derived photogrammetrically with mean elevation error of about 4mm. Surface grain size was mapped using a 7x7 pixel window and based on a calibrated relationship with the entropy values of the grey level co-occurrence matrix for the images. Consequently each pixel in the DEM also has an associated grain size. Over the 40 hour period the range of elevation and grain size variations over the river bed can be used to analyse the vertical particle-size sorting pattern within the morphological active layer (the layer between the maximum and minimum elevations at each point) and the presence of any vertical stratification in particle size. In braided channels with active bed scour and bar migration particle exchange occurs in a morphological active layer with thickness of the order of 10D90. The

  10. Insights into DNA-mediated interparticle interactions from a coarse-grained model.

    PubMed

    Ding, Yajun; Mittal, Jeetain

    2014-11-14

    DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system in metastable amorphous states. Therefore, it is vital to explore the molecular details of particle assembly processes in order to understand the underlying mechanisms. Molecular simulations based on coarse-grained models can provide a convenient route to explore these details. Most of the currently available coarse-grained models of DNA-functionalized particles ignore key chemical and structural details of DNA behavior. These models therefore are limited in scope for studying experimental phenomena. In this paper, we present a new coarse-grained model of DNA-functionalized particles which incorporates some of the desired features of DNA behavior. The coarse-grained DNA model used here provides explicit DNA representation (at the nucleotide level) and complementary interactions between Watson-Crick base pairs, which lead to the formation of single-stranded hairpin and double-stranded DNA. Aggregation between multiple complementary strands is also prevented in our model. We study interactions between two DNA-functionalized particles as a function of DNA grafting density, lengths of the hybridizing and non-hybridizing parts of DNA, and temperature. The calculated free energies as a function of pair distance between particles qualitatively resemble experimental measurements of DNA-mediated pair interactions. PMID:25399156

  11. Statistical model for grain boundary and grain volume oxidation kinetics in UO{sub 2} spent fuel

    SciTech Connect

    Stout, R.B.; Shaw, H.F.; Einziger, R.E.

    1989-09-01

    This paper addresses statistical characteristics for the simplest case of grain boundary/grain volume oxidation kinetics of UO{sub 2} to U{sub 3}O{sub 7} for a fragment of a spent fuel pellet. It also presents a limited discussion of future extensions to this simple case to represent the more complex cases of oxidation kinetics in spent fuels. 17 refs., 1 fig.

  12. Carbon and nitrogen dynamics in a soil profile: Model development

    NASA Astrophysics Data System (ADS)

    Batlle-Aguilar, Jordi; Brovelli, Alessandro; Barry, D. Andrew

    2010-05-01

    In order to meet demands for crops, pasture and firewood, the rate of land use change from forested to agricultural uses has steadily increased over several decades, resulting in an increased release of nutrients towards groundwater and surface water bodies. In parallel, the degradation of riparian zones has diminished their capacity to provide critical ecosystem functions, such as the ability to control and buffer nutrient cycles. In recent years, however, the key environmental importance of natural, healthy ecosystems has been progressively recognized and restoration of degraded lands towards their former natural state has become an area of active research worldwide. Land use changes and restoration practices are known to affect both soil nutrient dynamics and their transport to neighbouring areas. To this end, in order to interpret field experiments and elucidate the different mechanisms taking place, numerical tools are beneficial. Microbiological transformations of the soil organic matter, including decomposition and nutrient turnover are controlled to a large extent by soil water content, influenced in turn by climatic and environmental conditions such as precipitation and evapotranspiration. The work presented here is part of the Swiss RECORD project (http://www.cces.ethz.ch/projects/nature/Record), a large collaborative research effort undertaken to monitor the changes in ecosystem functioning in riparian areas undergoing restoration. In this context we have developed a numerical model to simulate carbon and nitrogen transport and turnover in a one-dimensional variably saturated soil profile. The model is based on the zero-dimensional mechanistic batch model of Porporato et al. (Adv. Water Res., 26: 45-58, 2003), but extends its capabilities to simulate (i) the transport of the mobile components towards deeper horizons, and (ii) the vertical evolution of the profile and the subsequent distribution of the organic matter. The soil is divided in four

  13. Systematic coarse graining flowing polymer melts: thermodynamically guided simulations and resulting constitutive model.

    PubMed

    Iig, Patrick

    2011-01-01

    Complex fluids, such as polymers, colloids, liquid-crystals etc., show intriguing viscoelastic properties, due to the complicated interplay between flow-induced structure formation and dynamical behavior. Starting from microscopic models of complex fluids, a systematic coarse-graining method is presented that allows us to derive closed-form and thermodynamically consistent constitutive equations for such fluids. Essential ingredients of the proposed approach are thermodynamically guided simulations within a consistent coarse-graining scheme. In addition to this new type of multiscale simulations, we reconstruct the building blocks that constitute the thermodynamically consistent coarse-grained model. We illustrate the method for low-molecular polymer melts, which are subject to different imposed flow fields like planar shear and different elongational flows. The constitutive equation for general flow conditions we obtain shows rheological behavior including shear thinning, normal stress differences, and elongational viscosities in good agreement with reference results. PMID:21678766

  14. Assessment of global nitrogen pollution in rivers using an integrated biogeochemical modeling framework.

    PubMed

    He, Bin; Kanae, Shinjiro; Oki, Taikan; Hirabayashi, Yukiko; Yamashiki, Yosuke; Takara, Kaoru

    2011-04-01

    This study has analyzed the global nitrogen loading of rivers resulting from atmospheric deposition, direct discharge, and nitrogenous compounds generated by residential, industrial, and agricultural sources. Fertilizer use, population distribution, land cover, and social census data were used in this study. A terrestrial nitrogen cycle model with a 24-h time step and 0.5° spatial resolution was developed to estimate nitrogen leaching from soil layers in farmlands, grasslands, and natural lands. The N-cycle in this model includes the major processes of nitrogen fixation, nitrification, denitrification, immobilization, mineralization, leaching, and nitrogen absorption by vegetation. The previously developed Total Runoff Integrating Pathways network was used to analyze nitrogen transport from natural and anthropogenic sources through river channels, as well as the collecting and routing of nitrogen to river mouths by runoff. Model performance was evaluated through nutrient data measured at 61 locations in several major world river basins. The dissolved inorganic nitrogen concentrations calculated by the model agreed well with the observed data and demonstrate the reliability of the proposed model. The results indicate that nitrogen loading in most global rivers is proportional to the size of the river basin. Reduced nitrate leaching was predicted for basins with low population density, such as those at high latitudes or in arid regions. Nitrate concentration becomes especially high in tropical humid river basins, densely populated basins, and basins with extensive agricultural activity. On a global scale, agriculture has a significant impact on the distribution of nitrogenous compound pollution. The map of nitrate distribution indicates that serious nitrogen pollution (nitrate concentration: 10-50 mg N/L) has occurred in areas with significant agricultural activities and small precipitation surpluses. Analysis of the model uncertainty also suggests that the nitrate

  15. Coarse grain modeling of imperfect networks and gels

    NASA Astrophysics Data System (ADS)

    Sliozberg, Yelena; Chantawansri, Tanya; Sirk, Timothy; Andzelm, Jan; Mrozek, Randy; Lenhart, Joseph

    2013-03-01

    There is a strong interest in chemically and physically cross-linked entangled polymer networks and gels due to their tailorability in respect to both mechanical and structural properties. Even so, these properties are sensitive to imperfections in the polymer networks, such as dangling ends and loops. Computational modeling is a viable tool to understand the effects of these imperfections on properties in a controlled environment, in which specific defects can be systematically created and varied. In this study, we have employed generic bead-spring models of flexible chains to study a chemically and physically cross-linked network. Our results will show the importance defects, such as dangling ends and loops, on the mechanical and structural properties of these networks. We will also discuss the effects of these defects on the time-dependent elastic modulus. The simulation results qualitatively agree with experimental results and the other theoretical predictions.

  16. Using simulation and budget models to scale-up nitrogen leaching from field to region in Canada.

    PubMed

    Huffman, E C; Yang, J Y; Gameda, S; De Jong, R

    2001-12-11

    Efforts are underway at Agriculture and Agri-Food Canada (AAFC) to develop an integrated, nationally applicable, socioeconomic/biophysical modeling capability in order to predict the environmental impacts of policy and program scenarios. This paper outlines our Decision Support System (DSS), which integrates the IROWCN (Indicator of the Risk of Water Contamination by Nitrogen) index with the agricultural policy model CRAM (Canadian Regional Agricultural Model) and presents an outline of our methodology to provide independent assessments of the IROWCN results through the use of nitrogen (N) simulation models in select, data-rich areas. Three field-level models--DSSAT, N_ABLE, and EPIC--were evaluated using local measured data. The results show that all three dynamic models can be used to simulate biomass, grain yield, and soil N dynamics at the field level; but the accuracy of the models differ, suggesting that models need to be calibrated using local measured data before they are used in Canada. Further simulation of IROWCN in a maize field using N_ABLE showed that soil-mineral N levels are highly affected by the amount of fertilizer N applied and the time of year, meaning that fertilizer and manure N applications and weather data are crucial for improving IROWCN. Methods of scaling-up simulated IROWCN from field-level to soil-landscape polygons and CRAM regions are discussed. PMID:12805754

  17. Gas and grain chemical composition in cold cores as predicted by the Nautilus 3-phase model

    NASA Astrophysics Data System (ADS)

    Ruaud, Maxime; Wakelam, Valentine; Hersant, Franck

    2016-04-01

    We present an extended version of the 2-phase gas-grain code NAUTILUS to the 3-phase modelling of gas and grain chemistry of cold cores. In this model, both the mantle and the surface are considered as chemically active. We also take into account the competition among reaction, diffusion and evaporation. The model predictions are confronted to ice observations in the envelope of low-mass and massive young stellar objects as well as toward background stars. Modelled gas-phase abundances are compared to species observed toward TMC-1 (CP) and L134N dark clouds. We find that our model successfully reproduces the observed ice species. It is found that the reaction-diffusion competition strongly enhances reactions with barriers and more specifically reactions with H2, which is abundant on grains. This finding highlights the importance to have a good approach to determine the abundance of H2 on grains. Consequently, it is found that the major N-bearing species on grains go from NH3 to N2 and HCN when the reaction-diffusion competition is accounted. In the gas-phase and before few 105 yrs, we find that the 3-phase model does not have a strong impact on the observed species compared to the 2-phase model. After this time, the computed abundances dramatically decrease due to the strong accretion on dust, which is not counterbalanced by the desorption less efficient than in the 2-phase model. This strongly constrains the chemical-age of cold cores to be of the order of few 105 yrs.

  18. Three-dimensional bonded-cell model for grain fragmentation

    NASA Astrophysics Data System (ADS)

    Cantor, D.; Azéma, E.; Sornay, P.; Radjai, F.

    2016-07-01

    We present a three-dimensional numerical method for the simulation of particle crushing in 3D. This model is capable of producing irregular angular fragments upon particle fragmentation while conserving the total volume. The particle is modeled as a cluster of rigid polyhedral cells generated by a Voronoi tessellation. The cells are bonded along their faces by a cohesive Tresca law with independent tensile and shear strengths and simulated by the contact dynamics method. Using this model, we analyze the mechanical response of a single particle subjected to diametral compression for varying number of cells, their degree of disorder, and intercell tensile and shear strength. In particular, we identify the functional dependence of particle strength on the intercell strengths. We find that two different regimes can be distinguished depending on whether intercell shear strength is below or above its tensile strength. In both regimes, we observe a power-law dependence of particle strength on both intercell strengths but with different exponents. The strong effect of intercell shear strength on the particle strength reflects an interlocking effect between cells. In fact, even at low tensile strength, the particle global strength can still considerably increase with intercell shear strength. We finally show that the Weibull statistics describes well the particle strength variability.

  19. Coarse-grained description of cosmic structure from Szekeres models

    NASA Astrophysics Data System (ADS)

    Sussman, Roberto A.; Delgado Gaspar, I.; Hidalgo, Juan Carlos

    2016-03-01

    We show that the full dynamical freedom of the well known Szekeres models allows for the description of elaborated 3-dimensional networks of cold dark matter structures (over-densities and/or density voids) undergoing ``pancake'' collapse. By reducing Einstein's field equations to a set of evolution equations, which themselves reduce in the linear limit to evolution equations for linear perturbations, we determine the dynamics of such structures, with the spatial comoving location of each structure uniquely specified by standard early Universe initial conditions. By means of a representative example we examine in detail the density contrast, the Hubble flow and peculiar velocities of structures that evolved, from linear initial data at the last scattering surface, to fully non-linear 10-20 Mpc scale configurations today. To motivate further research, we provide a qualitative discussion on the connection of Szekeres models with linear perturbations and the pancake collapse of the Zeldovich approximation. This type of structure modelling provides a coarse grained—but fully relativistic non-linear and non-perturbative —description of evolving large scale cosmic structures before their virialisation, and as such it has an enormous potential for applications in cosmological research.

  20. Meteorite nanoparticles as models for interstellar grains: synthesis and preliminary characterisation.

    PubMed

    Mautner, M N; Abdelsayed, V; El-Shall, M S; Thrower, J D; Green, S D; Collings, M P; McCoustra, M R S

    2006-01-01

    Dust particles and their interaction with gases play important roles in star formation and in solar nebulae. Appropriate model dust grains are needed for the laboratory simulation of gas-grain interactions. Nanoparticles formed from carbonaceous meteorites may be particularly suitable, as these particles are formed from materials that were formed originally from interstellar/nebula dust. Extending our previous studies with grounded meteorite powders, we demonstrate here the production of nanoparticles formed from meteorites using the laser desorption/controlled condensation method developed in our laboratory. The product nanoparticle aggregates have porous, web-like morphologies similar to interstellar dust grains, indicating that they can present large specific surface areas for gas/grain interactions. In this paper, we present polarisation modulation reflection-absorption infrared spectra (PM-RAIRS) of supported thin films and compare these spectra with the known silicate bands in the spectra of interstellar dust recorded during the ISO mission. We also report an ultrahigh vacuum (UHV) temperature programmed desorption (TPD) study of the adsorption of CO on the supported nanoparticle films. The latter allow us to estimate the CO binding energy on the meteorite nanoparticles as 13.5 +/- 3.0 kJ mol(-1), cf. a value of 9.8 +/- 0.2 kJ mol(-1) for CO binding to a water ice substrate. Such thermochemical data can be useful for computational modelling of gas-grain interactions under the diverse conditions in interstellar clouds and solar nebulae. PMID:17191444

  1. Fused coarse-grained model of aromatic ionic liquids and their behaviour at electrodes.

    PubMed

    Li, Bin; Ma, Ke; Wang, Yong-Lei; Turesson, Martin; Woodward, Clifford E; Forsman, Jan

    2016-03-01

    A fused coarse-grained model of aromatic ionic liquids 1-alkyl-3-methylimidazoliums tetrafluoroborate ([CnMIM(+)][BF4(-)]) has been constructed. Structural and dynamical properties calculated from our model are compared with experimental data as well as with corresponding results from simulations of other suggested models. Specifically, we adopt a fused-sphere coarse-grained model for cations and anions. This model is utilized to study structure and differential capacitance in models of flat and porous carbon electrodes. We find that the capacitance varies with pore size, in a manner that is related to the packing of ions inside the pore. For very narrow pores, diffusion is slow and the establishment of thermodynamic equilibrium may exceed the practical limits for our molecular dynamics simulations. PMID:26928079

  2. Numerical Modeling of Enhanced Nitrogen Dissolution During Gas Tungsten Arc Welding

    SciTech Connect

    Palmer, T A

    2001-08-17

    are filled with nitrogen gas, which has been rejected from the liquid iron. Outside the arc column, the nitrogen in solution in the iron is in equilibrium with diatomic nitrogen rather than monatomic nitrogen, which dominates the arc column. Models based on the role of the plasma phase in producing these enhanced nitrogen concentrations have also been developed. For example, Gedeon and Eaga have proposed that the diatomic gas introduced into the plasma phase in the arc column partially dissociates at a temperature higher than that at the sample surface. The monatomic species is then transported to the liquid metal surface, where it is absorbed at the temperature on the liquid metal surface. Mundra and DebRoy have used this same methodology to develop a semi-quantitative model to describe the temperature at which the diatomic gas dissociates in the plasma phase. In the two-temperature model, a hypothetical temperature, T{sub d}, equal to the temperature at which the equilibrium thermal dissociation of diatomic nitrogen produces the partial pressure of monatomic nitrogen in the plasma, is defined. This dissociation temperature is in a range of 100 to 300 K higher than the temperature at the metal surface, T{sub s}, and is a measure of the partial pressure of the atomic nitrogen in the plasma. This methodology provides an order-of-magnitude agreement between the calculated and experimental nitrogen concentrations but does not strictly provide a capability for predicting the nitrogen concentration. No quantitative means for predicting the nitrogen concentration in the weld metal currently exists. In developing a quantitative model, it must be recognized that nitrogen dissolution into the weld pool is intimately tied to several simultaneously occurring physical processes. These processes include the formation of various nitrogen species in the plasma phase above the weld pool, reactions at the interface between the plasma phase and the weld pool surface, and the transport

  3. Modeling nitrogen plasmas produced by intense electron beams

    NASA Astrophysics Data System (ADS)

    Angus, J. R.; Mosher, D.; Swanekamp, S. B.; Ottinger, P. F.; Schumer, J. W.; Hinshelwood, D. D.

    2016-05-01

    A new gas-chemistry model is presented to treat the breakdown of a nitrogen gas with pressures on the order of 1 Torr from intense electron beams with current densities on the order of 10 kA/cm2 and pulse durations on the order of 100 ns. For these parameter regimes, the gas transitions from a weakly ionized molecular state to a strongly ionized atomic state on the time scale of the beam pulse. The model is coupled to a 0D-circuit model using the rigid-beam approximation that can be driven by specifying the time and spatial profiles of the beam pulse. Simulation results are in good agreement with experimental measurements of the line-integrated electron density from experiments done using the Gamble II generator at the Naval Research Laboratory. It is found that the species are mostly in the ground and metastable states during the atomic phase, but that ionization proceeds predominantly through thermal ionization of optically allowed states with excitation energies close to the ionization limit.

  4. Soil Tillage Management Affects Maize Grain Yield by Regulating Spatial Distribution Coordination of Roots, Soil Moisture and Nitrogen Status.

    PubMed

    Wang, Xinbing; Zhou, Baoyuan; Sun, Xuefang; Yue, Yang; Ma, Wei; Zhao, Ming

    2015-01-01

    combination of deeper deployment of roots and resource (water and N) availability was realized where the soil was prone to leaching. The correlation between the depletion of resources and distribution of patchy roots endorsed the SS tillage practice. It resulted in significantly greater post-silking biomass and grain yield compared to the RT and NT treatments, for summer maize on the Huang-Huai-Hai plain. PMID:26098548

  5. Soil Tillage Management Affects Maize Grain Yield by Regulating Spatial Distribution Coordination of Roots, Soil Moisture and Nitrogen Status

    PubMed Central

    Wang, Xinbing; Zhou, Baoyuan; Sun, Xuefang; Yue, Yang; Ma, Wei; Zhao, Ming

    2015-01-01

    optimal combination of deeper deployment of roots and resource (water and N) availability was realized where the soil was prone to leaching. The correlation between the depletion of resources and distribution of patchy roots endorsed the SS tillage practice. It resulted in significantly greater post-silking biomass and grain yield compared to the RT and NT treatments, for summer maize on the Huang-Huai-Hai plain. PMID:26098548

  6. Vapor Pressure of Aqueous Solutions of Electrolytes Reproduced with Coarse-Grained Models without Electrostatics.

    PubMed

    Perez Sirkin, Yamila A; Factorovich, Matías H; Molinero, Valeria; Scherlis, Damian A

    2016-06-14

    The vapor pressure of water is a key property in a large class of applications from the design of membranes for fuel cells and separations to the prediction of the mixing state of atmospheric aerosols. Molecular simulations have been used to compute vapor pressures, and a few studies on liquid mixtures and solutions have been reported on the basis of the Gibbs Ensemble Monte Carlo method in combination with atomistic force fields. These simulations are costly, making them impractical for the prediction of the vapor pressure of complex materials. The goal of the present work is twofold: (1) to demonstrate the use of the grand canonical screening approach ( Factorovich , M. H. J. Chem. Phys. 2014 , 140 , 064111 ) to compute the vapor pressure of solutions and to extend the methodology for the treatment of systems without a liquid-vapor interface and (2) to investigate the ability of computationally efficient high-resolution coarse-grained models based on the mW monatomic water potential and ions described exclusively with short-range interactions to reproduce the relative vapor pressure of aqueous solutions. We find that coarse-grained models of LiCl and NaCl solutions faithfully reproduce the experimental relative pressures up to high salt concentrations, despite the inability of these models to predict cohesive energies of the solutions or the salts. A thermodynamic analysis reveals that the coarse-grained models achieve the experimental activity coefficients of water in solution through a compensation of severely underestimated hydration and vaporization free energies of the salts. Our results suggest that coarse-grained models developed to replicate the hydration structure and the effective ion-ion attraction in solution may lead to this compensation. Moreover, they suggest an avenue for the design of coarse-grained models that accurately reproduce the activity coefficients of solutions. PMID:27196963

  7. Box-modeling of the impacts of atmospheric nitrogen deposition and benthic remineralization on the nitrogen cycle of the eastern tropical South Pacific

    NASA Astrophysics Data System (ADS)

    Su, B.; Pahlow, M.; Oschlies, A.

    2015-09-01

    Both atmospheric deposition and benthic remineralization influence the marine nitrogen cycle, and hence ultimately also marine primary production. The biological and biogeochemical relations of the eastern tropical South Pacific (ETSP) to nitrogen deposition, benthic denitrification and phosphate regeneration are analysed in a prognostic box model of the oxygen, nitrogen and phosphorus cycles in the ETSP. In the model, atmospheric nitrogen deposition based on estimates for the years 2000-2009 is offset by half by reduced N2 fixation, with the other half transported out of the model domain. Both model- and data-based benthic denitrification are found to trigger nitrogen fixation, partly compensating for the NO3- loss. Since phosphate is the ultimate limiting nutrient in the model, enhanced sedimentary phosphate regeneration under suboxic conditions stimulates primary production and subsequent export production and NO3- loss in the oxygen minimum zone (OMZ). A sensitivity analysis of the local response to both atmospheric deposition and benthic remineralization indicates dominant stabilizing feedbacks in the ETSP, which tend to keep a balanced nitrogen inventory, i.e., nitrogen input by atmospheric deposition is counteracted by decreasing nitrogen fixation; NO3- loss via benthic denitrification is partly compensated by increased nitrogen fixation; enhanced nitrogen fixation stimulated by phosphate regeneration is partly removed by the stronger water-column denitrification. Even though the water column in our model domain acts as a NO3- source, the ETSP including benthic denitrification might become a NO3- sink.

  8. A simple, efficient polarizable coarse-grained water model for molecular dynamics simulations.

    PubMed

    Riniker, Sereina; van Gunsteren, Wilfred F

    2011-02-28

    The development of coarse-grained (CG) models that correctly represent the important features of compounds is essential to overcome the limitations in time scale and system size currently encountered in atomistic molecular dynamics simulations. Most approaches reported in the literature model one or several molecules into a single uncharged CG bead. For water, this implicit treatment of the electrostatic interactions, however, fails to mimic important properties, e.g., the dielectric screening. Therefore, a coarse-grained model for water is proposed which treats the electrostatic interactions between clusters of water molecules explicitly. Five water molecules are embedded in a spherical CG bead consisting of two oppositely charged particles which represent a dipole. The bond connecting the two particles in a bead is unconstrained, which makes the model polarizable. Experimental and all-atom simulated data of liquid water at room temperature are used for parametrization of the model. The experimental density and the relative static dielectric permittivity were chosen as primary target properties. The model properties are compared with those obtained from experiment, from clusters of simple-point-charge water molecules of appropriate size in the liquid phase, and for other CG water models if available. The comparison shows that not all atomistic properties can be reproduced by a CG model, so properties of key importance have to be selected when coarse graining is applied. Yet, the CG model reproduces the key characteristics of liquid water while being computationally 1-2 orders of magnitude more efficient than standard fine-grained atomistic water models. PMID:21361530

  9. A simple and transferable all-atom/coarse-grained hybrid model to study membrane processes.

    PubMed

    Genheden, Samuel; Essex, Jonathan W

    2015-10-13

    We present an efficient all-atom/coarse-grained hybrid model and apply it to membrane processes. This model is an extension of the all-atom/ELBA model applied previously to processes in water. Here, we improve the efficiency of the model by implementing a multiple-time step integrator that allows the atoms and the coarse-grained beads to be propagated at different timesteps. Furthermore, we fine-tune the interaction between the atoms and the coarse-grained beads by computing the potential of mean force of amino acid side chain analogs along the membrane normal and comparing to atomistic simulations. The model was independently validated on the calculation of small-molecule partition coefficients. Finally, we apply the model to membrane peptides. We studied the tilt angle of the Walp23 and Kalp23 helices in two different model membranes and the stability of the glycophorin A dimer. The model is efficient, accurate, and straightforward to use, as it does not require any extra interaction particles, layers of atomistic solvent molecules or tabulated potentials, thus offering a novel, simple approach to study membrane processes. PMID:26574264

  10. [Study on nitrogen cycling and transformations in a duckweed pond by means of modeling analysis].

