Science.gov

Sample records for modeling grain nitrogen

  1. Modeling Grain Nitrogen Accumulation and Protein Composition to Understand the Sink/Source Regulations of Nitrogen Remobilization for Wheat

    PubMed Central

    Martre, Pierre; Porter, John R.; Jamieson, Peter D.; Triboï, Eugène

    2003-01-01

    A functional explanation for the regulation of grain nitrogen (N) accumulation in cereal by environmental and genetic factors remains elusive. Here, new mechanistic hypotheses of grain N accumulation are proposed and tested for wheat (Triticum aestivum). First, we tested experimentally the hypothesis that grain N accumulation is mostly source regulated. Four contrasting cultivars, in terms of their grain N concentrations and yield potentials, were grown with non-limiting N supply. Grain number per ear was reduced by removing the top part of the ear at anthesis. Reduction in grain number gave a significant increase in N content per grain for all cultivars, showing that grain N accumulation was source regulated. However, on a per ear basis, cultivars with a high grain number fully compensated their N accumulation for reduced grain number at anthesis. Cultivars with a lower grain number did not compensate completely, and grain N per ear was decreased by 16%. Second, new mechanistic hypotheses of the origins of grain N source regulation and its response to environment were tested by simulation. The hypotheses were: (a) The regulation by N sources of grain N accumulation applies only for the storage proteins (i.e. gliadin and glutenin fractions); (b) accumulation of structural and metabolic proteins (i.e. albumin-globulin and amphiphilic fractions) is sink-regulated; and (c) N partitioning between gliadins and glutenins is constant during grain development and unmodified by growing conditions. Comparison of experimental and simulation results of the accumulation of grain protein fractions under wide ranges of N fertilization, temperatures, and irrigation supported these hypotheses. PMID:14630962

  2. Integrating remotely sensed leaf area index and leaf nitrogen accumulation with RiceGrow model based on particle swarm optimization algorithm for rice grain yield assessment

    NASA Astrophysics Data System (ADS)

    Wang, Hang; Zhu, Yan; Li, Wenlong; Cao, Weixing; Tian, Yongchao

    2014-01-01

    A regional rice (Oryza sativa) grain yield prediction technique was proposed by integration of ground-based and spaceborne remote sensing (RS) data with the rice growth model (RiceGrow) through a new particle swarm optimization (PSO) algorithm. Based on an initialization/parameterization strategy (calibration), two agronomic indicators, leaf area index (LAI) and leaf nitrogen accumulation (LNA) remotely sensed by field spectra and satellite images, were combined to serve as an external assimilation parameter and integrated with the RiceGrow model for inversion of three model management parameters, including sowing date, sowing rate, and nitrogen rate. Rice grain yield was then predicted by inputting these optimized parameters into the reinitialized model. PSO was used for the parameterization and regionalization of the integrated model and compared with the shuffled complex evolution-University of Arizona (SCE-UA) optimization algorithm. The test results showed that LAI together with LNA as the integrated parameter performed better than each alone for crop model parameter initialization. PSO also performed better than SCE-UA in terms of running efficiency and assimilation results, indicating that PSO is a reliable optimization method for assimilating RS information and the crop growth model. The integrated model also had improved precision for predicting rice grain yield.

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

    USDA-ARS?s Scientific Manuscript database

    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 (...

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

    USDA-ARS?s Scientific Manuscript database

    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)...

  5. 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.

  6. The Nitrogen Contribution of Different Plant Parts to Wheat Grains: Exploring Genotype, Water, and Nitrogen Effects

    PubMed Central

    Sanchez-Bragado, Rut; Serret, M. Dolors; Araus, José L.

    2017-01-01

    The flag leaf has been traditionally considered as the main contributor to grain nitrogen. However, during the reproductive stage, other organs besides the flag leaf may supply nitrogen to developing grains. Therefore, the contribution of the ear and other organs to the nitrogen supplied to the growing grains remains unclear. It is important to develop phenotypic tools to assess the relative contribution of different plant parts to the N accumulated in the grains of wheat which may helps to develop genotypes that use N more efficiently. We studied the effect of growing conditions (different levels of water and nitrogen in the field) on the nitrogen contribution of the spike and different vegetative organs of the plant to the grains. The natural abundance of δ15N and total N content in the flag blade, peduncle, whole spike, glumes and awns were compared to the δ15N and total N in mature grains to trace the origin of nitrogen redistribution to the grains. The δ15N and total N content of the different plant parts correlated positively with the δ15N and total N content of mature grains suggesting that all organs may contribute a portion of their N content to the grains. The potential contribution of the flag blade to grain N increased (by 46%) as the growing conditions improved, whereas the potential contribution of the glumes plus awns and the peduncle increased (46 and 31%, respectively) as water and nitrogen stress increased. In general, potential contribution of the ear providing N to growing grains was similar (42%) than that of the vegetative parts of the plants (30–40%), regardless of the growing conditions. Thus, the potential ear N content could be a positive trait for plant phenotyping, especially under water and nitrogen limiting conditions. In that sense, genotypic variability existed at least between old (tall) and modern (semidwarf) cultivars, with the ear from modern genotypes exhibiting less relative contribution to the total grain N. The combined

  7. The Nitrogen Contribution of Different Plant Parts to Wheat Grains: Exploring Genotype, Water, and Nitrogen Effects.

    PubMed

    Sanchez-Bragado, Rut; Serret, M Dolors; Araus, José L

    2016-01-01

    The flag leaf has been traditionally considered as the main contributor to grain nitrogen. However, during the reproductive stage, other organs besides the flag leaf may supply nitrogen to developing grains. Therefore, the contribution of the ear and other organs to the nitrogen supplied to the growing grains remains unclear. It is important to develop phenotypic tools to assess the relative contribution of different plant parts to the N accumulated in the grains of wheat which may helps to develop genotypes that use N more efficiently. We studied the effect of growing conditions (different levels of water and nitrogen in the field) on the nitrogen contribution of the spike and different vegetative organs of the plant to the grains. The natural abundance of δ(15)N and total N content in the flag blade, peduncle, whole spike, glumes and awns were compared to the δ(15)N and total N in mature grains to trace the origin of nitrogen redistribution to the grains. The δ(15)N and total N content of the different plant parts correlated positively with the δ(15)N and total N content of mature grains suggesting that all organs may contribute a portion of their N content to the grains. The potential contribution of the flag blade to grain N increased (by 46%) as the growing conditions improved, whereas the potential contribution of the glumes plus awns and the peduncle increased (46 and 31%, respectively) as water and nitrogen stress increased. In general, potential contribution of the ear providing N to growing grains was similar (42%) than that of the vegetative parts of the plants (30-40%), regardless of the growing conditions. Thus, the potential ear N content could be a positive trait for plant phenotyping, especially under water and nitrogen limiting conditions. In that sense, genotypic variability existed at least between old (tall) and modern (semidwarf) cultivars, with the ear from modern genotypes exhibiting less relative contribution to the total grain N. The

  8. Relationship between grain crop yield potential and nitrogen response

    USDA-ARS?s Scientific Manuscript database

    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 ...

  9. [Effects of soil fertility and nitrogen application rate on nitrogen absorption and translocation, grain yield, and grain protein content of wheat].

    PubMed

    Wang, Yuefu; Yu, Zhenwen; Li, Xiangxia; Yu, Songlie

    2003-11-01

    The results of this study showed that nitrogen application improved the nitrogen uptake by wheat, especially during its late growth stage. Although a higher nitrogen application rate could increase the amount of absorbed nitrogen, an excess of nitrogen would remain in vegetative organs at the stage after flowering, owing to the low translocation rate of nitrogen from these organs to the grain, and hence, the nitrogen use efficiency and nitrogen harvest index were decreased. Compared with that on high fertility soil, the ratio of nitrogen absorbed from fertilizer to total absorbed nitrogen was higher when the wheat was grown on low fertility soil. On high fertility soil, wheat plant absorbed more nitrogen from top-dressed fertilizer than from basis fertilizer, and top-dressed fertilizer contributed more nitrogen to the grain. It was reversed on low fertility soil.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  11. [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).

  12. [Effects of watering and nitrogen fertilization on the growth, grain yield, and water- and nitrogen use efficiency of winter wheat].

    PubMed

    Li, Li; Hong, Jian-Ping; Wang, Hong-Ting; Xiu, Ying-He; Zhang, Lu

    2013-05-01

    A field experiment with split-plot design was conducted to study the effects of watering, nitrogen fertilization, and their interactions on the growth, grain yield, and water- and nitrogen use efficiency of winter wheat. Four watering levels (0, 900, 1200, and 1500 m3 x hm(-2)) in main plots and five nitrogen fertilization levels (0, 90, 150, 210, and 270 kg N x hm(-2)) in sub-plots were designed. The results showed that the grain yield, nitrogen absorption, nitrogen use efficiency, and nitrogen productive efficiency of winter wheat increased with increasing level of watering, but the nitrogen use efficiency and nitrogen productive efficiency decreased with increasing nitrogen fertilization level. The grain yield, nitrogen absorption, and nitrogen harvest index were increased with increasing nitrogen fertilization level when the nitrogen application rate was 0-150 kg N x hm(-2), but not further increased significantly when the nitrogen application rate exceeded 150 kg x hm(-2). With the increasing level of watering, the water consumption amount (WCA) and the total water use efficiency increased, while the proportion of precipitation and soil water supply to WCA as well as the irrigation water use efficiency decreased. With the increasing level of nitrogen fertilization, the proportion of precipitation and watering amount to WCA increased, that of soil water supply to WCA decreased, and the total water use efficiency and irrigation water use efficiency decreased after an initial increase, with no significant differences among the treatments of 150, 210, and 270 kg N x hm(-2). It was considered that under our experimental condition, 1500 m3 x hm(-2) of watering amount plus 150 kg x hm(-2) of nitrogen fertilization could be the optimal combination for the high yielding and high efficiency.

  13. [Proteomics of rice leaf and grain at late growth stage under different nitrogen fertilization levels].

    PubMed

    Ning, Shu-ju; Zhao, Min; Xiang, Xiao-liang; Wei, Dao-zhi

    2010-10-01

    Taking super-rice Liangyoupeijiu as test material, and by the method of two-dimensional gel electrophoresis (2-DE), this paper studied the changes in the leaf and grain proteomics of the variety at its late growth stage under different levels of nitrogen fertilization (1/2 times of normal nitrogen level, 20 mg x L(-1); normal nitrogen level, 40 mg x L(-1); 2 times of normal nitrogen level, 80 mg x L(-1)), with the biological functions of 16 leaf proteins, 9 inferior grain proteins, and 4 superior grain proteins identified and analyzed. Nitrogen fertilization could affect and regulate the plant photosynthesis via affecting the activation of photosynthesis-related enzymes and of CO2, the light system unit, and the constitution of electron transfer chain at the late growth stage of the variety. It could also promote the expression of the enzymes related to the energy synthesis and growth in inferior grains. High nitrogen fertilization level was not beneficial to the synthesis of starch in superior grain, but sufficient nitrogen supply was still important for the substance accumulation and metabolism. Therefore, rational nitrogen fertilization could increase the photosynthesis rate of flag leaves, enhance the source function, delay the functional early ageing, and promote the grain-filling at late growth stage.

  14. 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.

  15. 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 ...

  16. 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 ...

  17. Nitrogen components in lunar soil 12023: Complex grains are not the carrier of isotopically light nitrogen

    NASA Astrophysics Data System (ADS)

    Brilliant, D. R.; Franchi, I. A.; Pillinger, C. T.

    1994-09-01

    High resolution stepped combustion is used to release isotopically distinct N components of different thermal stability in lunar soil 12023. The isotopically light gas in this soil appears to be the same as that found in the lunar breccia 79035, but the latter material has little of an isotopically heavy component of only slightly lower thermal stability. Complex grains in 12023, which probably only release their N on melting, contain a mixture of the heavy and light N in approximately the same proportions as the unaggregated soil. Ideas that require complex grains to be enriched in a light-N component, synonymous with the ancient solar wind, therefore, cannot be correct. The implications for models invoking solar-wind secular variation are discussed.

  18. HYBRID MESOSCALE MODELING OF DYNAMIC GRAIN FRAGMENTATION

    SciTech Connect

    R. SWIFT; C. HAGELBERG; M. HILTL

    2001-04-01

    Fines created by grain fragmentation from shaped-charge, jet perforation treatment often plug-up pores in the vicinity of the perforation tunnel. We analyze and model grain damage on samples recovered from impact tests of dry and water saturated sandstone at stress levels and duration similar to that of perforation loading. Analyses of Scanning Electron Microscope (SEM) images and laser particle size measurements on portions of the recovered samples characterize grain damage and changes in grain size distribution. Hybrid modeling that combines the Discrete Element Method (DEM) with Smooth Particle Hydrodynamics (SPH), and includes mesoscale representation of grain/pore structure, shows how grain damage evolves for dry and wet conditions. Modeling defines behavior in accord with recovered sample analyses as follows: (1) Increase in grain damage is obtained with an increase in stress level and pulse duration. (2) The grains in dry samples are extremely and irregularly fragmented with extensive reduced porosity. (3) Less grain damage and higher porosity is obtained in saturated samples. The influence of pore fluid mitigates the interaction between grains, thus reducing fragmentation damage. (4) Computed particle size distributions are similar in character to measurements.

  19. Stochastic modeling of grain-fabric formation

    NASA Astrophysics Data System (ADS)

    Naruse, H.

    2011-12-01

    In this study, we developed a stochastic model of the grain-fabric formation, and performed flume experiments and field observations to examine the model predictions. It has been suggested that the grain fabric (preferred orientation of grain long axes) of sand/sandstone provides significant sedimentological information such as paleocurrent direction, sediment-transport processes, and depositional environments . Grains orient along preferred directions because of interactions between fluids and sediment particles , and it has been known that there are two types of preferred grain orientations-a(p)a(i) and a(t)b(i). a(t)b(i)- and a(p)a(i)-type fabrics are preferred grain orientations that are perpendicular and parallel to the flow direction, respectively. River gravels tend to exhibit the a(t)b(i) fabric, whereas turbidite sandstones often exhibit the a(p)a(i) fabric; nonetheless, there exist many exceptions, and the grain-fabric tendency often fluctuates even in a single bed. The cause of the two types of grain fabric currently unknown, and the flow parameters that influence the fabric type have not yet been determined . Toward this end, we developed a stochastic model of grain-fabric formation that consider probabilistic density functions (PDFs) of the orientations of both influx and outflux grains to an active layer of surface sediments. Flume experiments using rice grains provided the PDFs of both influx and outflux grain orientation that can be well approximated by the von Mises distribution. On average, the orientations of influx and outflux grains were both perpendicular to the flow direction. This is because the projection area of a grain to the flow direction is maximized when the grain orients perpendicular to the flow. The proposed model predicts that larger grains or weaker flow (low Shields dimensionless stress) produces the a(t)b(i) fabric whereas an intense flow (high Shields dimensionless stress) produces the a(p)a(i) fabric. It also predicts that

  20. 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

  1. Effects of starter nitrogen fertilizer on soybean root activity, leaf photosynthesis and grain yield

    PubMed Central

    Gai, Zhijia; Zhang, Jingtao; Li, Caifeng

    2017-01-01

    The objective of this study was to examine the impact of starter nitrogen fertilizer on soybean root activity, leaf photosynthesis, grain yield and their relationship. To achieve this objective, field experiments were conducted in 2013 and 2014, using a randomized complete block design, with three replications. Nitrogen was applied at planting at rates of 0, 25, 50, and 75 kg N ha-1. In both years, starter nitrogen fertilizer benefited root activity, leaf photosynthesis, and consequently its yield. Statistically significant correlation was found among root activity, leaf photosynthetic rate, and grain yield at the developmental stage. The application of N25, N50, and N75 increased grain yield by 1.28%, 2.47%, and 1.58% in 2013 and by 0.62%, 2.77%, and 2.06% in 2014 compared to the N0 treatment. Maximum grain yield of 3238.91 kg ha-1 in 2013 and 3086.87 kg ha-1 in 2014 were recorded for N50 treatment. Grain yield was greater for 2013 than 2014, possibly due to more favorable environmental conditions. This research indicated that applying nitrogen as starter is necessary to increase soybean yield in Sangjiang River Plain in China. PMID:28388620

  2. 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…

  3. 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…

  4. Effects of Genotype, Season, and Nitrogen Nutrition on Gene Expression and Protein Accumulation in Wheat Grain

    PubMed Central

    2014-01-01

    Six commercial U.K. cultivars of winter wheat selected to represent different abilities to partition nitrogen into grain protein were grown in replicated field trials at five different sites over three seasons. The proportion of LMW glutenin subunits decreased and the proportion of gliadins increased during grain development and in response to N application. Differences were observed between the proportions of LMW glutenin subunits and gliadins in low- and high-protein grain, these two fractions being decreased and increased, respectively. There was little effect of grain protein content on the proportions of either the HMW glutenin subunits or large glutenin polymers, which are enriched in these subunits, with the latter increasing during development in all cultivars. The proportion of total protein present in polymers in the mature grain decreased with increasing N level. Correlations were also observed between the abundances of gliadin protein transcripts and the corresponding proteins. PMID:24786983

  5. Effect of carbon and nitrogen on grain boundary segregation in irradiated stainless steels

    NASA Astrophysics Data System (ADS)

    Kano, F.; Fukuya, K.; Hamada, S.; Miwa, Y.

    1998-10-01

    SUS304 stainless steels with carbon contents of 0.052%, 0.019% and 0.004% and SUS316L stainless steels with nitrogen contents of 0.095%, 0.032% and 0.003% were irradiated with 12 MeV Ni ions at 573 K to a dose of 1 dpa at 1 μm depth. Microstructure and grain boundary chemical composition were investigated using a transmission electron microscope with a field-emission-gun (FE-TEM) at the probe size of 0.5 nm. The number density of dislocation loop was higher as the carbon content was higher and was almost independent of nitrogen content. With increasing carbon and nitrogen content, the degree of Cr depletion and Si/Ni segregation was decreased. Both carbon and nitrogen suppressed the Cr depletion and Si/Ni segregation. The suppression effect of carbon was larger than that of nitrogen.

  6. 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.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  8. 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.

  9. 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

  10. 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.

  11. Grain subproteome responses to nitrogen and sulfur supply in diploid wheat Triticum monococcum ssp. monococcum.

    PubMed

    Bonnot, Titouan; Bancel, Emmanuelle; Alvarez, David; Davanture, Marlène; Boudet, Julie; Pailloux, Marie; Zivy, Michel; Ravel, Catherine; Martre, Pierre

    2017-09-01

    Wheat grain storage proteins (GSPs) make up most of the protein content of grain and determine flour end-use value. The synthesis and accumulation of GSPs depend highly on nitrogen (N) and sulfur (S) availability and it is important to understand the underlying control mechanisms. Here we studied how the einkorn (Triticum monococcum ssp. monococcum) grain proteome responds to different amounts of N and S supply during grain development. GSP composition at grain maturity was clearly impacted by nutrition treatments, due to early changes in the rate of GSP accumulation during grain filling. Large-scale analysis of the nuclear and albumin-globulin subproteomes during this key developmental phase revealed that the abundance of 203 proteins was significantly modified by the nutrition treatments. Our results showed that the grain proteome was highly affected by perturbation in the N:S balance. S supply strongly increased the rate of accumulation of S-rich α/β-gliadin and γ-gliadin, and the abundance of several other proteins involved in glutathione metabolism. Post-anthesis N supply resulted in the activation of amino acid metabolism at the expense of carbohydrate metabolism and the activation of transport processes including nucleocytoplasmic transit. Protein accumulation networks were analyzed. Several central actors in the response were identified whose variation in abundance was related to variation in the amounts of many other proteins and are thus potentially important for GSP accumulation. This detailed analysis of grain subproteomes provides information on how wheat GSP composition can possibly be controlled in low-level fertilization condition. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

  12. 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

  13. 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

  14. Grain Surface Models and Data for Astrochemistry

    NASA Astrophysics Data System (ADS)

    Cuppen, H. M.; Walsh, C.; Lamberts, T.; Semenov, D.; Garrod, R. T.; Penteado, E. M.; Ioppolo, S.

    2017-01-01

    The cross-disciplinary field of astrochemistry exists to understand the formation, destruction, and survival of molecules in astrophysical environments. Molecules in space are synthesized via a large variety of gas-phase reactions, and reactions on dust-grain surfaces, where the surface acts as a catalyst. A broad consensus has been reached in the astrochemistry community on how to suitably treat gas-phase processes in models, and also on how to present the necessary reaction data in databases; however, no such consensus has yet been reached for grain-surface processes. A team of {˜}25 experts covering observational, laboratory and theoretical (astro)chemistry met in summer of 2014 at the Lorentz Center in Leiden with the aim to provide solutions for this problem and to review the current state-of-the-art of grain surface models, both in terms of technical implementation into models as well as the most up-to-date information available from experiments and chemical computations. This review builds on the results of this workshop and gives an outlook for future directions.

  15. Wheat ear carbon assimilation and nitrogen remobilization contribute significantly to grain yield.

    PubMed

    Zhou, Bangwei; Serret, Maria Dolores; Elazab, Abdelhalim; Bort Pie, Jordi; Araus, José Luis; Aranjuelo, Iker; Sanz-Sáez, Álvaro

    2016-11-01

    The role of wheat ears as a source of nitrogen (N) and carbon (C) in the grain filling process has barely been studied. To resolve this question, five wheat genotypes were labeled with (15) N-enriched nutrient solution. N remobilization and absorption were estimated via the nitrogen isotope composition of total organic matter and Rubisco. Gas exchange analyses showed that ear photosynthesis contributed substantially to grain filling in spite of the great loss of C due to respiration. Of the total kernel N, 64.7% was derived from the N acquired between sowing and anthesis, while the remaining 35.3% was derived from the N acquired between anthesis and maturity. In addition, 1.87 times more N was remobilized to the developing kernel from the ear than from the flag leaf. The higher yielding genotypes showed an increased N remobilization to the kernel compared to the lower yielding genotypes. In addition, the higher yielding genotypes remobilized more N from the ears to the kernel than the lower yielding genotypes, while the lower yielding genotypes remobilized more N from the flag leaf to the kernel. Therefore, the ears contribute significantly toward fulfilling C and N demands during grain filling.

  16. Dynamics of Light and Nitrogen Distribution during Grain Filling within Wheat Canopy1[OA

    PubMed Central

    Bertheloot, Jessica; Martre, Pierre; Andrieu, Bruno

    2008-01-01

    In monocarpic species, during the reproductive stage the growing grains represent a strong sink for nitrogen (N) and trigger N remobilization from the vegetative organs, which decreases canopy photosynthesis and accelerates leaf senescence. The spatiotemporal distribution of N in a reproductive canopy has not been described in detail. Here, we investigated the role of the local light environment on the spatiotemporal distribution of leaf lamina N mass per unit leaf area (SLN) during grain filling of field-grown wheat (Triticum aestivum). In addition, in order to provide some insight into the coordination of N depletion between the different vegetative organs, N dynamics were studied for individual leaf laminae, leaf sheaths, internodes, and chaff of the top fertile culms. At the canopy scale, SLN distribution paralleled the light gradient below the flag leaf collar until almost the end of grain filling. On the contrary, the significant light gradient along the flag leaf lamina was not associated with a SLN gradient. Within the top fertile culms, the time course of total (alive + necrotic tissues) N concentration of the different laminae and sheaths displayed a similar pattern. Another common pattern was observed for internodes and chaff. During the period of no root N uptake, N depletion of individual laminae and sheaths followed a first-order kinetics independent of leaf age, genotype, or N nutrition. The results presented here show that during grain filling, N dynamics are integrated at the culm scale and strongly depend on the local light conditions determined by the canopy structure. PMID:18799664

  17. 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.

  18. 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

  19. 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

  20. 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.

  1. 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

  2. Coarse-grained model of glycosaminoglycans.

    PubMed

    Samsonov, Sergey A; Bichmann, Leon; Pisabarro, M Teresa

    2015-01-26

    Glycosaminoglycans (GAGs) represent a class of anionic periodic linear polysaccharides, which mediate cell communication processes by interactions with their protein targets in the extracellular matrix. Due to their high flexibility, charged nature, periodicity, and polymeric nature, GAGs are challenging systems for computational approaches. To deal with the length challenge, coarse-grained (CG) modeling could be a promising approach. In this work, we develop AMBER-compatible CG parameters for GAGs using all-atomic (AA) molecular dynamics (MD) simulations in explicit solvent and the Boltzmann conversion approach. We compare both global and local properties of GAGs obtained in the simulations with AA and CG approaches, and we conclude that our CG model is appropriate for the MD approach of long GAG molecules at long time scales.

  3. 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.

  4. 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.

  5. Modeling Nitrogen Cycling in Delaware Estuary

    NASA Astrophysics Data System (ADS)

    Tabatabai, A.; Wilkin, J.

    2016-02-01

    Estuaries play a critical role in transforming the biogeochemical properties of water that originates from fluvial sources before it is ultimately discharged to the coastal ocean. Nutrient cycling and export within the Delaware Estuary affect the ecosystem functions both within Delaware Bay and on the adjacent continental shelf. A realistic coupled hydrodynamical-biogeochemical modeling framework was developed for the Delaware Bay using ROMS (Regional Ocean Modeling System; myroms.org) to quantify nitrogen fluxes and budgets. The modeling system includes inert and age tracers to identify water transport pathways. Model skill assessment used a host of in-situ physical and biogeochemical data, and satellite products. The nitrogen budget was estimated for a five-year period of 2007-2011. A large portion of the incoming nitrogen from terrestrial sources is denitrified or buried in the Bay. Positive net ecosystem production contributes to organic nitrogen export to the shelf. There is strong interannual variability in riverine nitrogen inflows, but in years with greater riverine nitrogen input most of the excess nitrogen is buried, denitrified or exported to the shelf; the net ecosystem production shows less variability. By taking advantage of a process-based biogeochemical model and an ensemble of available observed and empirical evidence, this study provides more detailed information about nitrogen fluxes in Delaware Estuary than previously established.

  6. 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.

  7. 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...

  8. 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...

  9. 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

  10. Numerical Investigation of Grain Coarsening and Coalescence Model

    NASA Astrophysics Data System (ADS)

    Muradova, Aliki D.; Hristopulos, Dionisios T.

    2015-01-01

    A kinetic nonlinear model of mass transfer, grain coarsening and coalescence with potential applications in sintering processes is studied. The model involves nonlinear differential equations that determine the transport of mass between grains. The rate of mass transfer is controlled by the activation energy (an Arrhenius factor) leading to a nonlinear model of mass transfer and grain coarsening. The resulting dynamical system of coupled nonlinear differential equations with random initial conditions (i.e., initial grain mass configuration) is solved by means of the Runge-Kutta method. An analysis of the fixed points of the two-grain system is carried out, and the solution of the multi-grain system is studied. We incorporate coalescence of smaller grains with larger neighbors using a cellular automaton step in the evolution of the system.

  11. Nuclear magnetic resonance relaxation characterisation of water status of developing grains of maize (Zea mays L.) grown at different nitrogen levels.

    PubMed

    Krishnan, Prameela; Chopra, Usha Kiran; Verma, Ajay Pal Singh; Joshi, Devendra Kumar; Chand, Ishwar

    2014-04-01

    Changes in water status of developing grains of maize (Zea mays L.) grown under different nitrogen levels were characterized by nuclear magnetic resonance (NMR) spectroscopy. There were distinct changes in water status of grains due to the application of different levels of nitrogen (0, 120 and 180 kg N ha(-1)). A comparison of the grain developmental characteristics, composition and physical properties indicated that, not only the developmental characteristics like grain weight, grain number/ear, and rate of grain filling increased, but also bound water characterized by the T2 component of NMR relaxation increased with nitrogen application (50-70%) and developmental stages leading to maturation (10-60%). The consistency in the patterns of responses to free water and intermediate water to increasing levels of nitrogen application and grain maturity suggested that nitrogen application resulted in more proportion of water to both bound- and intermediate states and less in free state. These changes are further corroborated by the concomitant increases in protein and starch contents in grains from higher nitrogen treatments as macromolecules like protein and starch retain more amount of water in the bound state. The results of the changes in T2 showed that water status during grain development was not only affected by developmental processes but also by nitrogen supply to plants. This study strongly indicated a clear nutrient and developmental stage dependence of grain tissue water status in maize. Copyright © 2013 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  12. Modeling reactive nitrogen in North America: recent ...