    PubMed

    Peng, Jian-feng; Song, Yong-hui; Yuan, Peng; Wang, Bao-zhen

    2006-10-01

    Based on the simulated results from N cycling and transformation model of duckweed pond, the influences of different major transfer pathways on various nitrogen removal performances are investigated. The effects of seasonal variations of water conditions on nitrogen transformations are determined. The simulated results show that nitrification and denitrification were the major removal pathways for nitrogen in duckweed pond, and the removal contributions of organic nitrogen sedimentation and ammonia volatilization for total nitrogen removal were less than 2.1%. Furthermore, in duckweed pond, nitrification and denitrification decided the removal efficiencies of ammonia and NOx., respectively; both algae decaying and organic nitrogen ammonification controlled primarily the organic nitrogen removal performances; both organic nitrogen sedimentation and mineralization of sedimentary nitrogen determined the variations of sedimentary nitrogen. Duckweed pond with duckweed growing largely can increase sharply algae mortality and keep the low content of algae in effluent. Besides, through accelerating the nitrification and denitrification rate, duckweed can evidently improve the removal efficiencies of total nitrogen. PMID:17256592

  11. Modeling sustainable reuse of nitrogen-laden wastewater by poplar.

    PubMed

    Wang, Yusong; Licht, Louis; Just, Craig

    2016-06-01

    Numerical modeling was used to simulate the leaching of nitrogen (N) to groundwater as a consequence of irrigating food processing wastewater onto grass and poplar under various management scenarios. Under current management practices for a large food processor, a simulated annual N loading of 540 kg ha(-1) yielded 93 kg ha(-1) of N leaching for grass and no N leaching for poplar during the growing season. Increasing the annual growing season N loading to approximately 1,550 kg ha(-1) for poplar only, using "weekly", "daily" and "calculated" irrigation scenarios, yielded N leaching of 17 kg ha(-1), 6 kg ha(-1), and 4 kg ha(-1), respectively. Constraining the simulated irrigation schedule by the current onsite wastewater storage capacity of approximately 757 megaliters (Ml) yielded N leaching of 146 kg ha(-1) yr(-1) while storage capacity scenarios of 3,024 and 4,536 Ml yielded N leaching of 65 and 13 kg ha(-1) yr(-1), respectively, for a loading of 1,550 kg ha(-1) yr(-1). Further constraining the model by the current wastewater storage volume and the available land area (approximately 1,000 hectares) required a "diverse" irrigation schedule that was predicted to leach a weighted average of 13 kg-N ha(-1) yr(-1) when dosed with 1,063 kg-N ha(-1) yr(-1). PMID:26375195

  12. Grain boundaries

    SciTech Connect

    Balluffi, R.W.; Bristowe, P.D.

    1991-01-01

    The present document is a progress report describing the work accomplished to date during the second year of our four-year grant (February 15, 1990--February 14, 1994) to study grain boundaries. The research was focused on the following three major efforts: Study of the atomic structure of grain boundaries by means of x-ray diffraction, transmission electron microscopy and computer modeling; study of short-circuit diffusion along grain boundaries; and development of a Thin-film Deposition/Bonding Apparatus for the manufacture of high purity bicrystals.

  13. Predicting RNA 3D structure using a coarse-grain helix-centered model

    PubMed Central

    Kerpedjiev, Peter; Höner zu Siederdissen, Christian; Hofacker, Ivo L.

    2015-01-01

    A 3D model of RNA structure can provide information about its function and regulation that is not possible with just the sequence or secondary structure. Current models suffer from low accuracy and long running times and either neglect or presume knowledge of the long-range interactions which stabilize the tertiary structure. Our coarse-grained, helix-based, tertiary structure model operates with only a few degrees of freedom compared with all-atom models while preserving the ability to sample tertiary structures given a secondary structure. It strikes a balance between the precision of an all-atom tertiary structure model and the simplicity and effectiveness of a secondary structure representation. It provides a simplified tool for exploring global arrangements of helices and loops within RNA structures. We provide an example of a novel energy function relying only on the positions of stems and loops. We show that coupling our model to this energy function produces predictions as good as or better than the current state of the art tools. We propose that given the wide range of conformational space that needs to be explored, a coarse-grain approach can explore more conformations in less iterations than an all-atom model coupled to a fine-grain energy function. Finally, we emphasize the overarching theme of providing an ensemble of predicted structures, something which our tool excels at, rather than providing a handful of the lowest energy structures. PMID:25904133

  14. A Hybrid Approach for Highly Coarse-grained Lipid Bilayer Models

    PubMed Central

    Srivastava, Anand; Voth, Gregory A.

    2012-01-01

    We present a systematic methodology to develop highly coarse-grained (CG) lipid models for large scale bio-membrane simulations, in which we derive CG interactions using a powerful combination of the multiscale coarse-graining (MS-CG) method, and an analytical form of the CG potential to model interactions at short range. The resulting hybrid coarse-graining (HCG) methodology is used to develop a three-site solvent-free model for 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and a 1:1 mixture of 1,2-dioleoyl-sn-glycero-3-phospho-L-serine (DOPS) and DOPC. In addition, we developed a four-site model of DOPC, demonstrating the capability of the HCG methodology in designing model lipid systems of a desired resolution. We carried out microsecond-scale molecular dynamics (MD) simulations of large vesicles, highlighting the ability of the model to study systems at mesoscopic length and time scales. The models of DLPC, DOPC and DOPC-DOPS have elastic properties consistent with experiment and structural properties such as the radial distribution functions (RDF), bond and angle distributions, and the z-density distributions that compare well with reference all-atom systems. PMID:25100925

  15. Multiscale Simulations of Protein Landscapes: Using Coarse Grained Models as Reference Potentials to Full Explicit Models

    PubMed Central

    Messer, Benjamin M.; Roca, Maite; Chu, Zhen T.; Vicatos, Spyridon; Kilshtain, Alexandra Vardi; Warshel, Arieh

    2009-01-01

    Evaluating the free energy landscape of proteins and the corresponding functional aspects presents a major challenge for computer simulation approaches. This challenge is due to the complexity of the landscape and the enormous computer time needed for converging simulations. The use of simplified coarse grained (CG) folding models offers an effective way of sampling the landscape but such a treatment, however, may not give the correct description of the effect of the actual protein residues. A general way around this problem that has been put forward in our early work (Fan et al, Theor Chem Acc (1999) 103:77-80) uses the CG model as a reference potential for free energy calculations of different properties of the explicit model. This method is refined and extended here, focusing on improving the electrostatic treatment and on demonstrating key applications. This application includes: evaluation of changes of folding energy upon mutations, calculations of transition states binding free energies (which are crucial for rational enzyme design), evaluation of catalytic landscape and simulation of the time dependent responses to pH changes. Furthermore, the general potential of our approach in overcoming major challenges in studies of structure function correlation in proteins is discussed. PMID:20052756

  16. Systematic coarse-grained modeling of complexation between small interfering RNA and polycations

    NASA Astrophysics Data System (ADS)

    Wei, Zonghui; Luijten, Erik

    2015-12-01

    All-atom molecular dynamics simulations can provide insight into the properties of polymeric gene-delivery carriers by elucidating their interactions and detailed binding patterns with nucleic acids. However, to explore nanoparticle formation through complexation of these polymers and nucleic acids and study their behavior at experimentally relevant time and length scales, a reliable coarse-grained model is needed. Here, we systematically develop such a model for the complexation of small interfering RNA (siRNA) and grafted polyethyleneimine copolymers, a promising candidate for siRNA delivery. We compare the predictions of this model with all-atom simulations and demonstrate that it is capable of reproducing detailed binding patterns, charge characteristics, and water release kinetics. Since the coarse-grained model accelerates the simulations by one to two orders of magnitude, it will make it possible to quantitatively investigate nanoparticle formation involving multiple siRNA molecules and cationic copolymers.

  17. Moving beyond Watson-Crick models of coarse grained DNA dynamics

    NASA Astrophysics Data System (ADS)

    Linak, Margaret C.; Tourdot, Richard; Dorfman, Kevin D.

    2011-11-01

    DNA produces a wide range of structures in addition to the canonical B-form of double-stranded DNA. Some of these structures are stabilized by Hoogsteen bonds. We developed an experimentally parameterized, coarse-grained model that incorporates such bonds. The model reproduces many of the microscopic features of double-stranded DNA and captures the experimental melting curves for a number of short DNA hairpins, even when the open state forms complicated secondary structures. We demonstrate the utility of the model by simulating the folding of a thrombin aptamer, which contains G-quartets, and strand invasion during triplex formation. Our results highlight the importance of including Hoogsteen bonding in coarse-grained models of DNA.

  18. Capturing mechanical properties of biological cells using coarse-grained modeling

    NASA Astrophysics Data System (ADS)

    Mao, Wenbin; Chang, Monique; Alexeev, Alexander

    2013-11-01

    Understanding cell mechanics is important for a variety of biomedical applications. Our goal is to develop a coarse-grained computational model that can properly capture the micromechanics of biological cells. The coarse-grained cell model includes an elastic shell enclosing a cross-linked polymer network and a viscous fluid representing, respectively, cell membrane, cytoskeleton, and cytoplasm. We use this model to investigate the mechanical response of cells to external forces and compare the results with the experimental AFM measurements. We systematically vary the properties and structure of the internal polymer network and the outer membrane to assess their influence on the cell mechanical responses. This model not only reveals interesting insights into the cell mechanics, but also provides a promising tool for investigation of motile and multicellular systems. Acknowledge financial support from NSF under Award No. 0932510.

  19. Systematic coarse-grained modeling of complexation between small interfering RNA and polycations

    SciTech Connect

    Wei, Zonghui; Luijten, Erik

    2015-12-28

    All-atom molecular dynamics simulations can provide insight into the properties of polymeric gene-delivery carriers by elucidating their interactions and detailed binding patterns with nucleic acids. However, to explore nanoparticle formation through complexation of these polymers and nucleic acids and study their behavior at experimentally relevant time and length scales, a reliable coarse-grained model is needed. Here, we systematically develop such a model for the complexation of small interfering RNA (siRNA) and grafted polyethyleneimine copolymers, a promising candidate for siRNA delivery. We compare the predictions of this model with all-atom simulations and demonstrate that it is capable of reproducing detailed binding patterns, charge characteristics, and water release kinetics. Since the coarse-grained model accelerates the simulations by one to two orders of magnitude, it will make it possible to quantitatively investigate nanoparticle formation involving multiple siRNA molecules and cationic copolymers.

  20. Simulating Cellulose Structure, Properties, Thermodynamics, Synthesis, and Deconstruction with Atomistic and Coarse-Grain Models

    SciTech Connect

    Crowley, M. F.; Matthews, J.; Beckham, G.; Bomble, Y.; Hynninen, A. P.; Ciesielski, P. F.

    2012-01-01

    Cellulose is still a mysterious polymer in many ways: structure of microfibrils, thermodynamics of synthesis and degradation, and interactions with other plant cell wall components. Our aim is to uncover the details and mechanisms of cellulose digestion and synthesis. We report the details of the structure of cellulose 1-beta under several temperature conditions and report here the results of these studies and connections to experimental measurements and the measurement in-silico the free energy of decrystallization of several morphologies of cellulose. In spatially large modeling, we show the most recent work of mapping atomistic and coarse-grain models into tomographic images of cellulose and extreme coarse-grain modeling of interactions of large cellulase complexes with microfibrils. We discuss the difficulties of modeling cellulose and suggest future work both experimental and theoretical to increase our understanding of cellulose and our ability to use it as a raw material for fuels and materials.

  1. A Model for Predicting Grain Boundary Cracking in Polycrystalline Viscoplastic Materials Including Scale Effects

    SciTech Connect

    Allen, D.H.; Helms, K.L.E.; Hurtado, L.D.

    1999-04-06

    A model is developed herein for predicting the mechanical response of inelastic crystalline solids. Particular emphasis is given to the development of microstructural damage along grain boundaries, and the interaction of this damage with intragranular inelasticity caused by dislocation dissipation mechanisms. The model is developed within the concepts of continuum mechanics, with special emphasis on the development of internal boundaries in the continuum by utilizing a cohesive zone model based on fracture mechanics. In addition, the crystalline grains are assumed to be characterized by nonlinear viscoplastic mechanical material behavior in order to account for dislocation generation and migration. Due to the nonlinearities introduced by the crack growth and viscoplastic constitution, a numerical algorithm is utilized to solve representative problems. Implementation of the model to a finite element computational algorithm is therefore briefly described. Finally, sample calculations are presented for a polycrystalline titanium alloy with particular focus on effects of scale on the predicted response.

  2. Gene expression dynamics with stochastic bursts: Construction and exact results for a coarse-grained model

    NASA Astrophysics Data System (ADS)

    Lin, Yen Ting; Doering, Charles R.

    2016-02-01

    We present a theoretical framework to analyze the dynamics of gene expression with stochastic bursts. Beginning with an individual-based model which fully accounts for the messenger RNA (mRNA) and protein populations, we propose an expansion of the master equation for the joint process. The resulting coarse-grained model reduces the dimensionality of the system, describing only the protein population while fully accounting for the effects of discrete and fluctuating mRNA population. Closed form expressions for the stationary distribution of the protein population and mean first-passage times of the coarse-grained model are derived and large-scale Monte Carlo simulations show that the analysis accurately describes the individual-based process accounting for mRNA population, in contrast to the failure of commonly proposed diffusion-type models.

  3. Evolutionary models of the Earth with a grain size-dependent rheology

    NASA Astrophysics Data System (ADS)

    Rozel, Antoine; Golabek, Gregor; Tackley, Paul

    2015-04-01

    Thermodynamically consistent models of single phase grain size evolution have been proposed in the past years [Austin and Evans (2007), Ricard and Bercovici (2009), Rozel et al. (2011), Rozel (2012)]. Following the same physical approach, the mechanics of two-phase grain aggregates has been formulated [Bercovici and Ricard (2012a)]. Several non-linear mechanisms such as dynamic recrystallization or Zener pinning are now available in a single non-equilibrium formulation of grain size distributions evolution. The self-consistent generation of localized plate boundaries is predicted in [Bercovici and Ricard (2012b)] using this model, but it has not been tested in a dynamically consistent way. Our preliminary results have shown that out of equilibrium grain size dynamics leads to localization of deformation below the lithosphere rather than subduction initiation. Yet this result was obtained assuming indealized conditions. We study here, for the first time, the evolution of grain size in the mantle and lithosphere in evolutionary models, starting from a just-frozen magma ocean until the present day situation. Following complexities are considered in these models: melting, phase transitions, compressible convection, and different pressure-temperature-dependent composite rheologies in upper and lower mantles. We use a visco-plastic rheology in which the viscous strain rate is obtained by summation of dislocation and diffusion creep. Pressure and velocity fields are solved on a staggered grid using a SIMPLER-like method. Multigrid W-cycles and extra coarse-grid relaxations are employed to enhance the convergence of Stokes and continuity equations. The grain size is stored on a large number of tracers advected through the computational domain (a 2D spherical annulus), which prevent numerical diffusion and allows a high resolution. We also describe the physical formalism itself and derive a set of free parameters for the model. The results show that Normal growth, dynamic

  4. Food Prices and Climate Extremes: A Model of Global Grain Price Variability with Storage

    NASA Astrophysics Data System (ADS)

    Otto, C.; Schewe, J.; Frieler, K.

    2015-12-01

    Extreme climate events such as droughts, floods, or heat waves affect agricultural production in major cropping regions and therefore impact the world market prices of staple crops. In the last decade, crop prices exhibited two very prominent price peaks in 2007-2008 and 2010-2011, threatening food security especially for poorer countries that are net importers of grain. There is evidence that these spikes in grain prices were at least partly triggered by actual supply shortages and the expectation of bad harvests. However, the response of the market to supply shocks is nonlinear and depends on complex and interlinked processes such as warehousing, speculation, and trade policies. Quantifying the contributions of such different factors to short-term price variability remains difficult, not least because many existing models ignore the role of storage which becomes important on short timescales. This in turn impedes the assessment of future climate change impacts on food prices. Here, we present a simple model of annual world grain prices that integrates grain stocks into the supply and demand functions. This firstly allows us to model explicitly the effect of storage strategies on world market price, and thus, for the first time, to quantify the potential contribution of trade policies to price variability in a simple global framework. Driven only by reported production and by long--term demand trends of the past ca. 40 years, the model reproduces observed variations in both the global storage volume and price of wheat. We demonstrate how recent price peaks can be reproduced by accounting for documented changes in storage strategies and trade policies, contrasting and complementing previous explanations based on different mechanisms such as speculation. Secondly, we show how the integration of storage allows long-term projections of grain price variability under climate change, based on existing crop yield scenarios.

  5. Improved Coarse-Grained Modeling of Cholesterol-Containing Lipid Bilayers

    PubMed Central

    2015-01-01

    Cholesterol trafficking, which is an essential function in mammalian cells, is intimately connected to molecular-scale interactions through cholesterol modulation of membrane structure and dynamics and interaction with membrane receptors. Since these effects of cholesterol occur on micro- to millisecond time scales, it is essential to develop accurate coarse-grained simulation models that can reach these time scales. Cholesterol has been shown experimentally to thicken the membrane and increase phospholipid tail order between 0 and 40% cholesterol, above which these effects plateau or slightly decrease. Here, we showed that the published MARTINI coarse-grained force-field for phospholipid (POPC) and cholesterol fails to capture these effects. Using reference atomistic simulations, we systematically modified POPC and cholesterol bonded parameters in MARTINI to improve its performance. We showed that the corrections to pseudobond angles between glycerol and the lipid tails and around the oleoyl double bond particle (the “angle-corrected model”) slightly improves the agreement of MARTINI with experimentally measured thermal, elastic, and dynamic properties of POPC membranes. The angle-corrected model improves prediction of the thickening and ordering effects up to 40% cholesterol but overestimates these effects at higher cholesterol concentration. In accordance with prior work that showed the cholesterol rough face methyl groups are important for limiting cholesterol self-association, we revised the coarse-grained representation of these methyl groups to better match cholesterol-cholesterol radial distribution functions from atomistic simulations. In addition, by using a finer-grained representation of the branched cholesterol tail than MARTINI, we improved predictions of lipid tail order and bilayer thickness across a wide range of concentrations. Finally, transferability testing shows that a model incorporating our revised parameters into DOPC outperforms other

  6. a Nonequilibrium Plasmadynamics Model for Nitrogen/hydrogen Arcjets

    NASA Astrophysics Data System (ADS)

    Megli, Thomas W.

    Electrothermal arcjets offer significant cost advantage over conventional satellite propulsion systems. In these devices, the propellant is electrically heated, allowing for higher temperatures and specific impulse than chemical rockets. Despite the relative simplicity of the basic design, many complex physical processes are poorly understood. Less than 50% of the electrical power is converted to thrust kinetic power. A numerical model is developed to study arcjet plasma flowfields. The model employs a modified set of Navier-Stokes equations, which includes separate energy equations for the electrons and heavy species. A thermal nonequilibrium, chemical equilibrium model is first developed, and then generalized to chemical nonequilibrium. A seven -species plasma of molecules, atoms, and ions is assumed for a variable mixture ratio of nitrogen and hydrogen. This permits simulation of various propellants, including hydrogen, ammonia, and hydrazine. Equations for charge continuity and Ohm's Law are employed to predict the arc current distribution. A thermal model for the nozzle is also included. The combined features of thermal nonequilibrium, chemical nonequilibrium, and propellant flexibility distinguish this model from previous research efforts. Model calculations are presented for 1-2 kW-class arcjets operating with hydrogen and hydrazine propellants. Thermal equilibrium is predicted in the highly ionized arc core, while electron temperatures near the electrodes are an order of magnitude greater than heavy species temperatures. The thermal nonequilibrium enhances ionization and electrical conductivity, and thus governs the current attachment to the nozzle. A comparison of chemical equilibrium and nonequilibrium simulations indicates that ambipolar diffusion of electrons and ions also controls the current conduction. The model is compared with experimental measurements. Respective calculations for specific impulse and exhaust velocities are within approximately 5

  7. 2D models of gas flow and ice grain acceleration in Enceladus' vents using DSMC methods

    NASA Astrophysics Data System (ADS)

    Tucker, Orenthal J.; Combi, Michael R.; Tenishev, Valeriy M.

    2015-09-01

    The gas distribution of the Enceladus water vapor plume and the terminal speeds of ejected ice grains are physically linked to its subsurface fissures and vents. It is estimated that the gas exits the fissures with speeds of ∼300-1000 m/s, while the micron-sized grains are ejected with speeds comparable to the escape speed (Schmidt, J. et al. [2008]. Nature 451, 685-688). We investigated the effects of isolated axisymmetric vent geometries on subsurface gas distributions, and in turn, the effects of gas drag on grain acceleration. Subsurface gas flows were modeled using a collision-limiter Direct Simulation Monte Carlo (DSMC) technique in order to consider a broad range of flow regimes (Bird, G. [1994]. Molecular Gas Dynamics and the Direct Simulation of Gas Flows. Oxford University Press, Oxford; Titov, E.V. et al. [2008]. J. Propul. Power 24(2), 311-321). The resulting DSMC gas distributions were used to determine the drag force for the integration of ice grain trajectories in a test particle model. Simulations were performed for diffuse flows in wide channels (Reynolds number ∼10-250) and dense flows in narrow tubular channels (Reynolds number ∼106). We compared gas properties like bulk speed and temperature, and the terminal grain speeds obtained at the vent exit with inferred values for the plume from Cassini data. In the simulations of wide fissures with dimensions similar to that of the Tiger Stripes the resulting subsurface gas densities of ∼1014-1020 m-3 were not sufficient to accelerate even micron-sized ice grains to the Enceladus escape speed. In the simulations of narrow tubular vents with radii of ∼10 m, the much denser flows with number densities of 1021-1023 m-3 accelerated micron-sized grains to bulk gas speed of ∼600 m/s. Further investigations are required to understand the complex relationship between the vent geometry, gas source rate and the sizes and speeds of ejected grains.

  8. Only pick the right grains: Modelling the bias due to subjective grain-size interval selection for chronometric and fingerprinting approaches.

    NASA Astrophysics Data System (ADS)

    Dietze, Michael; Fuchs, Margret; Kreutzer, Sebastian

    2016-04-01

    Many modern approaches of radiometric dating or geochemical fingerprinting rely on sampling sedimentary deposits. A key assumption of most concepts is that the extracted grain-size fraction of the sampled sediment adequately represents the actual process to be dated or the source area to be fingerprinted. However, these assumptions are not always well constrained. Rather, they have to align with arbitrary, method-determined size intervals, such as "coarse grain" or "fine grain" with partly even different definitions. Such arbitrary intervals violate principal process-based concepts of sediment transport and can thus introduce significant bias to the analysis outcome (i.e., a deviation of the measured from the true value). We present a flexible numerical framework (numOlum) for the statistical programming language R that allows quantifying the bias due to any given analysis size interval for different types of sediment deposits. This framework is applied to synthetic samples from the realms of luminescence dating and geochemical fingerprinting, i.e. a virtual reworked loess section. We show independent validation data from artificially dosed and subsequently mixed grain-size proportions and we present a statistical approach (end-member modelling analysis, EMMA) that allows accounting for the effect of measuring the compound dosimetric history or geochemical composition of a sample. EMMA separates polymodal grain-size distributions into the underlying transport process-related distributions and their contribution to each sample. These underlying distributions can then be used to adjust grain-size preparation intervals to minimise the incorporation of "undesired" grain-size fractions.

  9. The ATAMM procedure model for concurrent processing of large grained control and signal processing algorithms

    NASA Technical Reports Server (NTRS)

    Stoughton, John W.; Mielke, Roland R.

    1988-01-01

    An overview is presented of a model for describing data and control flow associated with the execution of large-grained, decision-free algorithms in a special distributed computer environment. The ATAMM (Algorithm-To-Architecture Mapping Model) model provides a basis for relating an algorithm to its execution in a dataflow multicomputer environment. The ATAMM model features a marked graph Petri net description of the algorithm behavior with regard to both data and control flow. The model provides an analytical basis for calculating performance bounds on throughput characteristics which are demonstrated here.

  10. Interstellar grains

    NASA Technical Reports Server (NTRS)

    Snow, T. P.

    1986-01-01

    There are few aspects of interstellar grains that can be unambiguously defined. Very little can be said that is independent of models or presuppositions; hence issues are raised and questions categorized, rather than providing definitive answers. The questions are issues fall into three general areas; the general physical and chemical nature of the grains; the processes by which they are formed and destroyed; and future observational approaches.

  11. Genomic prediction models for grain yield of spring bread wheat in diverse agro-ecological zones

    PubMed Central

    Saint Pierre, C.; Burgueño, J.; Crossa, J.; Fuentes Dávila, G.; Figueroa López, P.; Solís Moya, E.; Ireta Moreno, J.; Hernández Muela, V. M.; Zamora Villa, V. M.; Vikram, P.; Mathews, K.; Sansaloni, C.; Sehgal, D.; Jarquin, D.; Wenzl, P.; Singh, Sukhwinder

    2016-01-01

    Genomic and pedigree predictions for grain yield and agronomic traits were carried out using high density molecular data on a set of 803 spring wheat lines that were evaluated in 5 sites characterized by several environmental co-variables. Seven statistical models were tested using two random cross-validations schemes. Two other prediction problems were studied, namely predicting the lines’ performance at one site with another (pairwise-site) and at untested sites (leave-one-site-out). Grain yield ranged from 3.7 to 9.0 t ha−1 across sites. The best predictability was observed when genotypic and pedigree data were included in the models and their interaction with sites and the environmental co-variables. The leave-one-site-out increased average prediction accuracy over pairwise-site for all the traits, specifically from 0.27 to 0.36 for grain yield. Days to anthesis, maturity, and plant height predictions had high heritability and gave the highest accuracy for prediction models. Genomic and pedigree models coupled with environmental co-variables gave high prediction accuracy due to high genetic correlation between sites. This study provides an example of model prediction considering climate data along-with genomic and pedigree information. Such comprehensive models can be used to achieve rapid enhancement of wheat yield enhancement in current and future climate change scenario. PMID:27311707

  12. On the representability problem and the physical meaning of coarse-grained models.

    PubMed

    Wagner, Jacob W; Dama, James F; Durumeric, Aleksander E P; Voth, Gregory A

    2016-07-28

    In coarse-grained (CG) models where certain fine-grained (FG, i.e., atomistic resolution) observables are not directly represented, one can nonetheless identify indirect the CG observables that capture the FG observable's dependence on CG coordinates. Often, in these cases it appears that a CG observable can be defined by analogy to an all-atom or FG observable, but the similarity is misleading and significantly undermines the interpretation of both bottom-up and top-down CG models. Such problems emerge especially clearly in the framework of the systematic bottom-up CG modeling, where a direct and transparent correspondence between FG and CG variables establishes precise conditions for consistency between CG observables and underlying FG models. Here we present and investigate these representability challenges and illustrate them via the bottom-up conceptual framework for several simple analytically tractable polymer models. The examples provide special focus on the observables of configurational internal energy, entropy, and pressure, which have been at the root of controversy in the CG literature, as well as discuss observables that would seem to be entirely missing in the CG representation but can nonetheless be correlated with CG behavior. Though we investigate these problems in the framework of systematic coarse-graining, the lessons apply to top-down CG modeling also, with crucial implications for simulation at constant pressure and surface tension and for the interpretations of structural and thermodynamic correlations for comparison to experiment. PMID:27475349

  13. Genomic prediction models for grain yield of spring bread wheat in diverse agro-ecological zones.

    PubMed

    Saint Pierre, C; Burgueño, J; Crossa, J; Fuentes Dávila, G; Figueroa López, P; Solís Moya, E; Ireta Moreno, J; Hernández Muela, V M; Zamora Villa, V M; Vikram, P; Mathews, K; Sansaloni, C; Sehgal, D; Jarquin, D; Wenzl, P; Singh, Sukhwinder

    2016-01-01

    Genomic and pedigree predictions for grain yield and agronomic traits were carried out using high density molecular data on a set of 803 spring wheat lines that were evaluated in 5 sites characterized by several environmental co-variables. Seven statistical models were tested using two random cross-validations schemes. Two other prediction problems were studied, namely predicting the lines' performance at one site with another (pairwise-site) and at untested sites (leave-one-site-out). Grain yield ranged from 3.7 to 9.0 t ha(-1) across sites. The best predictability was observed when genotypic and pedigree data were included in the models and their interaction with sites and the environmental co-variables. The leave-one-site-out increased average prediction accuracy over pairwise-site for all the traits, specifically from 0.27 to 0.36 for grain yield. Days to anthesis, maturity, and plant height predictions had high heritability and gave the highest accuracy for prediction models. Genomic and pedigree models coupled with environmental co-variables gave high prediction accuracy due to high genetic correlation between sites. This study provides an example of model prediction considering climate data along-with genomic and pedigree information. Such comprehensive models can be used to achieve rapid enhancement of wheat yield enhancement in current and future climate change scenario. PMID:27311707

  14. A Hybrid Method of Moment Equations and Rate Equations to Modeling Gas-Grain Chemistry

    NASA Astrophysics Data System (ADS)

    Pei, Y.; Herbst, E.

    2011-05-01

    Grain surfaces play a crucial role in catalyzing many important chemical reactions in the interstellar medium (ISM). The deterministic rate equation (RE) method has often been used to simulate the surface chemistry. But this method becomes inaccurate when the number of reacting particles per grain is typically less than one, which can occur in the ISM. In this condition, stochastic approaches such as the master equations are adopted. However, these methods have mostly been constrained to small chemical networks due to the large amounts of processor time and computer power required. In this study, we present a hybrid method consisting of the moment equation approximation to the stochastic master equation approach and deterministic rate equations to treat a gas-grain model of homogeneous cold cloud cores with time-independent physical conditions. In this model, we use the standard OSU gas phase network (version OSU2006V3) which involves 458 gas phase species and more than 4000 reactions, and treat it by deterministic rate equations. A medium-sized surface reaction network which consists of 21 species and 19 reactions accounts for the productions of stable molecules such as H_2O, CO, CO_2, H_2CO, CH_3OH, NH_3 and CH_4. These surface reactions are treated by a hybrid method of moment equations (Barzel & Biham 2007) and rate equations: when the abundance of a surface species is lower than a specific threshold, say one per grain, we use the ``stochastic" moment equations to simulate the evolution; when its abundance goes above this threshold, we use the rate equations. A continuity technique is utilized to secure a smooth transition between these two methods. We have run chemical simulations for a time up to 10^8 yr at three temperatures: 10 K, 15 K, and 20 K. The results will be compared with those generated from (1) a completely deterministic model that uses rate equations for both gas phase and grain surface chemistry, (2) the method of modified rate equations (Garrod

  15. Coarse-grained variables for particle-based models: diffusion maps and animal swarming simulations

    NASA Astrophysics Data System (ADS)

    Liu, Ping; Safford, Hannah R.; Couzin, Iain D.; Kevrekidis, Ioannis G.

    2014-12-01

    As microscopic (e.g. atomistic, stochastic, agent-based, particle-based) simulations become increasingly prevalent in the modeling of complex systems, so does the need to systematically coarse-grain the information they provide. Before even starting to formulate relevant coarse-grained equations, we need to determine the right macroscopic observables—the right variables in terms of which emergent behavior will be described. This paper illustrates the use of data mining (and, in particular, diffusion maps, a nonlinear manifold learning technique) in coarse-graining the dynamics of a particle-based model of animal swarming. Our computational data-driven coarse-graining approach extracts two coarse (collective) variables from the detailed particle-based simulations, and helps formulate a low-dimensional stochastic differential equation in terms of these two collective variables; this allows the efficient quantification of the interplay of "informed" and "naive" individuals in the collective swarm dynamics. We also present a brief exploration of swarm breakup and use data-mining in an attempt to identify useful predictors for it. In our discussion of the scope and limitations of the approach we focus on the key step of selecting an informative metric, allowing us to usefully compare different particle swarm configurations.

  16. Modeling Nucleation and Grain Growth in the Solar Nebula: Initial Progress Report

    NASA Technical Reports Server (NTRS)

    Nuth, Joseph A.; Paquette, J. A.; Ferguson, F. T.

    2010-01-01

    The primitive solar nebula was a violent and chaotic environment where high energy collisions, lightning, shocks and magnetic re-connection events rapidly vaporized some fraction of nebular dust, melted larger particles while leaving the largest grains virtually undisturbed. At the same time, some tiny grains containing very easily disturbed noble gas signatures (e.g., small, pre-solar graphite or SiC particles) never experienced this violence, yet can be found directly adjacent to much larger meteoritic components (chondrules or CAIs) that did. Additional components in the matrix of the most primitive carbonaceous chondrites and in some chondritic porous interplanetary dust particles include tiny nebular condensates, aggregates of condensates and partially annealed aggregates. Grains formed in violent transient events in the solar nebula did not come to equilibrium with their surroundings. To understand the formation and textures of these materials as well as their nebular abundances we must rely on Nucleation Theory and kinetic models of grain growth, coagulation and annealing. Such models have been very uncertain in the past: we will discuss the steps we are taking to increase their reliability.

  17. Coarse-grained cosmological perturbation theory: Stirring up the dust model

    NASA Astrophysics Data System (ADS)

    Uhlemann, Cora; Kopp, Michael

    2015-04-01

    We study the effect of coarse graining the dynamics of a pressureless self-gravitating fluid (coarse-grained dust) in the context of cosmological perturbation theory, in both the Eulerian and Lagrangian frameworks. We obtain recursion relations for the Eulerian perturbation kernels of the coarse-grained dust model by relating them to those of the standard pressureless fluid model. The effect of the coarse graining is illustrated by means of power and cross spectra for the density and velocity, which are computed up to one-loop order. In particular, the large-scale vorticity power spectrum that arises naturally from a mass-weighted velocity is derived from first principles. We find qualitatively good agreement for the magnitude, shape, and spectral index of the vorticity power spectrum with recent measurements from N -body simulations and results from the effective field theory of large-scale structure. To lay the ground for applications in the context of Lagrangian perturbation theory, we finally describe how the kernels obtained in Eulerian space can be mapped to Lagrangian ones.

  18. Computer Modeling of Transport of Oxidizing Species in Grain Boundaries during Zirconium Corrosion

    SciTech Connect

    Xian-Ming Bai; Yongfeng Zhang; Michael R. Tonks

    2014-06-01

    Zirconium (Zr) based alloys are widely used as the cladding materials in light-water reactors. The water-side corrosion of these alloys degrades their structural integrity and poses serious safety concerns. During the Zr corrosion process, a thin Zr oxide (ZrO2) layer forms on the alloy surface and serves as a barrier layer for further corrosion. The majority of the oxide has the monoclinic phase. At the transition region between the oxide and the metal, the oxide contains a thin layer of stabilized tetragonal phase. It is found that the texture of the tetragonal layer determines the protectiveness of the oxide for corrosion. The transport of oxidizing species, such as anion defects, cation defects, and electron through the tetragonal oxide layer could be the rate limiting step of the corrosion. The defect diffusion can be affected by the growing stresses and microstructures such as grain boundaries and dislocations. In this work molecular dynamics simulations are used to investigate the anion and cation diffusion in bulk and at grain boundaries in tetragonal ZrO2. The results show that defect diffusion at grain boundaries is complex and the behavior strongly depends on the grain boundary type. For most of the grain boundaries studied the defect diffusion are much slower than in the bulk, implying that grain boundaries may not be fast defect transport paths during corrosion. The connection between the modeling results and published experimental work will also be discussed. This work is funded by the Laboratory Directed Research and Development (LDRD) program at Idaho National Laboratory.

  19. Modelling nitrogen and carbon interactions in composting of animal manure in naturally aerated piles.

    PubMed

    Oudart, D; Robin, P; Paillat, J M; Paul, E

    2015-12-01

    Composting animal manure with natural aeration is a low-cost and low-energy process that can improve nitrogen recycling in millions of farms world-wide. Modelling can decrease the cost of choosing the best options for solid manure management in order to decrease the risk of loss of fertilizer value and ammonia emission. Semi-empirical models are suitable, considering the scarce data available in farm situations. Eleven static piles of pig or poultry manure were monitored to identify the main processes governing nitrogen transformations and losses. A new model was implemented to represent these processes in a pile considered as homogeneous. The model is based on four modules: biodegradation, nitrogen transformations and volatilization, thermal exchanges, and free air space evolution. When necessary, the parameters were calibrated with the data set. The results showed that microbial growth could reduce ammonia volatilization. Greatest nitrogen conservation is achieved when microbial growth was limited by nitrogen availability. PMID:26403389

  20. Models performance and robustness for simulating drainage and nitrate-nitrogen fluxes without recalibration

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Intensively grazed pastures generate nitrate-nitrogen (NO3-N) contaminated groundwater creating grave environmental concern. Computer models simulate and forecast appropriate agricultural practices to reduce environmental impact. Model validation is an essential process in evaluation and field appli...

  1. Global modeling of organic aerosol: the importance of reactive nitrogen

    NASA Astrophysics Data System (ADS)

    Pye, H. O. T.; Chan, A. W. H.; Barkley, M. P.; Seinfeld, J. H.

    2010-09-01

    Reactive nitrogen compounds, specifically NOx and NO3, likely influence global organic aerosol levels. To assess these interactions, GEOS-Chem, a chemical transport model, is updated to include improved biogenic emissions (following MEGAN v2.1/2.04), a new organic aerosol tracer lumping scheme, aerosol from nitrate radical (NO3) oxidation of isoprene, and NOx-dependent terpene aerosol yields. As a result of significant nighttime terpene emissions, fast reaction of monoterpenes with the nitrate radical, and relatively high aerosol yields from NO3 oxidation, biogenic hydrocarbon-NO3 reactions are expected to be a major contributor to surface level aerosol concentrations in anthropogenically influenced areas such as the United States. By including aerosol from nitrate radical oxidation in GEOS-Chem, terpene aerosol approximately doubles and isoprene aerosol is enhanced by 30 to 40% in the Southeast United States. In terms of the global budget of organic aerosol, however, aerosol from nitrate radical oxidation is somewhat minor (slightly more than 3 Tg/yr) due to the relatively high volatility of organic-NO3 oxidation products. Globally, 69 to 88 Tg/yr of organic aerosol is predicted to be produced annually, of which 14-15 Tg/yr is from oxidation of monoterpenes and sesquiterpenes and 8-9 Tg/yr from isoprene.

  2. Stress-dilatancy based modelling of granular materials and extensions to soils with crushable grains

    NASA Astrophysics Data System (ADS)

    Desimone, Antonio; Tamagnini, Claudio

    2005-01-01

    Stress-dilatancy relations have played a crucial role in the understanding of the mechanical behaviour of soils and in the development of realistic constitutive models for their response. Recent investigations on the mechanical behaviour of materials with crushable grains have called into question the validity of classical relations such as those used in critical state soil mechanics.In this paper, a method to construct thermodynamically consistent (isotropic, three-invariant) elasto-plastic models based on a given stress-dilatancy relation is discussed. Extensions to cover the case of granular materials with crushable grains are also presented, based on the interpretation of some classical model parameters (e.g. the stress ratio at critical state) as internal variables that evolve according to suitable hardening laws. Copyright

  3. Subsurface Gas Flow and Ice Grain Acceleration within Enceladus and Europa Fissures: 2D DSMC Models

    NASA Astrophysics Data System (ADS)

    Tucker, O. J.; Combi, M. R.; Tenishev, V.

    2014-12-01

    The ejection of material from geysers is a ubiquitous occurrence on outer solar system bodies. Water vapor plumes have been observed emanating from the southern hemispheres of Enceladus and Europa (Hansen et al. 2011, Roth et al. 2014), and N2plumes carrying ice and ark particles on Triton (Soderblom et al. 2009). The gas and ice grain distributions in the Enceladus plume depend on the subsurface gas properties and the geometry of the fissures e.g., (Schmidt et al. 2008, Ingersoll et al. 2010). Of course the fissures can have complex geometries due to tidal stresses, melting, freezing etc., but directly sampled and inferred gas and grain properties for the plume (source rate, bulk velocity, terminal grain velocity) can be used to provide a basis to constrain characteristic dimensions of vent width and depth. We used a 2-dimensional Direct Simulation Monte Carlo (DSMC) technique to model venting from both axi-symmetric canyons with widths ~2 km and narrow jets with widths ~15-40 m. For all of our vent geometries, considered the water vapor source rates (1027­ - 1028 s-1) and bulk gas velocities (~330 - 670 m/s) obtained at the surface were consistent with inferred values obtained by fits of the data for the plume densities (1026 - 1028 s-1, 250 - 1000 m/s) respectively. However, when using the resulting DSMC gas distribution for the canyon geometries to integrate the trajectories of ice grains we found it insufficient to accelerate submicron ice grains to Enceladus' escape speed. On the other hand, the gas distributions in the jet like vents accelerated grains > 10 μm significantly above Enceladus' escape speed. It has been suggested that micron-sized grains are ejected from the vents with speeds comparable to the Enceladus escape speed. Here we report on these results including comparisons to results obtained from 1D models as well as discuss the implications of our plume model results. We also show preliminary results for similar considerations applied to Europa

  4. Adaptive resolution simulation of polarizable supramolecular coarse-grained water models

    SciTech Connect

    Zavadlav, Julija; Praprotnik, Matej; Melo, Manuel N.; Marrink, Siewert J.

    2015-06-28

    Multiscale simulations methods, such as adaptive resolution scheme, are becoming increasingly popular due to their significant computational advantages with respect to conventional atomistic simulations. For these kind of simulations, it is essential to develop accurate multiscale water models that can be used to solvate biophysical systems of interest. Recently, a 4-to-1 mapping was used to couple the bundled-simple point charge water with the MARTINI model. Here, we extend the supramolecular mapping to coarse-grained models with explicit charges. In particular, the two tested models are the polarizable water and big multiple water models associated with the MARTINI force field. As corresponding coarse-grained representations consist of several interaction sites, we couple orientational degrees of freedom of the atomistic and coarse-grained representations via a harmonic energy penalty term. This additional energy term aligns the dipole moments of both representations. We test this coupling by studying the system under applied static external electric field. We show that our approach leads to the correct reproduction of the relevant structural and dynamical properties.

  5. Advanced modeling of nitrogen oxide emissions in circulating fluidized bed combustors: Parametric study of coal combustion and nitrogen compound chemistries

    SciTech Connect

    Kilpinen, P.; Kallio, S.; Hupa, M.

    1999-07-01

    This paper describes work-in-progress aimed at developing an emission model for circulating fluidized bed combustors using detailed homogeneous and heterogeneous chemical kinetics. The main emphasis is on nitrogen oxides (NO{sub x}, N{sub 2}O) but also unburned gases (CO, C{sub x}H{sub y}) and sulfur dioxide (SO{sub 2}) will be investigated in the long run. The hydrodynamics is described by a 1.5-dimensional model where the riser is divided into three regions: a dense bubbling bed at the bottom, a vigorously mixed splash zone, and a transport zone. The two latter zones are horizontally split into a core region and an annular region. The solids circulation rate is calculated from the known solids inventory and the pressure and mass balances over the entire circulation loop. The solids are divided into classes according to size and type or particle. The model assumes instantaneous fuel devolatilization at the bottom and an even distribution of volatiles in the suspension phase of the dense bed. For addition of secondary air, a complete penetration and an instantaneous mixing with the combustor gases in the core region is assumed. The temperature distribution is assumed to be known, and no energy balance is solved. A comprehensive kinetic scheme of about 300 elementary gas-phase reactions is used to describe the homogeneous oxidation of the volatiles including both hydrocarbon and volatile-nitrogen components (NH{sub 3}, HCN). Heterogeneous char combustion to CO and CO{sub 2}, and char-nitrogen conversion to NO, N{sub 2}O, and N{sub 2} are described by a single particle model that includes 15 reaction steps given in the form of 6 net reaction paths. In the paper, the model is briefly described. A special emphasis is put on the evaluation of chemistry submodels. Modeling results on nitrogen oxides' formation are compared with measured concentration profiles in a 12 MW CFBC riser from literature. The importance of accurate chemistry description on predictions is

  6. Denitrification, leaching, and river nitrogen export in the Community Earth System Model

    NASA Astrophysics Data System (ADS)

    Nevison, Cynthia; Hess, Peter; Riddick, Stuart; Ward, Dan

    2016-03-01

    River nitrogen export is simulated within the Community Earth System Model (CESM) by coupling nitrogen leaching and runoff fluxes from the Community Land Model (CLM) to the River Transport Model (RTM). The coupled CLM-RTM prognostically simulates the downstream impact of human N cycle perturbation on coastal areas. It also provides a framework for estimating denitrification fluxes of N2 and associated trace gases like N2O in soils and river sediments. An important limitation of the current model is that it only simulates dissolved inorganic nitrogen (DIN) river export, due to the lack of dissolved organic nitrogen (DON) and particulate nitrogen (PN) leaching fluxes in CLM. In addition, the partitioning of soil N loss in CLM between the primary loss pathways of denitrification and N leaching/runoff appears heavily skewed toward denitrification compared to other literature estimates, especially in nonagricultural regions, and also varies considerably among the four model configurations presented here. River N export is generally well predicted in the model configurations that include midlatitude crops, but tends to be underpredicted in rivers that are less perturbed by human agriculture. This is especially true in the tropics, where CLM likely underestimates leaching and runoff of all forms of nitrogen. River export of DIN is overpredicted in some relatively unperturbed Arctic rivers, which may result from excessive N inputs to those regions in CLM. Better representation of N loss in CLM can improve confidence in model results with respect to the core model objective of simulating nitrogen limitation of the carbon cycle.

  7. Quantifying depositional processes in sediment archives using end-member modelling of grain size data

    NASA Astrophysics Data System (ADS)

    Dietze, Elisabeth; Diekmann, Bernhard; Opitz, Stephan; Hartmann, Kai

    2013-04-01

    Key proxies in sedimentary archives typically are derived from detrital grain size distributions, precisely measured by particle size analysers with often more than 80 grain size classes. Although grain size distributions contain a lot of information on past depositional environments, research typically neglects the complete distribution and uses instead only integrated measures of moments (i.e. mean sand/silt/clay content, sorting, skewness, kurtosis). These are biased, when applied to multi-modal distributions. Such distributions indicate different sources and sorting by different transport processes. To decipher the genetic fingerprints of sources and transport processes, grain size distributions need to be unmixed. Principles of eigenspace analysis and several scaling procedures are integrated in an end-member modelling algorithm (EMMA), which aims to reduce redundancy in the large grain size datasets producing only limited numbers of meaningful end-member distributions related to sedimentary processes. Their contribution to each sample in space and time as well as associated uncertainties can be quantified and the most robust sedimentation processes can be derived from several similarly-likely model runs. Here we present the application of EMMA considering sediment archives in Donggi Cona lake system at the north-eastern Tibetan Plateau, China. Quantitative reconstructions of lacustrine, littoral, fluvial and aeolian sediment end-members are provided from modern and fossil offshore lake sediments and from onshore sequences of lake high-stand sediments. Knowledge on local catchment configuration is embedded in the conceptual frame of a catchment-wide sediment cascade. In a synthesis, Late Quaternary lake level changes, related sedimentary processes, and further regional reconstructions allow first inferences of dominant driving forces (i.e., climate, geomorphological, and neo-tectonic dynamics).

  8. Linking Agricultural Crop Management and Air Quality Models for Regional to National-Scale Nitrogen Assessments

    EPA Science Inventory

    While nitrogen (N) is an essential element for life, human population growth and demands for energy, transportation and food can lead to excess nitrogen in the environment. A modeling framework is described and implemented to promote a more integrated, process-based and system le...

  9. Multiscale Modeling of Grain Boundary Segregation and Embrittlement in Tungsten for Mechanistic Design of Alloys for Coal Fired Plants

    SciTech Connect

    Luo, Jian; Tomar, Vikas; Zhou, Naixie; Lee, Hongsuk

    2013-06-30

    Based on a recent discovery of premelting-like grain boundary segregation in refractory metals occurring at high temperatures and/or high alloying levels, this project investigated grain boundary segregation and embrittlement in tungsten (W) based alloys. Specifically, new interfacial thermodynamic models have been developed and quantified to predict high-temperature grain boundary segregation in the W-Ni binary alloy and W-Ni-Fe, W-Ni-Ti, W-Ni-Co, W-Ni-Cr, W-Ni-Zr and W-Ni-Nb ternary alloys. The thermodynamic modeling results have been experimentally validated for selected systems. Furthermore, multiscale modeling has been conducted at continuum, atomistic and quantum-mechanical levels to link grain boundary segregation with embrittlement. In summary, this 3-year project has successfully developed a theoretical framework in combination with a multiscale modeling strategy for predicting grain boundary segregation and embrittlement in W based alloys.

  10. Generalized coarse-grained model based on point multipole and Gay-Berne potentials

    NASA Astrophysics Data System (ADS)

    Golubkov, Pavel A.; Ren, Pengyu

    2006-08-01

    This paper presents a general coarse-grained molecular mechanics model based on electric point multipole expansion and Gay-Berne [J. Chem. Phys. 74, 3316 (1981)] potential. Coarse graining of van der Waals potential is achieved by treating molecules as soft uniaxial ellipsoids interacting via a generalized anisotropic Gay-Berne function. The charge distribution is represented by point multipole expansion, including point charge, dipole, and quadrupole moments placed at the center of mass. The Gay-Berne and point multipole potentials are combined in the local reference frame defined by the inertial frame of the all-atom counterpart. The coarse-grained model has been applied to rigid-body molecular dynamics simulations of molecular liquids including benzene and methanol. The computational efficiency is improved by several orders of magnitude, while the results are in reasonable agreement with all-atom models and experimental data. We also discuss the implications of using point multipole for polar molecules capable of hydrogen bonding and the applicability of this model to a broad range of molecular systems including highly charged biopolymers.