    EPA Pesticide Factsheets

    Nitrogen is an essential building block of all proteins and thus an essential nutrient for all life. The bulk of nitrogen in the environment is tightly bound as non-reactive N2. Reactive nitrogen, which is naturally produced via enzymatic reactions, forest fires and lightning, is continually recycled and cascades through air, water, and soil media (Galloway et al., 2003). Human activity has perturbed this cycle through the combustion of fossil fuels and synthesis of fertilizers. The anthropogenic contribution to this cycle is now larger than natural sources in the United States and globally (Galloway et al., 2004). Reactive nitrogen enters the biosphere primarily from emissions of oxidized nitrogen to the atmosphere from combustion sources, as inorganic fertilizer applied to crops as reduced nitrogen fixed from atmospheric N2 through the Haber-Bosch process, as organic fertilizers such as manure, and through the cultivation of nitrogen fixing crops (Canfield et al., 2010). Both the United States (US) Clean Air Act and the Canadian Environmental Protection Act (CEPA) have substantially reduced the emissions of oxidized nitrogen in North America through NOx controls on smokestacks and exhaust pipes (Sickles and Shadwick, 2015; AQA, 2015). However, reduced nitrogen emissions have remained constant during the last few decades of emission reductions. The National Exposure Research Laboratory’s Atmospheric Modeling Division (AMAD) c

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

    PubMed Central

    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

  14. Next Generation Carbon-Nitrogen Dynamics Model

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

    Nitrogen is a key regulator of vegetation dynamics, soil carbon release, and terrestrial carbon cycles. Thus, to assess energy impacts on the global carbon cycle and future climates, it is critical that we have a mechanism-based and data-calibrated nitrogen model that simulates nitrogen limitation upon both above and belowground carbon dynamics. In this study, we developed a next generation nitrogen-carbon dynamic model within the NCAR Community Earth System Model (CESM). This next generation nitrogen-carbon dynamic model utilized 1) a mechanistic model of nitrogen limitation on photosynthesis with nitrogen trade-offs among light absorption, electron transport, carboxylation, respiration and storage; 2) an optimal leaf nitrogen model that links soil nitrogen availability and leaf nitrogen content; and 3) an ecosystem demography (ED) model that simulates the growth and light competition of tree cohorts and is currently coupled to CLM. Our three test cases with changes in CO2 concentration, growing temperature and radiation demonstrate the model's ability to predict the impact of altered environmental conditions on nitrogen allocations. Currently, we are testing the model against different datasets including soil fertilization and Free Air CO2 enrichment (FACE) experiments across different forest types. We expect that our calibrated model will considerably improve our understanding and predictability of vegetation-climate interactions.itrogen allocation model evaluations. The figure shows the scatter plots of predicted and measured Vc,max and Jmax scaled to 25 oC (i.e.,Vc,max25 and Jmax25) at elevated CO2 (570 ppm, test case one), reduced radiation in canopy (0.1-0.9 of the radiation at the top of canopy, test case two) and reduced growing temperature (15oC, test case three). The model is first calibrated using control data under ambient CO2 (370 ppm), radiation at the top of the canopy (621 μmol photon/m2/s), the normal growing temperature (30oC). The fitted model

  15. 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

  16. Effect of irrigation and nitrogen application on grain amino acid composition and protein quality in winter wheat.

    PubMed

    Zhang, Panpan; Ma, Geng; Wang, Chenyang; Lu, Hongfang; Li, Shasha; Xie, Yingxin; Ma, Dongyun; Zhu, Yunji; Guo, Tiancai

    2017-01-01

    Water management and nitrogen application are critical factors in wheat grain yield and protein quality. This study aimed to evaluate the effect of irrigation and nitrogen application on the grain yield, protein content and amino acid composition of winter wheat. Field experiments were conducted in a split-plot design with three replications in high-yielding land on the North China Plain in 2012/2013, 2013/2014 and 2014/2015. Three irrigation treatments were examined in main plots: no irrigation, irrigation at jointing, and irrigation at jointing plus anthesis, while subplots were assigned to nitrogen treatment at four different rates: 0, 180, 240, 300 kg N ha-1, respectively. The results indicated that irrigation at jointing and at jointing plus anthesis improved grain yield by an average of 12.79 and 18.65% across three cropping seasons, respectively, compared with no irrigation. However, different irrigation treatments had no significant effect on grain protein content in any cropping season. Compared with no N treatment, 180, 240, and 300 kg N ha-1 N application significantly increased grain yield, by 58.66, 61.26 and 63.42% respectively, averaged over three cropping seasons. Grain protein and the total, essential and non-essential amino acid content significantly increased with increasing nitrogen application. Irrigation significantly improved the essential amino acid index (EAAI) and protein-digestibility-corrected amino acid score (PDCAAS) compared with no irrigation; however, N application decreased them by an average of 7.68 and 11.18% across three cropping seasons, respectively. EAAI and PDCAAS were positively correlated, however, they were highly negatively correlated with yield and grain protein content.

  17. Effect of irrigation and nitrogen application on grain amino acid composition and protein quality in winter wheat

    PubMed Central

    Ma, Geng; Wang, Chenyang; Lu, Hongfang; Li, Shasha; Xie, Yingxin; Ma, Dongyun; Zhu, Yunji; Guo, Tiancai

    2017-01-01

    Water management and nitrogen application are critical factors in wheat grain yield and protein quality. This study aimed to evaluate the effect of irrigation and nitrogen application on the grain yield, protein content and amino acid composition of winter wheat. Field experiments were conducted in a split-plot design with three replications in high-yielding land on the North China Plain in 2012/2013, 2013/2014 and 2014/2015. Three irrigation treatments were examined in main plots: no irrigation, irrigation at jointing, and irrigation at jointing plus anthesis, while subplots were assigned to nitrogen treatment at four different rates: 0, 180, 240, 300 kg N ha-1, respectively. The results indicated that irrigation at jointing and at jointing plus anthesis improved grain yield by an average of 12.79 and 18.65% across three cropping seasons, respectively, compared with no irrigation. However, different irrigation treatments had no significant effect on grain protein content in any cropping season. Compared with no N treatment, 180, 240, and 300 kg N ha-1 N application significantly increased grain yield, by 58.66, 61.26 and 63.42% respectively, averaged over three cropping seasons. Grain protein and the total, essential and non-essential amino acid content significantly increased with increasing nitrogen application. Irrigation significantly improved the essential amino acid index (EAAI) and protein-digestibility-corrected amino acid score (PDCAAS) compared with no irrigation; however, N application decreased them by an average of 7.68 and 11.18% across three cropping seasons, respectively. EAAI and PDCAAS were positively correlated, however, they were highly negatively correlated with yield and grain protein content. PMID:28594830

  18. 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.

  19. Potts-model grain growth simulations: Parallel algorithms and applications

    SciTech Connect

    Wright, S.A.; Plimpton, S.J.; Swiler, T.P.

    1997-08-01

    Microstructural morphology and grain boundary properties often control the service properties of engineered materials. This report uses the Potts-model to simulate the development of microstructures in realistic materials. Three areas of microstructural morphology simulations were studied. They include the development of massively parallel algorithms for Potts-model grain grow simulations, modeling of mass transport via diffusion in these simulated microstructures, and the development of a gradient-dependent Hamiltonian to simulate columnar grain growth. Potts grain growth models for massively parallel supercomputers were developed for the conventional Potts-model in both two and three dimensions. Simulations using these parallel codes showed self similar grain growth and no finite size effects for previously unapproachable large scale problems. In addition, new enhancements to the conventional Metropolis algorithm used in the Potts-model were developed to accelerate the calculations. These techniques enable both the sequential and parallel algorithms to run faster and use essentially an infinite number of grain orientation values to avoid non-physical grain coalescence events. Mass transport phenomena in polycrystalline materials were studied in two dimensions using numerical diffusion techniques on microstructures generated using the Potts-model. The results of the mass transport modeling showed excellent quantitative agreement with one dimensional diffusion problems, however the results also suggest that transient multi-dimension diffusion effects cannot be parameterized as the product of the grain boundary diffusion coefficient and the grain boundary width. Instead, both properties are required. Gradient-dependent grain growth mechanisms were included in the Potts-model by adding an extra term to the Hamiltonian. Under normal grain growth, the primary driving term is the curvature of the grain boundary, which is included in the standard Potts-model Hamiltonian.

  20. Free Energy-Based Coarse-Grained Force Field for Binary Mixtures of Hydrocarbons, Nitrogen, Oxygen, and Carbon Dioxide.

    PubMed

    Cao, Fenglei; Deetz, Joshua D; Sun, Huai

    2017-01-23

    The free energy based Lennard-Jones 12-6 (FE-12-6) coarse-grained (CG) force field developed for alkanes1 has been extended to model small molecules of light hydrocarbons (methane, ethane, propane, butane, and isobutane), nitrogen, oxygen, and carbon dioxide. The adjustable parameters of the FE-12-6 potential are determined by fitting against experimental vapor-liquid equilibrium (VLE) curves and heat of vaporization (HOV) data for pure substance liquids. Simulations using the optimized FE-12-6 parameters correctly reproduced experimental measures of the VLE, HOV, density, vapor pressure, compressibility, critical point, and surface tension for pure substances over a wide range of thermodynamic states. The force field parameters optimized for pure substances were tested on methane/butane, nitrogen/decane, and carbon dioxide/decane binary mixtures to predict their vapor-liquid equilibrium phase diagrams. It is found that for nonpolar molecules represented by different sized beads, a common scaling factor (0.08) that reduces the strength of the interaction potential between unlike beads, generated using Lorentz-Berthelot (LB) combination rules, is required to predict vapor-liquid phase equilibria accurately.

  1. 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

  2. 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

  3. A Unified Model of Grain Alignment: Radiative Alignment of Interstellar Grains with Magnetic Inclusions

    NASA Astrophysics Data System (ADS)

    Hoang, Thiem; Lazarian, A.

    2016-11-01

    The radiative torque (RAT) alignment of interstellar grains with ordinary paramagnetic susceptibilities has been supported by earlier studies. The alignment of such grains depends on the so-called RAT parameter q max, which is determined by the grain shape. In this paper, we elaborate on our model of RAT alignment for grains with enhanced magnetic susceptibility due to iron inclusions, such that RAT alignment is magnetically enhanced, which we term the MRAT mechanism. Such grains can be aligned with high angular momentum at the so-called high-J attractor points, achieving a high degree of alignment. Using our analytical model of RATs, we derive the critical value of the magnetic relaxation parameter δ m to produce high-J attractor points as functions of q max and the anisotropic radiation angle relative to the magnetic field ψ. We find that if about 10% of the total iron abundance present in silicate grains is forming iron clusters, this is sufficient to produce high-J attractor points for all reasonable values of q max. To calculate the degree of grain alignment, we carry out numerical simulations of MRAT alignment by including stochastic excitations from gas collisions and magnetic fluctuations. We show that large grains can achieve perfect alignment when the high-J attractor point is present, regardless of the values of q max. Our obtained results pave the way for the physical modeling of polarized thermal dust emission as well as magnetic dipole emission. We also find that millimeter-sized grains in accretion disks may be aligned with the magnetic field if they are incorporated with iron nanoparticles.

  4. Active sensing: An innovative tool for evaluating grain yield and nitrogen use efficiency of multiple wheat genotypes

    NASA Astrophysics Data System (ADS)

    Naser, Mohammed Abdulridha

    Precision agricultural practices have significantly contributed to the improvement of crop productivity and profitability. Remote sensing based indices, such as Normalized Difference Vegetative Index (NDVI) have been used to obtain crop information. It is used to monitor crop development and to provide rapid and nondestructive estimates of plant biomass, nitrogen (N) content and grain yield. Remote sensing tools are helping improve nitrogen use efficiency (NUE) through nitrogen management and could also be useful for high NUE genotype selection. The objectives of this study were: (i) to determine if active sensor based NDVI readings can differentiate wheat genotypes, (ii) to determine if NDVI readings can be used to classify wheat genotypes into grain yield productivity classes, (iii) to identify and quantify the main sources of variation in NUE across wheat genotypes, and (iv) to determine if normalized difference vegetation index (NDVI) could characterize variability in NUE across wheat genotypes. This study was conducted in north eastern Colorado for two years, 2010 and 2011. The NDVI readings were taken weekly during the winter wheat growing season from March to late June, in 2010 and 2011 and NUE were calculated as partial factor productivity and as partial nitrogen balance at the end of the season. For objectives i and ii, the correlation between NDVI and grain yield was determined using Pearson's product-moment correlation coefficient (r) and linear regression analysis was used to explain the relationship between NDVI and grain yield. The K-means clustering algorithm was used to classify mean NDVI and mean grain yield into three classes. For objectives iii and iv, the parameters related to NUE were also calculated to measure their relative importance in genotypic variation of NUE and power regression analysis between NDVI and NUE was used to characterize the relationship between NDVI and NUE. The results indicate more consistent association between grain

  5. 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.

  6. 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.

  7. 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

  8. [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.

  9. 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.

  10. Simple Reaction Time and Statistical Facilitation: A Parallel Grains Model

    ERIC Educational Resources Information Center

    Miller, Jeff; Ulrich, Rolf

    2003-01-01

    A race-like model is developed to account for various phenomena arising in simple reaction time (RT) tasks. Within the model, each stimulus is represented by a number of grains of information or activation processed in parallel. The stimulus is detected when a criterion number of activated grains reaches a decision center. Using the concept of…

  11. 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

  12. 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.

  13. [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.

  14. 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.

  15. Comparative Phosphoproteomic Analysis under High-Nitrogen Fertilizer Reveals Central Phosphoproteins Promoting Wheat Grain Starch and Protein Synthesis

    PubMed Central

    Zhen, Shoumin; Deng, Xiong; Zhang, Ming; Zhu, Gengrui; Lv, Dongwen; Wang, Yaping; Zhu, Dong; Yan, Yueming

    2017-01-01

    Nitrogen (N) is a macronutrient important for plant growth and development. It also strongly influences starch and protein synthesis, closely related to grain yield and quality. We performed the first comparative phosphoproteomic analysis of developing wheat grains in response to high-N fertilizer. Physiological and biochemical analyses showed that application of high-N fertilizer resulted in significant increases in leaf length and area, chlorophyll content, the activity of key enzymes in leaves such as nitrate reductase (NR), and in grains such as sucrose phosphate synthase (SPS), sucrose synthase (SuSy), and ADP glucose pyrophosphorylase (AGPase). This enhanced enzyme activity led to significant improvements in starch content, grain yield, and ultimately, bread making quality. Comparative phosphoproteomic analysis of developing grains under the application of high-N fertilizer performed 15 and 25 days post-anthesis identified 2470 phosphosites among 1372 phosphoproteins, of which 411 unique proteins displayed significant changes in phosphorylation level (>2-fold or <0.5-fold). These phosphoproteins are involved mainly in signaling transduction, starch synthesis, energy metabolism. Pro-Q diamond staining and Western blotting confirmed our phosphoproteomic results. We propose a putative pathway to elucidate the important roles of the central phosphoproteins regulating grain starch and protein synthesis. Our results provide new insights into the molecular mechanisms of protein phosphorylation modifications involved in grain development, yield and quality formation. PMID:28194157

  16. Nitrogen chemistry on dust grains: the formation of hydroxylamine, precursor to glycine

    NASA Astrophysics Data System (ADS)

    Vidali, Gianfranco; Lemaire, Jean Louis; Shi, Jianming; Hopkins, Tyler; Garrod, Rob; He, Jiao

    2015-08-01

    In ices coating dust grains in molecular clouds, nitrogen-containing molecules - mostly NH3 - are present in sizable quantity, up to 15-20% with respect to water ice, the largest component. We studied the oxidation of ammonia in a series of experiments using beams of oxygen and ammonia in various configurations (co-deposition and sequential deposition with various NH3:O ratios). We detected the formation of hydroxylamine (NH2OH) and other products, depending on the degree of oxidation. A simulation of a dense cloud with input from experimental data shows that on and in ices at 14 K and with modest activation energy for reaction, NH2OH is easily formed and its abundance never falls below a tenth of the NH3 abundance. Strategies for detection of hydroxylamine in the ISM will be presented.This work is supported by the NSF Astronomy and Astrophysics Division (grant No.1311958 to G.V.). R.T.G. acknowledges the support of the NASA Astrophysics Theory Program (grant No. NNX11AC38G).

  17. Co-production of Nitrogen-15 and Oxygen-18 in Explosive Helium Burning and Implications for Supernova Graphite Grains

    NASA Astrophysics Data System (ADS)

    Bojazi, Michael

    My Masters research involves simulations of a supernova whereby a shock wave of constant Mach number is sent through a 15-solar-mass star evolved to the point of core-collapse. The resulting nucleosynthesis is examined with the intent of explaining the overproduction, relative to solar values, of nitrogen-15 and oxygen-18 abundances in supernova presolar graphite grains, as experimentally determined by Groopman et al. via a NanoSIMS analysis. We find such overabundances to be present in the helium-rich zone. Oxygen-18 is leftover from presupernova helium burning while nitrogen-15 is produced by explosive helium burning. Interestingly, anomalous excesses in molybdenum-95 and molybdenum-97 abundances in SiC X grains, discovered by Pellin et al. using the CHARISMA instrument, probably arise from explosive helium burning as well. These results signal the importance of the helium-rich zone for supernova presolar grain growth. We suggest that matter deep from the supernova, which is rich in iron-peak elements, gets injected into the helium-rich zone. Small TiC grains form in this material. These subgrains then traverse the helium-rich zone and serve as seeds for the growth of the graphite or SiC X grains.

  18. Measurement and modeling of radiation-induced grain boundary grain boundary segregation in stainless steels

    SciTech Connect

    Bruemmer, S.M.; Charlot, L.A.; Simonen, E.P.

    1995-08-01

    Grain boundary radiation-induced segregation (RIS) in Fe-Ni-Cr stainless alloys has been measured and modelled as a function of irradiation temperature and dose. Heavy-ion irradiation was used to produce damage levels from 1 to 20 displacements per atom (dpa) at temperatures from 175 to 550{degrees}C. Measured Fe, Ni, and Cr segregation increased sharply with irradiation dose (from 0 to 5 dpa) and temperature (from 175 to about 350{degrees}C). However, grain boundary concentrations did not change significantly as dose or temperatures were further increased. Impurity segregation (Si and P) was also measured, but only Si enrichment appeared to be radiation-induced. Grain boundary Si levels peaked at an intermediate temperature of {approximately}325{degrees}C reaching levels of {approximately}8 at. %. Equilibrium segregation of P was measured in the high-P alloys, but interfacial concentration did not increase with irradiation exposure. Examination of reported RIS in neutron-irradiated stainless steels revealed similar effects of irradiation dose on grain boundary compositional changes for both major alloying and impurity element`s. The Inverse Kirkendall model accurately predicted major alloying element RIS in ion- and neutron-irradiated alloys over the wide range of temperature and dose conditions. In addition, preliminary calculations indicate that the Johnson-Lam model can reasonably estimate grain boundary Si enrichment if back diffusion is enhanced.

  19. 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

  20. 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.

  1. A coarse-grained model for PETN crystals

    SciTech Connect

    Gee, R; Wu, C; Maiti, A

    2006-02-10

    Using the energetic material Pentaerythritol Tetranitrate (PETN) as a specific example of molecular crystal, we describe the development of a simple coarse-graining procedure by grouping several atoms or whole functional groups into single charge-neutral beads. As compared to fully atomistic calculations the coarse-grained model speeds up simulations by more than two orders of magnitude. Yet, by adjusting only two parameters in the coarse-grained interaction, the model accurately predicts the lattice constants, sublimation energy, pressure-volume curve up to P=10 GPa, and energetically the most stable facets. Computed surface and desorption energies, bulk modulus, and equilibrium morphology are reported as well.

  2. Modelling of grain boundary dynamics using amplitude equations

    NASA Astrophysics Data System (ADS)

    Hüter, Claas; Neugebauer, Jörg; Boussinot, Guillaume; Svendsen, Bob; Prahl, Ulrich; Spatschek, Robert

    2017-07-01

    We discuss the modelling of grain boundary dynamics within an amplitude equations description, which is derived from classical density functional theory or the phase field crystal model. The relation between the conditions for periodicity of the system and coincidence site lattices at grain boundaries is investigated. Within the amplitude equations framework, we recover predictions of the geometrical model by Cahn and Taylor for coupled grain boundary motion, and find both {<100\\rangle} and {<110\\rangle} coupling. No spontaneous transition between these modes occurs due to restrictions related to the rotational invariance of the amplitude equations. Grain rotation due to coupled motion is also in agreement with theoretical predictions. Whereas linear elasticity is correctly captured by the amplitude equations model, open questions remain for the case of nonlinear deformations.

  3. Nitrogen Controls on Climate Model Evapotranspiration.

    NASA Astrophysics Data System (ADS)

    Dickinson, Robert E.; Berry, Joseph A.; Bonan, Gordon B.; Collatz, G. James; Field, Christopher B.; Fung, Inez Y.; Goulden, Michael; Hoffmann, William A.; Jackson, Robert B.; Myneni, Ranga; Sellers, Piers J.; Shaikh, Muhammad

    2002-02-01

    Most evapotranspiration over land occurs through vegetation. The fraction of net radiation balanced by evapotranspiration depends on stomatal controls. Stomates transpire water for the leaf to assimilate carbon, depending on the canopy carbon demand, and on root uptake, if it is limiting. Canopy carbon demand in turn depends on the balancing between visible photon-driven and enzyme-driven steps in the leaf carbon physiology. The enzyme-driven component is here represented by a Rubisco-related nitrogen reservoir that interacts with plant-soil nitrogen cycling and other components of a climate model. Previous canopy carbon models included in GCMs have assumed either fixed leaf nitrogen, that is, prescribed photosynthetic capacities, or an optimization between leaf nitrogen and light levels so that in either case stomatal conductance varied only with light levels and temperature.A nitrogen model is coupled to a previously derived but here modified carbon model and includes, besides the enzyme reservoir, additional plant stores for leaf structure and roots. It also includes organic and mineral reservoirs in the soil; the latter are generated, exchanged, and lost by biological fixation, deposition and fertilization, mineralization, nitrification, root uptake, denitrification, and leaching. The root nutrient uptake model is a novel and simple, but rigorous, treatment of soil transport and root physiological uptake. The other soil components are largely derived from previously published parameterizations and global budget constraints.The feasibility of applying the derived biogeochemical cycling model to climate model calculations of evapotranspiration is demonstrated through its incorporation in the Biosphere-Atmosphere Transfer Scheme land model and a 17-yr Atmospheric Model Inter comparison Project II integration with the NCAR CCM3 GCM. The derived global budgets show land net primary production (NPP), fine root carbon, and various aspects of the nitrogen cycling are

  4. Absorbing ice model of interstellar grains.

    NASA Technical Reports Server (NTRS)

    Swamy, K. S. K.; Jackson, W. M.; Donn, B. D.

    1971-01-01

    Extinction curves have been calculated for Mie scattering by grains with a refractive index m equals to n - ik, where n was between 1.3 and 2.0 and k varied from 0 to 0.5. A good fit for the observed interstellar extinction in the wavelength region of 0.1 to 2.0 microns was obtained for particles with a radius of 0.1 micron and m equal to 1.3 - 0.2i. Inclusion of the changes in the refractive index in the vacuum ultraviolet region due to the strong absorptions of methane, ammonia and water does not appreciably alter these results. Theoretical extinction curves for the composite medium of H2O, NH3, CH4, and graphite show a general agreement with the observed interstellar reddening curve over the whole spectral range, in addition to producing kinks in the far-ultraviolet region.

  5. Time-dependent models of grain-forming stellar atmospheres

    SciTech Connect

    Woodrow, J.E.J.; Auman, J.R

    1982-06-01

    Completely time-dependent models of the expanding atmospheres of cool, carbon-rich stars were calculated. The driving force for the expansion was radiation pressure on grains. The grains were assumed to have the structure of graphite with sigma = 1000 ergs cm/sup -2/. The stellar parameters adopted for the models were M = 1.5 M/sub x/O, L = 1.94 x 10/sup 4/ L/sub x/O, C/H = 1.22 x 10/sup -3/, and C/O = 1.76. Two models were generated. Model 1 had T( = 2500 K and model 2, T( = 2400 K. In both models grain nucleation was negligible at supersaturation levels less than 5. At higher supersaturation levels condensation of small (aroughly-equal5.5 x 10/sup -8/ cm) grains was sufficiently great to generate mass flows. The calculated mass loss rate for model 1 was 6.2 x 10/sup -9/ M/sub sun/ yr/sup -1/ and for model 2, 7.4 x 10/sup -8/ M/sub sun/ yr/sup -1/. The mass flow approached a steady state in model 1, but in model 2 a small amplitude pulsation was superposed upon the outward flow. Initially this pulsation was very irregular, but after an elapsed time of 27 x 10/sup 7/ s the model had relaxed into a steady pulsation mode with a period of 6.4 x 10/sup 7/ s. This mode was followed for four periods during which the amplitude of the pulses remained constant. The driving force for this pulsation appears to be an opacity-controlled feedback mechanism which operated between the grain-forming region of the model and the hydrogen dissociation zone. In model 1 the opacity of the grains was too small for this mechanism to produce pulsations.

  6. Interactions of Nitrogen Source and Rate and Weed Removal Timing Relative to Nitrogen Content in Corn and Weeds and Corn Grain Yield.

    PubMed

    Knight, Alexandra M; Everman, Wesley J; Jordan, David L; Heiniger, Ronnie W; Smyth, T Jot

    2017-01-01

    Adequate fertility combined with effective weed management is important in maximizing corn (Zea mays L.) grain yield. Corn uptake of nitrogen (N) is dependent upon many factors including weed species and density and the rate and formulation of applied N fertilizer. Understanding interactions among corn, applied N, and weeds is important in developing management strategies. Field studies were conducted in North Carolina to compare corn and weed responses to urea ammonium nitrate (UAN), sulfur-coated urea (SCU), and composted poultry litter (CPL) when a mixture of Palmer amaranth (Amaranthus palmeri S. Wats.) and large crabgrass (Digitaria sanguinalis L.) was removed with herbicides at heights of 8 or 16 cm. These respective removal timings corresponded with 22 and 28 days after corn planting or V2 and V3 stages of growth, respectively. Differences in N content in above-ground biomass of corn were noted early in the season due to weed interference but did not translate into differences in corn grain yield. Interactions of N source and N rate were noted for corn grain yield but these factors did not interact with timing of weed control. These results underscore that timely implementation of control tactics regardless of N fertility management is important to protect corn grain yield.

  7. Interactions of Nitrogen Source and Rate and Weed Removal Timing Relative to Nitrogen Content in Corn and Weeds and Corn Grain Yield

    PubMed Central

    Knight, Alexandra M.; Heiniger, Ronnie W.; Smyth, T. Jot

    2017-01-01

    Adequate fertility combined with effective weed management is important in maximizing corn (Zea mays L.) grain yield. Corn uptake of nitrogen (N) is dependent upon many factors including weed species and density and the rate and formulation of applied N fertilizer. Understanding interactions among corn, applied N, and weeds is important in developing management strategies. Field studies were conducted in North Carolina to compare corn and weed responses to urea ammonium nitrate (UAN), sulfur-coated urea (SCU), and composted poultry litter (CPL) when a mixture of Palmer amaranth (Amaranthus palmeri S. Wats.) and large crabgrass (Digitaria sanguinalis L.) was removed with herbicides at heights of 8 or 16 cm. These respective removal timings corresponded with 22 and 28 days after corn planting or V2 and V3 stages of growth, respectively. Differences in N content in above-ground biomass of corn were noted early in the season due to weed interference but did not translate into differences in corn grain yield. Interactions of N source and N rate were noted for corn grain yield but these factors did not interact with timing of weed control. These results underscore that timely implementation of control tactics regardless of N fertility management is important to protect corn grain yield. PMID:28487878

  8. 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.