  11. Generalized coarse-grained model based on point multipole and Gay-Berne potentials.

    PubMed

    Golubkov, Pavel A; Ren, Pengyu

    2006-08-14

    This paper presents a general coarse-grained molecular mechanics model based on electric point multipole expansion and Gay-Berne [J. Chem. Phys. 74, 3316 (1981)] potential. Coarse graining of van der Waals potential is achieved by treating molecules as soft uniaxial ellipsoids interacting via a generalized anisotropic Gay-Berne function. The charge distribution is represented by point multipole expansion, including point charge, dipole, and quadrupole moments placed at the center of mass. The Gay-Berne and point multipole potentials are combined in the local reference frame defined by the inertial frame of the all-atom counterpart. The coarse-grained model has been applied to rigid-body molecular dynamics simulations of molecular liquids including benzene and methanol. The computational efficiency is improved by several orders of magnitude, while the results are in reasonable agreement with all-atom models and experimental data. We also discuss the implications of using point multipole for polar molecules capable of hydrogen bonding and the applicability of this model to a broad range of molecular systems including highly charged biopolymers. PMID:16942269

  12. Properties of Coarse-Grained Polymer Models: Statics, Dynamics, and Crystallinity

    NASA Astrophysics Data System (ADS)

    Grest, Gary; Salerno, K. Michael; Agrawal, Anupriya; Perahia, Dvora

    2015-03-01

    To capture large length and time scales, coarse-grained (CG) models that combine multiple atoms into one bead have been developed to model polymer melts. In the process microscopic detail is discarded in exchange for computational efficiency. However it is not well-understood how the scale of coarse-graining affects the polymer structure and dynamics. We compare results of atomistic simulations with CG models in which each CG bead represents three, four, or six methylene groups for C96H194, C480H962,andC960H1922. The CG potential is developed at 500K by iterative Boltzmann inversion. While static properties such as end-to-end distance and radius of gyration are captured by all CG models, the entanglement length deviates from experimental results with increased CG scale. The mean squared displacement of CG models is used to determine scale factors between the atomistic and CG models. During cooling to low temperature, the three and four-carbon models form a semi-crystalline structure while the six-carbon model and a four-carbon model based on the MARTINI force field remain amorphous at all temperatures. These findings show that the level of coarse-graining and CG interactions can strongly affect model temperature transferability. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's NNSA under Contract DE-AC04-94AL85000.

  13. Cross-Species Extrapolation of Prediction Models for Cadmium Transfer from Soil to Corn Grain

    PubMed Central

    Yang, Hua; Li, Zhaojun; Lu, Lu; Long, Jian; Liang, Yongchao

    2013-01-01

    Cadmium (Cd) is a highly toxic heavy metal for both plants and animals. The presence of Cd in agricultural soils is of great concern regarding its transfer in the soil-plant system. This study investigated the transfer of Cd (exogenous salts) from a wide range of Chinese soils to corn grain (Zhengdan 958). Through multiple stepwise regressions, prediction models were developed, with the combination of Cd bioconcentration factor (BCF) of Zhengdan 958 and soil pH, organic matter (OM) content, and cation exchange capacity (CEC). Moreover, these prediction models from Zhengdan 958 were applied to other non-model corn species through cross-species extrapolation approach. The results showed that the pH of the soil was the most important factor that controlled Cd uptake and lower pH was more favorable for Cd bioaccumulation in corn grain. There was no significant difference among three prediction models in the different Cd levels. When the prediction models were applied to other non-model corn species, the ratio ranges between the predicted BCF values and the measured BCF values were within an interval of 2 folds and close to the solid line of 1∶1 relationship. Furthermore, these prediction models also reduced the measured BCF intra-species variability for all non-model corn species. Therefore, the prediction models established in this study can be applied to other non-model corn species and be useful for predicting the Cd bioconcentration in corn grain and assessing the ecological risk of Cd in different soils. PMID:24324636

  14. Dynamic force matching: A method for constructing dynamical coarse-grained models with realistic time dependence

    SciTech Connect

    Davtyan, Aram; Dama, James F.; Voth, Gregory A.; Andersen, Hans C.

    2015-04-21

    Coarse-grained (CG) models of molecular systems, with fewer mechanical degrees of freedom than an all-atom model, are used extensively in chemical physics. It is generally accepted that a coarse-grained model that accurately describes equilibrium structural properties (as a result of having a well constructed CG potential energy function) does not necessarily exhibit appropriate dynamical behavior when simulated using conservative Hamiltonian dynamics for the CG degrees of freedom on the CG potential energy surface. Attempts to develop accurate CG dynamic models usually focus on replacing Hamiltonian motion by stochastic but Markovian dynamics on that surface, such as Langevin or Brownian dynamics. However, depending on the nature of the system and the extent of the coarse-graining, a Markovian dynamics for the CG degrees of freedom may not be appropriate. In this paper, we consider the problem of constructing dynamic CG models within the context of the Multi-Scale Coarse-graining (MS-CG) method of Voth and coworkers. We propose a method of converting a MS-CG model into a dynamic CG model by adding degrees of freedom to it in the form of a small number of fictitious particles that interact with the CG degrees of freedom in simple ways and that are subject to Langevin forces. The dynamic models are members of a class of nonlinear systems interacting with special heat baths that were studied by Zwanzig [J. Stat. Phys. 9, 215 (1973)]. The properties of the fictitious particles can be inferred from analysis of the dynamics of all-atom simulations of the system of interest. This is analogous to the fact that the MS-CG method generates the CG potential from analysis of equilibrium structures observed in all-atom simulation data. The dynamic models generate a non-Markovian dynamics for the CG degrees of freedom, but they can be easily simulated using standard molecular dynamics programs. We present tests of this method on a series of simple examples that demonstrate that

  15. MODELING NANOCRYSTALLINE GRAIN GROWTH DURING THE PULSED ELECTRODEPOSITION OF GOLD-COPPER

    SciTech Connect

    Jankowski, A F

    2005-10-27

    The process parameters of current density, pulse duration, and cell potential affect both the structure and composition of electrodeposits. The mechanism for nucleation and growth as determined from current transients yield relationships for nucleus density and nucleation rate. To develop an understanding of the role of the process parameters on grain size, as a design structural parameter to control strength for example, a formulation is presented to model the affects of the deposition energy on grain size and morphology. An activation energy for the deposition process is modeled that reveals different growth mechanisms, wherein nucleation and diffusion effects are each dominant as dependent upon pulse duration. A diffusion coefficient common for each of the pulsed growth modes demarcates an observed transition in growth from smooth to rough surfaces.

  16. Classical density functional theory & simulations on a coarse-grained model of aromatic ionic liquids.

    PubMed

    Turesson, Martin; Szparaga, Ryan; Ma, Ke; Woodward, Clifford E; Forsman, Jan

    2014-05-14

    A new classical density functional approach is developed to accurately treat a coarse-grained model of room temperature aromatic ionic liquids. Our major innovation is the introduction of charge-charge correlations, which are treated in a simple phenomenological way. We test this theory on a generic coarse-grained model for aromatic RTILs with oligomeric forms for both cations and anions, approximating 1-alkyl-3-methyl imidazoliums and BF₄⁻, respectively. We find that predictions by the new density functional theory for fluid structures at charged surfaces are very accurate, as compared with molecular dynamics simulations, across a range of surface charge densities and lengths of the alkyl chain. Predictions of interactions between charged surfaces are also presented. PMID:24718295

  17. A Numerical Model of Anisotropic Mass Transport Through Grain Boundary Networks

    NASA Astrophysics Data System (ADS)

    Wang, Yibo

    Tin (Sn) thin films are commonly used in electronic circuit applications as coatings on contacts and solders for joining components. It is widely observed, for some such system, that whiskers---long, thin crystalline structures---emerge and grow from the film. The Sn whisker phenomenon has become a highly active research area since Sn whiskers have caused a large amount of damage and loss in manufacturing, military, medical and power industries. Though lead (Pb) addition to Sn has been used to solve this problem for over five decades, the adverse environmental and health effects of Pb have motivated legislation to severely constrain Pb use in society. People are researching and seeking the reasons which cause whiskers and corresponding methods to solve the problem. The contributing factors to cause a Sn whisker are potentially many and much still remains unknown. Better understanding of fundamental driving forces should point toward strategies to improve (a) the accuracy with which we can predict whisker formation, and (b) our ability to mitigate the phenomenon. This thesis summarizes recent important research achievements in understanding Sn whisker formation and growth, both experimentally and theoretically. Focus is then placed on examining the role that anisotropy in grain boundary diffusivity plays in determining whisker characteristics (specifically, whether they form and, if so, where on a surface). To study this aspect of the problem and to enable future studies on stress driven grain boundary diffusion, this thesis presents a numerical anisotropic mass transport model. In addition to presenting details of the model and implementation, model predictions for a set of increasingly complex grain boundary networks are discussed. Preliminary results from the model provide evidence that anisotropic grain boundary diffusion may be a primary driving mechanism in whisker formation.

  18. Modeled contributions of three types of diazotrophs to nitrogen fixation at Station ALOHA.

    PubMed

    Goebel, Nicole L; Edwards, Christopher A; Church, Matthew J; Zehr, Jonathan P

    2007-11-01

    A diagnostic model based on biomass and growth was used to assess the relative contributions of filamentous nonheterocystous Trichodesmium and unicellular cyanobacteria, termed Groups A and B, to nitrogen fixation at the North Pacific Station ALOHA over a 2-year period. Average (and 95% confidence interval, CI) annual rates of modeled monthly values for Trichodesmium, Group B and Group A were 92 (52), 14 (4) and 12 (8) mmol N per m(2) per year, respectively. The fractional contribution to modeled instantaneous nitrogen fixation by each diazotroph fluctuated on interannual, seasonal and shorter time scales. Trichodesmium fixed substantially more nitrogen in year 1 (162) than year 2 (12). Group B fixed almost two times more nitrogen in year 1 (17) than year 2 (9). In contrast, Group A fixed two times more nitrogen in year 2 (16) than year 1 (8). When including uncertainties in our estimates using the bootstrap approach, the range of unicellular nitrogen fixation extended from 10% to 68% of the total annual rate of nitrogen fixation for all three diazotrophs. Furthermore, on a seasonal basis, the model demonstrated that unicellular diazotrophs fixed the majority (51%-97%) of nitrogen during winter and spring, whereas Trichodesmium dominated nitrogen fixation during summer and autumn (60%-96%). Sensitivity of the modeled rates to some parameters suggests that this unique attempt to quantify relative rates of nitrogen fixation by different diazotrophs may need to be reevaluated as additional information on cell size, variability in biomass and C:N, and growth characteristics of the different cyanobacterial diazotrophs become available. PMID:18043668

  19. A coarse-grained model for amorphous and crystalline fatty acids

    NASA Astrophysics Data System (ADS)

    Hadley, K. R.; McCabe, C.

    2010-04-01

    Fatty acids constitute one of the main components of the lipid lamellae in the top layer of the skin, known as the stratum corneum, which acts as a barrier to foreign substances entering the body and to water leaving the body. To better understand the mechanics of the skin, a molecular-level understanding of the structure of the lamellae needs to be investigated. As a first step toward this goal, the current work involves the development of a coarse-grained model for fatty acids in an amorphous and a crystalline state. In order to retain the structural details of the atomistic molecules, radial distribution functions have been used to provide target data against which the coarse-grained force field is optimized. The optimization was achieved using the method developed by Reith, Pütz, and Müller-Plathe with a damping factor introduced into the updating scheme to facilitate the convergence against the crystalline radial distribution functions. Using this approach, a transferable force field has been developed for both crystalline and amorphous systems that can be used to describe fatty acids of different chain lengths. We are unaware of any other coarse-grained model in the literature that has been developed to study solid phases. Additionally, the amorphous force field has been shown to accurately model mixtures of different free fatty acids based on the potentials derived from pure lipid systems.

  20. Laboratory investigations of the role of the grain surface in astrochemical models.

    PubMed

    Brown, Wendy A; Viti, Serena; Wolff, Angela J; Bolina, Amandeep S

    2006-01-01

    The rich chemistry often detected in star forming regions is now recognized to be a consequence of solid-state astrochemistry and the thermal desorption of its products. In recent experimental studies, desorption of a range of ices from a gold surface was investigated using temperature programmed desorption (TPD). These data were then used in astrochemical models. In this paper we investigate the sensitivity of these models to the inclusion of TPD data obtained from different surfaces (simulating different dust grains) and different thicknesses of the icy mantles. Detailed laboratory TPD studies of the desorption of ices from a highly oriented pyrolytic graphite (HOPG) surface have been performed. Desorption temperatures and kinetic parameters have been determined directly from the TPD data and have been used to determine the expected desorption temperature for the ices from grain surfaces. The results of these experiments have been incorporated into astrochemical models of high mass star forming regions and have then been compared with the results of previous experiments. From this comparison, we are able to determine whether the nature and composition of the grain surface is important in dictating the chemistry that occurs in star forming regions. PMID:17191445

  1. Dynamic and impact contact mechanics of geologic materials: Grain-scale experiments and modeling

    SciTech Connect

    Cole, David M.; Hopkins, Mark A.; Ketcham, Stephen A.

    2013-06-18

    High fidelity treatments of the generation and propagation of seismic waves in naturally occurring granular materials is becoming more practical given recent advancements in our ability to model complex particle shapes and their mechanical interaction. Of particular interest are the grain-scale processes that are activated by impact events and the characteristics of force transmission through grain contacts. To address this issue, we have developed a physics based approach that involves laboratory experiments to quantify the dynamic contact and impact behavior of granular materials and incorporation of the observed behavior indiscrete element models. The dynamic experiments do not involve particle damage and emphasis is placed on measured values of contact stiffness and frictional loss. The normal stiffness observed in dynamic contact experiments at low frequencies (e.g., 10 Hz) are shown to be in good agreement with quasistatic experiments on quartz sand. The results of impact experiments - which involve moderate to extensive levels of particle damage - are presented for several types of naturally occurring granular materials (several quartz sands, magnesite and calcium carbonate ooids). Implementation of the experimental findings in discrete element models is discussed and the results of impact simulations involving up to 5 Multiplication-Sign 105 grains are presented.

  2. Coarse-graining molecular dynamics models using an extended Galerkin method

    NASA Astrophysics Data System (ADS)

    Li, Xiantao

    2013-03-01

    I will present a systematic approach to coarse-grain molecular dynamics models for solids. The coarse-grained models are derived by Galerkin projection to a sequence of Krylov subspaces. On the coarsest space, the model corresponds to a finite element discretization of the continuum elasto-dynamics model. On the other hand, the projection to the finest space yields the full molecular dynamics description. The models in between serve as a smooth transition between the two scales. We start with a molecular dynamics (MD) model, mix¨i = -∂V/∂xi . First, let Y0 be the approximation space for the continuum model. By projecting the MD model onto the subspace, we obtain a coarse-grained model, M q ¨ = F (q) . Using the Cauchy-Born approximation, this model can be shown to coincide with the finite element representation of the continuum elastodynamics model. This model has limited accuracy near lattice defects. One natural idea is to switch to the MD model in regions surround local defect. As a result, one creates an interface between the continuum and atomistic description, where coupling conditions are needed. Direct coupling methods may involve enforcing constraints or mixing the energy or forces. Such an approach may suffer from large phonon reflections at the interface, and introduce large modeling error. In order to seamlessly couple this model to MD, we successively expand the approximation space to the Krylov spaces, Kl =Y0 + AY0 + ⋯ +AlY0 . Here A is the force constant matrix, computed from the atomistic model. Due to the translational invariance, only a smaller number of such matrices need to be computed. By projecting the MD model onto this new subspace, we obtain an extended system, M q .. =F0 (q ,ξ1 , ... ,ξl) ,ξ̈1 =F1 (q ,ξ1 , ... ,ξl) , ... ... ,ξ̈l =Fl (q ,ξ1 , ... ,ξl) . The additional variables ξj represent the coefficients in the extended approximation space. Using this systematic approach, one can build a hierarchy of models with

  3. Grain-scale modeling of arbitrary fluid saturation in random packings

    NASA Astrophysics Data System (ADS)

    Melnikov, Konstantin; Mani, Roman; Wittel, Falk K.; Thielmann, Marcel; Herrmann, Hans J.

    2015-08-01

    We propose a model for increasing liquid saturation in a granular packing, which can account for liquid redistribution at saturation levels beyond the well-studied capillary bridge regime. The model is capable of resolving and combining capillary bridges, menisci, and fully saturated pores to form local liquid clusters of any shape. They can exchange volume due to the local Laplace pressure gradient via a liquid film on the surfaces of grains. Local instabilities such as Haines jumps trigger the discontinuous evolution of the liquid front. The applicability of the model is demonstrated and compared to benchmark experiments on the level of individual liquid structures as well as on larger systems.

  4. Computer simulation of topological evolution in 2-d grain growth using a continuum diffuse-interface field model

    SciTech Connect

    Fan, D.; Geng, C.; Chen, L.Q.

    1997-03-01

    The local kinetics and topological phenomena during normal grain growth were studied in two dimensions by computer simulations employing a continuum diffuse-interface field model. The relationships between topological class and individual grain growth kinetics were examined, and compared with results obtained previously from analytical theories, experimental results and Monte Carlo simulations. It was shown that both the grain-size and grain-shape (side) distributions are time-invariant and the linear relationship between the mean radii of individual grains and topological class n was reproduced. The moments of the shape distribution were determined, and the differences among the data from soap froth. Potts model and the present simulation were discussed. In the limit when the grain size goes to zero, the average number of grain edges per grain is shown to be between 4 and 5, implying the direct vanishing of 4- and 5-sided grains, which seems to be consistent with recent experimental observations on thin films. Based on the simulation results, the conditions for the applicability of the familiar Mullins-Von Neumann law and the Hillert`s equation were discussed.

  5. A mathematical model of phloem sucrose transport as a new tool for designing rice panicle structure for high grain yield.

    PubMed

    Seki, Motohide; Feugier, François Gabriel; Song, Xian-Jun; Ashikari, Motoyuki; Nakamura, Haruka; Ishiyama, Keiki; Yamaya, Tomoyuki; Inari-Ikeda, Mayuko; Kitano, Hidemi; Satake, Akiko

    2015-04-01

    Rice (Oryza sativa) is one of the most important food crops in the world. Numerous quantitative trait loci or genes controlling panicle architecture have been identified to increase grain yield. Yet grain yield, defined as the product of the number of well-ripened grains and their weight, is a complex trait that is determined by multiple factors such as source, sink and translocation capacity. Mechanistic modelling capturing capacities of source, sink and transport will help in the theoretical design of crop ideotypes that guarantee high grain yield. Here we present a mathematical model simulating sucrose transport and grain growth within a complex phloem network. The model predicts that the optimal panicle structure for high yield shows a simple grain arrangement with few higher order branches. In addition, numerical analyses revealed that inefficient delivery of carbon to panicles with higher order branches prevails regardless of source capacity, indicating the importance of designing grain arrangement and phloem structure. Our model highlights the previously unexplored effect of grain arrangement on the yield, and provides numerical solutions for optimal panicle structure under various source and sink capacities. PMID:25516572

  6. Nitrogen feedbacks increase future terrestrial ecosystem carbon uptake in an individual-based dynamic vegetation model

    NASA Astrophysics Data System (ADS)

    Wårlind, D.; Smith, B.; Hickler, T.; Arneth, A.

    2014-11-01

    Recently a considerable amount of effort has been put into quantifying how interactions of the carbon and nitrogen cycle affect future terrestrial carbon sinks. Dynamic vegetation models, representing the nitrogen cycle with varying degree of complexity, have shown diverging constraints of nitrogen dynamics on future carbon sequestration. In this study, we use LPJ-GUESS, a dynamic vegetation model employing a detailed individual- and patch-based representation of vegetation dynamics, to evaluate how population dynamics and resource competition between plant functional types, combined with nitrogen dynamics, have influenced the terrestrial carbon storage in the past and to investigate how terrestrial carbon and nitrogen dynamics might change in the future (1850 to 2100; one representative "business-as-usual" climate scenario). Single-factor model experiments of CO2 fertilisation and climate change show generally similar directions of the responses of C-N interactions, compared to the C-only version of the model as documented in previous studies using other global models. Under an RCP 8.5 scenario, nitrogen limitation suppresses potential CO2 fertilisation, reducing the cumulative net ecosystem carbon uptake between 1850 and 2100 by 61%, and soil warming-induced increase in nitrogen mineralisation reduces terrestrial carbon loss by 31%. When environmental changes are considered conjointly, carbon sequestration is limited by nitrogen dynamics up to the present. However, during the 21st century, nitrogen dynamics induce a net increase in carbon sequestration, resulting in an overall larger carbon uptake of 17% over the full period. This contrasts with previous results with other global models that have shown an 8 to 37% decrease in carbon uptake relative to modern baseline conditions. Implications for the plausibility of earlier projections of future terrestrial C dynamics based on C-only models are discussed.

  7. Multiscale coarse-grained modelling of chromatin components: DNA and the nucleosome.

    PubMed

    Korolev, Nikolay; Nordenskiöld, Lars; Lyubartsev, Alexander P

    2016-06-01

    To model large biomolecular systems, such as cell and organelles an atomistic description is not currently achievable and is not generally practical. Therefore, simplified coarse-grained (CG) modelling becomes a necessity. One of the most important cellular components is chromatin, a large DNA-protein complex where DNA is highly compacted. Recent progress in coarse graining modelling of the major chromatin components, double helical DNA and the nucleosome core particle (NCP) is presented. First, general principles and approaches allowing rigorous bottom-to-top generation of interaction potentials in the CG models are presented. Then, recent CG models of DNA are reviewed and their adequacy is benchmarked against experimental data on the salt dependence of DNA flexibility (persistence length). Furthermore, a few recent CG models of the NCP are described and their application for studying salt-dependent NCP-NCP interaction is discussed. An example of a multiscale approach to CG modelling of chromatin is presented where interactions and self-assembly of thousands of NCPs in solution are observed. PMID:26956528

  8. Physics-Based Reactive Burn Model: Grain size effects and binder effects

    NASA Astrophysics Data System (ADS)

    Lu, Xia; Hamate, Yuichio; Horie, Yasuyuki

    2007-06-01

    We have been developing a physics-based reactive burn (PBRB) model aiming at expanding predictive capability. The PBRB model was formulated based on the concept of a statistical hot spot cell. In the model, thermomechanics and physiochemical features are explicitly modeled. In this paper, we have extended the statistical hot spot model to explicitly describe the ignition and growth of hot spots. In particular, grain size effects are explicitly delineated through introduction of a size-dependent thickness of the hot-region thickness, a size-dependent energy deposition criterion, and a specific surface area. Besides the linear relationships between the run distance to detonation and critical diameter with the reciprocal specific surface area of HE, as discussed in a parallel paper in this meeting, parametric studies have also shown that the PBRB can predict a non-monotonous variation of shock sensitivity with grain size, as observed by Moulard et al. The purpose of this work is to extend the model to include the effects of explosive binders explicitly. As a first step we investigate the thermomechanical effects of a binder by using direct mesoscale simulations. The results will be used in the extending the PBRB model to include binder thermomechanics explicitly.

  9. Coarse-graining to the meso and continuum scales with molecular-dynamics-like models

    NASA Astrophysics Data System (ADS)

    Plimpton, Steve

    Many engineering-scale problems that industry or the national labs try to address with particle-based simulations occur at length and time scales well beyond the most optimistic hopes of traditional coarse-graining methods for molecular dynamics (MD), which typically start at the atomic scale and build upward. However classical MD can be viewed as an engine for simulating particles at literally any length or time scale, depending on the models used for individual particles and their interactions. To illustrate I'll highlight several coarse-grained (CG) materials models, some of which are likely familiar to molecular-scale modelers, but others probably not. These include models for water droplet freezing on surfaces, dissipative particle dynamics (DPD) models of explosives where particles have internal state, CG models of nano or colloidal particles in solution, models for aspherical particles, Peridynamics models for fracture, and models of granular materials at the scale of industrial processing. All of these can be implemented as MD-style models for either soft or hard materials; in fact they are all part of our LAMMPS MD package, added either by our group or contributed by collaborators. Unlike most all-atom MD simulations, CG simulations at these scales often involve highly non-uniform particle densities. So I'll also discuss a load-balancing method we've implemented for these kinds of models, which can improve parallel efficiencies. From the physics point-of-view, these models may be viewed as non-traditional or ad hoc. But because they are MD-style simulations, there's an opportunity for physicists to add statistical mechanics rigor to individual models. Or, in keeping with a theme of this session, to devise methods that more accurately bridge models from one scale to the next.

  10. Hierarchical coarse-graining model for photosystem II including electron and excitation-energy transfer processes.

    PubMed

    Matsuoka, Takeshi; Tanaka, Shigenori; Ebina, Kuniyoshi

    2014-03-01

    We propose a hierarchical reduction scheme to cope with coupled rate equations that describe the dynamics of multi-time-scale photosynthetic reactions. To numerically solve nonlinear dynamical equations containing a wide temporal range of rate constants, we first study a prototypical three-variable model. Using a separation of the time scale of rate constants combined with identified slow variables as (quasi-)conserved quantities in the fast process, we achieve a coarse-graining of the dynamical equations reduced to those at a slower time scale. By iteratively employing this reduction method, the coarse-graining of broadly multi-scale dynamical equations can be performed in a hierarchical manner. We then apply this scheme to the reaction dynamics analysis of a simplified model for an illuminated photosystem II, which involves many processes of electron and excitation-energy transfers with a wide range of rate constants. We thus confirm a good agreement between the coarse-grained and fully (finely) integrated results for the population dynamics. PMID:24418347

  11. Limited impact of atmospheric nitrogen deposition on marine productivity due to biogeochemical feedbacks in a global ocean model

    NASA Astrophysics Data System (ADS)

    Somes, Christopher J.; Landolfi, Angela; Koeve, Wolfgang; Oschlies, Andreas

    2016-05-01

    The impact of increasing anthropogenic atmospheric nitrogen deposition on marine biogeochemistry is uncertain. We performed simulations to quantify its effect on nitrogen cycling and marine productivity in a global 3-D ocean biogeochemistry model. Nitrogen fixation provides an efficient feedback by decreasing immediately to deposition, whereas water column denitrification increases more gradually in the slowly expanding oxygen deficient zones. Counterintuitively, nitrogen deposition near oxygen deficient zones causes a net loss of marine nitrogen due to the stoichiometry of denitrification. In our idealized atmospheric deposition simulations that only account for nitrogen cycle perturbations, these combined stabilizing feedbacks largely compensate deposition and suppress the increase in global marine productivity to <2%, in contrast to a simulation that neglects nitrogen cycle feedbacks that predicts an increase of >15%. Our study emphasizes including the dynamic response of nitrogen fixation and denitrification to atmospheric nitrogen deposition to predict future changes of the marine nitrogen cycle and productivity.

  12. Folding of small knotted proteins: Insights from a mean field coarse-grained model

    SciTech Connect

    Najafi, Saeed; Potestio, Raffaello

    2015-12-28

    A small but relevant number of proteins whose native structure is known features nontrivial topology, i.e., they are knotted. Understanding the process of folding from a swollen unknotted state to the biologically relevant native conformation is, for these proteins, particularly difficult, due to their rate-limiting topological entanglement. To shed some light into this conundrum, we introduced a structure-based coarse-grained model of the protein, where the information about the folded conformation is encoded in bonded angular interactions only, which do not favor the formation of native contacts. A stochastic search scheme in parameter space is employed to identify a set of interactions that maximizes the probability to attain the knotted state. The optimal knotting pathways of the two smallest knotted proteins, obtained through this approach, are consistent with the results derived by means of coarse-grained as well as full atomistic simulations.

  13. Coarse-Grain Model Simulations of Nonequilibrium Dynamics in Heterogeneous Materials.

    PubMed

    Brennan, John K; Lísal, Martin; Moore, Joshua D; Izvekov, Sergei; Schweigert, Igor V; Larentzos, James P

    2014-06-19

    A suite of computational tools is described for particle-based mesoscale simulations of the nonequilibrium dynamics of energetic solids, including mechanical deformation, phase transitions, and chemical reactivity triggered by shock or thermal loading. The method builds upon our recent advances both in generating coarse-grain models under high strains and in developing a variant of dissipative particle dynamics (DPD) that includes chemical reactions. To describe chemical reactivity, a coarse-grain particle equation-of-state was introduced into the constant-energy DPD variant that rigorously treats complex chemical reactions and the associated chemical energy release. As illustration of these developments, we present simulations of shock compression of an RDX crystal and its thermal decomposition under high temperatures. We also discuss our current efforts toward a highly scalable domain-decomposition implementation that extends applicability to micrometer-size simulations. With appropriate parametrization, the method is applicable to other materials whose dynamic response is driven by microstructural heterogeneities. PMID:26270506

  14. Nitrogen Management Modeling Techniques: Assessing Cropping Systems/Landscape Combinations.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nitrogen use efficiency (NUE) in production agriculture often is too low resulting in losses of excess N to ground water as NO3-N, to gaseous emissions of NH3 and N2O, and to N losses in surface runoff and erosion. Best management practices (BMPs) are needed to improve efficiency levels while maint...

  15. Modeling landscape-scale nitrogen management for conservation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There are concerns about how agriculture will adapt to a changing climate and other environmental challenges during the twenty-first century to provide food security for the ever-increasing global population. Designing and implementing best nitrogen management practices will be key in global food se...

  16. Multiobjective Sensitivity Analysis Of Sediment And Nitrogen Processes With A Watershed Model

    EPA Science Inventory

    This paper presents a computational analysis for evaluating critical non-point-source sediment and nutrient (specifically nitrogen) processes and management actions at the watershed scale. In the analysis, model parameters that bear key uncertainties were presumed to reflect the ...

  17. Reconciling modeled and observed atmospheric deposition of soluble organic nitrogen at coastal locations

    NASA Astrophysics Data System (ADS)

    Ito, Akinori; Lin, Guangxing; Penner, Joyce E.

    2014-06-01

    Atmospheric deposition of reactive nitrogen (N) species from air pollutants is a significant source of exogenous nitrogen in marine ecosystems. Here we use an atmospheric chemical transport model to investigate the supply of soluble organic nitrogen (ON) from anthropogenic sources to the ocean. Comparisons of modeled deposition with observations at coastal and marine locations show good overall agreement for inorganic nitrogen and total soluble nitrogen. However, previous modeling approaches result in significant underestimates of the soluble ON deposition if the model only includes the primary soluble ON and the secondary oxidized ON in gases and aerosols. Our model results suggest that including the secondary reduced ON in aerosols as a source of soluble ON contributes to an improved prediction of the deposition rates (g N m-2 yr-1). The model results show a clear distinction in the vertical distribution of soluble ON in aerosols between different processes from the primary sources and the secondary formation. The model results (excluding the biomass burning and natural emission changes) suggest an increase in soluble ON outflow from atmospheric pollution, in particular from East Asia, to the oceans in the twentieth century. These results highlight the necessity of improving the process-based quantitative understanding of the chemical reactions of inorganic nitrogen species with organics in aerosol and cloud water.

  18. A Coupled Land Surface-Subsurface Biogeochemical Model for Aqueous and Gaseous Nitrogen Losses

    NASA Astrophysics Data System (ADS)

    Gu, C.; Maggi, F.; Riley, W.; Pan, L.; Xu, T.; Oldenburg, C.; Miller, N.

    2008-12-01

    In recent years concern has grown over the contribution of nitrogen (N) fertilizers to nitrate (NOB3PB-P) water pollution and atmospheric pollution of nitrous oxide (NB2BO), nitric oxide (NO), and ammonia (NHB3B). Characterizing the amount and species of N losses is therefore essential in developing a strategy to estimate and mitigate N leaching and emission to the atmosphere. Indeed, transformations of nitrogen depend strongly on water content, soil temperature, and nitrogen concentration. Land surface processes therefore have to be taken into account to properly characterize N biogeochemical cycling. However, most current nitrogen biogeochemical models take the land surface as the upper boundary by lumping the complex processes above the surface as known boundary conditions. In this study, an extant subsurface mechanistic N cycle model (TOUGHREACT-N) was coupled with the community land model (CLM). The resulting coupled model extends the modeling capability of TOUGHREACT-N to include the important energy, momentum, and moisture dynamics provided by CLM. The coupled model showed a significant impact of land-surface diurnal forcing on soil temperature and moisture and on nitrogen fluxes. We also discuss field applications of the model and discuss how temporal dynamics of nitrogen fluxes are affected by land surface processes.

  19. How well does end-member modelling analysis of grain size data work?

    NASA Astrophysics Data System (ADS)

    Schulte, Philipp; Dietze, Michael; Dietze, Elisabeth

    2014-05-01

    End-member modelling analysis (EMMA) is a powerful and flexible statistic approach to identify and quantify generic sediment transport processes from multimodal grain-size distributions. EMMA has been introduced over 15 years ago and is now available in different approaches as encapsulated FORTRAN code (Weltje, 1997), Matlab-script (Dietze et al., 2012) and the R-package EMMAgeo (Dietze and Dietze, 2013). EMMA was mainly used to reconstruct past sedimentation processes in a variety of sedimentary environments (marine, aeolian, lacustrine). Typically, it is rather difficult to assess how meaningful and well the model performs in a certain environment, since neither the actual process end-members (generic grain-size distributions sorted by a certain sediment transport) nor their individual contributions to each sample are known a priori. To allow a comprehensive performance test, we sampled a set of four known process end-members: alluvial sand (main mode: 0.70±0.55 φ), dune sand (main mode: 1.35±0.60 φ), loess (main mode: 4.71±0.65 φ) and overbank deposit (main mode: 5.81±1.62 φ). High resolution grain-size information is based on laser-diffraction analysis (116 classes). The four process end-members were artificially mixed with random, but known proportions to yield 100 samples. This mixed data set was measured again with the laser particle size analyser and served as input for EMMA within the R-package EMMAgeo. This contribution discusses the ability of EMMA to identify and characterise the four distinct process end-members and quantify their contributions to each sample. Different ways to estimate uncertainties are presented. Further evaluations focus on the influence of numbers of included samples, numbers of grain-size classes, vertical mixing of samples (simulating turbation) and self-similarity of process end-members. Dietze E, et al. 2012. An end-member algorithm for deciphering modern detrital processes from lake sediments of Lake Donggi Cona, NE

  20. A Coarse-Grained Protein Model in a Water-like Solvent

    NASA Astrophysics Data System (ADS)

    Sharma, Sumit; Kumar, Sanat K.; Buldyrev, Sergey V.; Debenedetti, Pablo G.; Rossky, Peter J.; Stanley, H. Eugene

    2013-05-01

    Simulations employing an explicit atom description of proteins in solvent can be computationally expensive. On the other hand, coarse-grained protein models in implicit solvent miss essential features of the hydrophobic effect, especially its temperature dependence, and have limited ability to capture the kinetics of protein folding. We propose a free space two-letter protein (``H-P'') model in a simple, but qualitatively accurate description for water, the Jagla model, which coarse-grains water into an isotropically interacting sphere. Using Monte Carlo simulations, we design protein-like sequences that can undergo a collapse, exposing the ``Jagla-philic'' monomers to the solvent, while maintaining a ``hydrophobic'' core. This protein-like model manifests heat and cold denaturation in a manner that is reminiscent of proteins. While this protein-like model lacks the details that would introduce secondary structure formation, we believe that these ideas represent a first step in developing a useful, but computationally expedient, means of modeling proteins.

  1. Modelling the nitrogen loadings from large yellow croaker (Larimichthys crocea) cage aquaculture.

    PubMed

    Cai, Huiwen; Ross, Lindsay G; Telfer, Trevor C; Wu, Changwen; Zhu, Aiyi; Zhao, Sheng; Xu, Meiying

    2016-04-01

    Large yellow croaker (LYC) cage farming is a rapidly developing industry in the coastal areas of the East China Sea. However, little is known about the environmental nutrient loadings resulting from the current aquaculture practices for this species. In this study, a nitrogenous waste model was developed for LYC based on thermal growth and bioenergetic theories. The growth model produced a good fit with the measured data of the growth trajectory of the fish. The total, dissolved and particulate nitrogen outputs were estimated to be 133, 51 and 82 kg N tonne(-1) of fish production, respectively, with daily dissolved and particulate nitrogen outputs varying from 69 to 104 and 106 to 181 mg N fish(-1), respectively, during the 2012 operational cycle. Greater than 80 % of the nitrogen input from feed was predicted to be lost to the environment, resulting in low nitrogen retention (<20 %) in the fish tissues. Ammonia contributed the greatest proportion (>85 %) of the dissolved nitrogen generated from cage farming. This nitrogen loading assessment model is the first to address nitrogenous output from LYC farming and could be a valuable tool to examine the effects of management and feeding practices on waste from cage farming. The application of this model could help improve the scientific understanding of offshore fish farming systems. Furthermore, the model predicts that a 63 % reduction in nitrogenous waste production could be achieved by switching from the use of trash fish for feed to the use of pelleted feed. PMID:26728289

  2. A SIMPLE MODEL OF THE EFFECTS OF NITROGEN LOADING, FRESHWATER RESIDENCE TIME, AND INTERNAL LOSSES ON THE NITROGEN CONCENTRATIONS AND EXPORT IN ESTUARIES

    EPA Science Inventory

    This simple model uses the annual loading rate of total nitrogen (TN) and the water residence time to calculate average annual TN concentration and internal loss rates (e.g. denitrification and incorporation in sediments) in an estuary, and rate of nitrogen export across the seaw...

  3. Effect of a nitrogen-carbon interaction on terrestrial carbon fluxes estimated by biosphere model

    NASA Astrophysics Data System (ADS)

    Sasai, T.; Yamaguchi, Y.

    2007-12-01

    It is important for the global warming to accurately understand the terrestrial carbon fluxes at global scale. Estimating spatial and temporal patterns in the carbon fluxes, recently, many global biosphere models were proposed and developed. However, since the model analyses have always some uncertainties. One of the major uncertainties is an effect of nitrogen cycle on the carbon cycle, as nitrogen largely controls carbon dynamics as plant and soil microbe nutrients. A goal of this study is to investigate the effect of terrestrial carbon-nitrogen interaction on NPP using new biosphere model. Firstly, a new nitrogen cycle model was constructed including twelve main nitrogen flows (nitrogen fixation, deposition, nitrifications, volatilization, nitrate leaching, plant uptake, allocation, translocation, retranslocation, soil organic and inorganic nitrogen dynamics), and fourteen pools (three biomass, four litter fall, five soil organic, and two inorganic). Secondly, the nitrogen model was integrated to the existing biosphere model, BEAMS (Biosphere model integrating Eco-physiological And Mechanistic approaches using Satellite data) [Sasai et al., 2005, 2007]. The new biosphere model was run for 20 years (1982-2001) at a global scale. The inputs datasets used were NCEP/NCAR re-analysis and fPAR/LAI based on NOAA/AVHRR produced by Boston University. The two-dimensional distributions of monthly GPP and NPP were calculated. And, the GPP estimates by the original and new BEAMS were compared with ground measurements at flux-tower sites. We compared seasonal changes in GPP between the new model and eddy covariance measurements at flux sites. As a result, the GPP estimates had good agreement with the GPP measurements (r2 = 0.91). In view of a comparison in GPP between the measurements and the original BEAMS (r2 = 0.84), the new model is better than the original BEAMS. Especially, we could observe an indisputable improvement of the new model on a seasonal change in the growing

  4. Eastern oyster (Crassostrea virginica) δ15N as a bioindicator of nitrogen sources: Observations and modeling

    PubMed Central

    Fertig, B.; Carruthers, T.J.B.; Dennison, W.C.; Fertig, E.J.; Altabet, M.A.

    2013-01-01

    Stable nitrogen isotopes (δ15N) in bioindicators are increasingly employed to identify nitrogen sources in many ecosystems and biological characteristics of the eastern oyster (Crassostrea virginica) make it an appropriate species for this purpose. To assess nitrogen isotopic fractionation associated with assimilation and baseline variations in oyster mantle, gill, and muscle tissue δ15N, manipulative fieldwork in Chesapeake Bay and corresponding modeling exercises were conducted. This study (1) determined that five individuals represented an optimal sample size; (2) verified that δ15N in oysters from two locations converged after shared deployment to a new location reflecting a change in nitrogen sources; (3) identified required exposure time and temporal integration (four months for muscle, two to three months for gill and mantle); and (4) demonstrated seasonal δ15N increases in seston (summer) and oysters (winter). As bioindicators, oysters can be deployed for spatial interpolation of nitrogen sources, even in areas lacking extant populations. PMID:20381097

  5. Tracer experiment and model evidence for macrofaunal shaping of microbial nitrogen functions along rocky shores

    NASA Astrophysics Data System (ADS)

    Pfister, Catherine A.; Altabet, Mark A.; Pather, Santhiska; Dwyer, Greg

    2016-06-01

    Seawater microbes as well as those associated with macrobiota are increasingly recognized as a key feature affecting nutrient cycling. Tidepools are ideal natural mesocosms to test macrofauna and microbe interactions, and we quantified rates of microbial nitrogen processing using tracer enrichment of ammonium (15NNH4) or nitrate (15NNO3) when tidepools were isolated from the ocean during low intertidal periods. Experiments were conducted during both day and night as well as in control tidepools and those from which mussels had been removed, allowing us to determine the role of both mussels and daylight in microbial nitrogen processing. We paired time series observations of 15N enrichment in NH4+, NO2- and NO3- with a differential equation model to quantify multiple, simultaneous nitrogen transformations. Mussel presence and daylight increased remineralization and photosynthetic nitrogen uptake. When we compared ammonium gain or loss that was attributed to any tidepool microbes vs. photosynthetic uptake, microbes accounted for 32 % of this ammonium flux on average. Microbial transformations averaged 61 % of total nitrate use; thus, microbial activity was almost 3 times that of photosynthetic nitrate uptake. Because it accounted for processes that diluted our tracer, our differential equation model assigned higher rates of nitrogen processing compared to prior source-product models. Our in situ experiments showed that animals alone elevate microbial nitrogen transformations by 2 orders of magnitude, suggesting that coastal macrobiota are key players in complex microbial nitrogen transformations.

  6. Atomic structures and energies of grain boundaries in Mg2SiO4 forsterite from atomistic modeling

    NASA Astrophysics Data System (ADS)

    Adjaoud, Omar; Marquardt, Katharina; Jahn, Sandro

    2012-10-01

    Grain boundaries influence many physical and chemical properties of crystalline materials. Here, we perform molecular dynamics simulations to study the structure of a series of [100] symmetric tilt grain boundaries in Mg2SiO4 forsterite. The present results show that grain boundary energies depend significantly on misorientation angle. For small misorientation angles (up to 22°), grain boundary structures consist of an array of partial edge dislocations with Burgers vector 1/2[001] associated with stacking faults and their energies can be readily fit with a model which adds the Peach-Koehler equation to the Read-Shockley dislocation model for grain boundaries. The core radius of partial dislocations and the spacing between the partials derived from grain boundary energies show that the transition from low- to high-angle grain boundaries occurs for a misorientation angle between 22° and 32°. For high misorientation angles (32.1° and 60.8°), the cores of dislocations overlap and form repeated structural units. Finally, we use a low energy atomic configuration obtained by molecular dynamics for the misorientation of 12.18° as input to simulate a high-resolution transmission electron microscopy (HRTEM) image. The simulated image is in good agreement with an observed HRTEM image, which indicates the power of the present approach to predict realistic atomic structures of grain boundaries in complex silicates.

  7. Cross-Species Extrapolation of Models for Predicting Lead Transfer from Soil to Wheat Grain.

    PubMed

    Liu, Ke; Lv, Jialong; Dai, Yunchao; Zhang, Hong; Cao, Yingfei

    2016-01-01

    The transfer of Pb from the soil to crops is a serious food hygiene security problem in China because of industrial, agricultural, and historical contamination. In this study, the characteristics of exogenous Pb transfer from 17 Chinese soils to a popular wheat variety (Xiaoyan 22) were investigated. In addition, bioaccumulation prediction models of Pb in grain were obtained based on soil properties. The results of the analysis showed that pH and OC were the most important factors contributing to Pb uptake by wheat grain. Using a cross-species extrapolation approach, the Pb uptake prediction models for cultivar Xiaoyan 22 in different soil Pb levels were satisfactorily applied to six additional non-modeled wheat varieties to develop a prediction model for each variety. Normalization of the bioaccumulation factor (BAF) to specific soil physico-chemistry is essential, because doing so could significantly reduce the intra-species variation of different wheat cultivars in predicted Pb transfer and eliminate the influence of soil properties on ecotoxicity parameters for organisms of interest. Finally, the prediction models were successfully verified against published data (including other wheat varieties and crops) and used to evaluate the ecological risk of Pb for wheat in contaminated agricultural soils. PMID:27518712

  8. Cross-Species Extrapolation of Models for Predicting Lead Transfer from Soil to Wheat Grain

    PubMed Central

    Liu, Ke; Lv, Jialong; Dai, Yunchao; Zhang, Hong; Cao, Yingfei

    2016-01-01

    The transfer of Pb from the soil to crops is a serious food hygiene security problem in China because of industrial, agricultural, and historical contamination. In this study, the characteristics of exogenous Pb transfer from 17 Chinese soils to a popular wheat variety (Xiaoyan 22) were investigated. In addition, bioaccumulation prediction models of Pb in grain were obtained based on soil properties. The results of the analysis showed that pH and OC were the most important factors contributing to Pb uptake by wheat grain. Using a cross-species extrapolation approach, the Pb uptake prediction models for cultivar Xiaoyan 22 in different soil Pb levels were satisfactorily applied to six additional non-modeled wheat varieties to develop a prediction model for each variety. Normalization of the bioaccumulation factor (BAF) to specific soil physico-chemistry is essential, because doing so could significantly reduce the intra-species variation of different wheat cultivars in predicted Pb transfer and eliminate the influence of soil properties on ecotoxicity parameters for organisms of interest. Finally, the prediction models were successfully verified against published data (including other wheat varieties and crops) and used to evaluate the ecological risk of Pb for wheat in contaminated agricultural soils. PMID:27518712

  9. Parameterizing the Morse potential for coarse-grained modeling of blood plasma

    SciTech Connect

    Zhang, Na; Zhang, Peng; Kang, Wei; Bluestein, Danny; Deng, Yuefan

    2014-01-15

    Multiscale simulations of fluids such as blood represent a major computational challenge of coupling the disparate spatiotemporal scales between molecular and macroscopic transport phenomena characterizing such complex fluids. In this paper, a coarse-grained (CG) particle model is developed for simulating blood flow by modifying the Morse potential, traditionally used in Molecular Dynamics for modeling vibrating structures. The modified Morse potential is parameterized with effective mass scales for reproducing blood viscous flow properties, including density, pressure, viscosity, compressibility and characteristic flow dynamics of human blood plasma fluid. The parameterization follows a standard inverse-problem approach in which the optimal micro parameters are systematically searched, by gradually decoupling loosely correlated parameter spaces, to match the macro physical quantities of viscous blood flow. The predictions of this particle based multiscale model compare favorably to classic viscous flow solutions such as Counter-Poiseuille and Couette flows. It demonstrates that such coarse grained particle model can be applied to replicate the dynamics of viscous blood flow, with the advantage of bridging the gap between macroscopic flow scales and the cellular scales characterizing blood flow that continuum based models fail to handle adequately.

  10. Parameterizing the Morse Potential for Coarse-Grained Modeling of Blood Plasma

    PubMed Central

    Zhang, Na; Zhang, Peng; Kang, Wei; Bluestein, Danny; Deng, Yuefan

    2014-01-01

    Multiscale simulations of fluids such as blood represent a major computational challenge of coupling the disparate spatiotemporal scales between molecular and macroscopic transport phenomena characterizing such complex fluids. In this paper, a coarse-grained (CG) particle model is developed for simulating blood flow by modifying the Morse potential, traditionally used in Molecular Dynamics for modeling vibrating structures. The modified Morse potential is parameterized with effective mass scales for reproducing blood viscous flow properties, including density, pressure, viscosity, compressibility and characteristic flow dynamics of human blood plasma fluid. The parameterization follows a standard inverse-problem approach in which the optimal micro parameters are systematically searched, by gradually decoupling loosely correlated parameter spaces, to match the macro physical quantities of viscous blood flow. The predictions of this particle based multiscale model compare favorably to classic viscous flow solutions such as Counter-Poiseuille and Couette flows. It demonstrates that such coarse grained particle model can be applied to replicate the dynamics of viscous blood flow, with the advantage of bridging the gap between macroscopic flow scales and the cellular scales characterizing blood flow that continuum based models fail to handle adequately. PMID:24910470

  11. A coarse-grained model to study calcium activation of the cardiac thin filament

    NASA Astrophysics Data System (ADS)

    Zhang, Jing; Schwartz, Steven

    2015-03-01

    Familial hypertrophic cardiomyopathy (FHC) is one of the most common heart disease caused by genetic mutations. Cardiac muscle contraction and relaxation involve regulation of crossbridge binding to the cardiac thin filament, which regulates actomyosin interactions through calcium-dependent alterations in the dynamics of cardiac troponin (cTn) and tropomyosin (Tm). An atomistic model of cTn complex interacting with Tm has been studied by our group. A more realistic model requires the inclusion of the dynamics of actin filament, which is almost 6 times larger than cTn and Tm in terms of atom numbers, and extensive sampling of the model becomes very resource-demanding. By using physics-based protein united-residue force field, we introduce a coarse-grained model to study the calcium activation of the thin filament resulting from cTn's allosteric regulation of Tm dynamics on actin. The time scale is much longer than that of all-atom molecular dynamics simulation because of the reduction of the degrees of freedom. The coarse-grained model is a good template for studying cardiac thin filament mutations that cause FHC, and reduces the cost of computational resources.