  9. Zinc, Iron, Manganese and Copper Uptake Requirement in Response to Nitrogen Supply and the Increased Grain Yield of Summer Maize

    PubMed Central

    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, 18.1and 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. UO2 Grain Growth: Developing Phase Field Models for Pore Dragging, Solute Dragging and Anisotropic Grain Boundary Energies

    SciTech Connect

    Ahmed, K.; Tonks, M.; Zhang, Y.; Biner, B.

    2016-09-28

    A detailed phase field model for the effect of pore drag on grain growth kinetics was implemented in MARMOT. The model takes into consideration both the curvature-driven grain boundary motion and pore migration by surface diffusion. As such, the model accounts for the interaction between pore and grain boundary kinetics, which tends to retard the grain growth process. Our 2D and 3D simulations demonstrate that the model capture all possible pore-grain boundary interactions proposed in theoretical models. For high enough surface mobility, the pores move along with the migrating boundary as a quasi-rigid-body, albeit hindering its migration rate compared to the pore-free case. For less mobile pores, the migrating boundary can separate from the pores. For the pore-controlled grain growth kinetics, the model predicts a strong dependence of the growth rate on the number of pores, pore size, and surface diffusivity in agreement with theroretical models. An evolution equation for the grain size that includes these parameters was derived and showed to agree well with numerical solution. It shows a smooth transition from boundary-controlled kinetics to pore-controlled kinetics as the surface diffusivity decreases or the number of pores or their size increases. This equation can be utilized in BISON to give accurate estimate for the grain size evolution. This will be accomplished in the near future. The effect of solute drag and anisotropy of grain boundary on grain growth will be investigated in future studies.

  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. [Effects of shading on the nitrogen redistribution in wheat plant and the wheat grain quality].

    PubMed

    Mu, Hui-rong; Jiang, Dong; Dai, Ting-bo; Cao, Wei-xing

    2010-07-01

    Taking winter wheat (Triticum aestivum L.) cultivars Yangmai 158 (shading-tolerant) and Yangmai 11 (shading-sensitive) as test materials, this paper studied the effects of shading at the stages from jointing to maturity on the plant N redistribution, grain yield, and grain- and dough quality of the cultivars. The treatments were non-shading, 22% shading, and 33% shading. Under shading, the grain yield and its protein content of Yangmai 158 and Yangmai 11 decreased by 4.1%-9.9% and 3.0%-8.3%, and 15.3%-25.8% and 10.4%-14.1%, respectively, compared with non-shading. With the increase of shading intensity, the grain N content was increasingly dependent on the N accumulated after anthesis. Shading decreased the redistribution of N stored pre-anthesis in the vegetative organs to the grain, but increased the redistribution efficiency of N accumulated pre-anthesis (RENP) in leaves while decreased the RENP in sheathes and stems, and in hulls and rachises. Therefore, the mean RENP in the vegetative organs was not essentially altered by shading. The grain protein content increased significantly under shading, which could be related to the "condense effect", i.e., the decrement of grain protein content was much less than that of grain yield. In addition, shading had less effects on the contents of grain albumin and globulin but increased the contents of grain gliadin and glutinin significantly, and accordingly, the grain wet gluten content, dough development time, and dough stability time increased, while the dough softening degree decreased.

  13. Modeling of migrating grains on asteroid's surface

    NASA Astrophysics Data System (ADS)

    Yu, Yang; Baoyin, Hexi

    2015-01-01

    We present a numerical method based on the polyhedral data of asteroid shape for simulation of individual grain's dynamics around the asteroid surface, with application to migration of regolith material on specific asteroid. Surface gravitational attraction and potential are computed using polyhedral method with a correction on possible singularities; asteroid surface is approximated with continuous quartic Bézier patches based on the division of polyhedral mesh, which provides sufficient geometrical information for the simulation. Orbital motion and surface motion are processed separately by checking if the particle touches or leaves the surface. Collisions are treated as instantaneous point-contact events with the local quartic curved surface. The subpoint is recorded throughout the process to track the ID of the particle. We provide full description of this method including very detailed treatments in numeric. Several basic tests are conducted to examine the performance of this method, and the potential application of this method is also discussed. The test results of seismic regolith migration on crater walls show consistent conclusions with former investigation.

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

    PubMed

    Poulain, P; Saladin, A; Hartmann, B; Prévost, C

    2008-11-30

    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 acid side chains strengthen the binding. Overall, this work demonstrates that coarse grain modeling can reveal itself a precious auxiliary for a general and complete description and understanding of protein-DNA association mechanisms.

  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. 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

  19. Effect of baking and fermentation on the stable carbon and nitrogen isotope ratios of grain-based food.

    PubMed

    Bostic, Joshua N; Palafox, Sherilyn J; Rottmueller, Marina E; Jahren, A Hope

    2015-05-30

    Isotope ratio mass spectrometry (IRMS) is used extensively to reconstruct general attributes of prehistoric and modern diets in both humans and animals. In order to apply these methods to the accurate determination of specific intakes of foods/nutrients of interest, the isotopic signature of individually consumed foods must be constrained. For example, 86% of the calories consumed in the USA are derived from processed and prepared foods, but the relationship between the stable isotope composition of raw ingredients and the resulting products has not been characterized. To examine the effect of common cooking techniques on the stable isotope composition of grain-based food items, we prepared yeast buns and sugar cookies from standardized recipes and measured bulk δ(13) C and δ(15) N values of samples collected throughout a 75 min fermentation process (buns) and before and after baking at 190°C (buns and cookies). Simple isotope mixing models were used to determine if the isotopic signatures of 13 multi-ingredient foods could be estimated from the isotopic signatures of their constituent raw ingredients. No variations in δ(13) C or δ(15) N values were detected between pre- and post-baked yeast buns (pre: -24.78‰/2.61‰, post: -24.75‰/2.74‰), beet-sugar cookies (pre: -24.48‰/3.84‰, post: -24.47‰/3.57‰), and cane-sugar cookies (pre: -19.07‰/2.97‰, post: -19.02‰/3.21‰), or throughout a 75 min fermentation process in yeast buns. Using isotopic mass balance equations, the δ(13) C/δ(15) N values of multi-ingredient foods were estimated from the isotopic composition of constituent raw ingredients to within 0.14 ± 0.13‰/0.24 ± 0.17‰ for gravimetrically measured recipes and 0.40 ± 0.38‰/0.58 ± 0.53‰ for volumetrically measured recipes. Two common food preparation techniques, baking and fermentation, do not substantially affect the carbon or nitrogen isotopic signature of grain-based foods. Mass-balance equations can be used to

  20. [Effects of nitrogen supply on flag leaf photosynthesis and grain starch accumulation of wheat from its anthesis to maturity under drought or waterlogging].

    PubMed

    Fan, Xuemei; Jiang, Dong; Dai, Tingbo; Jing, Qi; Cao, Weixing

    2005-10-01

    In this paper, a cement pool culture experiment with three water treatments (waterlogging, drought, and moderate water supply) and two nitrogen levels (120 and 240 kg x hm(-2)) was conducted to study the effects of nitrogen supply on the flag leaf photosynthesis and grain starch accumulation of two wheat varieties from anthesis to maturity under soil drought and waterlogging. In comparing with moderate water supply, soil drought and waterlogging reduced the photosynthesis rate (Pn) and SPAD of flag leaf and dry matter accumulation. Nitrogen supply under drought increased Pn and SPAD, while that under waterlogging was in adverse. The total soluble sugar content in grain was reduced under both drought and waterlogging, while that in leaf was decreased under waterlogging but increased under drought. Under waterlogging, increasing nitrogen application rate reduced starch accumulation. The unit grain weight and the yields of grain and starch were reduced under both drought and waterlogging, but nitrogen application favored them under drought while in adverse under waterlogging. It was indicated that both leaf photosynthesis and grain starch accumulation could be regulated by nitrogen supply under stress of soil drought or waterlogging from anthesis to maturity of wheat.

  1. [Effects of combined application of nitrogen and phosphorus on diurnal variation of photosynthesis at grain-filling stage and grain yield of super high-yielding wheat].

    PubMed

    Zhao, Hai-bo; Lin, Qi; Liu, Yi-guo; Jiang, Wen; Liu, Jian-jun; Zhai, Yan-ju

    2010-10-01

    Taking super high-yielding wheat cultivar Jimai 22 as test material, a field experiment was conducted to study the effects of combined application of nitrogen (N) and phosphorus (P) on the diurnal variation of photosynthesis at grain-filling stage and the grain yield of the cultivar. In treatments CK (without N and P application) and low N/P application (225 kg N x hm(-2) and 75 kg P x hm(-2)), the diurnal variation of net photosynthetic rate (Pn) was presented as double-peak curve, and there existed obvious midday depression of photosynthesis. Under reasonable application of N/P (300 kg N x hm(-2) and 150 kg P x hm(-2), treatment N2P2), the midday depression of photosynthesis weakened or even disappeared. Stomatal and non-stomatal limitations could be the causes of the midday depression. Increasing N and P supply increased the Pn, stomatal conductance (Gs), stomatal limitation value (Ls), and transpiration rate (Tr). Fertilizer P had less effects on the photosynthesis, compared with fertilizer N. When the P supply was over 150 kg x hm(-2), the increment of Pn was alleviated and even decreased. Among the fertilization treatments, treatment N2P2 had the highest Pn, Gs, and water use efficiency, being significantly different from CK. It appeared that fertilizer N had greater regulatory effect on the diurnal variation of photosynthesis, compared with fertilizer P, while the combined application of N and P had significant co-effect on the Pn, Gs, and Tr. A combined application of 300 kg N x hm(-2) and 150 kg P x hm(-2) benefited the enhancement of Pn and grain yield.

  2. 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).

  3. A coarse grain model for DNA.

    PubMed

    Knotts, Thomas A; Rathore, Nitin; Schwartz, David C; de Pablo, Juan J

    2007-02-28

    Understanding the behavior of DNA at the molecular level is of considerable fundamental and engineering importance. While adequate representations of DNA exist at the atomic and continuum level, there is a relative lack of models capable of describing the behavior of DNA at mesoscopic length scales. We present a mesoscale model of DNA that reduces the complexity of a nucleotide to three interactions sites, one each for the phosphate, sugar, and base, thereby rendering the investigation of DNA up to a few microns in length computationally tractable. The charges on these sites are considered explicitly. The model is parametrized using thermal denaturation experimental data at a fixed salt concentration. The validity of the model is established by its ability to predict several aspects of DNA behavior, including salt-dependent melting, bubble formation and rehybridization, and the mechanical properties of the molecule as a function of salt concentration.

  4. A coarse grain model for DNA

    NASA Astrophysics Data System (ADS)

    Knotts, Thomas A.; Rathore, Nitin; Schwartz, David C.; de Pablo, Juan J.

    2007-02-01

    Understanding the behavior of DNA at the molecular level is of considerable fundamental and engineering importance. While adequate representations of DNA exist at the atomic and continuum level, there is a relative lack of models capable of describing the behavior of DNA at mesoscopic length scales. We present a mesoscale model of DNA that reduces the complexity of a nucleotide to three interactions sites, one each for the phosphate, sugar, and base, thereby rendering the investigation of DNA up to a few microns in length computationally tractable. The charges on these sites are considered explicitly. The model is parametrized using thermal denaturation experimental data at a fixed salt concentration. The validity of the model is established by its ability to predict several aspects of DNA behavior, including salt-dependent melting, bubble formation and rehybridization, and the mechanical properties of the molecule as a function of salt concentration.

  5. Monte Carlo grain growth modeling with local temperature gradients

    NASA Astrophysics Data System (ADS)

    Tan, Y.; Maniatty, A. M.; Zheng, C.; Wen, J. T.

    2017-09-01

    This work investigated the development of a Monte Carlo (MC) simulation approach to modeling grain growth in the presence of non-uniform temperature field that may vary with time. We first scale the MC model to physical growth processes by fitting experimental data. Based on the scaling relationship, we derive a grid site selection probability (SSP) function to consider the effect of a spatially varying temperature field. The SSP function is based on the differential MC step, which allows it to naturally consider time varying temperature fields too. We verify the model and compare the predictions to other existing formulations (Godfrey and Martin 1995 Phil. Mag. A 72 737-49 Radhakrishnan and Zacharia 1995 Metall. Mater. Trans. A 26 2123-30) in simple two-dimensional cases with only spatially varying temperature fields, where the predicted grain growth in regions of constant temperature are expected to be the same as for the isothermal case. We also test the model in a more realistic three-dimensional case with a temperature field varying in both space and time, modeling grain growth in the heat affected zone of a weld. We believe the newly proposed approach is promising for modeling grain growth in material manufacturing processes that involves time-dependent local temperature gradient.

  6. 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.

  7. Obtaining fully dynamic coarse-grained models from MD.

    PubMed

    Español, Pep; Zúñiga, Ignacio

    2011-06-14

    We present a general method to obtain parametrised models for the drift and diffusion terms of the Fokker-Planck equation of a coarse-grained description of molecular systems. The method is based on the minimisation of the relative entropy defined in terms of the two-time joint probability and thus captures the full dynamics of the coarse-grained description. In addition, we show an alternative Bayesian argument that starts from the path probability of a diffusion process which allows one to obtain the best parametrised model that fits an actual observed path of the coarse-grained variables. Both approaches lead to exactly the same optimisation function giving strong support to the methodology. We provide an heuristic argument that explains how both approaches are connected.

  8. Modelling of nitrogen release from MBT waste

    SciTech Connect

    Mostbauer, P. . E-mail: peter.mostbauer@boku.ac.at; Heiss-Ziegler, C.

    2005-07-01

    The 'LaNDy' model (landfill nitrogen dynamics model) is a new mathematical tool for the evaluation of the long-term behaviour of nitrogen in mechanical-biologically pretreated (MBP) waste. LaNDy combines a hydraulic model based on RICHARD's equation with one-dimensional heat flow in landfills, kinetics of biological degradation, gas diffusion, nitrification and denitrification. A suitable temperature-dependent N mineralisation sub-model was based on numerous data from the literature and own LSR-experiments. With the 'nitrification modus' of the LaNDy model, kinetic data of nitrification, thermodynamic data of denitrification and diffusion characteristics of gaseous components (especially of oxygen and methane) are used as an additional input for the preliminary calculation of the long-time impact of nitrification and denitrification. Examples of predicted temperature distribution and leachate ammonium concentrations, using different landfill size, age of the landfill (10 to {approx}100 a) and hydraulic conductivity of the MBP waste, are presented in this paper.

  9. 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

  10. [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.

  11. 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.

  12. 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.

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

    USDA-ARS?s Scientific Manuscript database

    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. Nitrogen Fertilizer Deep Placement for Increased Grain Yield and Nitrogen Recovery Efficiency in Rice Grown in Subtropical China.

    PubMed

    Wu, Meng; Li, Guilong; Li, Weitao; Liu, Jia; Liu, Ming; Jiang, Chunyu; Li, Zhongpei

    2017-01-01

    Field plot experiments were conducted over 3 years (from April 2014 to November 2016) in a double-rice (Oryza sativa L.) cropping system in subtropical China to evaluate the effects of N fertilizer placement on grain yield and N recovery efficiency (NRE). Different N application methods included: no N application (CK); N broadcast application (NBP); N and NPK deep placement (NDP and NPKDP, respectively). Results showed that grain yield and apparent NRE significantly increased for NDP and NPKDP as compared to NBP. The main reason was that N deep placement (NDP) increased the number of productive panicle per m(-2). To further evaluate the increase, a pot experiment was conducted to understand the N supply in different soil layers in NDP during the whole rice growing stage and a (15)N tracing technique was used in a field experiment to investigate the fate of urea-(15)N in the rice-soil system during rice growth and at maturity. The pot experiment indicated that NDP could maintain a higher N supply in deep soil layers than N broadcast for 52 days during rice growth. The (15)N tracing study showed that NDP could maintain much higher fertilizer N in the 5-20 cm soil layer during rice growth and could induce plant to absorb more N from fertilizer and soil than NBP, which led to higher NRE. One important finding was that NDP and NPKDP significantly increased fertilizer NRE but did not lead to N declined in soil compared to NBP. Compared to NPK, NPKDP induced rice plants to absorb more fertilizer N rather than soil N.

  15. Nitrogen Fertilizer Deep Placement for Increased Grain Yield and Nitrogen Recovery Efficiency in Rice Grown in Subtropical China

    PubMed Central

    Wu, Meng; Li, Guilong; Li, Weitao; Liu, Jia; Liu, Ming; Jiang, Chunyu; Li, Zhongpei

    2017-01-01

    Field plot experiments were conducted over 3 years (from April 2014 to November 2016) in a double-rice (Oryza sativa L.) cropping system in subtropical China to evaluate the effects of N fertilizer placement on grain yield and N recovery efficiency (NRE). Different N application methods included: no N application (CK); N broadcast application (NBP); N and NPK deep placement (NDP and NPKDP, respectively). Results showed that grain yield and apparent NRE significantly increased for NDP and NPKDP as compared to NBP. The main reason was that N deep placement (NDP) increased the number of productive panicle per m-2. To further evaluate the increase, a pot experiment was conducted to understand the N supply in different soil layers in NDP during the whole rice growing stage and a 15N tracing technique was used in a field experiment to investigate the fate of urea-15N in the rice–soil system during rice growth and at maturity. The pot experiment indicated that NDP could maintain a higher N supply in deep soil layers than N broadcast for 52 days during rice growth. The 15N tracing study showed that NDP could maintain much higher fertilizer N in the 5–20 cm soil layer during rice growth and could induce plant to absorb more N from fertilizer and soil than NBP, which led to higher NRE. One important finding was that NDP and NPKDP significantly increased fertilizer NRE but did not lead to N declined in soil compared to NBP. Compared to NPK, NPKDP induced rice plants to absorb more fertilizer N rather than soil N. PMID:28744302

  16. Nitrogen utilization in growing lambs: effects of grain (starch) and protein sources with various rates of ruminal degradation.

    PubMed

    Matras, J; Bartle, S J; Preston, R L

    1991-01-01

    The potential interaction between grain (starch) and protein sources with varying ruminal degradation rates on N utilization in growing lambs was evaluated. Three grain sources with varying ruminal degradation rates, (barley greater than steam-flaked sorghum [SFSG] greater than dry-rolled sorghum [DRSG]) and three protein sources (urea greater than a 50:25:25 mixture of urea: blood meal:corn gluten meal [N basis, U/BC] greater than 50:50 mixture of meal:corn gluten meal [N basis, BC]), were evaluated in a 3 x 3 factorial arrangement. Supplemental protein sources provided 33% of dietary N (CP = 11.0%). For each grain-protein combination, a 3 x 3 Latin square metabolism trial was conducted using two sets of three lambs and three periods. Within-square treatments were 1.4, 1.7 and 2.0 times maintenance intake levels. No interactions were observed (P greater than .2) between dietary treatments and intake level. Grain sources did not differ (P greater than .2) in N balance or the proportion of N retained. Lambs fed urea diets retained less N (3.6 vs 4.2 and 4.1 g/d for urea vs U/BC and BC, respectively; linear, P = .07; quadratic, P = .12) and utilized N less efficiently (43.1 vs 51.9 and 52.5%, respectively; linear, P less than .001; quadratic, P = .10) than lambs fed BC diets. The grain x protein interaction was significant for most variables. Nitrogen utilization was most efficient (24 to 27% of N intake retained) when rapidly degraded sources (barley and urea) and slowly degraded sources (sorghum and BC) were fed together or when U/BC was the supplemental protein source (interaction P less than .08). An advantage was found for selection of starch and protein sources with similar ruminal degradation rates.

  17. 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.

  18. 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.

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

    PubMed

    Choi, Eunsong; Mondal, Jagannath; Yethiraj, Arun

    2014-01-09

    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.

  20. [Effects of nitrogen fertilization and root separation on the plant growth and grain yield of maize and its rhizosphere microorganisms].

    PubMed

    Zhang, Xiang-Qian; Huang, Guo-Qin; Bian, Xin-Min; Zhao, Qi-Guo

    2012-12-01

    A field experiment with root separation was conducted to study the effects of root interaction in maize-soybean intercropping system on the plant growth and grain yield of maize and its rhizosphere microorganisms under different nitrogen fertilization levels (0.1, 0.3, 0.5, and 0.7 g x kg(-1)). Root interaction and nitrogen fertilization had positive effects on the plant height, leaf length and width, and leaf chlorophyll content of maize. Less difference was observed in the root dry mass of maize at maturing stage between the treatments root separation and no root separation. However, as compared with root separation, no root separation under the nitrogen fertilization levels 0.1, 0.3, 0.5, and 0.7 g x kg(-1) increased the biomass per maize plant by 8.8%, 6.3%, 3.6%, and 0.7%, and the economic yield per maize plant by 17.7%, 10.0%, 8.2%, and 0.9%, respectively. No root separation increased the quantity of rhizosphere fungi and azotobacteria significantly, as compared with root separation. With increasing nitrogen fertilization level, the quantity of rhizosphere bacteria, fungi, and actinomycetes presented an increasing trend, while that of rhizosphere azotobacteria decreased after an initial increase. The root-shoot ratio of maize at maturing stage was significantly negatively correlated with the quantity of rhizosphere bacteria, fungi, and actinomycetes, but less correlated with the quantity of rhizosphere azotobacteria. It was suggested that the root interaction in maize-soybean intercropping system could improve the plant growth of maize and increase the maize yield and rhizosphere microbial quantity, but the effect would be decreased with increasing nitrogen fertilization level.

  1. 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

  2. A Forecasting Model for Feed Grain Demand Based on Combined Dynamic Model.

    PubMed

    Yang, Tiejun; Yang, Na; Zhu, Chunhua

    2016-01-01

    In order to improve the long-term prediction accuracy of feed grain demand, a dynamic forecast model of long-term feed grain demand is realized with joint multivariate regression model, of which the correlation between the feed grain demand and its influence factors is analyzed firstly; then the change trend of various factors that affect the feed grain demand is predicted by using ARIMA model. The simulation results show that the accuracy of proposed combined dynamic forecasting model is obviously higher than that of the grey system model. Thus, it indicates that the proposed algorithm is effective.

  3. A Forecasting Model for Feed Grain Demand Based on Combined Dynamic Model

    PubMed Central

    Yang, Tiejun

    2016-01-01

    In order to improve the long-term prediction accuracy of feed grain demand, a dynamic forecast model of long-term feed grain demand is realized with joint multivariate regression model, of which the correlation between the feed grain demand and its influence factors is analyzed firstly; then the change trend of various factors that affect the feed grain demand is predicted by using ARIMA model. The simulation results show that the accuracy of proposed combined dynamic forecasting model is obviously higher than that of the grey system model. Thus, it indicates that the proposed algorithm is effective. PMID:27698661

  4. 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.

  5. Nitrogen-doped rice grain-shaped titanium dioxide nanostructures by electrospinning: Frequency and temperature dependent conductivity

    NASA Astrophysics Data System (ADS)

    Babu, Veluru Jagadeesh; Rao, Rayavarapu Prasada; Nair, A. Sreekumaran; Ramakrishna, Seeram

    2011-09-01

    Rice grain-shaped, nitrogen-doped titanium dioxide (N-TiO2) nanostructures are synthesized using sol-gel method and followed by electrospinning. The as-spun composite fibers are sintered at 500 °C for 1 h in air. SEM images of the sintered samples showed rice grain-shaped nanostructures. The nanostructures were made up of spherical nanoparticles with average diameters of ˜ 20 nm, and the average diameter decreased with increase of N doping level. The temperature and frequency dependent electrical characterization has carried on nanostructures using impedance spectroscopy in the range of 298 K to 498 K and 30 Hz to 7 MHz, respectively. The magnitude of the ac conductivity is obtained from Nyquist plots and is proved that the ac conductivity is strongly dependent on temperature. The activation energy (Ea) is obtained from Arrhenius plots, and it is lowered from 0.31 to 0.22 eV with increasing N content. Therefore, the rice-grain shaped nanostructures can be employed in the low temperature gas sensor applications.

  6. 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

  7. Toward a Mechanistic Modeling of Nitrogen Limitation on Vegetation Dynamics

    PubMed Central

    Xu, Chonggang; Fisher, Rosie; Wullschleger, Stan D.; Wilson, Cathy J.; Cai, Michael; McDowell, Nate G.

    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 CO2 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 CO2 concentration, temperature, and radiation when evaluated against published data of Vc,max (maximum carboxylation rate) and Jmax (maximum electron transport rate). A sensitivity analysis of the model for herbaceous plants, deciduous and evergreen trees implies that elevated CO2 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 and the vegetation feedbacks

  8. 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.

  9. 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.

  10. Recent Advances in Transferable Coarse-Grained Modeling of Proteins

    PubMed Central

    Kar, Parimal; Feig, Michael

    2017-01-01

    Computer simulations are indispensable tools for studying the structure and dynamics of biological macromolecules. Biochemical processes occur on different scales of length and time. Atomistic simulations cannot cover the relevant spatiotemporal scales at which the cellular processes occur. To address this challenge, coarse-grained (CG) modeling of the biological systems are employed. Over the last few years, many CG models for proteins continue to be developed. However, many of them are not transferable with respect to different systems and different environments. In this review, we discuss those CG protein models that are transferable and that retain chemical specificity. We restrict ourselves to CG models of soluble proteins only. We also briefly review recent progress made in the multi-scale hybrid all-atom/coarse-grained simulations of proteins. PMID:25443957

  11. 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

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    USDA-ARS?s Scientific Manuscript database

    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 ‘...

  14. 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

  15. Climatic Warming Increases Winter Wheat Yield but Reduces Grain Nitrogen Concentration in East China

    PubMed Central

    Deng, Aixing; Song, Zhenwei; Zhang, Baoming; Zhang, Weijian

    2014-01-01

    Climatic warming is often predicted to reduce wheat yield and grain quality in China. However, direct evidence is still lacking. We conducted a three-year experiment with a Free Air Temperature Increase (FATI) facility to examine the responses of winter wheat growth and plant N accumulation to a moderate temperature increase of 1.5°C predicted to prevail by 2050 in East China. Three warming treatments (AW: all-day warming; DW: daytime warming; NW: nighttime warming) were applied for an entire growth period. Consistent warming effects on wheat plant were recorded across the experimental years. An increase of ca. 1.5°C in daily, daytime and nighttime mean temperatures shortened the length of pre-anthesis period averagely by 12.7, 8.3 and 10.7 d (P<0.05), respectively, but had no significant impact on the length of the post-anthesis period. Warming did not significantly alter the aboveground biomass production, but the grain yield was 16.3, 18.1 and 19.6% (P<0.05) higher in the AW, DW and NW plots than the non-warmed plot, respectively. Warming also significantly increased plant N uptake and total biomass N accumulation. However, warming significantly reduced grain N concentrations while increased N concentrations in the leaves and stems. Together, our results demonstrate differential impacts of warming on the depositions of grain starch and protein, highlighting the needs to further understand the mechanisms that underlie warming impacts on plant C and N metabolism in wheat. PMID:24736557

  16. Climatic warming increases winter wheat yield but reduces grain nitrogen concentration in east China.

    PubMed

    Tian, Yunlu; Zheng, Chengyan; Chen, Jin; Chen, Changqing; Deng, Aixing; Song, Zhenwei; Zhang, Baoming; Zhang, Weijian

    2014-01-01

    Climatic warming is often predicted to reduce wheat yield and grain quality in China. However, direct evidence is still lacking. We conducted a three-year experiment with a Free Air Temperature Increase (FATI) facility to examine the responses of winter wheat growth and plant N accumulation to a moderate temperature increase of 1.5°C predicted to prevail by 2050 in East China. Three warming treatments (AW: all-day warming; DW: daytime warming; NW: nighttime warming) were applied for an entire growth period. Consistent warming effects on wheat plant were recorded across the experimental years. An increase of ca. 1.5°C in daily, daytime and nighttime mean temperatures shortened the length of pre-anthesis period averagely by 12.7, 8.3 and 10.7 d (P<0.05), respectively, but had no significant impact on the length of the post-anthesis period. Warming did not significantly alter the aboveground biomass production, but the grain yield was 16.3, 18.1 and 19.6% (P<0.05) higher in the AW, DW and NW plots than the non-warmed plot, respectively. Warming also significantly increased plant N uptake and total biomass N accumulation. However, warming significantly reduced grain N concentrations while increased N concentrations in the leaves and stems. Together, our results demonstrate differential impacts of warming on the depositions of grain starch and protein, highlighting the needs to further understand the mechanisms that underlie warming impacts on plant C and N metabolism in wheat.

  17. 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

  18. 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

  19. Atmospheric nitrogen deposition to China: a model analysis on nitrogen budget and critical load exceedance

    NASA Astrophysics Data System (ADS)

    Zhao, Y.; Zhang, L.; Chen, Y.; Liu, X.; Xu, W.; Pan, Y.; Duan, L.

    2016-12-01

    We present a national-scale model analysis of the sources and processes of inorganic nitrogen deposition over China using the GEOS-Chem model at 1/2°×1/3° horizontal resolution. Averaged model results for 2008-2012 are evaluated with an ensemble of surface measurements of nitrogen wet deposition flux and concentration, and satellite measurements of tropospheric NO2 columns. Annual inorganic nitrogen deposition fluxes are shown to be generally less than 10 kg N ha-1 a-1 in the western China, 15-50 kg N ha-1 a-1 in the eastern China, and 15.6 kg N ha-1 a-1 averaged over China. The model simulates an annual total deposition flux of 16.4 Tg N to China, with 10.3 Tg N (63%) from reduced nitrogen (NHx) and 6.2 Tg N from oxidized nitrogen (NOy). Domestic anthropogenic sources contribute 86% of the total deposition; foreign anthropogenic sources 7% and natural sources 7%. Annually 23% of domestically emitted NH3 and 36% for NOx are exported out of China. We also find while nitrogen deposition to China is comparable to the nitrogen input from fertilizer application (16.5 Tg N a-1) on the national scale, it is much more widely distributed spatially. The deposition flux is also much higher than natural biological fixation (7.3 Tg N a-1). A comparison with estimates of nitrogen critical load for eutrophication indicates that about 40% of the land over China faces nitrogen critical load exceedances. However, 45% of the exceeding areas, mainly in Beijing-Tianjin-Hebei, Central China, East China, and South China, will not occur in the absence of nitrogen deposition, demonstrating the necessity of nitrogen emission controls to avoid potential negative ecological effects over these areas.

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. Dynamical coarse grained models with realistic time dependence

    NASA Astrophysics Data System (ADS)

    Andersen, Hans

    2015-03-01

    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. 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 an 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 was studied by Zwanzig [R. Zwanzig, J. Stat. Phys. 9, 215 (1973)]. The dynamic models generate a non-Markovian dynamics for the CG degrees of freedom, but they can be easily simulated using standard molecular dynamics simulation programs. We present tests of this method on a series of simple examples that demonstrate that the method provides realistic dynamical CG models that have non-Markovian or close to Markovian behavior that is consistent with the actual dynamical behavior of the all-atom system used to construct the CG model. The dynamic CG models have computational requirements that are similar to

  5. A dynamic nitrogen budget model of a Pacific Northwest salt ...

    EPA Pesticide Factsheets

    The role of salt marshes as either nitrogen sinks or sources in relation to their adjacent estuaries has been a focus of ecosystem service research for many decades. The complex hydrology of these systems is driven by tides, upland surface runoff, precipitation, evapotranspiration, and groundwater inputs, all of which can vary significantly on timescales ranging from sub-daily to seasonal. Additionally, many of these hydrologic drivers may vary with a changing climate. Due to this temporal variation in hydrology, it is difficult to represent salt marsh nitrogen budgets as steady-state models. A dynamic nitrogen budget model that varies based on hydrologic conditions may more accurately describe the role of salt marshes in nitrogen cycling. In this study we aim to develop a hydrologic model that is coupled with a process-based nitrogen model to simulate nitrogen dynamics at multiple temporal scales. To construct and validate our model we will use hydrologic and nitrogen species data collected from 2010 to present, from a 1.8 hectare salt marsh in the Yaquina Estuary, OR, USA. Hydrologic data include water table levels at two transects, upland tributary flow, tidal channel stage and flow, and vertical hydraulic head gradients. Nitrogen pool data include concentrations of nitrate and ammonium in porewater, tidal channel water, and extracted from soil cores. Nitrogen flux data include denitrification rates, nitrogen concentrations in upland runoff, and tida

  6. A dynamic nitrogen budget model of a Pacific Northwest salt ...

    EPA Pesticide Factsheets

    The role of salt marshes as either nitrogen sinks or sources in relation to their adjacent estuaries has been a focus of ecosystem service research for many decades. The complex hydrology of these systems is driven by tides, upland surface runoff, precipitation, evapotranspiration, and groundwater inputs, all of which can vary significantly on timescales ranging from sub-daily to seasonal. Additionally, many of these hydrologic drivers may vary with a changing climate. Due to this temporal variation in hydrology, it is difficult to represent salt marsh nitrogen budgets as steady-state models. A dynamic nitrogen budget model that varies based on hydrologic conditions may more accurately describe the role of salt marshes in nitrogen cycling. In this study we aim to develop a hydrologic model that is coupled with a process-based nitrogen model to simulate nitrogen dynamics at multiple temporal scales. To construct and validate our model we will use hydrologic and nitrogen species data collected from 2010 to present, from a 1.8 hectare salt marsh in the Yaquina Estuary, OR, USA. Hydrologic data include water table levels at two transects, upland tributary flow, tidal channel stage and flow, and vertical hydraulic head gradients. Nitrogen pool data include concentrations of nitrate and ammonium in porewater, tidal channel water, and extracted from soil cores. Nitrogen flux data include denitrification rates, nitrogen concentrations in upland runoff, and tida

  7. [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.

  8. 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.

  9. 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

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

    PubMed

    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 × 10(9) g N yr(-1)) split roughly 60:40 between inorganic:organic components. Much of this was denitrified (34 × 10(9) g N yr(-1)) and buried (46 × 10(9) 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 × 10(9) 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.

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

    PubMed Central

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

    2015-01-01

    Abstract 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. PMID:27668137

  12. Interactions between barley grain processing and source of supplemental dietary fat on nitrogen metabolism and urea-nitrogen recycling in dairy cows.

    PubMed

    Gozho, G N; Hobin, M R; Mutsvangwa, T

    2008-01-01

    The objective of this study was to determine the effects of methods of barley grain processing and source of supplemental fat on urea-N transfer to the gastrointestinal tract (GIT) and the utilization of this recycled urea-N in lactating dairy cows. Four ruminally cannulated Holstein cows (656.3 +/- 27.7 kg of BW; 79.8 +/- 12.3 d in milk) were used in a 4 x 4 Latin square design with 28-d periods and a 2 x 2 factorial arrangement of dietary treatments. Experimental diets contained dry-rolled barley or pelleted barley in combination with whole canola or whole flaxseed as supplemental fat sources. Nitrogen balance was measured from d 15 to 19, with concurrent measurements of urea-N kinetics using continuous intrajugular infusions of [15N 15N]-urea. Dry matter intake and N intake were higher in cows fed dry-rolled barley compared with those fed pelleted barley. Nitrogen retention was not affected by diet, but fecal N excretion was higher in cows fed dry-rolled barley than in those fed pelleted barley. Actual and energy-corrected milk yield were not affected by diet. Milk fat content and milk fat yield were higher in cows fed dry-rolled barley compared with those fed pelleted barley. Source of supplemental fat did not affect urea-N kinetics. Urea-N production was higher (442.2 vs. 334.3 g of N/d), and urea-N entering the GIT tended to be higher (272.9 vs. 202.0 g of N/d), in cows fed dry-rolled barley compared with those fed pelleted barley. The amount of urea-N entry into the GIT that was returned to the ornithine cycle was higher (204.1 vs. 159.5 g of N/d) in cows fed dry-rolled barley than in pelleted barley-fed cows. The amount of urea-N recycled to the GIT and used for anabolic purposes, and the amounts lost in the urine or feces were not affected by dietary treatment. Microbial nonammonia N supply, estimated using total urinary excretion of purine derivatives, was not affected by diet. These results show that even though barley grain processing altered urea

  13. 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.

  14. A coarse grain model for protein-surface interactions.

    PubMed

    Wei, Shuai; Knotts, Thomas A

    2013-09-07

    The interaction of proteins with surfaces is important in numerous applications in many fields-such as biotechnology, proteomics, sensors, and medicine--but fundamental understanding of how protein stability and structure are affected by surfaces remains incomplete. Over the last several years, molecular simulation using coarse grain models has yielded significant insights, but the formalisms used to represent the surface interactions have been rudimentary. We present a new model for protein surface interactions that incorporates the chemical specificity of both the surface and the residues comprising the protein in the context of a one-bead-per-residue, coarse grain approach that maintains computational efficiency. The model is parameterized against experimental adsorption energies for multiple model peptides on different types of surfaces. The validity of the model is established by its ability to quantitatively and qualitatively predict the free energy of adsorption and structural changes for multiple biologically-relevant proteins on different surfaces. The validation, done with proteins not used in parameterization, shows that the model produces remarkable agreement between simulation and experiment.

  15. A coarse grain model for protein-surface interactions

    NASA Astrophysics Data System (ADS)

    Wei, Shuai; Knotts, Thomas A.

    2013-09-01

    The interaction of proteins with surfaces is important in numerous applications in many fields—such as biotechnology, proteomics, sensors, and medicine—but fundamental understanding of how protein stability and structure are affected by surfaces remains incomplete. Over the last several years, molecular simulation using coarse grain models has yielded significant insights, but the formalisms used to represent the surface interactions have been rudimentary. We present a new model for protein surface interactions that incorporates the chemical specificity of both the surface and the residues comprising the protein in the context of a one-bead-per-residue, coarse grain approach that maintains computational efficiency. The model is parameterized against experimental adsorption energies for multiple model peptides on different types of surfaces. The validity of the model is established by its ability to quantitatively and qualitatively predict the free energy of adsorption and structural changes for multiple biologically-relevant proteins on different surfaces. The validation, done with proteins not used in parameterization, shows that the model produces remarkable agreement between simulation and experiment.

  16. Effects of ruminally degradable nitrogen in diets containing wet corn distiller's grains and steam-flaked corn on feedlot cattle performance and carcass characteristics

    USDA-ARS?s Scientific Manuscript database

    Assessment of degradable nitrogen (N) needs in diets containing wet corn distiller's grains with solubles (WCDGS) is needed to aid the cattle industry in managing feed costs. Yearling steers (n = 525; initial weight = 373 +/- 13 kg) were housed in 54 pens (9 to 10 steers/pen) and received treatments...

  17. Effects of non-protein nitrogen in diets containing 15% wet distiller's grains with solubles and steam-flaked corn on feedlot cattle performance and carcass characteristics

    USDA-ARS?s Scientific Manuscript database

    Our previous data suggest that the non-protein nitrogen (NPN) need in diets with 15% wet distiller's grains with solubles (WDGS) for optimum growth performance may be slightly less than in 0% WDGS diets. The objective of the present study was to more clearly define the NPN need in diets with 15% WDG...

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

    PubMed

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

    2008-06-28

    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(+)NO(3) (-) ionic liquid are provided to illustrate the method.

  19. 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.

  20. Nitrogen

    USGS Publications Warehouse

    Apodaca, Lori E.

    2013-01-01

    The article presents an overview of the nitrogen chemical market as of July 2013, including the production of ammonia compounds. Industrial uses for ammonia include fertilizers, explosives, and plastics. Other topics include industrial capacity of U.S. ammonia producers CF Industries Holdings Inc., Koch Nitrogen Co., PCS Nitrogen, Inc., and Agrium Inc., the impact of natural gas prices on the nitrogen industry, and demand for corn crops for ethanol production.

  1. 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

  2. [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.

  3. Coarse-grained modeling of RNA 3D structure.

    PubMed

    Dawson, Wayne K; Maciejczyk, Maciej; Jankowska, Elzbieta J; Bujnicki, Janusz M

    2016-07-01

    Functional RNA molecules depend on three-dimensional (3D) structures to carry out their tasks within the cell. Understanding how these molecules interact to carry out their biological roles requires a detailed knowledge of RNA 3D structure and dynamics as well as thermodynamics, which strongly governs the folding of RNA and RNA-RNA interactions as well as a host of other interactions within the cellular environment. Experimental determination of these properties is difficult, and various computational methods have been developed to model the folding of RNA 3D structures and their interactions with other molecules. However, computational methods also have their limitations, especially when the biological effects demand computation of the dynamics beyond a few hundred nanoseconds. For the researcher confronted with such challenges, a more amenable approach is to resort to coarse-grained modeling to reduce the number of data points and computational demand to a more tractable size, while sacrificing as little critical information as possible. This review presents an introduction to the topic of coarse-grained modeling of RNA 3D structures and dynamics, covering both high- and low-resolution strategies. We discuss how physics-based approaches compare with knowledge based methods that rely on databases of information. In the course of this review, we discuss important aspects in the reasoning process behind building different models and the goals and pitfalls that can result.

  4. [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.

  5. 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

  6. 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.

  7. MARTINI Coarse-Grained Models of Polyethylene and Polypropylene.

    PubMed

    Panizon, Emanuele; Bochicchio, Davide; Monticelli, Luca; Rossi, Giulia

    2015-06-25

    The understanding of the interaction of nanoplastics with living organisms is crucial both to assess the health hazards of degraded plastics and to design functional polymer nanoparticles with biomedical applications. In this paper, we develop two coarse-grained models of everyday use polymers, polyethylene (PE) and polypropylene (PP), aimed at the study of the interaction of hydrophobic plastics with lipid membranes. The models are compatible with the popular MARTINI force field for lipids, and they are developed using both structural and thermodynamic properties as targets in the parametrization. The models are then validated by showing their reliability at reproducing structural properties of the polymers, both linear and branched, in dilute conditions, in the melt, and in a PE-PP blend. PE and PP radius of gyration is correctly reproduced in all conditions, while PE-PP interactions in the blend are slightly overestimated. Partitioning of PP and PE oligomers in phosphatidylcholine membranes as obtained at CG level reproduces well atomistic data.

  8. 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.

  9. A shock initiation model for fine-grained hexanitrostilbene

    SciTech Connect

    Kipp, M.E.; Setchell, R.E.

    1989-01-01

    An established body of data indicates that very fine-grained hexanitrostilbene (HNS), when pressed to 92% of crystal density, exhibits shock initiation characteristics unlike those typical of porous, granular explosives. That is, a progressive buildup towards detonation from an initial shock by hot spot formation and growth processes is not observed. Instead, this particular HNS exhibits shock initiation characteristics normally associated with homogeneous explosives (e.g., the formation of a superdetonation wave after an initial shock has been introduced). In the present work, a comprehensive effort has been made to develop a predictive model for shock initiation in this material. This model is based on a theory of homogeneous reactive mixtures, and includes a refined equation of state for porous HNS reactant and a JWL equation of state for gaseous reaction products. The model has been incorporated into wave propagation codes, and comparisons with available initiation data are made. 22 refs., 8 figs.

  10. Sequence transferable coarse-grained model of amphiphilic copolymers

    NASA Astrophysics Data System (ADS)

    De Silva, Chathuranga C.; Leophairatana, Porakrit; Ohkuma, Takahiro; Koberstein, Jeffrey T.; Kremer, Kurt; Mukherji, Debashish

    2017-08-01

    Polymer properties are inherently multi-scale in nature, where delicate local interaction details play a key role in describing their global conformational behavior. In this context, deriving coarse-grained (CG) multi-scale models for polymeric liquids is a non-trivial task. Further complexities arise when dealing with copolymer systems with varying microscopic sequences, especially when they are of amphiphilic nature. In this work, we derive a segment-based generic CG model for amphiphilic copolymers consisting of repeat units of hydrophobic (methylene) and hydrophilic (ethylene oxide) monomers. The system is a simulation analogue of polyacetal copolymers [S. Samanta et al., Macromolecules 49, 1858 (2016)]. The CG model is found to be transferable over a wide range of copolymer sequences and also to be consistent with existing experimental data.

  11. One-bead coarse-grained model for RNA dynamics.

    PubMed

    Villada-Balbuena, Mario; Carbajal-Tinoco, Mauricio D

    2017-01-28

    We present a revised version of a coarse-grained model for RNA dynamics. In such approach, the description of nucleotides is reduced to single points that interact between them through a series of effective pair potentials that were obtained from an improved analysis of RNA structures from the Protein Data Bank. These interaction potentials are the main constituents of a Brownian dynamics simulation algorithm that allows to perform a variety of tasks by taking advantage of the reduced number of variables. Such tasks include the prediction of the three-dimensional configuration of a series of test molecules. Moreover, the model permits the inclusion of effective magnesium ions and the ends of the RNA chains can be pulled with an external force to study the process of unfolding. In spite of the simplicity of the model, we obtain a good agreement with the experimental results.

  12. One-bead coarse-grained model for RNA dynamics

    NASA Astrophysics Data System (ADS)

    Villada-Balbuena, Mario; Carbajal-Tinoco, Mauricio D.

    2017-01-01

    We present a revised version of a coarse-grained model for RNA dynamics. In such approach, the description of nucleotides is reduced to single points that interact between them through a series of effective pair potentials that were obtained from an improved analysis of RNA structures from the Protein Data Bank. These interaction potentials are the main constituents of a Brownian dynamics simulation algorithm that allows to perform a variety of tasks by taking advantage of the reduced number of variables. Such tasks include the prediction of the three-dimensional configuration of a series of test molecules. Moreover, the model permits the inclusion of effective magnesium ions and the ends of the RNA chains can be pulled with an external force to study the process of unfolding. In spite of the simplicity of the model, we obtain a good agreement with the experimental results.

  13. Atmospheric nitrogen deposition to China: A model analysis on nitrogen budget and critical load exceedance

    NASA Astrophysics Data System (ADS)

    Zhao, Yuanhong; Zhang, Lin; Chen, Youfan; Liu, Xuejun; Xu, Wen; Pan, Yuepeng; Duan, Lei

    2017-03-01

    We present a national-scale model analysis on the sources and processes of inorganic nitrogen deposition over China using the GEOS-Chem model at 1/2° × 1/3° horizontal resolution. Model results for 2008-2012 are evaluated with an ensemble of surface measurements of wet deposition flux and gaseous ammonia (NH3) concentration, and satellite measurements of tropospheric NO2 columns. Annual total inorganic nitrogen deposition fluxes are simulated to be generally less than 10 kg N ha-1 a-1 in western China (less than 2 kg N ha-1 a-1 over Tibet), 15-50 kg N ha-1 a-1 in eastern China, and 16.4 kg N ha-1 a-1 averaged over China. Annual total deposition to China is 16.4 Tg N, with 10.2 Tg N (62%) from reduced nitrogen (NHx) and 6.2 Tg N from oxidized nitrogen (NOy). Domestic anthropogenic sources contribute 86% of the total deposition; foreign anthropogenic sources 7% and natural sources 7%. Annually 23% of domestically emitted NH3 and 36% for NOx are exported outside the terrestrial land of China. We find that atmospheric nitrogen deposition is about half of the nitrogen input from fertilizer application (29.6 Tg N a-1), and is much higher than that from natural biological fixation (7.3 Tg N a-1) over China. A comparison of nitrogen deposition with critical load estimates for eutrophication indicates that about 15% of the land over China experiences critical load exceedances, demonstrating the necessity of nitrogen emission controls to avoid potential negative ecological effects.

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. Modelling the optical properties of composite and porous interstellar grains

    NASA Astrophysics Data System (ADS)

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

    2005-01-01

    There are indications that interstellar and interplanetary dust grains have an inhomogeneous and fluffy structure. We investigate different methods to describe light scattering by such composite particles. Both a model of layered particles and discrete dipole calculations for particles with Rayleigh and non-Rayleigh inclusions are used. The calculations demonstrate that porosity is a key parameter for determining light scattering. We find that the optical properties of the layered particles depend on the number and position of layers if the number of layers is small (⪉ 15). For a larger number of layers the scattering characteristics become independent of the layer sequence. The optical properties of particles with inclusions depend on the size of inclusions provided the porosity is large. The scattering characteristics of very porous particles with inclusions of different sizes are found to be close to those of multi-layered spheres. We compare the results of these calculations with the predictions of the effective medium theories (EMT) which are often used in astronomy as a tool to calculate the optical properties of composite particles. The results of our analysis show that the internal structure of grains (layers versus inclusions) only slightly affects the optics of particles provided the porosity does not exceed 50%. It is also demonstrated that in this case the optical properties of composite grains calculated with EMT agree with the results of the exact method for layered particles. For larger porosity, the standard EMT rules (i.e., Garnett and Bruggeman rules) give reliable results for particles with Rayleigh inclusions only.

  19. Modeling composite and fluffy grains: The effects of porosity

    NASA Technical Reports Server (NTRS)

    Wolff, Michael J.; Clayton, Geoffrey C.; Martin, P. G.; Schulte-Ladbeck, Regina E.

    1994-01-01

    Recent studies of interplanetary and interstellar dust provide evidence that cosmic dust grains are fluffy, composite objects, highlighting the need for models of the electromagnetic scattering by these grains. Effective medium theory (EMT) with Mie-type series solutions has been used to explore the effects of porosity which would be important in composite dust particles. While this indirect approach is both flexible and computationally efficient, it is not necessarily a good approximation. The need for EMT and its rather restrictive assumptions may be circumvented through a direct computation of the scattering properties via finite element methods, such as the discrete dipole approximation (DDA). Recently, the utility of the DDA method has been advanced significantly through improvements in theory, in numerical algorithms, and in computer hardware. Extensive calculations with the DDA method are used here to examine more directly the effects of porosity. A particular emphasis is placed upon developing a valid methodology. For both solid and porous targets we establish both numerical and physical convergence properties over the range of size parameter that is required for our study. DDA cross sections for grains with a range of porosity are compared to those computed by the EMT/series expansion technique to examine the applicability of several mixing rules, including two extensions of the Bruggeman rule. We show that for particles with Rayleigh vacuum inclusions, the extension proposed by Rouleau & Martin is quite successful. We also investigate the effects of larger, non-Rayleigh vacuum inclusions for various levels of porosity and find that they can be significant.

  20. 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.

  1. 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

  2. An Updated Gas/grain Sulfur Network for Astrochemical Models

    NASA Astrophysics Data System (ADS)

    Laas, Jacob; Caselli, Paola

    2017-06-01

    Sulfur is a chemical element that enjoys one of the highest cosmic abundances. However, it has traditionally played a relatively minor role in the field of astrochemistry, being drowned out by other chemistries after it depletes from the gas phase during the transition from a diffuse cloud to a dense one. A wealth of laboratory studies have provided clues to its rich chemistry in the condensed phase, and most recently, a report by a team behind the Rosetta spacecraft has significantly helped to unveil its rich cometary chemistry. We have set forth to use this information to greatly update/extend the sulfur reactions within the OSU gas/grain astrochemical network in a systematic way, to provide more realistic chemical models of sulfur for a variety of interstellar environments. We present here some results and implications of these models.

  3. 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.

  4. 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.

  5. 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.

  6. Modeling the nitrogen cycle one gene at a time

    NASA Astrophysics Data System (ADS)

    Coles, V.; Stukel, M. R.; Hood, R. R.; Moran, M. A.; Paul, J. H.; Satinsky, B.; Zielinski, B.; Yager, P. L.

    2016-02-01

    Marine ecosystem models are lagging the revolution in microbial oceanography. As a result, modeling of the nitrogen cycle has largely failed to leverage new genomic information on nitrogen cycling pathways and the organisms that mediate them. We developed a nitrogen based ecosystem model whose community is determined by randomly assigning functional genes to build each organism's "DNA". Microbes are assigned a size that sets their baseline environmental responses using allometric response curves. These responses are modified by the costs and benefits conferred by each gene in an organism's genome. The microbes are embedded in a general circulation model where environmental conditions shape the emergent population. This model is used to explore whether organisms constructed from randomized combinations of metabolic capability alone can self-organize to create realistic oceanic biogeochemical gradients. Community size spectra and chlorophyll-a concentrations emerge in the model with reasonable fidelity to observations. The model is run repeatedly with randomly-generated microbial communities and each time realistic gradients in community size spectra, chlorophyll-a, and forms of nitrogen develop. This supports the hypothesis that the metabolic potential of a community rather than the realized species composition is the primary factor setting vertical and horizontal environmental gradients. Vertical distributions of nitrogen and transcripts for genes involved in nitrification are broadly consistent with observations. Modeled gene and transcript abundance for nitrogen cycling and processing of land-derived organic material match observations along the extreme gradients in the Amazon River plume, and they help to explain the factors controlling observed variability.

  7. 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

  8. 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

  9. GAS-GRAIN MODELS FOR INTERSTELLAR ANION CHEMISTRY

    SciTech Connect

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

    2012-04-20

    Long-chain hydrocarbon anions C{sub n}H{sup -} (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 H{sub 2}}{approx}>10{sup 5} cm{sup -3}). 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 C{sub 6}H{sup -} 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 C{sub 6}O, C{sub 7}O, HC{sub 6}O, and HC{sub 7}O, the abundances of which depend on the assumed branching ratios for associative electron detachment.

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

    PubMed

    Deng, Mingsen; Shen, Hujun

    2016-02-04

    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.

  11. Coarse Grained Model for Biological Simulations: Recent Refinements and Validation

    PubMed Central

    Vicatos, Spyridon; Rychkova, Anna; Mukherjee, Shayantani; Warshel, Arieh

    2014-01-01

    Exploring the free energy landscape of proteins and modeling 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 various simplified coarse grained (CG) models offers an effective way of sampling the landscape, but most current models are not expected to give a reliable description of protein stability and functional aspects. The main problem is associated with insufficient focus on the electrostatic features of the model. In this respect our recent CG model offers significant advantage as it has been refined while focusing on its electrostatic free energy. Here we review the current state of our model, describing recent refinement, extensions and validation studies while focusing on demonstrating key applications. These include studies of protein stability, extending the model to include membranes and electrolytes and electrodes as well as studies of voltage activated proteins, protein insertion trough the translocon, the action of molecular motors and even the coupling of the stalled ribosome and the translocon. Our example illustrates the general potential of our approach in overcoming major challenges in studies of structure function correlation in proteins and large macromolecular complexes. PMID:25050439

  12. 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

  13. Modeling the dependence of strength on grain sizes in nanocrystalline materials.

    PubMed

    He, Wei; Bhole, Sanjeev D; Chen, DaoLun

    2008-01-01

    A model was developed to describe the grain size dependence of hardness (or strength) in nanocrystalline materials by combining the Hall-Petch relationship for larger grains with a coherent polycrystal model for nanoscale grains and introducing a log-normal distribution of grain sizes. The transition from the Hall-Petch relationship to the coherent polycrystal mechanism was shown to be a gradual process. The hardness in the nanoscale regime was observed to increase with decreasing grain boundary affected zone (or effective grain boundary thickness, Δ) in the form of Δ(-1/2). The critical grain size increased linearly with increasing Δ. The variation of the calculated hardness value with the grain size was observed to be in agreement with the experimental data reported in the literature.

  14. Optimizing irrigation and nitrogen for wheat through empirical modeling under semi-arid environment.

    PubMed

    Saeed, Umer; Wajid, Syed Aftab; Khaliq, Tasneem; Zahir, Zahir Ahmad

    2017-04-01

    Nitrogen fertilizer availability to plants is strongly linked with water availability. Excessive or insufficient use of nitrogen can cause reduction in grain yield of wheat and environmental issues. The per capita per annum water availability in Pakistan has reduced to less than 1000 m(3) and is expected to reach 800 m(3) during 2025. Irrigating crops with 3 or more than 3 in. of depth without measuring volume of water is not a feasible option anymore. Water productivity and economic return of grain yield can be improved by efficient management of water and nitrogen fertilizer. A study was conducted at post-graduate agricultural research station, University of Agriculture Faisalabad, during 2012-2013 and 2013-2014 to optimize volume of water per irrigation and nitrogen application. Split plot design with three replications was used to conduct experiment; four irrigation levels (I300 = 300 mm, I240 = 240 mm, I180 = 180 mm, I120 = 120 mm for whole growing season at critical growth stages) and four nitrogen levels (N60 = 60 kg ha(-1), N120 = 120 kg ha(-1), N180 = 180 kg ha(-1), and N240 = 240 kg ha(-1)) were randomized as main and sub-plot factors, respectively. The recorded data on grain yield was used to develop empirical regression models. The results based on quadratic equations and economic analysis showed 164, 162, 158, and 107 kg ha(-1) nitrogen as economic optimum with I300, I240, I180, and I120 mm water, respectively, during 2012-2013. During 2013-2014, quadratic equations and economic analysis showed 165, 162, 161, and 117 kg ha(-1) nitrogen as economic optimum with I300, I240, I180, and I120 mm water, respectively. The optimum irrigation level was obtained by fitting economic optimum nitrogen as function of total water. Equations predicted 253 mm as optimum irrigation water for whole growing season during 2012-2013 and 256 mm water as optimum for 2013-2014. The results also revealed that reducing irrigation from I300 to

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

    USDA-ARS?s Scientific Manuscript database

    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...