  12. Two-Component Coarse-Grained Molecular-Dynamics Model for the Human Erythrocyte Membrane

    PubMed Central

    Li, He; Lykotrafitis, George

    2012-01-01

    We present a two-component coarse-grained molecular-dynamics model for simulating the erythrocyte membrane. The proposed model possesses the key feature of combing the lipid bilayer and the erythrocyte cytoskeleton, thus showing both the fluidic behavior of the lipid bilayer and the elastic properties of the erythrocyte cytoskeleton. In this model, three types of coarse-grained particles are introduced to represent clusters of lipid molecules, actin junctions, and band-3 complexes, respectively. The proposed model facilitates simulations that span large length scales (approximately micrometers) and timescales (approximately milliseconds). By tuning the interaction potential parameters, we were able to control the diffusivity and bending rigidity of the membrane model. We studied the membrane under shearing and found that at a low shear strain rate, the developed shear stress was due mainly to the spectrin network, whereas the viscosity of the lipid bilayer contributed to the resulting shear stress at higher strain rates. In addition, we investigated the effects of a reduced spectrin network connectivity on the shear modulus of the membrane. PMID:22225800

  13. Measurement and modeling of ozone and nitrogen oxides produced by laser breakdown in oxygen-nitrogen atmospheres.

    PubMed

    Gornushkin, Igor B; Stevenson, Chris L; Galbács, Gábor; Smith, Ben W; Winefordner, James D

    2003-11-01

    The production of ozone nad nitrogen oxides was studied during multiple laser breakdown in oxygen-nitrogen mixtures at atmospheric pressure. About 2000 laser shots at 10(10) W cm-2 were delivered into a sealed reaction chamber. The chamber with a long capillary was designed to measure absorption of O3, NO, and NO2 as a function of the number of laser shots. The light source for absorption measurements was the continuum radiation emitted by the plasma during the first 0.2 microsecond of its evolution. A kinetic model was developed that encompassed the principal chemical reactions between the major atmospheric components and the products of laser breakdown. In the model, the laser plasma was treated as a source of nitric oxide and atomic oxygen, whose rates of production were calculated using measured absorption by NO, NO2, and O3. The calculated concentration profiles for NO, NO2, and O3 were in good agreement with measured profiles over a time scale of 0-200 s. The steady-state concentration of ozone was measured in a flow cell in air. For a single breakdown in air, the estimated steady-state yield of ozone was 2 x 10(12) molecules, which agreed with the model prediction. This study can be of importance for general understanding of laser plasma chemistry and for elucidating the nature of spectral interferences and matrix effects that may take place in applied spectrochemical analysis. PMID:14658160

  14. Modeling Grain Size and Strain Rate in Linear Friction Welded Waspaloy

    NASA Astrophysics Data System (ADS)

    Chamanfar, Ahmad; Jahazi, Mohammad; Gholipour, Javad; Wanjara, Priti; Yue, Stephen

    2013-09-01

    The high-temperature deformation behavior of the Ni-base superalloy, Waspaloy, using uniaxial isothermal compression testing was investigated at temperatures above the γ' solvus, 1333 K, 1373 K, and 1413 K (1060 °C, 1100 °C, and 1140 °C) for constant true strain rates of 0.001, 0.01, 0.1, and 1 s-1 and up to a true strain of 0.83. Flow softening and microstructural investigation indicated that dynamic recrystallization took place during deformation. For the investigated conditions, the strain rate sensitivity factor and the activation energy of hot deformation were 0.199 and 462 kJ/mol, respectively. Constitutive equations relating the dynamic recrystallized grain size to the deformation temperature and strain rate were developed and used to predict the grain size and strain rate in linear friction-welded (LFWed) Waspaloy. The predictions were validated against experimental findings and data reported in the literature. It was found that the equations can reliably predict the grain size of LFWed Waspaloy. Furthermore, the estimated strain rate was in agreement with finite element modeling data reported in the literature.

  15. Coarse-grained model of conformation-dependent electrophoretic mobility and its influence on DNA dynamics.

    PubMed

    Pandey, Harsh; Underhill, Patrick T

    2015-11-01

    The electrophoretic mobility of molecules such as λ-DNA depends on the conformation of the molecule. It has been shown that electrohydrodynamic interactions between parts of the molecule lead to a mobility that depends on conformation and can explain some experimental observations. We have developed a new coarse-grained model that incorporates these changes of mobility into a bead-spring chain model. Brownian dynamics simulations have been performed using this model. The model reproduces the cross-stream migration that occurs in capillary electrophoresis when pressure-driven flow is applied parallel or antiparallel to the electric field. The model also reproduces the change of mobility when the molecule is stretched significantly in an extensional field. We find that the conformation-dependent mobility can lead to a new type of unraveling of the molecule in strong fields. This occurs when different parts of the molecule have different mobilities and the electric field is large. PMID:26651689

  16. Coarse-Grained Structural Modeling of Molecular Motors Using Multibody Dynamics

    PubMed Central

    Parker, David; Bryant, Zev; Delp, Scott L.

    2010-01-01

    Experimental and computational approaches are needed to uncover the mechanisms by which molecular motors convert chemical energy into mechanical work. In this article, we describe methods and software to generate structurally realistic models of molecular motor conformations compatible with experimental data from different sources. Coarse-grained models of molecular structures are constructed by combining groups of atoms into a system of rigid bodies connected by joints. Contacts between rigid bodies enforce excluded volume constraints, and spring potentials model system elasticity. This simplified representation allows the conformations of complex molecular motors to be simulated interactively, providing a tool for hypothesis building and quantitative comparisons between models and experiments. In an example calculation, we have used the software to construct atomically detailed models of the myosin V molecular motor bound to its actin track. The software is available at www.simtk.org. PMID:20428469

  17. Development of DPD coarse-grained models: From bulk to interfacial properties

    NASA Astrophysics Data System (ADS)

    Solano Canchaya, José G.; Dequidt, Alain; Goujon, Florent; Malfreyt, Patrice

    2016-08-01

    A new Bayesian method was recently introduced for developing coarse-grain (CG) force fields for molecular dynamics. The CG models designed for dissipative particle dynamics (DPD) are optimized based on trajectory matching. Here we extend this method to improve transferability across thermodynamic conditions. We demonstrate the capability of the method by developing a CG model of n-pentane from constant-NPT atomistic simulations of bulk liquid phases and we apply the CG-DPD model to the calculation of the surface tension of the liquid-vapor interface over a large range of temperatures. The coexisting densities, vapor pressures, and surface tensions calculated with different CG and atomistic models are compared to experiments. Depending on the database used for the development of the potentials, it is possible to build a CG model which performs very well in the reproduction of the surface tension on the orthobaric curve.

  18. Development of DPD coarse-grained models: From bulk to interfacial properties.

    PubMed

    Solano Canchaya, José G; Dequidt, Alain; Goujon, Florent; Malfreyt, Patrice

    2016-08-01

    A new Bayesian method was recently introduced for developing coarse-grain (CG) force fields for molecular dynamics. The CG models designed for dissipative particle dynamics (DPD) are optimized based on trajectory matching. Here we extend this method to improve transferability across thermodynamic conditions. We demonstrate the capability of the method by developing a CG model of n-pentane from constant-NPT atomistic simulations of bulk liquid phases and we apply the CG-DPD model to the calculation of the surface tension of the liquid-vapor interface over a large range of temperatures. The coexisting densities, vapor pressures, and surface tensions calculated with different CG and atomistic models are compared to experiments. Depending on the database used for the development of the potentials, it is possible to build a CG model which performs very well in the reproduction of the surface tension on the orthobaric curve. PMID:27497539

  19. A polarizable coarse-grained protein model for dissipative particle dynamics.

    PubMed

    Peter, Emanuel K; Lykov, Kirill; Pivkin, Igor V

    2015-10-01

    We present a new coarse-grained polarizable protein model for dissipative particle dynamics (DPD) method. This method allows large timesteps in particle-based systems and speeds up sampling by many orders of magnitude. Our new model is based on the electrostatic polarization of the protein backbone and a detailed representation of the sidechains in combination with a polarizable water model. We define our model parameters using the experimental structures of two proteins, TrpZip2 and TrpCage. Backmapping and subsequent short replica-exchange molecular dynamics runs verify our approach and show convergence to the experimental structures on the atomistic level. We validate our model on five different proteins: GB1, the WW-domain, the B-domain of Protein A, the peripheral binding subunit and villin headpiece. PMID:26339692

  20. Coarse-grained model of conformation-dependent electrophoretic mobility and its influence on DNA dynamics

    NASA Astrophysics Data System (ADS)

    Pandey, Harsh; Underhill, Patrick T.

    2015-11-01

    The electrophoretic mobility of molecules such as λ -DNA depends on the conformation of the molecule. It has been shown that electrohydrodynamic interactions between parts of the molecule lead to a mobility that depends on conformation and can explain some experimental observations. We have developed a new coarse-grained model that incorporates these changes of mobility into a bead-spring chain model. Brownian dynamics simulations have been performed using this model. The model reproduces the cross-stream migration that occurs in capillary electrophoresis when pressure-driven flow is applied parallel or antiparallel to the electric field. The model also reproduces the change of mobility when the molecule is stretched significantly in an extensional field. We find that the conformation-dependent mobility can lead to a new type of unraveling of the molecule in strong fields. This occurs when different parts of the molecule have different mobilities and the electric field is large.

  1. Systematic coarse-graining of spectrin-level red blood cell models

    PubMed Central

    Fedosov, Dmitry A.; Caswell, Bruce; Karniadakis, George Em

    2013-01-01

    We present a rigorous procedure to derive coarse-grained red blood cell (RBC) models, which yield accurate mechanical response. Based on a semi-analytic theory the linear and nonlinear elastic properties of healthy and infected RBCs in malaria can be matched with those obtained in optical tweezers stretching experiments. The present analysis predicts correctly the membrane Young’s modulus in contrast to about 50% error in predictions by previous models. In addition, we develop a stress-free model which avoids a number of pitfalls of existing RBC models, such as non-smooth or poorly controlled equilibrium shape and dependence of the mechanical properties on the initial triangulation quality. Here we employ dissipative particle dynamics for the implementation but the proposed model is general and suitable for use in many existing continuum and particle-based numerical methods. PMID:24353352

  2. Predicting Bed Grain Size in Threshold Channels Using Lidar Digital Elevation Models

    NASA Astrophysics Data System (ADS)

    Snyder, N. P.; Nesheim, A. O.; Wilkins, B. C.; Edmonds, D. A.

    2011-12-01

    Over the past 20 years, researchers have developed GIS-based algorithms to extract channel networks and measure longitudinal profiles from digital elevation models (DEMs), and have used these to study stream morphology in relation to tectonics, climate and ecology. The accuracy of stream elevations from traditional DEMs (10-50 m pixels) is typically limited by the contour interval (3-20 m) of the rasterized topographic map source. This is a particularly severe limitation in low-relief watersheds, where 3 m of channel elevation change may occur over several km. Lidar DEMs (~1 m pixels) allow researchers to resolve channel elevation changes of ~0.5 m, enabling reach-scale calculations of gradient, which is the most important parameter for understanding channel processes at that scale. Lidar DEMs have the additional advantage of allowing users to make estimates of channel width. We present a process-based model that predicts median bed grain size in threshold gravel-bed channels from lidar slope and width measurements using the Shields and Manning equations. We compare these predictions to field grain size measurements in segments of three Maine rivers. Like many paraglacial rivers, these have longitudinal profiles characterized by relatively steep (gradient >0.002) and flat (gradient <0.0005) segments, with length scales of several km. This heterogeneity corresponds to strong variations in channel form, sediment supply, bed grain size, and aquatic habitat characteristics. The model correctly predicts bed sediment size within a factor of two in ~70% of the study sites. The model works best in single-thread channels with relatively low sediment supply, and poorly in depositional, multi-thread and/or fine (median grain size <20 mm) reaches. We evaluate the river morphology (using field and lidar measurements) in the context of the Parker et al. (2007) hydraulic geometry relations for single-thread gravel-bed rivers, and find correspondence in the locations where both

  3. Numerical micromagnetic modeling of shifted hysteresis loops in two-phase grains.

    NASA Astrophysics Data System (ADS)

    Shcherbakov, V. P.; Sycheva, N. K.

    2003-04-01

    The shifted hysteresis loops (SHL) are usually referred to the exchange anisotropy resulting from superexchange interaction across the interface of a two-phase ferrimagnetic (FM) - antiferrimagnetic (AF) system like maghemite-hematite or ordered-disordered hemoilmenite intergrowths. The three-dimensional numerical micromagnetic modeling including the self-magnetostatic energy of the FM-AFM system is carried out. For this the rectangular grain was subdivided into 63x31x31 cells; in so doing the FM phase occupied the (N)x31x31 cells while the neighbouring AFM phase took the rest (63-N)x31x31 cells. The equilibrium state was obtained by the minimization of the total energy. The solution is specified mainly by the parameters N, K/Ms and relations of the domain wall (DW) width to the sizes L of the FM phase and M of the AFM phase. Here Ms is the spontaneous magnetization, K is the magnetocrystalline constant. Calculations performed under different given parameters of the grain had shown that, in accordance with the predictions of the analytical approach, in large enough grains, when the DW width < L and L < M, the process of re-magnetization proceeds by yielding the DW on the interface boundary and the SHL are indeed observed in such the grains. The magnitude of the shift Hsh of the hysteresis loop can be estimated as the DW energy/LMs = (0.01-0.1)T. If both AF and FM phases are of order (or thinner) than the corresponding DW widths, neither DW nor shifted loops do appear. The work is supported by INTAS grant 99-1273.

  4. Propagation of Source Grain-size Distribution Uncertainty by Using a Lagrangian Volcanic Particle Dispersal Model

    NASA Astrophysics Data System (ADS)

    Neri, A.; De'Michieli Vitturi, M.; Pardini, F.; Salvetti, M. V.; Spanu, A.

    2014-12-01

    Lagrangian particle dispersal models are commonly used for tracking ash particles emitted from volcanic plumes and transported under the action of atmospheric wind fields. In this work, we adopted a Lagrangian particle model to carry out an uncertainty quantification analysis of volcanic ash dispersal in the atmosphere focused on the uncertainties affecting particle source conditions. To this aim the Eulerian fully compressible mesoscale non-hydrostatic model WRF was used to generate the driving wind field. The Lagrangian particle model LPAC (de'Michieli Vitturi et al., JGR 2010) was then used to simulate the transport of mass particles under the action of atmospheric conditions. The particle motion equations were derived by expressing the Lagrangian particle acceleration as the sum of the forces acting along its trajectory, with drag forces calculated as a function of particle diameter, density, shape and Reynolds number. The simulations were representative of weak plume events of Mt. Etna and aimed to quantify the effect on the dispersal process of the uncertainty in the mean and variance of a Gaussian density function describing the grain-size distribution of the mixture and in the particle sphericity. In order to analyze the sensitivity of particle dispersal to these uncertain parameters with a reasonable number of simulations, and therefore with affordable computational costs, response surfaces in the parameter space were built by using the generalized polynomial chaos technique. The uncertainty analysis allowed to quantify the most probable values, as well as their pdf, of the number of particles as well as of the mean and variance of the grain size distribution at various distances from the source, both in air and on the ground. In particular, results highlighted the strong reduction of the uncertainty ranges of the mean and variance of the grain-size distribution with increasing distance from source and the significant control of particle sphericity on the

  5. Coarse-grained simulations of polyelectrolyte complexes: MARTINI models for poly(styrene sulfonate) and poly(diallyldimethylammonium)

    NASA Astrophysics Data System (ADS)

    Vögele, Martin; Holm, Christian; Smiatek, Jens

    2015-12-01

    We present simulations of aqueous polyelectrolyte complexes with new MARTINI models for the charged polymers poly(styrene sulfonate) and poly(diallyldimethylammonium). Our coarse-grained polyelectrolyte models allow us to study large length and long time scales with regard to chemical details and thermodynamic properties. The results are compared to the outcomes of previous atomistic molecular dynamics simulations and verify that electrostatic properties are reproduced by our MARTINI coarse-grained approach with reasonable accuracy. Structural similarity between the atomistic and the coarse-grained results is indicated by a comparison between the pair radial distribution functions and the cumulative number of surrounding particles. Our coarse-grained models are able to quantitatively reproduce previous findings like the correct charge compensation mechanism and a reduced dielectric constant of water. These results can be interpreted as the underlying reason for the stability of polyelectrolyte multilayers and complexes and validate the robustness of the proposed models.

  6. Coarse-grained simulations of polyelectrolyte complexes: MARTINI models for poly(styrene sulfonate) and poly(diallyldimethylammonium)

    SciTech Connect

    Vögele, Martin; Holm, Christian; Smiatek, Jens

    2015-12-28

    We present simulations of aqueous polyelectrolyte complexes with new MARTINI models for the charged polymers poly(styrene sulfonate) and poly(diallyldimethylammonium). Our coarse-grained polyelectrolyte models allow us to study large length and long time scales with regard to chemical details and thermodynamic properties. The results are compared to the outcomes of previous atomistic molecular dynamics simulations and verify that electrostatic properties are reproduced by our MARTINI coarse-grained approach with reasonable accuracy. Structural similarity between the atomistic and the coarse-grained results is indicated by a comparison between the pair radial distribution functions and the cumulative number of surrounding particles. Our coarse-grained models are able to quantitatively reproduce previous findings like the correct charge compensation mechanism and a reduced dielectric constant of water. These results can be interpreted as the underlying reason for the stability of polyelectrolyte multilayers and complexes and validate the robustness of the proposed models.

  7. A wheat grazing model for simulating grain and beef production: Part 1 - model development

    Technology Transfer Automated Retrieval System (TEKTRAN)

    It is a common practice to grow winter wheat (Triticum aestivum L.) as a dual-purpose crop in the U.S. Southern Great Plains to capitalize added value by cattle production. Management of the dual-purpose wheat is complex because of the interactions and tradeoffs between grain and beef production. ...

  8. A wheat grazing model for simulating grain and beef production: model evaluation and validation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    One of the major livestock-cropping enterprises in the southern Great Palins is the grazing of winter wheat (Triticum aestivum L.) in the fall and winter and harvesting grain in June. For example, nearly one million hectares of winter wheat were grazed in 2000 in Oklahoma. Grazing winter wheat duri...

  9. Atmospheric Chemistry Transport Modeling of Organic Nitrogen Input to the Ocean

    NASA Astrophysics Data System (ADS)

    Ito, A.; Lin, G.; Penner, J. E.

    2013-12-01

    Atmospheric deposition of reactive nitrogen (N) species from air pollutants is a significant source of exogenous nitrogen in marine ecosystems. Here we use an atmospheric chemical transport model to investigate the supply of soluble organic nitrogen (ON) from anthropogenic sources to the ocean. Comparisons of modeled deposition with observations at coastal and marine locations show good overall agreement for inorganic nitrogen and total soluble nitrogen, but significant underestimates for soluble ON when we include the primary soluble ON from combustion sources and the secondary carbon-containing oxidized N in gases and aerosols. The model results suggest that including the secondary carbon-containing reduced N in aerosols contributes to a better predictive capability of the deposition rates. The model results show a clear distinction in the vertical distribution of soluble ON in aerosols between different processes from the primary sources and the secondary formation. The model results (excluding the biomass burning and natural emission changes) suggest an increase in soluble ON outflow from atmospheric pollution, in particular from East Asia, to the oceans in the twentieth century. These results highlight the necessity of improving the process-based quantitative understanding of the chemical reactions of inorganic nitrogen species with organics in aerosol and cloud water.

  10. An integrated model for simulating nitrogen trading in an agricultural catchment with complex hydrogeology.

    PubMed

    Cox, T J; Rutherford, J C; Kerr, S C; Smeaton, D C; Palliser, C C

    2013-09-30

    Nitrogen loads to several New Zealand lakes are dominated by nonpoint runoff from pastoral farmland which adversely affects lake water quality. A 'cap and trade' scheme is being considered to help meet targets set for nitrogen loads to Lake Rotorua, and a numerical model, NTRADER, has been developed to simulate and compare alternative schemes. NTRADER models both the geophysics of nitrogen generation and transport, including groundwater lag times, and the economics of 'cap and trade' schemes. It integrates the output from several existing models, including a farm-scale nitrogen leaching and abatement model, a farm-scale management economic model, and a catchment-scale nitrogen transport model. This paper details modeling methods and compares possible trading program design features for the Lake Rotorua catchment. Model simulations demonstrate how a cap and trade program could be used to effectively achieve challenging environmental goals in the targeted catchment. However, results also show that, due to complex hydrogeology, satisfactory environmental outcomes may be not achieved unless groundwater lag times are incorporated into the regulatory scheme. One way to do this, as demonstrated here, would be to explicitly include lag times in the cap and trade program. The utility of the model is further demonstrated by quantifying relative differences in abatement costs across potential regulatory schemes. PMID:23771202

  11. Improving dynamic phytoplankton reserve-utilization models with an indirect proxy for internal nitrogen.

    PubMed

    Malerba, Martino E; Heimann, Kirsten; Connolly, Sean R

    2016-09-01

    Ecologists have often used indirect proxies to represent variables that are difficult or impossible to measure directly. In phytoplankton, the internal concentration of the most limiting nutrient in a cell determines its growth rate. However, directly measuring the concentration of nutrients within cells is inaccurate, expensive, destructive, and time-consuming, substantially impairing our ability to model growth rates in nutrient-limited phytoplankton populations. The red chlorophyll autofluorescence (hereafter "red fluorescence") signal emitted by a cell is highly correlated with nitrogen quota in nitrogen-limited phytoplankton species. The aim of this study was to evaluate the reliability of including flow cytometric red fluorescence as a proxy for internal nitrogen status to model phytoplankton growth rates. To this end, we used the classic Quota model and designed three approaches to calibrate its model parameters to data: where empirical observations on cell internal nitrogen quota were used to fit the model ("Nitrogen-Quota approach"), where quota dynamics were inferred only from changes in medium nutrient depletion and population density ("Virtual-Quota approach"), or where red fluorescence emission of a cell was used as an indirect proxy for its internal nitrogen quota ("Fluorescence-Quota approach"). Two separate analyses were carried out. In the first analysis, stochastic model simulations were parameterized from published empirical relationships and used to generate dynamics of phytoplankton communities reared under nitrogen-limited conditions. Quota models were fitted to the dynamics of each simulated species with the three different approaches and the performance of each model was compared. In the second analysis, we fit Quota models to laboratory time-series and we calculate the ability of each calibration approach to describe the observed trajectories of internal nitrogen quota in the culture. Results from both analyses concluded that the

  12. Modelling Nitrogen Cycling in a Mariculture Ecosystem as a Tool to Evaluate its Outflow

    NASA Astrophysics Data System (ADS)

    Lefebvre, S.; Bacher, C.; Meuret, A.; Hussenot, J.

    2001-03-01

    A model was constructed to describe an intensive mariculture ecosystem growing sea bass ( Dicentrarchus labrax), located in the salt marshes of the Fiers d'Ars Bay on the French Atlantic coast, in order to assess nitrogen cycling within the system and nitrogen outflow from the system. The land-based system was separated into three main compartments: a seawater reservoir, fish ponds and a lagoon (sedimentation pond). Three submodels were built for simulation purposes: (1) a hydrological submodel which simulated water exchange; (2) a fish growth and excretion bioenergetic submodel; and (3) a nitrogen compound transformation and loss submodel (i.e. ammonification, nitrification and assimilation processes). A two-year sampling period of nitrogen water quality concentrations and fish growth was used to validate the model. The model fitted the observations of dissolved nitrogen components, fish growth and water fluxes on a daily basis in all the compartments. The dissolved inorganic nitrogen ranged widely and over time from 0·5 to 9 g N m -3within the system, depending on seawater supply and water temperature, without affecting fish growth. Fish feed was the most important input of nitrogen into the system. The mean average input of nitrogen in the feed was 205 kg N day -1, of which 19% was retained by fish, 4% accumulated in the sediment and 61% flowed from the system as dissolved components. The farm represented about 25% of the total dissolved nitrogen export from the bay, although the farm surface area was 100 times smaller than that of the bay.

  13. Development of a new model for vibration-dissociation coupling in nitrogen

    NASA Technical Reports Server (NTRS)

    Landrum, D. B.; Candler, Graham V.

    1992-01-01

    A new model for vibration-dissociation coupling is derived using knowledge obtained from a simulation of the vibrational relaxation of heated nitrogen by collisional processes. This bilevel model is based on the assumption that nitrogen can be represented by two molecular species. The vibrational energy relaxation is represented by a modified form of the Landau-Teller equation. The effects of the bilevel model on a typical hypervelocity flowfield computation are examined and compared to the Park TTv model. Specifically, it is found that the bilevel model exhibits a decreased dissociation rate. This is believed to be due to the inhibition of dissociation by nonequilibrium vibrational relaxation.