  16. 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.

  17. 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. © 2016 John Wiley & Sons Ltd.

  18. 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. Published by Elsevier Ltd.

  19. Coarse-grained modeling of polyethylene melts: Effect on dynamics

    DOE PAGES

    Peters, Brandon L.; Salerno, K. Michael; Agrawal, Anupriya; ...

    2017-05-23

    The distinctive viscoelastic behavior of polymers results from a coupled interplay of motion on multiple length and time scales. Capturing the broad time and length scales of polymer motion remains a challenge. Using polyethylene (PE) as a model macromolecule, we construct coarse-grained (CG) models of PE with three to six methyl groups per CG bead and probe two critical aspects of the technique: pressure corrections required after iterative Boltzmann inversion (IBI) to generate CG potentials that match the pressure of reference fully atomistic melt simulations and the transferability of CG potentials across temperatures. While IBI produces nonbonded pair potentials thatmore » give excellent agreement between the atomistic and CG pair correlation functions, the resulting pressure for the CG models is large compared with the pressure of the atomistic system. We find that correcting the potential to match the reference pressure leads to nonbonded interactions with much deeper minima and slightly smaller effective bead diameter. However, simulations with potentials generated by IBI and pressure-corrected IBI result in similar mean-square displacements (MSDs) and stress autocorrelation functions G(t) for PE melts. While the time rescaling factor required to match CG and atomistic models is the same for pressure- and non-pressure-corrected CG models, it strongly depends on temperature. Furthermore, transferability was investigated by comparing the MSDs and stress autocorrelation functions for potentials developed at different temperatures.« less

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. Coarse-grained models of protein folding: toy models or predictive tools?

    PubMed

    Clementi, Cecilia

    2008-02-01

    Coarse-grained models are emerging as a practical alternative to all-atom simulations for the characterization of protein folding mechanisms over long time scales. While a decade ago minimalist toy models were mainly designed to test general hypotheses on the principles regulating protein folding, the latest coarse-grained models are increasingly realistic and can be used to characterize quantitatively the detailed folding mechanism of specific proteins. The ability of such models to reproduce the essential features of folding dynamics suggests that each single atomic degree of freedom is not by itself particularly relevant to folding and supports a statistical mechanical approach to characterize folding transitions. When combined with more refined models and with experimental studies, the systematic investigation of protein systems and complexes using coarse-grained models can advance our theoretical understanding of the actual organizing principles that emerge from the complex network of interactions among protein atomic constituents.

  6. Modeling of multi-phase interactions of reactive nitrogen between snow and air in Antarctica

    NASA Astrophysics Data System (ADS)

    McCrystall, M.; Chan, H. G. V.; Frey, M. M.; King, M. D.

    2016-12-01

    In polar and snow-covered regions, the snowpack is an important link between atmospheric, terrestrial and oceanic systems. Trace gases, including nitrogen oxides, produced via photochemical reactions in snow are partially released to the lower atmosphere with considerable impact on its composition. However, the post-depositional processes that change the chemical composition and physical properties of the snowpack are still poorly understood. Most current snow chemistry models oversimplify as they assume air-liquid interactions and aqueous phase chemistry taking place at the interface between the snow grain and air. Here, we develop a novel temperature dependent multi-phase (gas-liquid-ice) physical exchange model for reactive nitrogen. The model is validated with existing year-round observations of nitrate in the top 0.5-2 cm of snow and the overlying atmosphere at two very different Antarctic locations: Dome C on the East Antarctic Plateau with very low annual mean temperature (-54ºC) and accumulation rate (<30 kg m-2 yr-1); and Halley, a coastal site with at times at or above freezing temperatures during summer, high accumulation rate and high background level of sea salt aerosol. We find that below the eutectic temperature of the H2O/dominant ion mixture the surface snow nitrate is controlled by kinetic adsorption onto the surface of snow grains followed by grain diffusion. Above the eutectic temperature, in addition to the former two processes, thermodynamic equilibrium of HNO3 between interstitial air and liquid water pockets, possibly present at triple junctions or grooves at grain boundaries, greatly enhances the nitrate uptake by snow in agreement with the concentration peak observed in summer.

  7. Estimation of phenotypic variability in symbiotic nitrogen fixation ability of common bean under drought stress using (15)N natural abundance in grain.

    PubMed

    Polania, Jose; Poschenrieder, Charlotte; Rao, Idupulapati; Beebe, Stephen

    2016-09-01

    Common bean (Phaseolus vulgaris L.) is the most important food legume, cultivated by small farmers and is usually exposed to unfavorable conditions with minimum use of inputs. Drought and low soil fertility, especially phosphorus and nitrogen (N) deficiencies, are major limitations to bean yield in smallholder systems. Beans can derive part of their required N from the atmosphere through symbiotic nitrogen fixation (SNF). Drought stress severely limits SNF ability of plants. The main objectives of this study were to: (i) test and validate the use of (15)N natural abundance in grain to quantify phenotypic differences in SNF ability for its implementation in breeding programs of common bean with bush growth habit aiming to improve SNF, and (ii) quantify phenotypic differences in SNF under drought to identify superior genotypes that could serve as parents. Field studies were conducted at CIAT-Palmira, Colombia using a set of 36 bean genotypes belonging to the Middle American gene pool for evaluation in two seasons with two levels of water supply (irrigated and drought stress). We used (15)N natural abundance method to compare SNF ability estimated from shoot tissue sampled at mid-pod filling growth stage vs. grain tissue sampled at harvest. Our results showed positive and significant correlation between nitrogen derived from the atmosphere (%Ndfa) estimated using shoot tissue at mid-pod filling and %Ndfa estimated using grain tissue at harvest. Both methods showed phenotypic variability in SNF ability under both drought and irrigated conditions and a significant reduction in SNF ability was observed under drought stress. We suggest that the method of estimating Ndfa using grain tissue (Ndfa-G) could be applied in bean breeding programs to improve SNF ability. Using this method of Ndfa-G, we identified four bean lines (RCB 593, SEA 15, NCB 226 and BFS 29) that combine greater SNF ability with greater grain yield under drought stress and these could serve as potential

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. Transferable coarse-grained model for perfluorosulfonic acid polymer membranes

    NASA Astrophysics Data System (ADS)

    Kuo, An-Tsung; Okazaki, Susumu; Shinoda, Wataru

    2017-09-01

    Perfluorosulfonic acid (PFSA) polymer membranes are widely used as proton exchange membranes. Because the structure of the aqueous domain within the PFSA membrane is expected to directly influence proton conductance, many coarse-grained (CG) simulation studies have been performed to investigate the membrane morphology; these studies mostly used phenomenological models, such as dissipative particle dynamics. However, a chemically accurate CG model is required to investigate the morphology in realistic membranes and to provide a concrete molecular design. Here, we attempt to construct a predictive CG model for the structure and morphology of PFSA membranes that is compatible with the Sinoda-DeVane-Klein (SDK) CG water model [Shinoda et al., Mol. Simul. 33, 27 (2007)]. First, we extended the parameter set for the SDK CG force field to examine a hydrated PFSA membrane based on thermodynamic and structural data from experiments and all-atom (AA) molecular dynamics (MD) simulations. However, a noticeable degradation of the morphology motivated us to improve the structural properties by using the iterative Boltzmann inversion (IBI) approach. Thus, we explored a possible combination of the SDK and IBI approaches to describe the nonbonded interaction. The hybrid SDK/IBI model improved the structural issues of SDK, showing a better agreement with AA-MD in the radial distribution functions. The hybrid SDK/IBI model was determined to reasonably reproduce both the thermodynamic and structural properties of the PFSA membrane for all examined water contents. In addition, the model demonstrated good transferability and has considerable potential for application to realistic long-chained PFSA membranes.

  13. Transferable coarse-grained model for perfluorosulfonic acid polymer membranes.

    PubMed

    Kuo, An-Tsung; Okazaki, Susumu; Shinoda, Wataru

    2017-09-07

    Perfluorosulfonic acid (PFSA) polymer membranes are widely used as proton exchange membranes. Because the structure of the aqueous domain within the PFSA membrane is expected to directly influence proton conductance, many coarse-grained (CG) simulation studies have been performed to investigate the membrane morphology; these studies mostly used phenomenological models, such as dissipative particle dynamics. However, a chemically accurate CG model is required to investigate the morphology in realistic membranes and to provide a concrete molecular design. Here, we attempt to construct a predictive CG model for the structure and morphology of PFSA membranes that is compatible with the Sinoda-DeVane-Klein (SDK) CG water model [Shinoda et al., Mol. Simul. 33, 27 (2007)]. First, we extended the parameter set for the SDK CG force field to examine a hydrated PFSA membrane based on thermodynamic and structural data from experiments and all-atom (AA) molecular dynamics (MD) simulations. However, a noticeable degradation of the morphology motivated us to improve the structural properties by using the iterative Boltzmann inversion (IBI) approach. Thus, we explored a possible combination of the SDK and IBI approaches to describe the nonbonded interaction. The hybrid SDK/IBI model improved the structural issues of SDK, showing a better agreement with AA-MD in the radial distribution functions. The hybrid SDK/IBI model was determined to reasonably reproduce both the thermodynamic and structural properties of the PFSA membrane for all examined water contents. In addition, the model demonstrated good transferability and has considerable potential for application to realistic long-chained PFSA membranes.

  14. 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.

  15. 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.

  16. 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.

  17. Coarse-grained modeling of protein unspecifically bound to DNA

    NASA Astrophysics Data System (ADS)

    Guardiani, Carlo; Cencini, Massimo; Cecconi, Fabio

    2014-04-01

    There is now a certain consensus that transcription factors (TFs) reach their target sites, where they regulate gene transcription, via a mechanism dubbed facilitated diffusion (FD). In FD, the TF cycles between events of 3D diffusion in solution (jumps), 1D diffusion along DNA (sliding), and small jumps (hopping), achieving association rates higher than for 3D diffusion alone. We investigate the FD phenomenology through molecular dynamics simulations in the framework of coarse-grained modeling. We show that, despite the crude approximations, the model generates, upon varying the equilibrium distance of the DNA-TF interaction, a phenomenology matching a number of experimental and numerical results obtained with more refined models. In particular, focusing on the kinematics of the process, we characterize the geometrical properties of TF trajectories during sliding. We find that sliding occurs via helical paths around the DNA helix, leading to a coupling of translation along the DNA axis with rotation around it. The 1D diffusion constant measured in simulations is found to be interwoven with the geometrical properties of sliding and we develop a simple argument that can be used to quantitatively reproduce the measured values.

  18. Continuous modeling of a grain boundary in MgO and its disclination induced grain-boundary migration mechanism

    NASA Astrophysics Data System (ADS)

    Cordier, P.; Sun, X.; Taupin, V.; Fressengeas, C.

    2016-12-01

    Grain boundaries (GBs) are thin material layers where the lattice rotates from one orientation to the next one within a few nanometers. Because they treat these layers as infinitely thin interfaces, large-scale polycrystalline representations fail to describe their structure. Conversely, atomistic representations provide a detailed description of the GBs, but their character remains discrete and not prone to coarse-graining procedures. Continuum descriptions based on kinematic and crystal defect fields defined at interatomic scale are appealing because they can provide smooth and thorough descriptions of GBs, recovering in some sense the atomistic description and potentially serving as a basis for coarse-grained polycrystalline representations. In this work, a crossover between atomistic description and continuous representation of a MgO tilt boundary in polycrystals is set-up to model the periodic arrays of structural units by using dislocation and disclination dipole arrays along GBs. The strain, rotation, curvature, disclination and dislocation density fields are determined in the boundary area by using the discrete atomic positions generated by molecular dynamics simulations. Then, this continuous disclination/dislocation model is used as part of the initial conditions in elasto-plastic continuum mechanics simulations to investigate the shear-coupled boundary migration of tilt boundaries. The present study leads to better understanding of the structure and mechanical architecture of grain boundaries.

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

    NASA Astrophysics Data System (ADS)

    Kovacs, G. J.

    2003-04-01

    In the early 1980-es the author published interpretations of his observations on special adaptation processes of crops. Those days it was not yet timely 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 build these into systems models. From practical reasons 4M system model was chosen for this work. 4M has been developed at RISSAC, Budapest, Hungary based on CERES model and the advices of J.T. Ritchie. It includes the work of several Hungarian scientists. The newly modelled processes were as follows: (1) nitrate and ammonium concentration of soil solution in soil layers influenced by water transport processes and nitrogen transformation and transport processes, (2) root growth and distribution by the influence of available soil water and soil nitrogen, (3) changed transpiration rate influenced by radical change of availability of nitrogen. (4) changed distribution rate and redistribution of dry matter and nutrients in plants influenced by water and nitrogen stress. These processes have different consequences in the plant production depending on the phenological stage when the stress occurs. There are weather situations under the climate of the Carpathian base under which these the summer stress reactions can cause tons of losses in biomass and yield despite of abundant supply of fertilizers in spring. The phenomena can be characterised as spoiled maize stand interrupted by a heavy rainy period with strong nitrate leaching. In the dry period after the rainy period nitrogen shortage intensifies transpiration then the lack of water supply makes the plant to grow the roots fast in the deeper horizons. That leads to redistribution of biomass, loss of above ground DM, and deficiency of nutrients in the plant. In flowering stage it may lead to poor fertilization and smaller grain numbers consequently lower yield potential.

  20. 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

  1. 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.

  2. 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.

  3. Toward a model of grain surface exposure in planetary regoliths

    NASA Technical Reports Server (NTRS)

    Housley, R. M.

    1980-01-01

    The interpretation of solar wind implanted gas concentration versus particle size for lunar regolith samples is considered. In so doing, interparticle adhesive forces are considered explicitly and the simplest possible grain exposure law consistent with the existence of such forces is hypothesized. Namely, for particles small enough that these forces exceed the lunar gravitational force, any element of area has equal probability of being in the regolith surface regardless of the size of the grain on which it is situated. This law leads to the expectation that concentrations will depend inversely on mean grain radius for small grains and gradually become independent of radius for very large grains consistent with observations. Therefore, such a concentration dependence cannot by used to infer the presence of saturation losses.

  4. Modelling of grain boundary effects in nanocrystalline/multicrystalline silicon heterojunction solar cells

    NASA Astrophysics Data System (ADS)

    Farrokh-Baroughi, Mahdi; Sivoththaman, Siva

    2006-07-01

    Heterojunction solar cells formed by nanocrystalline silicon films on fine-grained multicrystalline silicon substrates are simulated in the presence of grain boundaries. The effects of grain boundaries on the dark and illuminated current-voltage (I-V) characteristics and spectral response (SR) of heterojunction (HJ) solar cells are assessed using 1D and 2D device simulations. The grain boundary in fine-grained multicrystalline silicon is modelled in two ways: as a defective surface with continuous defect distribution throughout the bandgap, and as a hypothetical sheet with a certain recombination velocity for electrons and holes. The SR and I-V characteristics of HJs are exploited to characterize grain boundary effects on the photovoltaic properties of the solar cells and photodetectors. Simulation results show noticeable differences on the dark I-V and SR of on- and off-grain boundary HJs. Grain boundary effects become important when fine-grained multicrystalline substrates are used. Measurement results of tiny test structures fabricated on the grain boundary show consistently inferior dark I-V and SR characteristics compared to those fabricated away from the grain and allow us to quantify the recombination at the grain boundary.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  7. Nitrogen

    USGS Publications Warehouse

    Apodaca, L.E.

    2012-01-01

    Ammonia was produced by 12 companies at 27 plants in 15 states in the United States during 2011. Sixty-one percent of total U.S. ammonia production capacity was centered in Louisiana, Oklahoma and Texas because of those states' large reserves of natural gas, the dominant domestic feedstock. In 2011, U.S. producers operated at about 84 percent of their rated capacity (excluding plants that were idle for the entire year). Four companies — CF Industries Holdings Inc.; Koch Nitrogen Co.; PCS Nitrogen Inc. and Agrium Inc., in descending order — accounted for 77 percent of the total U.S. ammonia production capacity.

  8. 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.

  9. Coarse-grained modeling of hybrid block copolymer system

    NASA Astrophysics Data System (ADS)

    Su, Yongrui

    This thesis is comprised of three major projects of my research. In the first project, I proposed a nanoparticle model and combined it with the Theoretically Informed Coarse Grained (TICG) model for pure polymer systems and the grand canonical slip springs model developed in our group to build a new model for entangled nanocomposites. With Molecule Dynamics(MD) simulation, I studied the mechanic properties of the nanocomposites, for example the influence of nanoparticles size and volume fraction on entanglements, the diffusion of polymers and nanoparticles, and the influence of nanoparticles size and volume fraction on viscosity et al.. We found that the addition of small-size nanoparticles reduces the viscosity of the nanocomposites, which is in contrary to what Einstein predicted a century ago. However, when particle increases its size to micrometers the Einstein predictions is recovered. From our simulation, we believe that small-size nanoparticles can more effectively decrease the entanglements of nanocomposites than larger particles. The free volume effect introduced by small-size nanoparticles also helps decrease the viscosity of the whole system. In the second project, I combined the Ohta-Kawasaki (OK) model [3] and the Covariance Matrix Adaptation Evolutionary Strategy(CMA-ES) to optimize the block copolymer blends self-assembly in the hole-shrink process. The aim is to predict the optimal composition and the optimal surface energy to direct the block copolymer blends self-assembly process in the confined hole. After optimization in the OK model, we calibrated the optimal results by the more reliable TICG model and got the same morphology. By comparing different optimization process, we found that the homopolymers which are comprised of the same monomers as either block of the block copolymer can form a perfect perforated hole and might have better performance than the pure block copolymer. While homopolymers which are comprised of a third-party monomers

  10. 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.

  11. 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.

  12. 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

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

    PubMed

    Zhang, Guoyou; Sakai, Hidemitsu; Tokida, Takeshi; Usui, Yasuhiro; Zhu, Chunwu; Nakamura, Hirofumi; Yoshimoto, Mayumi; Fukuoka, Minehiko; Kobayashi, Kazuhiko; Hasegawa, Toshihiro

    2013-08-01

    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].

  14. 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.

  15. Watershed Models for Predicting Nitrogen Loads from Artificially Drained Lands

    Treesearch

    R. Wayne Skaggs; George M. Chescheir; Glenn Fernandez; Devendra M. Amatya

    2003-01-01

    Non-point sources of pollutants originate at the field scale but water quality problems usually occur at the watershed or basin scale. This paper describes a series of models developed for poorly drained watersheds. The models use DRAINMOD to predict hydrology at the field scale and a range of methods to predict channel hydraulics and nitrogen transport. In-stream...

  16. Coarse Grained Model for Exploring Voltage Dependent Ion Channels

    PubMed Central

    Dryga, Anatoly; Chakrabarty, Suman; Vicatos, Spyridon; Warshel, Arieh

    2011-01-01

    The relationship between the membrane voltage and the gating of voltage activated ion channels and other systems have been a problem of great current interest. Unfortunately, reliable molecular simulations of external voltage effects present a major challenge, since meaningful converging microscopic simulations are not yet available and macroscopic treatments involve major uncertainties in terms of the dielectric used and other key features. This work extends our coarse grained (CG) model to simulations of membrane/protein systems under external potential. Special attention has been devoted to a consistent modeling of the effect of external potential due to the electrodes, emphasizing semimacroscopic description of the electrolytes in the solution regions between the membranes and the electrodes, as well as the coupling between the combined potential from the electrodes and electrolytes, and the protein ionization states. We also provide a clear connection to microscopic treatment of the electrolytes and thus can explore possible conceptual problems that are hard to resolve by other current approaches. For example, we obtain a clear description of the charge distribution in the entire electrolyte system, including near the electrodes in membrane/electrodes systems (where continuum models do not seem to provide the relevant results). Furthermore, the present treatment provides an insight on the distribution of the electrolyte charges before and after equilibration across the membrane, and thus on the nature of the gating charge. The different aspects of the model have been carefully validated by considering problems ranging for the simple Debye-Huckel, Gouy-Chapman models to the evaluation of the electrolyte distribution between two electrodes, as well as the effect of extending the simulation system by periodic replicas. Overall the clear connection to microscopic descriptions combined with the power of the CG modeling seems to offer a powerful tool for exploring

  17. Coarse graining approach to First principles modeling of structural materials

    SciTech Connect

    Odbadrakh, Khorgolkhuu; Nicholson, Don M; Rusanu, Aurelian; Samolyuk, German D; Wang, Yang; Stoller, Roger E; Zhang, X.-G.; Stocks, George Malcolm

    2013-01-01

    Classical Molecular Dynamic (MD) simulations characterizing extended defects typically require millions of atoms. First principles calculations employed to understand these defect systems at an electronic level cannot, and should not deal with such large numbers of atoms. We present an e cient coarse graining (CG) approach to calculate local electronic properties of large MD-generated structures from the rst principles. We used the Locally Self-consistent Multiple Scattering (LSMS) method for two types of iron defect structures 1) screw-dislocation dipoles and 2) radiation cascades. The multiple scattering equations are solved at fewer sites using the CG. The atomic positions were determined by MD with an embedded atom force eld. The local moments in the neighborhood of the defect cores are calculated with rst-principles based on full local structure information, while atoms in the rest of the system are modeled by representative atoms with approximated properties. This CG approach reduces computational costs signi cantly and makes large-scale structures amenable to rst principles study. Work is sponsored by the USDoE, O ce of Basic Energy Sciences, Center for Defect Physics, an Energy Frontier Research Center. This research used resources of the Oak Ridge Leadership Computing Facility at the ORNL, which is supported by the O ce of Science of the USDoE under Contract No. DE-AC05-00OR22725.

  18. 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.

  19. Coarse grained model for calculating the ion mobility of hydrocarbons

    NASA Astrophysics Data System (ADS)

    Kuroboshi, Y.; Takemura, K.

    2016-12-01

    Hydrocarbons are widely used as insulating compounds. However, their fundamental characteristics in conduction phenomena are not completely understood. A great deal of effort is required to determine reasonable ionic behavior from experiments because of their complicated procedures and tight controls of the temperature and the purity of the liquids. In order to understand the conduction phenomena, we have theoretically calculated the ion mobilities of hydrocarbons and investigated their characteristics using the coarse grained model in molecular dynamics simulations. We assumed a molecule of hydrocarbons to be a bead and simulated its dependence on the viscosity, electric field, and temperature. Furthermore, we verified the suitability of the conformation, scale size, and long-range interactions for the ion mobility. The results of the simulations show that the ion mobility values agree reasonably well with the values from Walden's rule and depend on the viscosity but not on the electric field. The ion mobility and self-diffusion coefficient exponentially increase with increasing temperature, while the activation energy decreases with increasing molecular size. These values and characteristics of the ion mobility are in reasonable agreement with experimental results. In the future, we can understand not only the ion mobilies of hydrocarbons in conduction, but also we can predict general phenomena in electrochemistry with molecular dynamics simulations.

  20. [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.

  1. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

    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.

  3. 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.

  4. 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

  5. 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

  6. 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

  7. Carbon-nitrogen-water interactions: is model parsimony fruitful?

    NASA Astrophysics Data System (ADS)

    Puertes, Cristina; González-Sanchis, María; Lidón, Antonio; Bautista, Inmaculada; Lull, Cristina; Francés, Félix

    2017-04-01

    It is well known that carbon and nitrogen cycles are highly intertwined and both should be explained through the water balance. In fact, in water-controlled ecosystems nutrient deficit is related to this water scarcity. For this reason, the present study compares the capability of three models in reproducing the interaction between the carbon and nitrogen cycles and the water cycle. The models are BIOME-BGCMuSo, LEACHM and a simple carbon-nitrogen model coupled to the hydrological model TETIS. Biome-BGCMuSo and LEACHM are two widely used models that reproduce the carbon and nitrogen cycles adequately. However, their main limitation is that these models are quite complex and can be too detailed for watershed studies. On the contrary, the TETIS nutrient sub-model is a conceptual model with a vertical tank distribution over the active soil depth, dividing it in two layers. Only the input of the added litter and the losses due to soil respiration, denitrification, leaching and plant uptake are considered as external fluxes. Other fluxes have been neglected. The three models have been implemented in an experimental plot of a semi-arid catchment (La Hunde, East of Spain), mostly covered by holm oak (Quercus ilex). Plant transpiration, soil moisture and runoff have been monitored daily during nearly two years (26/10/2012 to 30/09/2014). For the same period, soil samples were collected every two months and taken to the lab in order to obtain the concentrations of dissolved organic carbon, microbial biomass carbon, ammonium and nitrate. In addition, between field trips soil samples were placed in PVC tubes with resin traps and were left incubating (in situ buried cores). Thus, mineralization and nitrification accumulated fluxes for two months, were obtained. The ammonium and nitrate leaching accumulated for two months were measured using ion-exchange resin cores. Soil respiration was also measured every field trip. Finally, water samples deriving from runoff, were collected

  8. 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.

  9. Nitrogen

    USGS Publications Warehouse

    Apodaca, L.E.

    2010-01-01

    Ammonia was produced by 13 companies at 23 plants in 16 states during 2009. Sixty percent of all U.S. ammonia production capacity was centered in Louisiana. Oklahoma and Texas because of those states' large reserves of natural gas, the dominant domestic feedstock. In 2009, U.S. producers operated at about 83 percent of their rated capacity (excluding plants that were idle for the entire year). Five companies — Koch Nitrogen Co.; Terra Industries Inc.; CF Industries Inc.; PCS Nitrogen Inc. and Agrium Inc., in descending order — accounted for 80 percent of the total U.S. ammonia production capacity. U.S. production was estimated to be 7.7 Mt (8.5 million st) of nitrogen (N) content in 2009 compared with 7.85 Mt (8.65 million st) of N content in 2008. Apparent consumption was estimated to have decreased to 12.1 Mt (13.3 million st) of N, a 10-percent decrease from 2008. 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.

  10. Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models

    NASA Astrophysics Data System (ADS)

    Genheden, Samuel

    2017-09-01

    We present the estimation of solvation free energies of small solutes in water, n-octanol and hexane using molecular dynamics simulations with two MARTINI models at different resolutions, viz. the coarse-grained (CG) and the hybrid all-atom/coarse-grained (AA/CG) models. From these estimates, we also calculate the water/hexane and water/octanol partition coefficients. More than 150 small, organic molecules were selected from the Minnesota solvation database and parameterized in a semi-automatic fashion. Using either the CG or hybrid AA/CG models, we find considerable deviations between the estimated and experimental solvation free energies in all solvents with mean absolute deviations larger than 10 kJ/mol, although the correlation coefficient is between 0.55 and 0.75 and significant. There is also no difference between the results when using the non-polarizable and polarizable water model, although we identify some improvements when using the polarizable model with the AA/CG solutes. In contrast to the estimated solvation energies, the estimated partition coefficients are generally excellent with both the CG and hybrid AA/CG models, giving mean absolute deviations between 0.67 and 0.90 log units and correlation coefficients larger than 0.85. We analyze the error distribution further and suggest avenues for improvements.

  11. A Grain Structure Model based on Voronoi polygon of Non- oriented Electrical Steel in Blanking Process

    NASA Astrophysics Data System (ADS)

    Wang, Zhe; Li, Shuhui; Dong, Liang; He, Ji

    2016-08-01

    World-wide there is a trend to develop higher permeability grades, thin thickness and coarse grain of non-oriented electrical steels, a core function material of motors. Blanking is the most popular technique for producing the motor laminations. However, the deformation of material is significantly influenced by grain size. In this paper, Voronoi polygon is used for generate the random microstructures of the studied non-oriented electrical steel. Finite Element (FE) model considering grain size is thus established to analysis the blanking process. The material behaviour of grains is derived from the widely accepted surface layer model. Compared to the conventional model without considering the grain size, the novel model shows good matching with the experimental results.

  12. The proportion of nitrate in leaf nitrogen, but not changes in root growth, are associated with decreased grain protein in wheat under elevated [CO2].

    PubMed

    Bahrami, Helale; De Kok, Luit J; Armstrong, Roger; Fitzgerald, Glenn J; Bourgault, Maryse; Henty, Samuel; Tausz, Michael; Tausz-Posch, Sabine

    2017-09-01

    The atmospheric CO2 concentration ([CO2]) is increasing and predicted to reach ∼550ppm by 2050. Increasing [CO2] typically stimulates crop growth and yield, but decreases concentrations of nutrients, such as nitrogen ([N]), and therefore protein, in plant tissues and grains. Such changes in grain composition are expected to have negative implications for the nutritional and economic value of grains. This study addresses two mechanisms potentially accountable for the phenomenon of elevated [CO2]-induced decreases in [N]: N uptake per unit length of roots as well as inhibition of the assimilation of nitrate (NO3(-)) into protein are investigated and related to grain protein. We analysed two wheat cultivars from a similar genetic background but contrasting in agronomic features (Triticum aestivum L. cv. Scout and Yitpi). Plants were field-grown within the Australian Grains Free Air CO2 Enrichment (AGFACE) facility under two atmospheric [CO2] (ambient, ∼400ppm, and elevated, ∼550ppm) and two water treatments (rain-fed and well-watered). Aboveground dry weight (ADW) and root length (RL, captured by a mini-rhizotron root growth monitoring system), as well as [N] and NO3(-) concentrations ([NO3(-)]) were monitored throughout the growing season and related to grain protein at harvest. RL generally increased under e[CO2] and varied between water supply and cultivars. The ratio of total aboveground N (TN) taken up per RL was affected by CO2 treatment only later in the season and there was no significant correlation between TN/RL and grain protein concentration across cultivars and [CO2] treatments. In contrast, a greater percentage of N remained as unassimilated [NO3(-)] in the tissue of e[CO2] grown crops (expressed as the ratio of NO3(-) to total N) and this was significantly correlated with decreased grain protein. These findings suggest that e[CO2] directly affects the nitrate assimilation capacity of wheat with direct negative implications for grain quality. Crown

  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. Effects of dietary combination of corn and rice as whole crop silage and grain sources on carbohydrate digestion and nitrogen use in steers.

    PubMed

    Li, Zongfu; Sugino, Toshihisa; Obitsu, Taketo; Taniguchi, Kohzo

    2014-02-01

    Four Holstein steers were used to evaluate the combination effects of whole crop corn (Cs) or rice (Rs) silage with steam-flaked corn (Cg) or rice (Rg) grain (four dietary treatments) on ruminal carbohydrate digestion, duodenal nitrogen (N) flow and plasma essential amino acid (EAA) concentration. The ruminal digestibility of starch and nonfiber carbohydrate (NFC) for Rs and Rg diets compared with Cs and Cg diets was greater, but that of neutral detergent fiber (aNDFom) was less. Because the ruminal disappearance of NFC plus aNDFom was similar across four dietary treatments, microbial N flow was not affected by the diets. There was an interaction of methionine (Met) flow by silage and grain sources: greatest for CsRg and least for RsRg diet, and blood plasma concentration of Met after feeding was lower for Rg than Cg diets. Postprandial reduction degree of plasma EAA varied with the diets and individual EAA. The Cs diets compared with the Rs diets tended to be greater in N retention because of greater digestible organic matter (OM) intake. These results suggest that silage source combined with corn or rice grain affects N use in steers through the digestible OM intake, and the kinds of limiting AA may differ among the combination of silage and grain sources.

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

    DOE PAGES

    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.

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

    SciTech Connect

    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. Modelling Ontogenetic Changes of Nitrogen and Water Content in Lettuce

    PubMed Central

    SEGINER, IDO; BLEYAERT, PETER; BREUGELMANS, MAAIKE

    2004-01-01

    • Background and Aims It is well established that the nitrogen content of plants, including lettuce, decreases with time. It has also been observed that water content of lettuce increases between planting and harvest. This paper is an attempt at modelling these observations. • Methods An existing dynamic model (Nicolet), designed to predict growth and nitrate content of glasshouse lettuce, is modified to accommodate the ontogenetic changes of reduced-nitrogen and water contents (on a dry matter basis). The decreasing reduced-N content and the increasing water content are mimicked by dividing the originally uniform plant into ‘metabolically active’ tissue and ‘support’ tissue. The ‘metabolic’ tissue is assumed to contain a higher nitrogen content and a lower water content than the ‘support’ tissue. As the plants grow, the ratio of ‘support’ to ‘metabolic’ tissue increases, resulting in an increased mean water content and a decreased reduced-N content. Simulations with the new model are compared with experimental glasshouse data over four seasons. • Key Results The empirical linear relationship between water and reduced-N contents, matches, to a good approximation, the corresponding relationship based on the model. The agreement between the two makes it possible to effectively uncouple the estimation of the ‘ontogenetic’ parameters from the estimation of the other parameters. The growth and nitrate simulation results match the data rather well and are hardly affected by the new refinement. The reduced-N and water contents are predicted much better with the new model. • Conclusion Prediction of nitrogen uptake for the substantial nitrate pool of lettuce depends on the water content. Hence, the modified model may assist in making better fertilization decisions and better estimates of nitrogen leaching. PMID:15294851

  19. 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.

  20. Grain-scale modeling and splash parametrization for aeolian sand transport

    NASA Astrophysics Data System (ADS)

    Lämmel, Marc; Dzikowski, Kamil; Kroy, Klaus; Oger, Luc; Valance, Alexandre

    2017-02-01

    The collision of a spherical grain with a granular bed is commonly parametrized by the splash function, which provides the velocity of the rebounding grain and the velocity distribution and number of ejected grains. Starting from elementary geometric considerations and physical principles, like momentum conservation and energy dissipation in inelastic pair collisions, we derive a rebound parametrization for the collision of a spherical grain with a granular bed. Combined with a recently proposed energy-splitting model [Ho et al., Phys. Rev. E 85, 052301 (2012), 10.1103/PhysRevE.85.052301] that predicts how the impact energy is distributed among the bed grains, this yields a coarse-grained but complete characterization of the splash as a function of the impact velocity and the impactor-bed grain-size ratio. The predicted mean values of the rebound angle, total and vertical restitution, ejection speed, and number of ejected grains are in excellent agreement with experimental literature data and with our own discrete-element computer simulations. We extract a set of analytical asymptotic relations for shallow impact geometries, which can readily be used in coarse-grained analytical modeling or computer simulations of geophysical particle-laden flows.

  1. Accounting for nitrogen fixation in simple models of lake nitrogen loading/export.

    PubMed

    Ruan, Xiaodan; Schellenger, Frank; Hellweger, Ferdi L

    2014-05-20

    Coastal eutrophication, an important global environmental problem, is primarily caused by excess nitrogen and management efforts consequently focus on lowering watershed N export (e.g., by reducing fertilizer use). Simple quantitative models are needed to evaluate alternative scenarios at the watershed scale. Existing models generally assume that, for a specific lake/reservoir, a constant fraction of N loading is exported downstream. However, N fixation by cyanobacteria may increase when the N loading is reduced, which may change the (effective) fraction of N exported. Here we present a model that incorporates this process. The model (Fixation and Export of Nitrogen from Lakes, FENL) is based on a steady-state mass balance with loading, output, loss/retention, and N fixation, where the amount fixed is a function of the N/P ratio of the loading (i.e., when N/P is less than a threshold value, N is fixed). Three approaches are used to parametrize and evaluate the model, including microcosm lab experiments, lake field observations/budgets and lake ecosystem model applications. Our results suggest that N export will not be reduced proportionally with N loading, which needs to be considered when evaluating management scenarios.

  2. Nitrogen-corrected True Metabolizable Energy and Amino Acid Digestibility of Chinese Corn Distillers Dried Grains with Solubles in Adult Cecectomized Roosters

    PubMed Central

    Li, F.; Liu, Y.; Yin, R. Q.; Yang, X. J.; Yao, J. H.; Sun, F. F.; Li, G. J.; Liu, Y. R.; Sun, Y. J.

    2013-01-01

    This study was conducted to evaluate chemical composition, nitrogen-corrected true metabolizable energy (TMEn) and true amino acids digestibility of corn distillers dried grains with solubles (DDGS) produced in China. Twenty five sources of corn DDGS was collected from 8 provinces of China. A precision-fed rooster assay was used to determine TMEn and amino acids digestibility with 35 adult cecectomized roosters, in which each DDGS sample was tube fed (30 g). The average content of ash, crude protein, total amino acid, ether extract, crude fiber and neutral detergent fiber were 4.81, 27.91, 22.51, 15.22, 6.35 and 37.58%, respectively. TMEn of DDGS ranged from 1,779 to 3,071 kcal/kg and averaged 2,517 kcal/kg. Coefficient of variation for non-amino acid crude protein, ether extract, crude fiber and TMEn were 55.0, 15.7, 15.9 and 17.1%, respectively. The average true amino acid digestibility was 77.32%. Stepwise regression analysis obtained the following equation: TMEn, kcal/kg = −2,995.6+0.88×gross energy+49.63×a* (BIC = 248.8; RMSE = 190.8; p<0.01). Removing gross energy from the model obtained the following equation: TMEn, kcal/kg = 57.88×ether extracts+87.62×a* (BIC = 254.3, RMSE = 223.5; p<0.01). No correlation was found between color scores and lysine true digestibility (p>0.05). These results suggest that corn DDGS produced in China has a large variation in chemical composition, and gross energy and a* value can be used to generate TMEn predict equation. PMID:25049858

  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

    USDA-ARS?s Scientific Manuscript database

    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. 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.

  6. ACCURATE MODELING OF X-RAY EXTINCTION BY INTERSTELLAR GRAINS

    SciTech Connect

    Hoffman, John; Draine, B. T. E-mail: draine@astro.princeton.edu

    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.

  7. 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.

  8. Nitrogen component in nonpoint source pollution models

    USDA-ARS?s Scientific Manuscript database

    Pollutants entering a water body can be very destructive to the health of that system. Best Management Practices (BMPs) and/or conservation practices are used to reduce these pollutants, but understanding the most effective practices is very difficult. Watershed models are an effective tool to aid...

  9. 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.

  10. 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

  11. 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

  12. Grain Boundary Curvature in a Model Ni-Based Superalloy (Preprint)

    DTIC Science & Technology

    2006-07-01

    AFRL-ML-WP-TP-2006-482 GRAIN BOUNDARY CURVATURE IN A MODEL Ni-BASED SUPERALLOY (PREPRINT) Kai Song and Mark Aindow JULY 2006... MODEL Ni-BASED SUPERALLOY (PREPRINT) 5c. PROGRAM ELEMENT NUMBER 62712E 5d. PROJECT NUMBER K720 5e. TASK NUMBER 01 6. AUTHOR(S) Kai Song...AFRL/WS 06-1882, 09 Aug 2006. 14. ABSTRACT The local grain boundary curvature in a model Ni-based superalloy was measured experimentally using

  13. Phase field modeling of grain structure evolution during directional solidification of multi-crystalline silicon sheet

    NASA Astrophysics Data System (ADS)

    Lin, H. K.; Lan, C. W.

    2017-10-01

    Evolution of grain structures and grain boundaries (GBs), especially the coincident site lattice GBs, during directional solidification of multi-crystalline silicon sheet are simulated by using a phase field model for the first time. Since the coincident site lattice GBs having lower mobility, tend to follow their own crystallographic directions despite thermal gradients, the anisotropic energy and mobility of GBs are considered in the model. Three basic interactions of GBs during solidification are examined and they are consistent with experiments. The twinning process for new grain formation is further added in the simulation by considering twin nucleation. The effect of initial distribution of GB types and grain orientations is also investigated for the twinning frequency and the evolution of grain size and GB types.

  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. 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.

  16. 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.

  17. Parametrizing coarse grained models for molecular systems at equilibrium

    NASA Astrophysics Data System (ADS)

    Kalligiannaki, E.; Chazirakis, A.; Tsourtis, A.; Katsoulakis, M. A.; Plecháč, P.; Harmandaris, V.

    2016-10-01

    Hierarchical coarse graining of atomistic molecular systems at equilibrium has been an intensive research topic over the last few decades. In this work we (a) review theoretical and numerical aspects of different parametrization methods (structural-based, force matching and relative entropy) to derive the effective interaction potential between coarse-grained particles. All methods approximate the many body potential of mean force; resulting, however, in different optimization problems. (b) We also use a reformulation of the force matching method by introducing a generalized force matching condition for the local mean force in the sense that allows the approximation of the potential of mean force under both linear and non-linear coarse graining mappings (E. Kalligiannaki, et al., J. Chem. Phys. 2015). We apply and compare these methods to: (a) a benchmark system of two isolated methane molecules; (b) methane liquid; (c) water; and (d) an alkane fluid. Differences between the effective interactions, derived from the various methods, are found that depend on the actual system under study. The results further reveal the relation of the various methods and the sensitivities that may arise in the implementation of numerical methods used in each case.

  18. 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.

  19. Statistical models for carbon-nitrogen film growth

    PubMed

    Aarao Reis FD; Franceschini

    2000-04-01

    We studied models of deposition and erosion, with two species of particles, that represent quantitatively many features of amorphous carbon-nitrogen film grown under plasma enhanced chemical vapor deposition. In the original model, the columns of the deposit are independent, and particles C and N are released with probabilities p and 1-p, respectively. An incident C particle always aggregates upon contact with the surface. An N particle annihilates with a top C particle with probability q and aggregates with probability 1-q. An N particle always annihilates with a top N. A critical line separates the regimes of growth (p>q/2) and erosion (pnitrogen atmospheres. In order to represent the blocking of surface bonds by hydrogen atoms, we considered a second model in which any aggregation process is accepted with probability alpha, otherwise it is rejected. For q=0.25 and alpha=0.3, the rxx(N) curve agrees with data from films grown in methane-nitrogen and methane-ammonia atmospheres. The fitting values of q and alpha were inferred from related experiments. In order to test the influence of lattice structure and spatial correlations, we also studied those models in simple cubic lattices, considering that the aggregation must satisfy the restricted solid-on-solid model conditions for the difference of heights in neighboring columns, while the erosion is random. We obtained similar results for rxx(N) curves, confirming the validity of those models to represent the kinetics of amorphous films growth. It was also observed that the surface roughness increases with x(N), which agrees qualitatively with several experiments on carbon-nitrogen films growth with ion bombardment.

  20. 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).

  1. 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).

  2. Understanding hydrological and nitrogen interactions by sensitivity analysis of a catchment-scale nitrogen model

    NASA Astrophysics Data System (ADS)

    Medici, Chiara; Wade, Andrew; Frances, Felix

    2010-05-01

    Nitrogen is present in both terrestrial and aquatic ecosystems and research is needed to understand its storage, transportation and transformations in river catchments world-wide because of its importance in controlling plant growth and freshwater trophic status (Vitousek et al. 2009; Chu et al. 2008; Schlesinger et al 2006; Ocampo et al. 2006; Green et al., 2004; Arheimer et al., 1996). Numerous mathematical models have been developed to describe the nitrogen dynamics, but there is a substantial gap between the outputs now expected from these models and what modellers are able to provide with scientific justification (McIntyre et al., 2005). In fact, models will always necessarily be simplification of reality; hence simplifying assumptions are sources of uncertainty that must be well understood for an accurate model results interpretation. Therefore, estimating prediction uncertainties in water quality modelling is becoming increasingly appreciated (Dean et al., 2009, Kruger et al., 2007, Rode et al., 2007). In this work the lumped LU4-N model (Medici et al., 2008; Medici et al., EGU2009-7497) is subjected to an extensive regionalised sensitivity analysis (GSA, based on Monte Carlo simulations) in application to the Fuirosos catchment, Catalonia. The main results are: 1) the hydrological model is greatly affected by the maximum static storage water content (Hu_max), which defines the amount of water held in soil that can leave the catchment only by evapotranspiration. Thus, it defines also the amount of water not retained that is free to move and supplies the other model tanks; 2) the use of several objective functions in order to take into account different hydrograph characteristic helped to constrain parameter values; 3) concerning nitrogen, to obtain a sufficient level of behavioural parameter sets for the statistical analysis, not very severe criteria could be adopted; 4) stream water concentrations are sensitive to the shallow aquifer parameters, especially

  3. 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.

  4. Coarse graining from variationally enhanced sampling applied to the Ginzburg–Landau model

    PubMed Central

    Invernizzi, Michele; Valsson, Omar; Parrinello, Michele

    2017-01-01

    A powerful way to deal with a complex system is to build a coarse-grained model capable of catching its main physical features, while being computationally affordable. Inevitably, such coarse-grained models introduce a set of phenomenological parameters, which are often not easily deducible from the underlying atomistic system. We present a unique approach to the calculation of these parameters, based on the recently introduced variationally enhanced sampling method. It allows us to obtain the parameters from atomistic simulations, providing thus a direct connection between the microscopic and the mesoscopic scale. The coarse-grained model we consider is that of Ginzburg–Landau, valid around a second-order critical point. In particular, we use it to describe a Lennard–Jones fluid in the region close to the liquid–vapor critical point. The procedure is general and can be adapted to other coarse-grained models. PMID:28292890

  5. Grain Nucleation Parameters for Aluminum Alloys: Experimental Determination and Model Validation

    NASA Astrophysics Data System (ADS)

    Ahmadein, M.; Pustal, B.; Berger, R.; Subašić, E.; Bührig-Polaczek, A.

    2009-03-01

    A statistical grain nucleation model was implemented as a part of a multiphase flow and solidification simulation code for metallic alloys. Three characteristic parameters control the solution accuracy of the nucleation model: the total grain density, the mean undercooling, and the standard deviation of the undercooling. These parameters were obtained experimentally for grain-refined (GR) A356, GR AlCu4, and unrefined (UR) AlCu4 aluminum alloys. An apparatus was constructed and equipped with a cooling system to provide different cooling rates throughout the cast sample. The local grain density related to each cooling rate and undercooling was determined. The model parameters were obtained via statistical tools and were used to perform a simulation for the solidification of the cast sample. Calculated results were compared to experimental results, and the model exhibited good agreement with the experiments.

  6. Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model.

    PubMed

    Invernizzi, Michele; Valsson, Omar; Parrinello, Michele

    2017-03-28

    A powerful way to deal with a complex system is to build a coarse-grained model capable of catching its main physical features, while being computationally affordable. Inevitably, such coarse-grained models introduce a set of phenomenological parameters, which are often not easily deducible from the underlying atomistic system. We present a unique approach to the calculation of these parameters, based on the recently introduced variationally enhanced sampling method. It allows us to obtain the parameters from atomistic simulations, providing thus a direct connection between the microscopic and the mesoscopic scale. The coarse-grained model we consider is that of Ginzburg-Landau, valid around a second-order critical point. In particular, we use it to describe a Lennard-Jones fluid in the region close to the liquid-vapor critical point. The procedure is general and can be adapted to other coarse-grained models.

  7. 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.

  8. 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.

  9. 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

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

    PubMed

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

    2012-07-01

    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. 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. 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 duration of grain filling. Source-sink modelling

  11. Dietary modeling shows that substitution of whole-grain for refined-grain ingredients of foods commonly consumed by US children and teens can increase intake of whole grains.

    PubMed

    Keast, Debra R; Rosen, Renee A; Arndt, Elizabeth A; Marquart, Len F

    2011-09-01

    Currently available whole-grain foods are not frequently consumed, and few children achieve the whole-grain intake recommendation. To investigate the influence on whole-grain consumption of substituting whole-grain for refined-grain ingredients of foods commonly consumed by children. Secondary cross-sectional analysis of publicly available food consumption data collected by the US Department of Agriculture. A nationally representative sample of US children aged 9 to 18 years (n=2,349) providing 24-hour dietary recall data in the 2003-2004 National Health and Nutrition Examination Survey. Whole-grain intake was modeled by replacing varying proportions of refined flour contained in foods such as pizza crust, pasta, breads, and other baked goods with whole-wheat flour, and by replacing a proportion of white rice with brown rice. Replacement levels were based on the acceptability of whole-grain foods tested among children in elementary schools, and ranged from 15% to 50%; the majority were ≤25%. Sample-weighted mean premodeled and postmodeled whole-grain intake, standard errors, and statistical significance of differences between demographic subgroups were determined using SUDAAN (version 9.0.3, 2007, Research Triangle Institute, Research Triangle Park, NC). Whole-grain intake increased 1.7 oz eq per day (from 0.5 to 2.2 oz eq/day). Premodeled and postmodeled whole-grain intakes were 6% and 28%, respectively, of total grain intake (7.7 oz eq/day). Major sources of postmodeled whole-grain intakes were breads/rolls (28.0%); pizza (14.2%); breakfast cereals (11.0%); rice/pasta (10.6%); quick breads such as tortillas, muffins, and waffles (10.8%); other baked goods (9.9%); and grain-based savory snacks other than popcorn (7.3%). Premodeled whole-grain intake differed by poverty level, but postmodeled whole-grain intake did not. The substitution of whole grain for a specific proportion of refined grain ingredients of commonly consumed foods increased whole-grain intake

  12. Multiscale modeling approach for calculating grain-boundary energies from first principles

    SciTech Connect

    Shenderova, O.A.; Brenner, D.W.; Nazarov, A.A.; Romanov, A.E.; Yang, L.H.

    1998-02-01

    A multiscale modeling approach is proposed for calculating energies of tilt-grain boundaries in covalent materials from first principles over an entire misorientation range for given tilt axes. The method uses energies from density-functional calculations for a few key structures as input into a disclination structural-units model. This approach is demonstrated by calculating energies of {l_angle}001{r_angle}-symmetrical tilt-grain boundaries in diamond. {copyright} {ital 1998} {ital The American Physical Society}

  13. 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.

  14. Establishment of canine models of lunatomalacia through liquid nitrogen freezing

    PubMed Central

    HUANG, QISHUN; FU, QIANG; ZHENG, HUAIYUAN; GAN, MENG; WONG, YUXIONG; CHEN, ZHENBING

    2013-01-01

    The aim of this study was to investigate the feasibility of establishing dog models of lunatomalacia through liquid nitrogen freezing. Twelve adult crossbred dogs were divided into three groups. Unilateral lunates were peeled off the parenchyma and frozen to result in avascular necrosis. They were observed dynamically through X-ray, computed tomography (CT) and magnetic resonance imaging (MRI). Furthermore, gross and histomorphological observations of samples were performed. Disseminated punctate hyperintense images and abnormal manifestations were detected, respectively. At 12 weeks after surgery, uneven bone density of the lunate and a flattened lunate of irregular shape were detected. A large area of irregular hypointense foci and hyperintensity was observed. Gross sample observation revealed a large area of dead bone. A decrease in the density of the trabecular bones and several vacant bone lacunas were visible. Liquid nitrogen freezing is a successful and reliable method for preparing animal models of lunatomalacia. PMID:23408726

  15. Establishment of canine models of lunatomalacia through liquid nitrogen freezing.

    PubMed

    Huang, Qishun; Fu, Qiang; Zheng, Huaiyuan; Gan, Meng; Wong, Yuxiong; Chen, Zhenbing

    2013-03-01

    The aim of this study was to investigate the feasibility of establishing dog models of lunatomalacia through liquid nitrogen freezing. Twelve adult crossbred dogs were divided into three groups. Unilateral lunates were peeled off the parenchyma and frozen to result in avascular necrosis. They were observed dynamically through X-ray, computed tomography (CT) and magnetic resonance imaging (MRI). Furthermore, gross and histomorphological observations of samples were performed. Disseminated punctate hyperintense images and abnormal manifestations were detected, respectively. At 12 weeks after surgery, uneven bone density of the lunate and a flattened lunate of irregular shape were detected. A large area of irregular hypointense foci and hyperintensity was observed. Gross sample observation revealed a large area of dead bone. A decrease in the density of the trabecular bones and several vacant bone lacunas were visible. Liquid nitrogen freezing is a successful and reliable method for preparing animal models of lunatomalacia.

  16. 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.

  17. 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

  18. Spatial variability analysis of within-field winter wheat nitrogen and grain quality using canopy fluorescence sensor measurements

    USDA-ARS?s Scientific Manuscript database

    Wheat grain protein content (GPC) is a key component when evaluating wheat nutrition. It is also important to determine wheat GPC before harvest for agricultural and food process enterprises in order to optimize the wheat grading process. Wheat GPC across a field is spatially variable due to the inh...

  19. Diagnostics of circumstellar grains in geometric models - I. Structure and composition

    NASA Astrophysics Data System (ADS)

    Dawes, J. H. P.; Greaves, J. S.

    2017-05-01

    The spectral energy distribution (SED) of circumstellar dust has been extensively used to diagnose the sizes and compositions of dust grains. We show that variations of SED slope in the long-wavelength (submillimetre to radio) regime can be used to diagnose the gross physical nature (and hence origins) of the dust, using simple geometric models that complement the use of detailed simulations. We consider two dust grain types: (i) clustered aggregates of smaller particles (monomers) and (ii) composite grains comprising ferrous inclusions within a silicate matrix. These types are intended to be analogous to fluffy cometary particles and fragments of compacted asteroids, respectively. Our results indicate that clusters of silicate grains produce a smooth SED, while composite grains with FeS inclusions produce an SED that has a pronounced drop at a wavelength an order of magnitude larger than the grain size, and is flatter at long wavelengths. As a test case, we compare the model predictions to flux measurements of the TW Hydrae disc. This SED shows a drop that only occurs in our models of compacted grains with inclusions. Since the TW Hya discs span approximately 10-40 au in radius, fluffy particles from comets were perhaps expected, as in the Sun's Kuiper belt.

  20. Diagnostics of circumstellar grains in geometric models I: structure and composition

    NASA Astrophysics Data System (ADS)

    Dawes, J. H. P.; Greaves, J. S.

    2017-01-01

    The spectral energy distribution (SED) of circumstellar dust has been extensively used to diagnose the sizes and compositions of dust grains. We show that variations of SED slope in the long wavelength (submillimetre to radio) regime can be used to diagnose the gross physical nature (and hence origins) of the dust, using simple geometric models that complement the use of detailed simulations. We consider two dust grain types: (i) clustered aggregates of smaller particles (monomers), and (ii) composite grains comprising ferrous inclusions within a silicate matrix. These types are intended to be analogous to fluffy cometary particles and fragments of compacted asteroids, respectively. Our results indicate that clusters of silicate grains produce a smooth SED, while composite grains with FeS inclusions produce an SED that has a pronounced drop at a wavelength an order of magnitude larger than the grain size, and is flatter at long wavelengths. As a test case, we compare the model predictions to flux measurements of the TW Hydrae disc. This SED shows a drop that only occurs in our models of compacted grains with inclusions. Since the TW Hya discs spans approximately 10-40 AU in radius, fluffy particles from comets were perhaps expected, as in the Sun's Kuiper belt.

  1. Investigating feedback mechanisms between stress and grain-size: preliminary findings from finite-element modelling

    NASA Astrophysics Data System (ADS)

    Cross, A. J.; Prior, D. J.; Ellis, S. M.

    2012-12-01

    It is widely accepted that changes in stress and grain size can induce a switch between grain-size insensitive (GSI) and sensitive (GSS) creep mechanisms. Under steady-state conditions, grains evolve to an equilibrium size in the boundary region between GSS and GSI, described by the paleopiezometer for a given material. Under these conditions, significant rheological weakening is not expected, as grain size reduction processes are balanced by grain growth processes. However, it has been shown that the stress field surrounding faults varies through the seismic cycle, with both rapid loading and unloading of stress possible in the co- and post-seismic stages. We propose that these changes in stress in the region of the brittle-ductile transition zone may be sufficient to force a deviation from the GSI-GSS boundary and thereby cause a change in grain size and creep mechanism prior to system re-equilibration. Here we present preliminary findings from numerical modelling of stress and grain size changes in response to loading of mechanical inhomogeneities. Our results are attained using a grain-size evolution (GSE) subroutine incorporated into the SULEC finite-element code developed by Susan Ellis and Susanne Buiter, which utilises an iterative approach of solving for spatial and temporal changes in differential stress, grain size and active creep mechanism. Preliminary models demonstrate that stress changes in response to the opening of a fracture in a flowing medium can be significant enough to cause a switch from GSI to GSS creep. These results are significant in the context of understanding spatial variations and feedback between stress, grain size and deformation mechanisms through the seismic cycle.