  14. Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism

    SciTech Connect

    Li, Zhen; Bian, Xin; Karniadakis, George Em; Li, Xiantao

    2015-12-28

    The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables, and the memory kernel is evaluated directly from microscopic dynamics. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons between the CG models with Markovian and non-Markovian approximations indicate that including the memory effects using NM-DPD yields similar results as the Markovian-based DPD if the system has clear time scale separation. However, for systems with small separation of time scales, NM-DPD can reproduce correct short-time properties that are related to how the system responds to high-frequency disturbances, which cannot be captured by the Markovian-based DPD model.

  15. Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism.

    PubMed

    Li, Zhen; Bian, Xin; Li, Xiantao; Karniadakis, George Em

    2015-12-28

    The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables, and the memory kernel is evaluated directly from microscopic dynamics. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons between the CG models with Markovian and non-Markovian approximations indicate that including the memory effects using NM-DPD yields similar results as the Markovian-based DPD if the system has clear time scale separation. However, for systems with small separation of time scales, NM-DPD can reproduce correct short-time properties that are related to how the system responds to high-frequency disturbances, which cannot be captured by the Markovian-based DPD model. PMID:26723613

  16. Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism

    NASA Astrophysics Data System (ADS)

    Li, Zhen; Bian, Xin; Li, Xiantao; Karniadakis, George Em

    2015-12-01

    The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables, and the memory kernel is evaluated directly from microscopic dynamics. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons between the CG models with Markovian and non-Markovian approximations indicate that including the memory effects using NM-DPD yields similar results as the Markovian-based DPD if the system has clear time scale separation. However, for systems with small separation of time scales, NM-DPD can reproduce correct short-time properties that are related to how the system responds to high-frequency disturbances, which cannot be captured by the Markovian-based DPD model.

  17. Necessity of high-resolution for coarse-grained modeling of flexible proteins.

    PubMed

    Jia, Zhiguang; Chen, Jianhan

    2016-07-01

    The popular MARTINI coarse-grained (CG) force field requires the protein structure to be fixed, and is unsuitable for simulating dynamic processes such as protein folding. Here, we examine the feasibility of developing a flexible protein model within the MARTINI framework. The results demonstrate that the MARTINI CG scheme does not properly describe the volume and packing of protein backbone and side chains and leads to excessive collapse without structural restraints in explicit CG water. Combining atomistic protein representation with the MARTINI CG solvent, such as in the PACE model, dramatically improves description of flexible protein conformations. Yet, the CG solvent is insufficient to capture the conformational dependence of protein-solvent interactions, and PACE is unable to properly model context dependent conformational transitions. Taken together, high physical resolution at or near the atomistic level is likely necessary for flexible protein models with explicit, microscopic solvents, and the coarse-graining needs to focus on possible simplification in interaction potentials. © 2016 Wiley Periodicals, Inc. PMID:27130454

  18. A sandpile model of grain blocking and consequences for sediment dynamics in step-pool streams

    NASA Astrophysics Data System (ADS)

    Molnar, P.

    2012-04-01

    Coarse grains (cobbles to boulders) are set in motion in steep mountain streams by floods with sufficient energy to erode the particles locally and transport them downstream. During transport, grains are often blocked and form width-spannings structures called steps, separated by pools. The step-pool system is a transient, self-organizing and self-sustaining structure. The temporary storage of sediment in steps and the release of that sediment in avalanche-like pulses when steps collapse, leads to a complex nonlinear threshold-driven dynamics in sediment transport which has been observed in laboratory experiments (e.g., Zimmermann et al., 2010) and in the field (e.g., Turowski et al., 2011). The basic question in this paper is if the emergent statistical properties of sediment transport in step-pool systems may be linked to the transient state of the bed, i.e. sediment storage and morphology, and to the dynamics in sediment input. The hypothesis is that this state, in which sediment transporting events due to the collapse and rebuilding of steps of all sizes occur, is analogous to a critical state in self-organized open dissipative dynamical systems (Bak et al., 1988). To exlore the process of self-organization, a cellular automaton sandpile model is used to simulate the processes of grain blocking and hydraulically-driven step collapse in a 1-d channel. Particles are injected at the top of the channel and are allowed to travel downstream based on various local threshold rules, with the travel distance drawn from a chosen probability distribution. In sandpile modelling this is a simple 1-d limited non-local model, however it has been shown to have nontrivial dynamical behaviour (Kadanoff et al., 1989), and it captures the essence of stochastic sediment transport in step-pool systems. The numerical simulations are used to illustrate the differences between input and output sediment transport rates, mainly focussing on the magnification of intermittency and

  19. Chemistry in disks. IV. Benchmarking gas-grain chemical models with surface reactions

    NASA Astrophysics Data System (ADS)

    Semenov, D.; Hersant, F.; Wakelam, V.; Dutrey, A.; Chapillon, E.; Guilloteau, St.; Henning, Th.; Launhardt, R.; Piétu, V.; Schreyer, K.

    2010-11-01

    Context. We describe and benchmark two sophisticated chemical models developed by the Heidelberg and Bordeaux astrochemistry groups. Aims: The main goal of this study is to elaborate on a few well-described tests for state-of-the-art astrochemical codes covering a range of physical conditions and chemical processes, in particular those aimed at constraining current and future interferometric observations of protoplanetary disks. Methods: We considered three physical models: a cold molecular cloud core, a hot core, and an outer region of a T Tauri disk. Our chemical network (for both models) is based on the original gas-phase osu_03_2008 ratefile and includes gas-grain interactions and a set of surface reactions for the H-, O-, C-, S-, and N-bearing molecules. The benchmarking was performed with the increasing complexity of the considered processes: (1) the pure gas-phase chemistry, (2) the gas-phase chemistry with accretion and desorption, and (3) the full gas-grain model with surface reactions. The chemical evolution is modeled within 109 years using atomic initial abundances with heavily depleted metals and hydrogen in its molecular form. Results: The time-dependent abundances calculated with the two chemical models are essentially the same for all considered physical cases and for all species, including the most complex polyatomic ions and organic molecules. This result, however, required a lot of effort to make all necessary details consistent through the model runs, e.g., definition of the gas particle density, density of grain surface sites, or the strength and shape of the UV radiation field. Conclusions: The reference models and the benchmark setup, along with the two chemical codes and resulting time-dependent abundances are made publicly available on the internet. This will facilitate and ease the development of other astrochemical models and provide nonspecialists with a detailed description of the model ingredients and requirements to analyze the cosmic

  20. The referential grain size and effective porosity in the Kozeny-Carman model

    NASA Astrophysics Data System (ADS)

    Urumović, Kosta; Urumović, Kosta, Sr.

    2016-05-01

    In this paper, the results of permeability and specific surface area analyses as functions of granulometric composition of various sediments (from silty clays to very well graded gravels) are presented. The effective porosity and the referential grain size are presented as fundamental granulometric parameters expressing an effect of the forces operating on fluid movement through the saturated porous media. This paper suggests procedures for calculating referential grain size and determining effective (flow) porosity, which result in parameters that reliably determine the specific surface area and permeability. These procedures ensure the successful application of the Kozeny-Carman model up to the limits of validity of Darcy's law. The value of effective porosity in the referential mean grain size function was calibrated within the range of 1.5 µm to 6.0 mm. The reliability of the parameters applied in the KC model was confirmed by a very high correlation between the predicted and tested hydraulic conductivity values (R2 = 0.99 for sandy and gravelly materials; R2 = 0.70 for clayey-silty materials). The group representation of hydraulic conductivity (ranging from 10-12 m s-1 up to 10-2 m s-1) presents a coefficient of correlation of R2 = 0.97 for a total of 175 samples of various deposits. These results present new developments in the research of the effective porosity, the permeability and the specific surface area distributions of porous materials. This is important because these three parameters are critical conditions for successful groundwater flow modeling and contaminant transport. Additionally, from a practical viewpoint, it is very important to identify these parameters swiftly and very accurately.

  1. Automated optimization of water-water interaction parameters for a coarse-grained model.

    PubMed

    Fogarty, Joseph C; Chiu, See-Wing; Kirby, Peter; Jakobsson, Eric; Pandit, Sagar A

    2014-02-13

    We have developed an automated parameter optimization software framework (ParOpt) that implements the Nelder-Mead simplex algorithm and applied it to a coarse-grained polarizable water model. The model employs a tabulated, modified Morse potential with decoupled short- and long-range interactions incorporating four water molecules per interaction site. Polarizability is introduced by the addition of a harmonic angle term defined among three charged points within each bead. The target function for parameter optimization was based on the experimental density, surface tension, electric field permittivity, and diffusion coefficient. The model was validated by comparison of statistical quantities with experimental observation. We found very good performance of the optimization procedure and good agreement of the model with experiment. PMID:24460506

  2. Automated Optimization of Water–Water Interaction Parameters for a Coarse-Grained Model

    PubMed Central

    2015-01-01

    We have developed an automated parameter optimization software framework (ParOpt) that implements the Nelder–Mead simplex algorithm and applied it to a coarse-grained polarizable water model. The model employs a tabulated, modified Morse potential with decoupled short- and long-range interactions incorporating four water molecules per interaction site. Polarizability is introduced by the addition of a harmonic angle term defined among three charged points within each bead. The target function for parameter optimization was based on the experimental density, surface tension, electric field permittivity, and diffusion coefficient. The model was validated by comparison of statistical quantities with experimental observation. We found very good performance of the optimization procedure and good agreement of the model with experiment. PMID:24460506

  3. A Model to Predict Nitrogen Losses in Advanced Soil-Based Wastewater Treatment Systems

    NASA Astrophysics Data System (ADS)

    Morales, I.; Cooper, J.; Loomis, G.; Kalen, D.; Amador, J.; Boving, T. B.

    2014-12-01

    Most of the non-point source Nitrogen (N) load in rural areas is attributed to onsite wastewater treatment systems (OWTS). Nitrogen compounds are considered environmental pollutants because they deplete the oxygen availability in water bodies and produce eutrophication. The objective of this study was to simulate the fate and transport of Nitrogen in OWTS. The commercially-available 2D/3D HYDRUS software was used to develop a transport and fate model. Experimental data from a laboratory meso-cosm study included the soil moisture content, NH4 and NO3- data. That data set was used to calibrate the model. Three types of OWTS were simulated: (1) pipe-and-stone (P&S), (2) advanced soil drainfields, pressurized shallow narrow drainfield (SND) and (3) Geomat (GEO), a variation of SND. To better understand the nitrogen removal mechanism and the performance of OWTS technologies, replicate (n = 3) intact soil mesocosms were used with 15N-labelled nitrogen inputs. As a result, it was estimated that N removal by denitrification was predominant in P&S. However, it is suggested that N was removed by nitrification in SND and GEO. The calibrated model was used to estimate Nitrogen fluxes for both conventional and advanced OWTS. Also, the model predicted the N losses from nitrification and denitrification in all OWTS. These findings help to provide practitioners with guidelines to estimate N removal efficiencies for OWTS, and predict N loads and spatial distribution for identifying non-point sources.

  4. Coarse-grained particle model for pedestrian flow using diffusion maps

    NASA Astrophysics Data System (ADS)

    Marschler, Christian; Starke, Jens; Liu, Ping; Kevrekidis, Ioannis G.

    2014-01-01

    Interacting particle systems constitute the dynamic model of choice in a variety of application areas. A prominent example is pedestrian dynamics, where good design of escape routes for large buildings and public areas can improve evacuation in emergency situations, avoiding exit blocking and the ensuing panic. Here we employ diffusion maps to study the coarse-grained dynamics of two pedestrian crowds trying to pass through a door from opposite sides. These macroscopic variables and the associated smooth embeddings lead to a better description and a clearer understanding of the nature of the transition to oscillatory dynamics. We also compare the results to those obtained through intuitively chosen macroscopic variables.

  5. Sediment transport modelling based on grain size trend analysis in Augusta Harbour (Sicily)

    NASA Astrophysics Data System (ADS)

    Barbera, Giuseppe; Feo, Roberto; Freni, Gabriele

    2015-12-01

    To support marine civil engineer in pollutant studies, sediment management or dredging operations, is useful to know how the sediments move in accumulation basin. This paper investigates the dynamic of the sediment path using a two-dimensional numeric model: the Grain Size Trend Analysis (GSTA). The GSTA was applied using GiSedTrend plugin, under GIS software. The case study is the Augusta Harbour, which is one of the most polluted Italian harbours. It is the marine part of the Site of National Interest (SNI) of Priolo Gargallo (Siracusa, Italy) and it can be hydrodynamically considered as a lagoon. Two scenarios were obtained by using different geostatistical criteria.

  6. Coarse Grained Modeling of The Interface BetweenWater and Heterogeneous Surfaces

    SciTech Connect

    Willard, Adam; Chandler, David

    2008-06-23

    Using coarse grained models we investigate the behavior of water adjacent to an extended hydrophobic surface peppered with various fractions of hydrophilic patches of different sizes. We study the spatial dependence of the mean interface height, the solvent density fluctuations related to drying the patchy substrate, and the spatial dependence of interfacial fluctuations. We find that adding small uniform attractive interactions between the substrate and solvent cause the mean position of the interface to be very close to the substrate. Nevertheless, the interfacial fluctuations are large and spatially heterogeneous in response to the underlying patchy substrate. We discuss the implications of these findings to the assembly of heterogeneous surfaces.

  7. Polarizable Water Model for the Coarse-Grained MARTINI Force Field

    PubMed Central

    Sengupta, Durba; Marrink, Siewert J.

    2010-01-01

    Coarse-grained (CG) simulations have become an essential tool to study a large variety of biomolecular processes, exploring temporal and spatial scales inaccessible to traditional models of atomistic resolution. One of the major simplifications of CG models is the representation of the solvent, which is either implicit or modeled explicitly as a van der Waals particle. The effect of polarization, and thus a proper screening of interactions depending on the local environment, is absent. Given the important role of water as a ubiquitous solvent in biological systems, its treatment is crucial to the properties derived from simulation studies. Here, we parameterize a polarizable coarse-grained water model to be used in combination with the CG MARTINI force field. Using a three-bead model to represent four water molecules, we show that the orientational polarizability of real water can be effectively accounted for. This has the consequence that the dielectric screening of bulk water is reproduced. At the same time, we parameterized our new water model such that bulk water density and oil/water partitioning data remain at the same level of accuracy as for the standard MARTINI force field. We apply the new model to two cases for which current CG force fields are inadequate. First, we address the transport of ions across a lipid membrane. The computed potential of mean force shows that the ions now naturally feel the change in dielectric medium when moving from the high dielectric aqueous phase toward the low dielectric membrane interior. In the second application we consider the electroporation process of both an oil slab and a lipid bilayer. The electrostatic field drives the formation of water filled pores in both cases, following a similar mechanism as seen with atomistically detailed models. PMID:20548957

  8. Phase-field modelling of rapid solidification in alloy systems: Spontaneous grain refinement effects

    NASA Astrophysics Data System (ADS)

    Mullis, A. M.

    2012-07-01

    Phase-field modelling of rapid alloy solidification, in which the rejection of latent heat from the growing solid cannot be ignored, has lagged significantly behind the modelling of conventional casting practises which can be approximated as isothermal. This is in large part due to the fact that if realistic materials properties are adopted the ratio of the thermal to solute diffusivity (the Lewis number) is typically 103 - 104, leading to severe multi-scale problems. However, use of state-of-the-art numerical techniques such as local mesh adaptivity, implicit time-stepping and a non-linear multi-grid solver allow these difficulties to be overcome. Here we describe how the application of this model, formulated in the thin-interface limit, can help to explain the long-standing phenomenon of spontaneous grain refinement in deeply undercooled melts. We find that at intermediate undercoolings the operating point parameter, σ*, may collapse to zero, resulting in the growth of non-dendritic morphologies such as doublons and 'dendritic seaweed'. Further increases in undercooling then lead to the re-establishment of stable dendritic growth. We postulate that remelting of such seaweed structures gives rise to the low undercooling instance of grain refinement observed in alloys.

  9. A Coarse-Grained Molecular Model for Glycosaminoglycans: Application to Chondroitin, Chondroitin Sulfate, and Hyaluronic Acid

    PubMed Central

    Bathe, Mark; Rutledge, Gregory C.; Grodzinsky, Alan J.; Tidor, Bruce

    2005-01-01

    A coarse-grained molecular model is presented for the study of the equilibrium conformation and titration behavior of chondroitin (CH), chondroitin sulfate (CS), and hyaluronic acid (HA)—glycosaminoglycans (GAGs) that play a central role in determining the structure and biomechanical properties of the extracellular matrix of articular cartilage. Systematic coarse-graining from an all-atom description of the disaccharide building blocks retains the polyelectrolytes' specific chemical properties while enabling the simulation of high molecular weight chains that are inaccessible to all-atom representations. Results are presented for the characteristic ratio, the ionic strength-dependent persistence length, the pH-dependent expansion factor for the end-to-end distance, and the titration behavior of the GAGs. Although 4-sulfation of the N-acetyl-D-galactosamine residue is found to increase significantly the intrinsic stiffness of CH with respect to 6-sulfation, only small differences in the titration behavior of the two sulfated forms of CH are found. Persistence length expressions are presented for each type of GAG using a macroscopic (wormlike chain-based) and a microscopic (bond vector correlation-based) definition. Model predictions agree quantitatively with experimental conformation and titration measurements, which support use of the model in the investigation of equilibrium solution properties of GAGs. PMID:15805173

  10. Coarse-grained model for the interconversion between different crystalline cellulose allomorphs

    SciTech Connect

    Langan, Paul

    2012-01-01

    We present the results of Langevin dynamics simulations on a coarse grained model for crystalline cellulose. In particular, we analyze two different cellulose crystalline forms: cellulose I (the natural form of cellulose) and cellulose IIII (obtained after cellulose I is treated with anhydrous liquid ammonia). Cellulose IIII has been the focus of wide interest in the field of cellulosic biofuels as it can be efficiently hydrolyzed to glucose (its enzymatic degradation rates are up to 5 fold higher than those of cellulose I ). In turn, glucose can eventually be fermented into fuels. The coarse-grained model presented in this study is based on a simplified geometry and on an effective potential mimicking the changes in both intracrystalline hydrogen bonds and stacking interactions during the transition from cellulose I to cellulose IIII. The model accurately reproduces both structural and thermomechanical properties of cellulose I and IIII. The work presented herein describes the structural transition from cellulose I to cellulose IIII as driven by the change in the equilibrium state of two degrees of freedom in the cellulose chains. The structural transition from cellulose I to cellulose IIII is essentially reduced to a search for optimal spatial arrangement of the cellulose chains.

  11. The ELBA Force Field for Coarse-Grain Modeling of Lipid Membranes

    PubMed Central

    Orsi, Mario; Essex, Jonathan W.

    2011-01-01

    A new coarse-grain model for molecular dynamics simulation of lipid membranes is presented. Following a simple and conventional approach, lipid molecules are modeled by spherical sites, each representing a group of several atoms. In contrast to common coarse-grain methods, two original (interdependent) features are here adopted. First, the main electrostatics are modeled explicitly by charges and dipoles, which interact realistically through a relative dielectric constant of unity (). Second, water molecules are represented individually through a new parametrization of the simple Stockmayer potential for polar fluids; each water molecule is therefore described by a single spherical site embedded with a point dipole. The force field is shown to accurately reproduce the main physical properties of single-species phospholipid bilayers comprising dioleoylphosphatidylcholine (DOPC) and dioleoylphosphatidylethanolamine (DOPE) in the liquid crystal phase, as well as distearoylphosphatidylcholine (DSPC) in the liquid crystal and gel phases. Insights are presented into fundamental properties and phenomena that can be difficult or impossible to study with alternative computational or experimental methods. For example, we investigate the internal pressure distribution, dipole potential, lipid diffusion, and spontaneous self-assembly. Simulations lasting up to 1.5 microseconds were conducted for systems of different sizes (128, 512 and 1058 lipids); this also allowed us to identify size-dependent artifacts that are expected to affect membrane simulations in general. Future extensions and applications are discussed, particularly in relation to the methodology's inherent multiscale capabilities. PMID:22194874

  12. Role of Grain Boundaries in the Coercivity of Magnetic Thin Films Investigated by a Two-Dimensional Ginzburg-Landau-Type Model

    NASA Astrophysics Data System (ADS)

    Iwano, Kaoru; Mitsumata, Chiharu; Ono, Kanta

    2016-07-01

    We investigate a two-dimensional Ginzburg-Landau-type model, with focus on grain boundaries that are prevalent in magnetic thin films with perpendicular magnetic anisotropy. The model covers four basic interactions, which are exchange, anisotropic, external, and dipole-dipole interactions, and describes magnetic thin films. Through numerical simulations for square grains, we find that there is a minimum grain-grain distance beyond which the interactions effectively vanish. Furthermore, we also find that magnetic reversals occur at the corners of grains and confirm that circular grains result in higher coercivity under similar packing ratio, because of the absence of corners.

  13. Coarse-grained models reveal functional dynamics--I. Elastic network models--theories, comparisons and perspectives.

    PubMed

    Yang, Lee-Wei; Chng, Choon-Peng

    2008-01-01

    In this review, we summarize the progress on coarse-grained elastic network models (CG-ENMs) in the past decade. Theories were formulated to allow study of conformational dynamics in time/space frames of biological interest. Several highlighted models and their underlined hypotheses are introduced in physical depth. Important ENM offshoots, motivated to reproduce experimental data as well as to address the slow-mode-encoded configurational transitions, are also introduced. With the theoretical developments, computational cost is significantly reduced due to simplified potentials and coarse-grained schemes. Accumulating wealth of data suggest that ENMs agree equally well with experiment in describing equilibrium dynamics despite their distinct potentials and levels of coarse-graining. They however do differ in the slowest motional components that are essential to address large conformational changes of functional significance. The difference stems from the dissimilar curvatures of the harmonic energy wells described for each model. We also provide our views on the predictability of 'open to close' (open-->close) transitions of biomolecules on the basis of conformational selection theory. Lastly, we address the limitations of the ENM formalism which are partially alleviated by the complementary CG-MD approach, to be introduced in the second paper of this two-part series. PMID:19812764

  14. Improving Model Representation of Reduced Nitrogen in the Greater Yellowstone Area

    NASA Astrophysics Data System (ADS)

    Thompson, T. M.

    2015-12-01

    Human activity, including fossil fuel combustion and agriculture has greatly increased the amount of reactive nitrogen (RN) in the atmosphere and its subsequent deposition to land. Increases in deposition of RN compounds can adversely affect sensitive ecosystems and is a growing problem in many natural areas. The National Park Service in conjunction with Colorado State University researchers and assistance from the Forest Service conducted the Grand Teton Reactive Nitrogen Deposition Study (GrandTReNDS) involving spatially and temporally detailed measurements of RN during spring/summer 2011. In this work it was found that during summer months at the high elevation site Grand Targhee, 62% of the nitrogen deposition was due to reduced nitrogen, about equally split between dry and wet deposition, oxidized nitrogen accounted for 27% of the total, and the remaining was wet deposited organic nitrogen. An important next step to GrandTReNDS is the use of chemical transport models (CTMs) to estimate source contributions to RN in the park. Given the large contribution of reduced nitrogen species to total nitrogen deposition in the park, understanding and properly characterizing ammonia in CTMs is critical to estimating the total nitrogen deposition. A model performance evaluation of the CAMx uni-directional model and CMAQ bi-direction and uni-directional 2011 model simulations versus GrandTReNDS and other datasets was conducted. Preliminary results suggest that, in some areas, model performance of ambient ammonia concentration is more sensitive to the spatial resolution of the model and the accuracy of the spatial representation of emissions than to the incorporation of bi-directional flux. Additional model sensitivity runs, including sensitivity to resolution (with and without bi-directional flux capabilities), changes to model estimated ammonia dry deposition velocities, and improved representation of the spatial distribution of ammonia emissions, are used to identify the

  15. A unique Critical State two-surface hyperplasticity model for fine-grained particulate media

    NASA Astrophysics Data System (ADS)

    Coombs, W. M.; Crouch, R. S.; Augarde, C. E.

    2013-01-01

    Even mild compression can cause re-arrangement of the internal structure of clay-like geomaterials, whereby clusters of particles rotate and collapse as face-to-face contacts between the constituent mineral platelets increase at the expense of edge-to-face (or edge-to-edge) contacts. The collective action of local particle re-orientation ultimately leads to path-independent isochoric macroscopic deformation under continuous shearing. This asymptotic condition is the governing feature of Critical State elasto-plasticity models. Unlike earlier formulations, the two-surface anisotropic model proposed herein is able to reproduce a unique isotropic Critical State stress envelope which agrees well with test data. Material point predictions are compared against triaxial experimental results and five other existing constitutive models. The hyperplastic formulation is seen to offer a significantly improved descriptor of the anisotropic behaviour of fine-grained particulate materials.

  16. Monte-Carlo simulations of a coarse-grained model for α-oligothiophenes

    NASA Astrophysics Data System (ADS)

    Almutairi, Amani; Luettmer-Strathmann, Jutta

    The interfacial layer of an organic semiconductor in contact with a metal electrode has important effects on the performance of thin-film devices. However, the structure of this layer is not easy to model. Oligothiophenes are small, π-conjugated molecules with applications in organic electronics that also serve as small-molecule models for polythiophenes. α-hexithiophene (6T) is a six-ring molecule, whose adsorption on noble metal surfaces has been studied extensively (see, e.g., Ref.). In this work, we develop a coarse-grained model for α-oligothiophenes. We describe the molecules as linear chains of bonded, discotic particles with Gay-Berne potential interactions between non-bonded ellipsoids. We perform Monte Carlo simulations to study the structure of isolated and adsorbed molecules

  17. The heliocentric evolution of cometary infrared spectra - Results from an organic grain model

    NASA Technical Reports Server (NTRS)

    Chyba, Christopher F.; Sagan, Carl; Mumma, Michael J.