  2. A Simple Model of Nitrogen Concentration, Throughput, and Denitrification in Estuaries

    EPA Science Inventory

    The Estuary Nitrogen Model (ENM) is a mass balance model that includes calculation of nitrogen losses within bays and estuaries using system flushing time. The model has been used to demonstrate the dependence of throughput and denitrification of nitrogen in bays and estuaries on...

  3. 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

  4. Modeling nitrogen plasmas produced by intense electron beams

    NASA Astrophysics Data System (ADS)

    Angus, Justin; Swanekamp, Steve; Richardson, Andrew; Schumer, Joseph; Mosher, David; Ottinger, Paul

    2016-10-01

    The Gamble II generator at the Naval Research Laboratory produces 100ns pulse duration, relativistic-electron beams with peak energies on the order of 1MV and peak currents of about 800kA with annular beam areas between 40-80cm2. This gives peak current densities 10 kA/cm2. For many different applications, a nitrogen gas in the 1Torr range is used as a charge- and current-neutralizing background to achieve beam transport. 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. A detailed gas-chemistry model is presented for a dynamical description of the nitrogen plasmas produced in such experiments. The model is coupled to a 0D circuit model representative of annular beams, and results for 1Torr nitrogen are in good agreement with experimental measurements of the line-integrated electron density and the net current. 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 the higher-lying optically-allowed states with excitation energies close to the ionization limit. Work is supported by AWE through NNSA.

  5. 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.

  6. On the approach to modeling of the mechanical behavior of a fine grained material

    NASA Astrophysics Data System (ADS)

    Bylya, O. I.; Bhaskaran, K.; Chistyakov, P. V.; Vasin, R. A.

    2012-07-01

    With the advent of technology, manufacturing of bulk materials from nano particles has been made possible. As a result, there has been an increased interest in modeling the mechanical behavior of ultra fine grain and nano scale materials. But their behavior differs markedly from that of coarse grain materials as their volume fraction of grain boundaries is inherently high. Conventional models of both phenomenological and physical character fail to give a satisfactory description of their behavior in a generic nature. In this paper, the reason for this is traced through the history of mechanics briefly and shortcomings of both the phenomenological approach and physical models are discussed. Need for a modified approach is emphasized and as a way of example, one such approach adopted by us, for describing near superplastic deformation of fine grained alloys, is discussed.

  7. Coupled Finite Element ? Potts Model Simulations of Grain Growth in Copper Interconnects

    SciTech Connect

    Radhakrishnan, Balasubramaniam; Gorti, Sarma B

    2009-01-01

    The paper addresses grain growth in copper interconnects in the presence of thermal expansion mismatch stresses. The evolution of grain structure and texture in copper in the simultaneous presence of two driving forces, curvature and elastic stored energy difference, is modeled by using a hybrid Potts model simulation approach. The elastic stored energy is calculated by using the commercial finite element code ABAQUS, where the effect of elastic anisotropy on the thermal mismatch stress and strain distribution within a polycrystalline grain structure is modeled through a user material (UMAT) interface. Parametric studies on the effect of trench width and the height of the overburden were carried out. The results show that the grain structure and texture evolution are significantly altered by the presence of elastic strain energy.

  8. 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.

  9. Evaluation of distributed parameters mathematical models applied to grain hydration with volume change

    NASA Astrophysics Data System (ADS)

    Nicolin, Douglas J.; Jorge, Regina Maria M.; Jorge, Luiz Mario M.

    2015-01-01

    Several studies have taken into account the volume change of foods that undergo hydration or drying. However, the simplest boundary condition at the surface is usually considered to facilitate the solution of variable volume models. This paper presents a model of moisture diffusion in soybean grains that considers the volume change of these grains when absorbing water and also the dependence of diffusivity on moisture content. The boundary condition of equality of diffusive and convective flows on the surface was used and compared with two other approaches commonly found in the literature of grain hydration. This boundary condition was also applied to the case of constant volume of the grains and it was concluded that there are significant differences when the change in volume is taken into account. An analysis of the diffusion coefficients determined as functions of moisture content, temperature, and hydration time is presented for the best model.

  10. Responses of super rice (Oryza sativa L.) to different planting methods for grain yield and nitrogen-use efficiency in the single cropping season.

    PubMed

    Chen, Song; Wang, Danying; Xu, Chunmei; Ji, Chenglin; Zhang, Xiaoguo; Zhao, Xia; Zhang, Xiufu; Chauhan, Bhagirath Singh

    2014-01-01

    To break the yield ceiling of rice production, a super rice project was developed in 1996 to breed rice varieties with super high yield. A two-year experiment was conducted to evaluate yield and nitrogen (N)-use response of super rice to different planting methods in the single cropping season. A total of 17 rice varieties, including 13 super rice and four non-super checks (CK), were grown under three N levels [0 (N0), 150 (N150), and 225 (N225) kg ha-1] and two planting methods [transplanting (TP) and direct-seeding in wet conditions (WDS)]. Grain yield under WDS (7.69 t ha-1) was generally lower than TP (8.58 t ha-1). However, grain yield under different planting methods was affected by N rates as well as variety groups. In both years, there was no difference in grain yield between super and CK varieties at N150, irrespective of planting methods. However, grain yield difference was dramatic in japonica groups at N225, that is, there was an 11.3% and 14.1% average increase in super rice than in CK varieties in WDS and TP, respectively. This suggests that high N input contributes to narrowing the yield gap in super rice varieties, which also indicates that super rice was bred for high fertility conditions. In the japonica group, more N was accumulated in super rice than in CK at N225, but no difference was found between super and CK varieties at N0 and N150. Similar results were also found for N agronomic efficiency. The results suggest that super rice varieties have an advantage for N-use efficiency when high N is applied. The response of super rice was greater under TP than under WDS. The results suggest that the need to further improve agronomic and other management practices to achieve high yield and N-use efficiency for super rice varieties in WDS.

  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. Possible model of an antiferroelectric twist grain boundary phase

    SciTech Connect

    Meier, J. G.; Carlsson, T.; Rudquist, P.; Lagerwall, S. T.; Nobili, M.; Brunet, M.

    2007-07-15

    Using x-ray and optical methods we have probed the structural organization of an antiferroelectric twist grain boundary phase (TGBC{sub a}) lying between the regular antiferroelectric smectic-C (SmC{sub a}{sup *}) and the smectic-Q (SmQ) or isotropic phase. We find that the twist axis is everywhere perpendicular to the local smectic layer normal and that the helical superstructure is incommensurate with the smectic layer structure. The twist grain boundaries consist of a periodic lattice of alternating +1/2 and -1/2 dispirations, i.e., unit screw dislocations in combination with half unit disclinations. The molecular tilt plane is alternatingly parallel and perpendicular to the twist axis. We find that the optically measured tilt angle in the SmC{sub a}{sup *} phase is smaller than that measured by x rays, which is the opposite to what is found in the SmC{sup *} phase. This means that the core part tilts less than the end chains in the SmC{sub a}{sup *} phase, while it tilts more in the SmC{sup *} phase. On entering the TGB phase a clear decrease is measured in the tilt angle. This is explained by the elastic influence from the disclinations, which appear in this phase.

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

    PubMed

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

    2015-10-01

    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.

  14. 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.

  15. Construction of ultra-coarse-grained model of protein with a Gō-like potential

    NASA Astrophysics Data System (ADS)

    Zhang, Yuwei; Cao, Zexing; Xia, Fei

    2017-08-01

    Ultra-Coarse-Grained (UCG) model whose resolution is less than residue-based coarse-grained model, is being developed in recent years. In this work, we attempt to construct a UCG model with a classical Gō-like potential. The heterogeneous parameters of local and nonlocal interactions in the energy potential function are derived by using fluctuation matching method. The simulated results with UCG models indicate that it could reproduce the root mean square fluctuations as accurate as that of long-time all-atom simulations. Therefore, the UCG model has great potential in the simulation of huge biological systems such as biomaterials.

  16. Excessive nitrogen application dampens antioxidant capacity and grain filling in wheat as revealed by metabolic and physiological analyses

    PubMed Central

    Kong, Lingan; Xie, Yan; Hu, Ling; Si, Jisheng; Wang, Zongshuai

    2017-01-01

    In this study, field-grown wheat (Triticum aestivum L.) was treated with normal (Nn) and excessive (Ne) levels of fertilizer N. Results showed that Ne depressed the activity of superoxide dismutase and peroxidase and increased the accumulation of reactive oxygen species (ROS) and malondialdehyde. The normalized difference vegetation index (NDVI) was higher under Ne at anthesis and medium milk but similar at the early dough stage and significantly lower at the hard dough stage than that under Nn. The metabolomics analysis of the leaf responses to Ne during grain filling showed 99 metabolites that were different between Ne and Nn treatments, including phenolic and flavonoid compounds, amino acids, organic acids and lipids, which are primarily involved in ROS scavenging, N metabolism, heat stress adaptation and disease resistance. Organic carbon (C) and total N contents were affected by the Ne treatment, with lower C/N ratios developing after medium milk. Ultimately, grain yields decreased with Ne. Based on these data, compared with the normal N fertilizer treatment, we concluded that excessive N application decreased the ability to scavenge ROS, increased lipid peroxidation and caused significant metabolic changes disturbing N metabolism, secondary metabolism and lipid metabolism, which led to reduced grain filling in wheat. PMID:28233811

  17. 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.

  18. 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

  19. A conduction model for semiconductor-grain-boundary-semiconductor barriers in polycrystalline-silicon films

    NASA Astrophysics Data System (ADS)

    Lu, N. C.-C.; Gerzberg, L.; Meindl, J. D.; Lu, C.-Y.

    1983-02-01

    A quantitative model is introduced to describe the electrical properties of a semiconductor-grain boundary-semiconductor barrier in polysilicon films over a wide temperature range. The model verifies the applicability of a single-crystal band diagram for the crystallite within which an impurity level exists. It describes a new analytical approach to the study of the grain-boundary effect on carrier transport under different experimental conditions by studying the behavior of grain-boundary potential barrier height and width. By characterizing the experimental data from a combination of these trapping effects and conduction processes, the electrical properties of polysilicon films with grain sizes of less than one micron, doping levels up to 8 x 10 to the 19th per cubic centimeter, and measurement temperatures from -176 C to 144 C can be better understood.

  20. A Cellular Automaton / Finite Element model for predicting grain texture development in galvanized coatings

    NASA Astrophysics Data System (ADS)

    Guillemot, G.; Avettand-Fènoël, M.-N.; Iosta, A.; Foct, J.

    2011-01-01

    Hot-dipping galvanizing process is a widely used and efficient way to protect steel from corrosion. We propose to master the microstructure of zinc grains by investigating the relevant process parameters. In order to improve the texture of this coating, we model grain nucleation and growth processes and simulate the zinc solid phase development. A coupling scheme model has been applied with this aim. This model improves a previous two-dimensional model of the solidification process. It couples a cellular automaton (CA) approach and a finite element (FE) method. CA grid and FE mesh are superimposed on the same domain. The grain development is simulated at the micro-scale based on the CA grid. A nucleation law is defined using a Gaussian probability and a random set of nucleating cells. A crystallographic orientation is defined for each one with a choice of Euler's angle (Ψ,θ,φ). A small growing shape is then associated to each cell in the mushy domain and a dendrite tip kinetics is defined using the model of Kurz [2]. The six directions of basal plane and the two perpendicular directions develop in each mushy cell. During each time step, cell temperature and solid fraction are then determined at micro-scale using the enthalpy conservation relation and variations are reassigned at macro-scale. This coupling scheme model enables to simulate the three-dimensional growing kinetics of the zinc grain in a two-dimensional approach. Grain structure evolutions for various cooling times have been simulated. Final grain structure has been compared to EBSD measurements. We show that the preferentially growth of dendrite arms in the basal plane of zinc grains is correctly predicted. The described coupling scheme model could be applied for simulated other product or manufacturing processes. It constitutes an approach gathering both micro and macro scale models.

  1. Modeling recrystallization kinetics, grain sizes, and textures during multipass hot rolling

    NASA Astrophysics Data System (ADS)

    Vatne, Hans Erik; Ørsund, Roar; Marthinsen, Knut; Nes, Erik

    1996-12-01

    A physically based model for the evolution of recrystallization microstructures and textures during hot rolling of aluminum is presented. The approach taken differs from similar models developed for steels. The present model is based on recent experimental investigations directed toward identifying the nature of the nucleation sites for recrystallized grains of different crystallographic orientations. Particle stimulated nucleation (PSN) and nucleation from cube bands and grain boundary regions have been incorporated in the model. The multipass aspect complicates the modeling due to partial recrystallization between the rolling passes. Two different approaches have been suggested to handle this. The model has been applied to predictions of recrystallization kinetics, recrystallized grain sizes, and recrystallization textures during multipass hot rolling of aluminum. The predictions are reasonable compared to experimental results.

  2. DDA Modeling for the Mid-IR Absorption of Irregularly Shaped Crystalline Forsterite Grains

    NASA Astrophysics Data System (ADS)

    Lindsay, Sean; Wooden, D. H.; Kelley, M. S.; Harker, D. E.; Woodward, C. E.; Murphy, J.

    2010-10-01

    An analysis of the Spitzer IRS spectra of the Deep Impact ejecta of comet 9P/Tempel 1 (Wooden et al. 2010, 42nd DPS Meeting) in conjunction with the dynamics of the ejecta grains (Kelley et al. 2010, 42nd DPS Meeting) strongly suggests that ecliptic comets have comae dominated by large (> 10 - 20 micron in radii) porous grains with Mg-rich crystal inclusions. In fact, Kelley et al. (2010) conclude that many ecliptic comets may be dominated by such grains with a high crystalline fraction, approximately 40% by mass, despite their generally weak silicate emission feature. To date, no model for the optical properties in the mid-IR of multi-mineralic large porous grains with silicate crystal inclusions, has been performed. We have initiated a program to compute the absorption and scattering efficiencies for these grains. Presented here are the 3 - 40 micron absorption efficiencies for models of sub-micron sized crystalline forsterite grains of irregular shape. We use the Discrete Dipole Approximation (DDA) to create discrete targets of forsterite that can be included in large porous aggregates. Computations are performed on the NAS Pleiades supercomputer. Our calculated absorption efficiencies for individual grains of forsterite are in agreement with laboratory measurements (Tamanai et al. 2006; Koike et al. 2003) and the continuous distribution of ellipsoids (CDE) method by Harker et al. (2007). We find for discrete grains that grain shape has a strong effect on the peak location of a crystalline resonance and that mimicking the physical properties of forsterite is important. Also presented are the absorption efficiencies for simple multi-component aggregates and for collections of forsterite crystals of different size and shape to replicate laboratory samples. This research is supported by the NASA GSRP Program.

  3. 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.

  4. 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

  5. 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

  6. 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

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

    PubMed

    Hämmerle, Martin; Höfle, Bernhard

    2014-12-16

    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.

  8. Significance of the model considering mixed grain-size for inverse analysis of turbidites

    NASA Astrophysics Data System (ADS)

    Nakao, K.; Naruse, H.; Tokuhashi, S., Sr.

    2016-12-01

    A method for inverse analysis of turbidity currents is proposed for application to field observations. Estimation of initial condition of the catastrophic events from field observations has been important for sedimentological researches. For instance, there are various inverse analyses to estimate hydraulic conditions from topography observations of pyroclastic flows (Rossano et al., 1996), real-time monitored debris-flow events (Fraccarollo and Papa, 2000), tsunami deposits (Jaffe and Gelfenbaum, 2007) and ancient turbidites (Falcini et al., 2009). These inverse analyses need forward models and the most turbidity current models employ uniform grain-size particles. The turbidity currents, however, are the best characterized by variation of grain-size distribution. Though there are numerical models of mixed grain-sized particles, the models have difficulty in feasibility of application to natural examples because of calculating costs (Lesshaft et al., 2011). Here we expand the turbidity current model based on the non-steady 1D shallow-water equation at low calculation costs for mixed grain-size particles and applied the model to the inverse analysis. In this study, we compared two forward models considering uniform and mixed grain-size particles respectively. We adopted inverse analysis based on the Simplex method that optimizes the initial conditions (thickness, depth-averaged velocity and depth-averaged volumetric concentration of a turbidity current) with multi-point start and employed the result of the forward model [h: 2.0 m, U: 5.0 m/s, C: 0.01%] as reference data. The result shows that inverse analysis using the mixed grain-size model found the known initial condition of reference data even if the condition where the optimization started is deviated from the true solution, whereas the inverse analysis using the uniform grain-size model requires the condition in which the starting parameters for optimization must be in quite narrow range near the solution. The

  9. Modeling organic nitrogen conversions in activated sludge bioreactors.

    PubMed

    Makinia, Jacek; Pagilla, Krishna; Czerwionka, Krzysztof; Stensel, H David

    2011-01-01

    For biological nutrient removal (BNR) systems designed to maximize nitrogen removal, the effluent total nitrogen (TN) concentration may range from 2.0 to 4.0 g N/m(3) with about 25-50% in the form of organic nitrogen (ON). In this study, current approaches to modeling organic N conversions (separate processes vs. constant contents of organic fractions) were compared. A new conceptual model of ON conversions was developed and combined with Activated Sludge Model No. 2d (ASM2d). The model addresses a new insight into the processes of ammonification, biomass decay and hydrolysis of particulate and colloidal ON (PON and CON, respectively). Three major ON fractions incorporated are defined as dissolved (DON) (<0.1 µm), CON (0.1-1.2 µm) and PON (41.2 µm). Each major fraction was further divided into two sub-fractions - biodegradable and non-biodegradable. Experimental data were collected during field measurements and lab experiments conducted at the ''Wschod'' WWTP (570,000 PE) in Gdansk (Poland). The accurate steady-state predictions of DON and CON profiles were possible by varying ammonification and hydrolysis rates under different electron acceptor conditions. With the same model parameter set, the behaviors of both inorganic N forms (NH4-N, NOX-N) and ON forms (DON, CON) in the batch experiments were predicted. The challenges to accurately simulate and predict effluent ON levels from BNR systems are due to analytical methods of direct ON measurement (replacing TKN) and lack of large enough database (in-process measurements, dynamic variations of the ON concentrations) which can be used to determine parameter value ranges.

  10. 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.

  11. Monte Carlo Modeling of Gas-Grain Chemistry in Star-Forming Regions

    NASA Astrophysics Data System (ADS)

    Vasyunin, A. I.; Herbst, E.

    2011-06-01

    An understanding of the complex grain-surface chemistry responsible for the formation of organic molecules in regions of star and planet formation requires the details of the structure of icy grain mantles to be included into astrochemical models. Here, we present a new macroscopic gas-grain Monte Carlo model with an icy grain mantle treated as a chemically reactive surface and a chemically inert bulk consisting of multiple molecular layers. The model allows us to track the chemical history of ice during its build-up in cold protostellar cores. Desorption processes important in the transition to the hot core stage of star formation are also included. The model is computationally efficient, which allows us to simulate a realistically complex chemistry based on the OSU.2008 network of gas-phase reactions and an extended set of grain-surface reactions, including the chemistry of complex organic species. The model is applied to simulate the chemistry that occurs during the evolution of protostellar matter from a cold core to a hot core phase. The results of modeling and their key differences from results obtained with traditional two-phase (gas-surface) astrochemical models will be presented.

  12. 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

  13. Modeling of grain size strengthening in tantalum at high pressures and strain rates

    NASA Astrophysics Data System (ADS)

    Rudd, Robert E.; Park, H.-S.; Cavallo, R. M.; Arsenlis, A.; Orlikowski, D. A.; Prisbrey, S. T.; Wehrenberg, C. E.; Remington, B. A.

    2017-01-01

    Laser-driven ramp wave compression experiments have been used to investigate the strength (flow stress) of tantalum and other metals at high pressures and high strain rates. Recently this kind of experiment has been used to assess the dependence of the strength on the average grain size of the material, finding no detectable variation with grain size. The insensitivity to grain size has been understood theoretically to result from the dominant effect of the high dislocation density generated at the extremely high strain rates of the experiment. Here we review the experiments and describe in detail the multiscale strength model used to simulate them. The multiscale strength model has been extended to include the effect of geometrically necessary dislocations generated at the grain boundaries during compatible plastic flow in the polycrystalline metal. We use the extended model to make predictions of the threshold strain rates and grain sizes below which grain size strengthening would be observed in the laser-driven Rayleigh-Taylor experiments.

  14. 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.

  15. Modeling of grain size strengthening in tantalum at high pressures and strain rates

    SciTech Connect

    Rudd, Robert E.; Park, H. -S.; Cavallo, R. M.; Arsenlis, A.; Orlikowski, D. A.; Prisbrey, S. T.; Wehrenberg, C. E.; Remington, B. A.

    2017-01-01

    Laser-driven ramp wave compression experiments have been used to investigate the strength (flow stress) of tantalum and other metals at high pressures and high strain rates. Recently this kind of experiment has been used to assess the dependence of the strength on the average grain size of the material, finding no detectable variation with grain size. The insensitivity to grain size has been understood theoretically to result from the dominant effect of the high dislocation density generated at the extremely high strain rates of the experiment. Here we review the experiments and describe in detail the multiscale strength model used to simulate them. The multiscale strength model has been extended to include the effect of geometrically necessary dislocations generated at the grain boundaries during compatible plastic flow in the polycrystalline metal. Lastly, we use the extended model to make predictions of the threshold strain rates and grain sizes below which grain size strengthening would be observed in the laser-driven Rayleigh-Taylor experiments.

  16. Modeling of grain size strengthening in tantalum at high pressures and strain rates

    DOE PAGES

    Rudd, Robert E.; Park, H. -S.; Cavallo, R. M.; ...

    2017-01-01

    Laser-driven ramp wave compression experiments have been used to investigate the strength (flow stress) of tantalum and other metals at high pressures and high strain rates. Recently this kind of experiment has been used to assess the dependence of the strength on the average grain size of the material, finding no detectable variation with grain size. The insensitivity to grain size has been understood theoretically to result from the dominant effect of the high dislocation density generated at the extremely high strain rates of the experiment. Here we review the experiments and describe in detail the multiscale strength model usedmore » to simulate them. The multiscale strength model has been extended to include the effect of geometrically necessary dislocations generated at the grain boundaries during compatible plastic flow in the polycrystalline metal. Lastly, we use the extended model to make predictions of the threshold strain rates and grain sizes below which grain size strengthening would be observed in the laser-driven Rayleigh-Taylor experiments.« less

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

    DOE PAGES

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

    2015-11-09

    Here, 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 simulatedmore » 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.« less

  18. Capturing the essence of folding and functions of biomolecules using coarse-grained models.

    PubMed

    Hyeon, Changbong; Thirumalai, D

    2011-09-27

    The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example, during chromosome organization. Describing phenomena that cover such diverse length, and also time, scales requires models that capture the underlying physics for the particular length scale of interest. Theoretical ideas, in particular, concepts from polymer physics, have guided the development of coarse-grained models to study folding of DNA, RNA and proteins. More recently, such models and their variants have been applied to the functions of biological nanomachines. Simulations using coarse-grained models are now poised to address a wide range of problems in biology.

  19. Global Land Use Regression Model for Nitrogen Dioxide Air Pollution.

    PubMed

    Larkin, Andrew; Geddes, Jeffrey A; Martin, Randall V; Xiao, Qingyang; Liu, Yang; Marshall, Julian D; Brauer, Michael; Hystad, Perry

    2017-06-20

    Nitrogen dioxide is a common air pollutant with growing evidence of health impacts independent of other common pollutants such as ozone and particulate matter. However, the worldwide distribution of NO2 exposure and associated impacts on health is still largely uncertain. To advance global exposure estimates we created a global nitrogen dioxide (NO2) land use regression model for 2011 using annual measurements from 5,220 air monitors in 58 countries. The model captured 54% of global NO2 variation, with a mean absolute error of 3.7 ppb. Regional performance varied from R(2) = 0.42 (Africa) to 0.67 (South America). Repeated 10% cross-validation using bootstrap sampling (n = 10,000) demonstrated a robust performance with respect to air monitor sampling in North America, Europe, and Asia (adjusted R(2) within 2%) but not for Africa and Oceania (adjusted R(2) within 11%) where NO2 monitoring data are sparse. The final model included 10 variables that captured both between and within-city spatial gradients in NO2 concentrations. Variable contributions differed between continental regions, but major roads within 100 m and satellite-derived NO2 were consistently the strongest predictors. The resulting model can be used for global risk assessments and health studies, particularly in countries without existing NO2 monitoring data or models.

  20. 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

  1. 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.

  2. A coarse grained protein-lipid model with application to lipoprotein particles

    PubMed Central

    Shih, Amy Y.; Arkhipov, Anton; Freddolino, Peter L.; Schulten, Klaus

    2008-01-01

    A coarse-grained model for molecular dynamics simulations is extended from lipids to proteins. In the framework of such models pioneered by Klein, atoms are described group-wise by beads, with the interactions between beads governed by effective potentials. The extension developed here is based on a coarse-grained lipid model previously developed by Marrink et al., though further versions will reconcile the approach taken with the systematic approach of Klein and other authors. Each amino acid of the protein is represented by two coarse-grained beads, one for the backbone (identical for all residues) and one for the side-chain (which differs depending on the residue type). The coarse-graining reduces system size about ten-fold and allows integration time steps of 25 to 50 fs. The model is applied to simulations of discoidal high-density lipoprotein particles, involving water, lipids, and two primarily helical proteins. These particles are an ideal test system for the extension of coarse-grained models. Our model proved reliable in maintaining the shape of pre-assembled particles and in accurately reproducing overall structural features of high-density lipoproteins. Microsecond simulations of lipoprotein assembly revealed formation of a protein-lipid complex in which two proteins are attached to either side of a discoidal lipid bilayer. PMID:16494423

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. Toward multiscale modelings of grain-fluid systems

    NASA Astrophysics Data System (ADS)

    Chareyre, Bruno; Yuan, Chao; Montella, Eduard P.; Salager, Simon

    2017-06-01

    Computationally efficient methods have been developed for simulating partially saturated granular materials in the pendular regime. In contrast, one hardly avoid expensive direct resolutions of 2-phase fluid dynamics problem for mixed pendular-funicular situations or even saturated regimes. Following previous developments for single-phase flow, a pore-network approach of the coupling problems is described. The geometry and movements of phases and interfaces are described on the basis of a tetrahedrization of the pore space, introducing elementary objects such as bridge, meniscus, pore body and pore throat, together with local rules of evolution. As firmly established local rules are still missing on some aspects (entry capillary pressure and pore-scale pressure-saturation relations, forces on the grains, or kinetics of transfers in mixed situations) a multi-scale numerical framework is introduced, enhancing the pore-network approach with the help of direct simulations. Small subsets of a granular system are extracted, in which multiphase scenario are solved using the Lattice-Boltzman method (LBM). In turns, a global problem is assembled and solved at the network scale, as illustrated by a simulated primary drainage.

  8. 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.

  9. 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.