    1989-01-01

    An emission feature peaking near 3.4 microns that is typical of C-H stretching in hydrocarbons and which fits a simple, two-component thermal emission model for dust in the cometary coma, has been noted in observations of Comets Halley and Wilson. A noteworthy consequence of this modeling is that, at about 1 AU, emission features at wavelengths longer than 3.4 microns come to be 'diluted' by continuum emission. A quantitative development of the model shows it to agree with observational data for Comet Halley for certain, plausible values of the optical constants; the observed heliocentric evolution of the 3.4-micron feature thereby furnishes information on the composition of the comet's organic grains.

  18. PEATBOG: a biogeochemical model for analyzing coupled carbon and nitrogen dynamics in northern peatlands

    NASA Astrophysics Data System (ADS)

    Wu, Y.; Blodau, C.

    2013-08-01

    Elevated nitrogen deposition and climate change alter the vegetation communities and carbon (C) and nitrogen (N) cycling in peatlands. To address this issue we developed a new process-oriented biogeochemical model (PEATBOG) for analyzing coupled carbon and nitrogen dynamics in northern peatlands. The model consists of four submodels, which simulate: (1) daily water table depth and depth profiles of soil moisture, temperature and oxygen levels; (2) competition among three plants functional types (PFTs), production and litter production of plants; (3) decomposition of peat; and (4) production, consumption, diffusion and export of dissolved C and N species in soil water. The model is novel in the integration of the C and N cycles, the explicit spatial resolution belowground, the consistent conceptualization of movement of water and solutes, the incorporation of stoichiometric controls on elemental fluxes and a consistent conceptualization of C and N reactivity in vegetation and soil organic matter. The model was evaluated for the Mer Bleue Bog, near Ottawa, Ontario, with regards to simulation of soil moisture and temperature and the most important processes in the C and N cycles. Model sensitivity was tested for nitrogen input, precipitation, and temperature, and the choices of the most uncertain parameters were justified. A simulation of nitrogen deposition over 40 yr demonstrates the advantages of the PEATBOG model in tracking biogeochemical effects and vegetation change in the ecosystem.

  19. PEATBOG: a biogeochemical model for analyzing coupled carbon and nitrogen dynamics in northern peatlands

    NASA Astrophysics Data System (ADS)

    Wu, Y.; Blodau, C.

    2013-03-01

    Elevated nitrogen deposition and climate change alter the vegetation communities and carbon (C) and nitrogen (N) cycling in peatlands. To address this issue we developed a new process-oriented biogeochemical model (PEATBOG) for analyzing coupled carbon and nitrogen dynamics in northern peatlands. The model consists of four submodels, which simulate: (1) daily water table depth and depth profiles of soil moisture, temperature and oxygen levels; (2) competition among three plants functional types (PFTs), production and litter production of plants; (3) decomposition of peat; and (4) production, consumption, diffusion and export of dissolved C and N species in soil water. The model is novel in the integration of the C and N cycles, the explicit spatial resolution belowground, the consistent conceptualization of movement of water and solutes, the incorporation of stoichiometric controls on elemental fluxes and a consistent conceptualization of C and N reactivity in vegetation and soil organic matter. The model was evaluated for the Mer Bleue Bog, near Ottawa, Ontario, with regards to simulation of soil moisture and temperature and the most important processes in the C and N cycles. Model sensitivity was tested for nitrogen input, precipitation, and temperature, and the choices of the most uncertain parameters were justified. A simulation of nitrogen deposition over 40 yr demonstrates the advantages of the PEATBOG model in tracking biogeochemical effects and vegetation change in the ecosystem.

  20. A Direct Method for Incorporating Experimental Data into Multiscale Coarse-Grained Models.

    PubMed

    Dannenhoffer-Lafage, Thomas; White, Andrew D; Voth, Gregory A

    2016-05-10

    To extract meaningful data from molecular simulations, it is necessary to incorporate new experimental observations as they become available. Recently, a new method was developed for incorporating experimental observations into molecular simulations, called experiment directed simulation (EDS), which utilizes a maximum entropy argument to bias an existing model to agree with experimental observations while changing the original model by a minimal amount. However, there is no discussion in the literature of whether or not the minimal bias systematically and generally improves the model by creating agreement with the experiment. In this work, we show that the relative entropy of the biased system with respect to an ideal target is always reduced by the application of a minimal bias, such as the one utilized by EDS. Using all-atom simulations that have been biased with EDS, one can then easily and rapidly improve a bottom-up multiscale coarse-grained (MS-CG) model without the need for a time-consuming reparametrization of the underlying atomistic force field. Furthermore, the improvement given by the many-body interactions introduced by the EDS bias can be maintained after being projected down to effective two-body MS-CG interactions. The result of this analysis is a new paradigm in coarse-grained modeling and simulation in which the "bottom-up" and "top-down" approaches are combined within a single, rigorous formalism based on statistical mechanics. The utility of building the resulting EDS-MS-CG models is demonstrated on two molecular systems: liquid methanol and ethylene carbonate. PMID:27045328

  1. Coarse-Grained Modeling of Nucleic Acids Using Anisotropic Gay-Berne and Electric Multipole Potentials.

    PubMed

    Li, Guohui; Shen, Hujun; Zhang, Dinglin; Li, Yan; Wang, Honglei

    2016-02-01

    In this work, we attempt to apply a coarse-grained (CG) model, which is based on anisotropic Gay-Berne and electric multipole (EMP) potentials, to the modeling of nucleic acids. First, a comparison has been made between the CG and atomistic models (AMBER point-charge model) in the modeling of DNA and RNA hairpin structures. The CG results have demonstrated a good quality in maintaining the nucleic acid hairpin structures, in reproducing the dynamics of backbone atoms of nucleic acids, and in describing the hydrogen-bonding interactions between nucleic acid base pairs. Second, the CG and atomistic AMBER models yield comparable results in modeling double-stranded DNA and RNA molecules. It is encouraging that our CG model is capable of reproducing many elastic features of nucleic acid base pairs in terms of the distributions of the interbase pair step parameters (such as shift, slide, tilt, and twist) and the intrabase pair parameters (such as buckle, propeller, shear, and stretch). Finally, The GBEMP model has shown a promising ability to predict the melting temperatures of DNA duplexes with different lengths. PMID:26717419

  2. A Coarse Grained Model for Methylcellulose: Spontaneous Ring Formation at Elevated Temperature

    NASA Astrophysics Data System (ADS)

    Huang, Wenjun; Larson, Ronald

    Methylcellulose (MC) is widely used as food additives and pharma applications, where its thermo-reversible gelation behavior plays an important role. To date the gelation mechanism is not well understood, and therefore attracts great research interest. In this study, we adopted coarse-grained (CG) molecular dynamics simulations to model the MC chains, including the homopolymers and random copolymers that models commercial METHOCEL A, in an implicit water environment, where each MC monomer modeled with a single bead. The simulations are carried using a LAMMPS program. We parameterized our CG model using the radial distribution functions from atomistic simulations of short MC oligomers, extrapolating the results to long chains. We used dissociation free energy to validate our CG model against the atomistic model. The CG model captured the effects of monomer substitution type and temperature from the atomistic simulations. We applied this CG model to simulate single chains up to 1000 monomers long and obtained persistence lengths that are close to those determined from experiment. We observed the chain collapse transition for random copolymer at 600 monomers long at 50C. The chain collapsed into a stable ring structure with outer diameter around 14nm, which appears to be a precursor to the fibril structure observed in the methylcellulose gel observed by Lodge et al. in the recent studies. Our CG model can be extended to other MC derivatives for studying the interaction between these polymers and small molecules, such as hydrophobic drugs.

  3. An Anisotropic Coarse-Grained Model for Proteins Based On Gay-Berne and Electric Multipole Potentials.

    PubMed

    Shen, Hujun; Li, Yan; Ren, Pengyu; Zhang, Dinglin; Li, Guohui

    2014-02-10

    Gay-Berne anisotropic potential has been widely used to evaluate the non-bonded interactions between coarse-grained particles being described as elliptical rigid bodies. In this paper, we are presenting a coarse-grained model for twenty kinds of amino acids and proteins, based on the anisotropic Gay-Berne and point electric multipole (EMP) potentials. We demonstrate that the anisotropic coarse-grained model, namely GBEMP model, is able to reproduce many key features observed from experimental protein structures (Dunbrack Library) as well as from atomistic force field simulations (using AMOEBA, AMBER and CHARMM force fields) while saving the computational cost by a factor of about 10~200 depending on specific cases and atomistic models. More importantly, unlike other coarse-grained approaches, our framework is based on the fundamental intermolecular forces with explicit treatment of electrostatic and repulsion-dispersion forces. As a result, the coarse-grained protein model presented an accurate description of non-bonded interactions (particularly electrostatic component) between hetero-/homo-dimers (such as peptide-peptide, peptide-water). In addition, the encouraging performance of the model was reflected by the excellent correlation between GBEMP and AMOEBA models in the calculations of the dipole moment of peptides. In brief, the GBEMP model given here is general and transferable, suitable for simulating complex biomolecular systems. PMID:24659927

  4. Acoustics of marine sediment under compaction: binary grain-size model and viscoelastic extension of Biot's theory.

    PubMed

    Leurer, Klaus C; Brown, Colin

    2008-04-01

    This paper presents a model of acoustic wave propagation in unconsolidated marine sediment, including compaction, using a concept of a simplified sediment structure, modeled as a binary grain-size sphere pack. Compressional- and shear-wave velocities and attenuation follow from a combination of Biot's model, used as the general framework, and two viscoelastic extensions resulting in complex grain and frame moduli, respectively. An effective-grain model accounts for the viscoelasticity arising from local fluid flow in expandable clay minerals in clay-bearing sediments. A viscoelastic-contact model describes local fluid flow at the grain contacts. Porosity, density, and the structural Biot parameters (permeability, pore size, structure factor) as a function of pressure follow from the binary model, so that the remaining input parameters to the acoustic model consist solely of the mass fractions and the known mechanical properties of each constituent (e.g., carbonates, sand, clay, and expandable clay) of the sediment, effective pressure, or depth, and the environmental parameters (water depth, salinity, temperature). Velocity and attenuation as a function of pressure from the model are in good agreement with data on coarse- and fine-grained unconsolidated marine sediments. PMID:18397002

  5. Contrasting Polymer Behavior Under Nanoconfinement using Thermomechanically Consistent Coarse-Grained Models

    NASA Astrophysics Data System (ADS)

    Keten, Sinan; Xia, Wenjie; Hsu, David

    2015-03-01

    We present a systematic, two-bead per monomer coarse graining strategy that simulates the thermomechanical behavior of polymers several hundred times faster than all-atom MD (Hsu et al. JCTC, 2014). The predictive capability of the technique is illustrated here for 5 different methacrylate monomers and polystyrene stereoisomers. The approach involves optimization of analytical bonded potentials from atomistic bonded distributions to emulate local structure, as validated by chain end-to-end length and the radius of gyration comparisons with experiments and random coil theory. Nonbonded Lennard-Jones potentials are tuned to reproduce the elastic modulus (E) and glass transition temperature (Tg) at a single thermodynamic state. Density-corrected parameters capture temperature-modulus dependence in the 150-600 K range. Flory-Fox constants of the CG models are commensurate with all atomistic and experimental results, even though all calibrations are done at a single molecular weight. Finally, we further demonstrate the predictive capabilities of the models by examining thin film nanoconfinement effects for different polymers, film thicknesses, interfacial energies, and molecular weights. Our technique, called thermomechanically consistent coarse graining (TCCG), is demonstrated, using polystyrene and poly(methylmethacrylate) as universal benchmarks, to be a robust and effective technique to understand the thermomechanical behavior of polymers thin films and nanocomposites.

  6. Order parameter re-mapping algorithm for 3D phase field model of grain growth using FEM

    DOE PAGESBeta

    Permann, Cody J.; Tonks, Michael R.; Fromm, Bradley; Gaston, Derek R.

    2016-01-14

    Phase field modeling (PFM) is a well-known technique for simulating microstructural evolution. To model grain growth using PFM, typically each grain is assigned a unique non-conserved order parameter and each order parameter field is evolved in time. Traditional approaches using a one-to-one mapping of grains to order parameters present a challenge when modeling large numbers of grains due to the computational expense of using many order parameters. This problem is exacerbated when using an implicit finite element method (FEM), as the global matrix size is proportional to the number of order parameters. While previous work has developed methods to reducemore » the number of required variables and thus computational complexity and run time, none of the existing approaches can be applied for an implicit FEM implementation of PFM. Here, we present a modular, dynamic, scalable reassignment algorithm suitable for use in such a system. Polycrystal modeling with grain growth and stress require careful tracking of each grain’s position and orientation which is lost when using a reduced order parameter set. In conclusion, the method presented in this paper maintains a unique ID for each grain even after reassignment, to allow the PFM to be tightly coupled to calculations of the stress throughout the polycrystal. Implementation details and comparative results of our approach are presented.« less

  7. Multiscale Modeling of Damage Processes in Aluminum Alloys: Grain-Scale Mechanisms

    NASA Technical Reports Server (NTRS)

    Hochhalter, J. D.; Veilleux, M. G.; Bozek, J. E.; Glaessgen, E. H.; Ingraffea, A. R.

    2008-01-01

    This paper has two goals related to the development of a physically-grounded methodology for modeling the initial stages of fatigue crack growth in an aluminum alloy. The aluminum alloy, AA 7075-T651, is susceptible to fatigue cracking that nucleates from cracked second phase iron-bearing particles. Thus, the first goal of the paper is to validate an existing framework for the prediction of the conditions under which the particles crack. The observed statistics of particle cracking (defined as incubation for this alloy) must be accurately predicted to simulate the stochastic nature of microstructurally small fatigue crack (MSFC) formation. Also, only by simulating incubation of damage in a statistically accurate manner can subsequent stages of crack growth be accurately predicted. To maintain fidelity and computational efficiency, a filtering procedure was developed to eliminate particles that were unlikely to crack. The particle filter considers the distributions of particle sizes and shapes, grain texture, and the configuration of the surrounding grains. This filter helps substantially reduce the number of particles that need to be included in the microstructural models and forms the basis of the future work on the subsequent stages of MSFC, crack nucleation and microstructurally small crack propagation. A physics-based approach to simulating fracture should ultimately begin at nanometer length scale, in which atomistic simulation is used to predict the fundamental damage mechanisms of MSFC. These mechanisms include dislocation formation and interaction, interstitial void formation, and atomic diffusion. However, atomistic simulations quickly become computationally intractable as the system size increases, especially when directly linking to the already large microstructural models. Therefore, the second goal of this paper is to propose a method that will incorporate atomistic simulation and small-scale experimental characterization into the existing multiscale

  8. Calibration and Uncertainty in Scenario Simulations with the HBV-N Nitrogen Model

    NASA Astrophysics Data System (ADS)

    Lindstrom, G.; Arheimer, B.

    2002-12-01

    The HBV model, a Swedish precipitation-runoff model has been used extensively in basins all over Sweden for 30 years. Recently, it has been complemented with routines for nitrogen transformation in groundwater, rivers and lakes. The aim is to develop a decision support tool for evaluation of nitrogen load on recipients due to different management practices and policies. The hydrological submodel has a large number of parameters, which are established by calibration, supported by experience from earlier model applications. The root zone leakage of nitrogen, used as input to the HBV model, is simulated by the SOIL-N model, a model for turnover of water, heat and nitrogen in the unsaturated zone. The nitrogen subroutines introduce additional parameters. It is clear that no unique optimum parameter set can be obtained from a single-site model calibation to runoff and nitrogen measurements. This equifinality results in a wide range of uncertainty in the scenario simulations, when studied by ordinary Monte Carlo simulation and acceptance of all parameter sets that produce a fitness criterion above a chosen limit. This is illustrated in a case study for the R”nne † basin in the agricultural region of southern Sweden. The objective of the uncertainty analysis is to explore the uncertainty in the scenario simulations, and to provide support for decision-makers to choose between measures according to expected results and the reliability of these results. However, an ordinary Monte Carlo simulation in which all parameters are simulated and combined randomly does not take advantage of the experience from earlier applications. Therefore, a method is proposed, in which parameter sets are judged not only according to the fitness to observations but also according to their agreement with earlier model applications and hydrological experience, by use of subjective likelihood weights. The range in the scenario simulations obtained from the combined approach is finally compared

  9. Evaluation of CALPUFF nitrogen deposition modeling in the Chesapeake Bay Watershed Area using NADP data

    SciTech Connect

    Garrison, M.; Mayes, P.; Sherwell, J.

    1998-12-31

    The CALMET/CALPUFF modeling system has been used to estimate nitrogen deposition in an area surrounding Baltimore and the northern portion of the Chesapeake Bay. Comprehensive NO{sub x} emissions inventories and meteorological data bases have been developed to conduct the modeling. This paper discusses the results of an evaluation of predicted nitrogen wet deposition rates compared to measured rates at two NADP/NTN sites in Maryland, Wye and White Rock. Underprediction of wet deposition rates is investigated through the use of sensitivity and diagnostic evaluations of model performance. A suggested change to the calculation of NO{sub x} transformation rates involving an alternative specification of minimum NO{sub x} concentrations was made to CALPUFF and the performance evaluation was re-done. Results of the new evaluation show significantly improved model performance, and therefore the modification is tentatively proposed for use in further applications of CALPUFF to the assessment of nitrogen deposition in the Chesapeake Bay watershed.

  10. Microscale deformation of a tempered martensite ferritic steel: Modelling and experimental study of grain and sub-grain interactions

    NASA Astrophysics Data System (ADS)

    Golden, Brian J.; Li, Dong-Feng; Guo, Yina; Tiernan, Peter; Leen, Sean B.; O'Dowd, Noel P.

    2016-01-01

    In this paper, a finite-element modelling framework is presented with explicit representation of polycrystalline microstructure for a tempered martensite ferritic steel. A miniature notched specimen was manufactured from P91 steel with a 20,000 h service history and tested at room temperature under three point bending. Deformation at the microscale is quantified by electron back scattered diffraction (EBSD) before and after mechanical loading. A representative volume element was developed, based on the initial EBSD scan, and a crystal plasticity model used to account for slip-based inelastic deformation in the material. The model showed excellent correlation with the experimental data when the relevant comparisons were made.

  11. Coarse-grained modeling of protein second osmotic virial coefficients: sterics and short-ranged attractions.

    PubMed

    Grünberger, Alexander; Lai, Pin-Kuang; Blanco, Marco A; Roberts, Christopher J

    2013-01-24

    A series of coarse-grained models, with different levels of structural resolution, were tested to calculate the steric contributions to protein osmotic second virial coefficients (B(22,S)) for proteins ranging from small single-domain molecules to large multidomain molecules, using the recently developed Mayer sampling method. B(22,S) was compared for different levels of coarse-graining: four-beads-per-amino-acid (4bAA), one-bead-per-amino-acid (1bAA), one-sphere-per-domain (1sD), and one-sphere-per-protein (1sP). Values for the 1bAA and 4bAA models were quantitatively indistinguishable for both spherical and nonspherical proteins, and the agreement with values from all-atom models improved with increasing protein size, making the CG approach attractive for large proteins of biotechnological interest. Interestingly, in the absence of detailed structural information, the hydrodynamic radius (R(h)) along with a simple 1sP approximation provided reasonably accurate values for B(22,S) for both globular and highly asymmetric protein structures, while other 1sP approximations gave poorer agreement; this helps to justify the currently empirical practice of estimating B(22,S) from R(h) for large proteins such as antibodies. The results also indicate that either 1bAA or 4bAA CG models may be good starting points for incorporating short-range attractions. Comparison of gD-crystallin B(22) values including both sterics and short-range attractions shows that 1bAA and 4bAA models give equivalent results when properly scaled to account for differences in the number of surface beads in the two CG descriptions. This provides a basis for future work that will also incorporate long-ranged electrostatic attractions and repulsions. PMID:23245189

  12. Bridging scales: from atoms to coarse-grained models for soft matter systems

    NASA Astrophysics Data System (ADS)

    Peter, Christine

    2015-03-01

    Molecular simulation has extended to increasingly complex soft matter systems, and time-scale and system-size requirements have instigated the use of simulation models on multiple levels of resolution. On the classical particle-based level, a large variety of methods to develop coarse grained (CG) simulation models has emerged, an important subgroup being those scale-bridging methods where the CG model is derived from and systematically linked to an underlying atomistic description. In my talk, I will introduce a few of these methods, address the underlying concepts as well as some of the ongoing challenges that are inherent to coarse graining. A natural consequence of reducing the level of resolution in a simulation model is a loss of transferability, i.e. a decreasing ability to correctly describe a system at several thermodynamic state points. Intimately linked to this is a loss of the ability to correctly represent all structural, thermodynamic and dynamic properties of the system. Examples for these limitations are easily found in all CG simulations of multicomponent or multiphase soft matter systems - ranging from liquid crystals, biomolecular aggregates, biomaterials to hard/soft nanocomposites. A correct representation of phase transitions, phase coexistence, environment-induced conformational transitions, or effects due to surfaces and interfaces is a severe challenge for bottom-up CG models. Addressing this challenge requires both a method of generating CG potentials as well as finding and rationalizing an appropriate reference state point to start out from. I will illustrate several of these aspects using examples from the biomolecular and (biomimetic-) materials world.

  13. Dynamic SPARROW Modeling of Nitrogen Flux with Climate and MODIS Vegetation Indices as Drivers

    NASA Astrophysics Data System (ADS)

    Smith, R. A.; Brakebill, J.; Schwarz, G.; Alexander, R. B.; Hirsch, R. M.; Nolin, A. W.; Macauley, M.; Zhang, Q.; Shih, J.; Wang, W.; Sproles, E.

    2011-12-01

    SPARROW models are widely used to identify and quantify the sources of contaminants in watersheds and to predict their flux and concentration at specified locations downstream. Conventional SPARROW models are statistically calibrated and describe the average relationship between sources and stream conditions based on long-term water quality monitoring data and spatially-referenced explanatory information. But many watershed management issues stem from intra- and inter-annual changes in contaminant sources, hydrologic forcing, or other environmental conditions which cause a temporary imbalance between inputs and stream water quality. Dynamic behavior of the system relating to changes in watershed storage and processing then becomes important. In this study, we describe a dynamically calibrated SPARROW model of total nitrogen flux in the Potomac River Basin based on seasonal water quality and watershed input data for 80 monitoring stations over the period 2000 to 2008. One challenge in dynamic modeling of reactive nitrogen is obtaining frequently-reported, spatially-detailed input data on the phenology of agricultural production and terrestrial vegetation. In this NASA-funded research, we use the Enhanced Vegetation Index (EVI) and gross primary productivity data from the Terra Satellite-borne MODIS sensor to parameterize seasonal uptake and release of nitrogen. The spatial reference frame of the model is a 16,000-reach, 1:100,000-scale stream network, and the computational time step is seasonal. Precipitation and temperature data are from PRISM. The model formulation allows for separate storage compartments for nonpoint sources including fertilized cropland, pasture, urban land, and atmospheric deposition. Removal of nitrogen from watershed storage to stream channels and to "permanent" sinks (deep groundwater and the atmosphere) occur as parallel first-order processes. We use the model to explore an important issue in nutrient management in the Potomac and other

  14. Neural networks modelling of nitrogen export: model development and application to unmonitored boreal forest watersheds.

    PubMed

    Li, X; Nour, M H; Smith, D W; Prepas, E E

    2010-04-14

    In remotely located boreal forest watersheds, monitoring nitrogen (N) export in stream discharge often is not feasible because of high costs and site inaccessibility. Therefore, modelling tools that can predict N export in unmonitored watersheds are urgently needed to support management decisions for these watersheds. The hydrological and biogeochemical processes that regulate N export in streams draining watersheds are complex and not fully understood, which makes artificial neural network (ANN) modelling suitable for such an application. This study developed ANN models to predict N export from watersheds relying only on easily accessible climate data and remote sensing (RS) data from the public domain. The models were able to predict the daily N export (g/km2/d) in five watersheds ranging in size from 5-130 km2 with reasonable accuracy. Similarity indices were developed between any two studied watersheds to quantify watershed similarity and guide the transferability of models from monitored watersheds to unmonitored ones. To demonstrate the applicability of the ANN models to unmonitored watersheds, the calibrated ANN models were used to predict N export in different watersheds (unmonitored watersheds in this perspective) without further calibration. The similarity index based upon a rainfall index, a peatland index and a RS normalized difference water index showed the best correlation with the transferability of the models. This study represents an important first step towards transferring ANN models developed for one watershed to unmonitored watersheds using similarity indices that rely on freely available climate and