  10. A screening-level modeling approach to estimate nitrogen ...

    EPA Pesticide Factsheets

    This paper presents a screening-level modeling approach that can be used to rapidly estimate nutrient loading and assess numerical nutrient standard exceedance risk of surface waters leading to potential classification as impaired for designated use. It can also be used to explore best management practice (BMP) implementation to reduce loading. The modeling framework uses a hybrid statistical and process based approach to estimate source of pollutants, their transport and decay in the terrestrial and aquatic parts of watersheds. The framework is developed in the ArcGIS environment and is based on the total maximum daily load (TMDL) balance model. Nitrogen (N) is currently addressed in the framework, referred to as WQM-TMDL-N. Loading for each catchment includes non-point sources (NPS) and point sources (PS). NPS loading is estimated using export coefficient or event mean concentration methods depending on the temporal scales, i.e., annual or daily. Loading from atmospheric deposition is also included. The probability of a nutrient load to exceed a target load is evaluated using probabilistic risk assessment, by including the uncertainty associated with export coefficients of various land uses. The computed risk data can be visualized as spatial maps which show the load exceedance probability for all stream segments. In an application of this modeling approach to the Tippecanoe River watershed in Indiana, USA, total nitrogen (TN) loading and risk of standard exce

  11. Grain dormancy and light quality effects on germination in the model grass Brachypodium distachyon.

    PubMed

    Barrero, José M; Jacobsen, John V; Talbot, Mark J; White, Rosemary G; Swain, Stephen M; Garvin, David F; Gubler, Frank

    2012-01-01

    • Lack of grain dormancy in cereal crops such as barley and wheat is a common problem affecting farming areas around the world, causing losses in yield and quality because of preharvest sprouting. Control of seed or grain dormancy has been investigated extensively using various approaches in different species, including Arabidopsis and cereals. However, the use of a monocot model plant such as Brachypodium distachyon presents opportunities for the discovery of new genes related to grain dormancy that are not present in modern commercial crops. • In this work we present an anatomical description of the Brachypodium caryopsis, and we describe the dormancy behaviour of six common diploid Brachypodium inbred genotypes. We also study the effect of light quality (blue, red and far-red) on germination, and analyse changes in abscisic acid levels and gene expression between a dormant and a non-dormant Brachypodium genotype. • Our results indicate that different genotypes display high natural variability in grain dormancy and that the characteristics of dormancy and germination are similar to those found in other cereals. • We propose that Brachypodium is an ideal model for studies of grain dormancy in grasses and can be used to identify new strategies for increasing grain dormancy in crop species. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.

  12. Cereal grain, rachis and pulse seed amino acid δ15N values as indicators of plant nitrogen metabolism.

    PubMed

    Styring, Amy K; Fraser, Rebecca A; Bogaard, Amy; Evershed, Richard P

    2014-01-01

    Natural abundance δ(15)N values of plant tissue amino acids (AAs) reflect the cycling of N into and within plants, providing an opportunity to better understand environmental and anthropogenic effects on plant metabolism. In this study, the AA δ(15)N values of barley (Hordeum vulgare) and bread wheat (Triticum aestivum) grains and rachis and broad bean (Vicia faba) and pea (Pisum sativum) seeds, grown at the experimental farm stations of Rothamsted, UK and Bad Lauchstädt, Germany, were determined by GC-C-IRMS. It was found that the δ(15)N values of cereal grain and rachis AAs could be largely attributed to metabolic pathways involved in their biosynthesis and catabolism. The relative (15)N-enrichment of phenylalanine can be attributed to its involvement in the phenylpropanoid pathway and glutamate has a δ(15)N value which is an average of the other AAs due to its central role in AA-N cycling. The relative AA δ(15)N values of broad bean and pea seeds were very different from one another, providing evidence for differences in the metabolic routing of AAs to the developing seeds in these leguminous plants. This study has shown that AA δ(15)N values relate to known AA biosynthetic pathways in plants and thus have the potential to aid understanding of how various external factors, such as source of assimilated N, influence metabolic cycling of N within plants.

  13. 3-D and quasi-2-D discrete element modeling of grain commingling in a bucket elevator boot system

    USDA-ARS?s Scientific Manuscript database

    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...

  14. Characterization and modeling of grain coarsening in powder metallurgical nickel-based superalloys

    NASA Astrophysics Data System (ADS)

    Payton, Eric John

    2009-08-01

    Accurate prediction of grain size as a function of processing conditions is highly sought after in many advanced alloy systems because specific grain sizes must be obtained to meet mechanical property requirements. In powder metallurgical nickel-based superalloys for turbine disk applications, physics-based modeling of grain coarsening is needed to accelerate alloy and process development and to meet demands for higher jet engine operating temperatures. Materials characterization and simulation techniques were integrated and applied simultaneously to enable quantitative representation of the microstructure, to clarify experimental results, and to validate mean-field descriptions of microstructural evolution. The key parameters controlling grain coarsening behavior were identified. A statistical-analytical mean-field model of grain coarsening with an adaptive spatio-temporal mesh was developed to enable rapid physics-based simulation of microstructural evolution. Experimental results were used as initial conditions and the model was then evaluated in the context of experimental results. Deviations of model predictions from experimental observations were then used to recommend future work to resolve remaining issues related to the microstructral evolution of powder metallurgical nickel-based superalloys, the mean-field modeling of microstructural evolution, and the quantitative characterization of materials.

  15. 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.

  16. A Model of Silicate Grain Nucleation and Growth in Circumstellar Outflows

    NASA Technical Reports Server (NTRS)

    Paquette, John A.; Ferguson, Frank T.; Nuth, Joseph A., III

    2011-01-01

    Based on its abundance, high bond energy, and recent measurements of its vapor pressure SiO is a natural candidate for dust nucleation in circumstellar outflows around asymptotic giant branch stars. In this paper, we describe a model of the nucleation and growth of silicate dust in such outflows. The sensitivity of the model to varying choices of poorly constrained chemical parameters is explored, and the merits of using scaled rather than classical nucleation theory are briefly considered, An elaboration of the model that includes magnesium and iron as growth species is then presented and discussed. The composition of the bulk of the grains derived from the model is consistent with olivines and pyroxenes, but somewhat metal-rich grains and very small, nearly pure SiO grains are also produced,

  17. A MODEL OF SILICATE GRAIN NUCLEATION AND GROWTH IN CIRCUMSTELLAR OUTFLOWS

    SciTech Connect

    Paquette, John A.; Ferguson, Frank T.; Nuth, Joseph A. III

    2011-05-10

    Based on its abundance, high bond energy, and recent measurements of its vapor pressure SiO is a natural candidate for dust nucleation in circumstellar outflows around asymptotic giant branch stars. In this paper, we describe a model of the nucleation and growth of silicate dust in such outflows. The sensitivity of the model to varying choices of poorly constrained chemical parameters is explored, and the merits of using scaled rather than classical nucleation theory are briefly considered. An elaboration of the model that includes magnesium and iron as growth species is then presented and discussed. The composition of the bulk of the grains derived from the model is consistent with olivines and pyroxenes, but somewhat metal-rich grains and very small, nearly pure SiO grains are also produced.

  18. Modeling of Nitrogen Oxides Emissions from CFB Combustion

    NASA Astrophysics Data System (ADS)

    Kallio, S.; Keinonen, M.

    In this work, a simplified description of combustion and nitrogen oxides chemistry was implemented in a 1.5D model framework with the aim to compare the results with ones earlier obtained with a detailed reaction scheme. The simplified chemistry was written using 12 chemical components. Heterogeneous chemistry is given by the same models as in the earlier work but the homogeneous and catalytic reactions have been altered. The models have been taken from the literature. The paper describes the numerical model with emphasis on the chemistry submodels. A simulation of combustion of bituminous coal in the Chalmers 12 MW boiler is conducted and the results are compared with the results obtained earlier with the detailed chemistry description. The results are also compared with measured O2, CO, NO and N2O profiles. The simplified reaction scheme produces equally good results as earlier obtained with the more elaborate chemistry description.

  19. A multiscale approach to triglycerides simulations: from atomistic to coarse-grained models and back.

    PubMed

    Brasiello, Antonio; Crescitelli, Silvestro; Milano, Giuseppe

    2012-01-01

    The aim of this paper is to provide a simulation strategy to study the liquid-solid transition of triglycerides. The strategy is based on a multiscale approach. A coarse-grained model, parameterized on the basis of reference atomistic simulations, has been used to model the liquid-solid transition. A reverse mapping procedure has been proposed to reconstruct atomistic models from coarse-grained configurations and validated against experimental structural properties. The nucleation and growth of the crystalline order have been analysed in terms of several properties.

  20. Porous grain model and equivalent elastic medium approach for predicting effective elastic properties of sedimentary rocks

    NASA Astrophysics Data System (ADS)

    Ruiz, Franklin J.

    This dissertation presents the results of using different inclusion and granular effective medium models and poroelasticity to predict the elastic properties of rocks with complex microstructures. Effective medium models account for the microstructure and texture of rocks, and can be used to predict the type of rock and microstructure from seismic velocities and densities. We introduce the elastic equivalency approach, using the differential effective medium model, to predict the effective elastic moduli of rocks and attenuation. We introduce the porous grain concept and develop rock physics models for rocks with microporosity. We exploit the porous grain concept to describe a variety of arrangements of uncemented and cemented grains with different degrees of hydraulic connectivity in the pore space. We first investigate the accuracy of the differential effective medium and self-consistent estimations of elastic properties of complex rock matrix using composites as analogs. We test whether the differential effective-medium (DEM) and self-consistent (SC) models can accurately estimate the elastic moduli of a complex rock matrix and compare the results with the average of upper and lower Hashin-Shtrikman bounds. We find that when the material microstructure is consistent with DEM, this model is more accurate than both SC and the bound-average method for a variety of inclusion aspect ratios, concentrations, and modulus contrasts. Based on these results, we next pose a question: can a theoretical inclusion model, specifically, the differential effective-medium model (DEM), be used to match experimental velocity data in rocks that are not necessarily made of inclusions (such as elastics)? We first approach this question by using empirical velocity-porosity equations as proxies for data. By finding a DEM inclusion aspect ratio (AR) to match these equations, we find that the required range of AR is remarkably narrow. Moreover, a constant AR of about 0.13 can be used to

  1. 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.

  2. Modeling Nitrogen Fate and Transport at the Sediment-Water ...

    EPA Pesticide Factsheets

    Diffusive mass transfer at media interfaces exerts control on the fate and transport of pollutants originating from agricultural and urban landscapes and affects the con-ditions of water bodies. Diffusion is essentially a physical process affecting the distribution and fate of various environmental pollutants such as nutrients, pesticides, metals, PCBs, PAHs, etc. Environmental problems caused by excessive use of agricultural chemicals (e.g., pesticides and fertilizers) and improper discharge of industrial waste and fuel leaks are all influenced by the diffusive nature of pollutants in the environment. Eutrophication is one such environmental problem where the sediment-water interface exerts a significant physical and geochemical control on the eutrophic condition of the stressed water body. Exposure of streams and lakes to contaminated sediment is another common environmental problem whereby transport of the contaminant (PCBs, PAHs, and other organic contaminants) across the sediment water can increase the risk for exposure to the chemicals and pose a significant health hazard to aquatic life and human beings. This chapter presents analytical and numerical models describing fate and transport phenomena at the sediment-water interface in freshwater ecosystems, with the primary focus on nitrogen cycling and the applicability of the models to real-world environmental problems and challenges faced in their applications. The first model deals with nitrogen cycling

  3. Laboratory-based grain-shape models for simulating dust infrared spectra

    NASA Astrophysics Data System (ADS)

    Mutschke, H.; Min, M.; Tamanai, A.

    2009-09-01

    Context: Analysis of thermal dust emission spectra for dust mineralogy and physical grain properties depends on comparison spectra, which are either laboratory-measured infrared extinction spectra or calculated extinction cross sections based on certain grain models. Often, the agreement between these two kinds of spectra, if available, is not yet satisfactory because of the strong influence of the grain morphology on the spectra. Aims: We investigate the ability of the statistical light-scattering model with a distribution of form factors (DFF) to reproduce measured infrared dust extinction spectra for particles that are small compared to the wavelength, i.e. in the size range of 1 μm and smaller. Methods: We take advantage of new experimental spectra measured for free particles dispersed in air with accompanying information on the grain morphology. For the calculations, we used DFFs that were derived for aggregates of spherical grains, as well as for compact grain shapes corresponding to Gaussian random spheres. In addition we used a fitting algorithm to obtain the best-fit DFFs for the various laboratory samples. In this way we can independently derive information on the shape of the grains from their infrared spectra. Results: With the DFF model, we achieve an adequate fit of the experimental IR spectra. The differences in the IR band profiles between the spectra of particulates with different grain shapes are simply reflected by different DFFs. Irregular particle shapes require a DFF similar to that of a Gaussian Random Sphere with σ=0.3, whereas roundish grain shapes are best fitted with that of a fractal aggregate of D_f=2.4-1.8. The fitted DFFs generally reproduce the measured spectral shapes quite well. For anisotropic materials, different DFFs are needed for the different crystallographic axes. The implications of this finding are discussed. Conclusions: The use of this model could be a step forward toward more realistic comparison data in infrared

  4. 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.

  5. Modeling the impact of bay breeze circulations on nitrogen deposition

    NASA Astrophysics Data System (ADS)

    Loughner, C. P.; Tzortziou, M.; Pickering, K. E.; Duffy, M.; Satam, C.

    2012-12-01

    Atmospheric gases and aerosols are deposited into watersheds and estuarine waters contributing to water quality degradation and affecting estuarine and coastal biogeochemical processes. Pollution that is deposited onto land can be transported into storm drains, groundwater, streams, and rivers where it is eventually transported into near-shore waters. Air quality models, which simulate the chemical transformation, atmospheric transport, and deposition of pollutants onto land and surface waters, can play an integral role in forecasting water quality, preparing water quality regulations and providing information on the sources of nutrients and pollutants for advanced estuarine biogeochemical models. Previous studies have found that Chesapeake Bay breezes cause localized areas of high air pollution concentrations and that model simulations with horizontal resolutions coarser than about 5 km are not able to capture bay breeze circulations. Here, we investigate the importance of capturing bay breeze circulations with high resolution model simulations (horizontal resolution of 1.33 km) to accurately simulate the spatial and temporal variability of nitrogen deposition into the Chesapeake Bay watershed. Nitrogen deposition into the watershed from air quality model simulations are compared with observed wet deposition and estimated dry deposition rates from the National Acid Deposition Program (NADP) and the Clean Air Status and Trends Network (CASTNET), respectively. The model simulation is conducted for the months of June and July 2011. Two concurrent air and water quality field campaigns, DISCOVER-AQ (Deriving Information on Surface Conditions from Column and Vertically Resolved Observations Relevant to Air Quality) and GeoCAPE-CBODAQ (Geostationary Coastal and Air Pollution Events-Chesapeake Bay Oceanographic Campaign with DISCOVER-AQ), were conducted in July 2011, and data obtained from these field experiments are used to evaluate the model simulations.

  6. Modelling of the effects of grain orientation on transformation-induced plasticity in multiphase carbon steels

    NASA Astrophysics Data System (ADS)

    Tjahjanto, D. D.; Turteltaub, S.; Suiker, A. S. J.; van der Zwaag, S.

    2006-06-01

    The effects of grain orientation on transformation-induced plasticity in multiphase steels are studied through three-dimensional finite element simulations. The boundary value problems analysed concern a uniaxially-loaded sample consisting of a grain of retained austenite surrounded by multiple grains of ferrite. For the ferritic phase, a rate-dependent crystal plasticity model is used that describes the elasto-plastic behaviour of body-centred cubic crystalline structures under large deformations. In this model, the critical-resolved shear stress for plastic slip consists of an evolving slip resistance and a stress-dependent term that corresponds to the projection of the stress tensor on a non-glide plane (i.e. a non-Schmid stress). For the austenitic phase, the transformation model developed by Turteltaub and Suiker (2006 Int. J. Solids Struct. at press, 2005 J. Mech. Phys. Solids 53 1747-88) is employed. This model simulates the displacive phase transformation of a face-centred cubic austenite into a body-centred tetragonal martensite under external mechanical loading. The effective transformation kinematics and the effective anisotropic elastic stiffness components in the model are derived from lower-scale information that follows from the crystallographic theory of martensitic transformations. In the boundary value problems studied, the mutual interaction between the transforming austenitic grain and the plastically deforming ferritic matrix is computed for several grain orientations. From the simulation results, specific combinations of austenitic and ferritic crystalline orientations are identified that either increase or decrease the effective strength of the material. This information is useful to further improve the mechanical properties of multiphase carbon steels. In order to quantify the anisotropic aspects of the crystal plasticity model, the simulation results for the uniaxially-loaded sample are compared with those obtained with an isotropic

  7. 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.

  8. A Three-Dimensional Cellular Automata Model Coupling Energy and Curvature-Driven Mechanisms for Austenitic Grain Growth

    NASA Astrophysics Data System (ADS)

    Wang, Min; Zhou, Jianxin; Yin, Yajun; Nan, Hai; Zhang, Dongqiao; Tu, Zhixin

    2017-10-01

    A 3D cellular automata model is used to simulate normal austenitic grain growth in this study. The proposed model considers both the curvature- and thermodynamics-driven mechanisms of growth. The 3D grain growth kinetics shows good agreement with the Beck equation. Moreover, the growth exponent and grain size distribution calculated by the proposed model coincides well with experimental and simulation results from other researchers. A linear relationship is found between the average relative grain size and the grain face number. More specifically, for average relative grain sizes exceeding 0.5, the number of faces increases linearly with relative grain size. For average relative grain sizes <0.5, this relationship is changed. Results simulated by the proposed model are translated to physical meaning by adjusting the actual temperature, space, and time for austenitic grain growth. The calibrated results are found to be in agreement with the simulation results from other research as well as the experimental results. By means of calibration of the proposed model, we can reliably predict the grain size in actual grain growth.

  9. Resolution-Adapted All-Atomic and Coarse-Grained Model for Biomolecular Simulations.

    PubMed

    Shen, Lin; Hu, Hao

    2014-06-10

    We develop here an adaptive multiresolution method for the simulation of complex heterogeneous systems such as the protein molecules. The target molecular system is described with the atomistic structure while maintaining concurrently a mapping to the coarse-grained models. The theoretical model, or force field, used to describe the interactions between two sites is automatically adjusted in the simulation processes according to the interaction distance/strength. Therefore, all-atomic, coarse-grained, or mixed all-atomic and coarse-grained models would be used together to describe the interactions between a group of atoms and its surroundings. Because the choice of theory is made on the force field level while the sampling is always carried out in the atomic space, the new adaptive method preserves naturally the atomic structure and thermodynamic properties of the entire system throughout the simulation processes. The new method will be very useful in many biomolecular simulations where atomistic details are critically needed.

  10. Stress and temperature dependence of recrystallized grain size: A subgrain misorientation model

    NASA Astrophysics Data System (ADS)

    Shimizu, Ichiko

    The steady-state grain size of Earth materials undergoing solid state flow is estimated based on a nucleation-and-growth model of dynamic recrystallization. Assuming a nucleation mechanism of subgrain rotation, the mean diameter d of recrystallized grains is obtained as d/b = A(σ/µ)-p exp[-((Qgb - Qv)/mkT)], where b is the length of the Burgers vector, σ is differential stress, µ is the shear modulus, Qgb is the activation energy for the jump of an atom across the grain boundary, Qv is that for self-diffusion in the grain volume, k is the Boltzmann constant, T is temperature, A is a constant, p = 1.25 and m = 4 for intracrystalline nucleation, and p = 1.33 and m = 3 for grain-boundary nucleation. The exponent p = 1.25 ˜ 1.33 agrees well with available data for high- temperature dislocation creep of rock-forming minerals. A weak negative dependence of grain size on temperature is expected from this theory.

  11. Reactive transport modeling of nitrogen in Seine River sediments

    NASA Astrophysics Data System (ADS)

    Akbarzadeh, Z.; Laverman, A.; Raimonet, M.; Rezanezhad, F.; Van Cappellen, P.

    2016-02-01

    Biogeochemical processes in sediments have a major impact on the fate and transport of nitrogen (N) in river systems. Organic matter decomposition in bottom sediments releases inorganic N species back to the stream water, while denitrification, anammox and burial of organic matter remove bioavailable N from the aquatic environment. To simulate N cycling in river sediments, a multi-component reactive transport model has been developed in MATLAB®. The model includes 3 pools of particulate organic N, plus pore water nitrate, nitrite, nitrous oxide and ammonium. Special attention is given to the production and consumption of nitrite, a N species often neglected in early diagenetic models. Although nitrite is usually considered to be short-lived, elevated nitrite concentrations have been observed in freshwater streams, raising concerns about possible toxic effects. We applied the model to sediment data sets collected at two locations in the Seine River, one upstream, the other downstream, of the largest wastewater treatment plant (WWTP) of the Paris conurbation. The model is able to reproduce the key features of the observed pore water depth profiles of the different nitrogen species. The modeling results show that the presence of oxygen in the overlying water plays a major role in controlling the exchanges of nitrite between the sediments and the stream water. In August 2012, sediments upstream of the WWTP switch from being a sink to a source of nitrite as the overlying water becomes anoxic. Downstream sediments remain a nitrite sink in oxic and anoxic conditions. Anoxic bottom waters at the upstream location promote denitrification, which produces nitrite, while at the downstream site, anammox and DNRA are important removal processes of nitrite.

  12. Guidance to Design Grain Boundary Mobility Experiments with Molecular Dynamics and Phase-Field Modeling

    SciTech Connect

    Michael R Tonks; Yongfeng Zhang; S.B. Biner; Paul C Millett; Xianming Bai

    2013-02-01

    Quantitative phase-field modeling can play an important role in designing experiments to measure the grain boundary (GB) mobility. In this work, molecular dynamics (MD) simulation is employed to determine the GB mobility using Cu bicrystals. Two grain configurations are considered: a shrinking circular grain and a half loop grain. The results obtained from the half loop configuration approaches asymptotically to that obtained from the circular configuration with increasing half loop width. We then verify the phase- field model by directly comparing to the MD simulation results, obtaining excellent agreement. Next, this phase-field model is used to predict the behavior in a common experimental setup that utilizes a half loop grain configuration in a bicrystal to measure the GB mobility. With a 3D simulation, we identify the two critical times within the experiments to reach an accurate value of the GB mobility. We use a series of 2D simulations to investigate the impact of the notch angle on these two critical times and we identify an angle of 60? as an optimal value. We also show that if the notch does not have a sharp tip, it may immobilize the GB migration indefinitely.

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

    PubMed

    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 F(1)-ATPase and the kinesin motor.

  14. 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.

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

    SciTech Connect

    Tonks, Michael R; Zhang, Yongfeng; Bai, Xianming

    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.

  16. 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.

  17. 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.

  18. 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.

  19. Numerical models for fluid-grains interactions: opportunities and limitations

    NASA Astrophysics Data System (ADS)

    Esteghamatian, Amir; Rahmani, Mona; Wachs, Anthony

    2017-06-01

    In the framework of a multi-scale approach, we develop numerical models for suspension flows. At the micro scale level, we perform particle-resolved numerical simulations using a Distributed Lagrange Multiplier/Fictitious Domain approach. At the meso scale level, we use a two-way Euler/Lagrange approach with a Gaussian filtering kernel to model fluid-solid momentum transfer. At both the micro and meso scale levels, particles are individually tracked in a Lagrangian way and all inter-particle collisions are computed by a Discrete Element/Soft-sphere method. The previous numerical models have been extended to handle particles of arbitrary shape (non-spherical, angular and even non-convex) as well as to treat heat and mass transfer. All simulation tools are fully-MPI parallel with standard domain decomposition and run on supercomputers with a satisfactory scalability on up to a few thousands of cores. The main asset of multi scale analysis is the ability to extend our comprehension of the dynamics of suspension flows based on the knowledge acquired from the high-fidelity micro scale simulations and to use that knowledge to improve the meso scale model. We illustrate how we can benefit from this strategy for a fluidized bed, where we introduce a stochastic drag force model derived from micro-scale simulations to recover the proper level of particle fluctuations. Conversely, we discuss the limitations of such modelling tools such as their limited ability to capture lubrication forces and boundary layers in highly inertial flows. We suggest ways to overcome these limitations in order to enhance further the capabilities of the numerical models.

  20. Stochastic and Deterministic Approaches to Gas-grain Modeling of Interstellar Sources

    NASA Astrophysics Data System (ADS)

    Vasyunin, Anton; Herbst, Eric; Caselli, Paola

    During the last decade, our understanding of the chemistry on surfaces of interstellar grains has been significantly enchanced. Extensive laboratory studies have revealed complex structure and dynamics in interstellar ice analogues, thus making our knowledge much more detailed. In addition, the first qualitative investigations of new processes were made, such as non-thermal chemical desorption of species from dust grains into the gas. Not surprisingly, the rapid growth of knowledge about the physics and chemistry of interstellar ices led to the development of a new generation of astrochemical models. The models are typically characterized by more detailed treatments of the ice physics and chemistry than previously. The utilized numerical approaches vary greatly from microscopic models, in which every single molecule is traced, to ``mean field'' macroscopic models, which simulate the evolution of averaged characteristics of interstellar ices, such as overall bulk composition. While microscopic models based on a stochastic Monte Carlo approach are potentially able to simulate the evolution of interstellar ices with an account of most subtle effects found in a laboratory, their use is often impractical due to limited knowledge about star-forming regions and huge computational demands. On the other hand, deterministic macroscopic models that often utilize kinetic rate equations are computationally efficient but experience difficulties in incorporation of such potentially important effects as ice segregation or discreteness of surface chemical reactions. In my talk, I will review the state of the art in the development of gas-grain astrochemical models. I will discuss how to incorporate key features of ice chemistry and dynamics in the gas-grain astrochemical models, and how the incorporation of recent laboratory findings into gas-grain models helps to better match observations.

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

    NASA Astrophysics Data System (ADS)

    Ding, Yajun; Mittal, Jeetain

    2014-11-01

    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.

  2. 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.

  3. 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...

  4. 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...

  5. 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.

  6. Comparison of two energy forest growth models based on photosynthesis and nitrogen productivity

    SciTech Connect

    Eckersten, H.

    1985-05-01

    Two energy forest growth models are compared. The growth rate in the first model (nitrogen model) is determined by the amount of nitrogen in leaves and the nitrogen productivity. The growth rate in the second model (photosynthetic model) is mainly determined by the photosynthetic process in the leaves, which in turn depends on climatic conditions and nitrogen status of the leaves, and on allocation. When two parameters related to those of the nitrogen model are derived from the photosynthetic model and the significances of these sets of parameters compared, some suggestions for changes to both models so as to make them consistent can be made. Allocation of biomass between stems, leaves and roots is shown to be a function of the nitrogen concentration in the leaves whereas the net fraction of growth lost through growth respiration in leaves and roots and death of fine roots is almost independent of the nitrogen concentration in leaves. It is also shown that the nitrogen model yields too large an influence for increasing leaf biomass on growth rate to be explained only by the effect of increasing self-shading in a growing canopy. In steady state conditions the photosynthetic model has no maximum leaf biomass when not considering death of biomass, while in the nitrogen model leaf biomass is limited even without death of leaf biomass.

  7. Mechanical behaviour of weak snow layers: modelling a porous structure of sintered grains

    NASA Astrophysics Data System (ADS)

    Mede, Tijan; Chambon, Guillaume; Hagenmuller, Pascal; Nicot, François

    2017-06-01

    Weak layers of snow are thin layers of low density and cohesion that consist of a complex network of sintered ice grains. These layers are very fragile and their collapse is considered to be the primary cause of dry slab snow avalanche release. This study reports on an attempt at modelling the mechanical response of these weak snow layers with discrete element (DEM) simulations, using x-ray tomographical images of real snow samples as input data on the microstructure of the material. An original method for representing irregular grain shapes in the DEM is first introduced. The method is based on utilizing the medial axis concept to represent an arbitrary grain shape with an optimal set of overlapping spheres. A thorough study of the effect of the grain approximating technique parameters on the key geometrical features of the grains is then carried out. Finally, the functionality of the model is demonstrated by performing an oedometric test on an image of a real snow sample.

  8. 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.

  9. Mechanical properties of desiccated ragweed pollen grains determined by micromanipulation and theoretical modelling.

    PubMed

    Liu, T; Zhang, Z

    2004-03-30

    The mechanical properties of desiccated ragweed pollen grains were determined using a micromanipulation technique and a theoretical model. Single pollen grains with a diameter of approximately 20 microm were compressed and held, compressed and released, and compressed to rupture at different speeds between two parallel surfaces. Simultaneously, the force being imposed on the pollen grains was measured. It has been found that the rupture force of pollen grains increased linearly with their displacement at rupture on average, but was independent of their diameter. The mean rupture force was 1.20 +/- 0.03 mN, and mean deformation (the ratio between the displacement and diameter) at rupture was 22 +/- 0.6%. Single pollen grains were modeled as a capsule with a core full of air and a non permeable wall. A constitutive equation based on Hookean law was used to determine the mechanical property parameters Eh (product of the Young's modulus and wall thickness), and the mean value of Eh of desiccated pollen gains was estimated to be 1653 +/- 36 N/m.

  10. Modelling carbon and nitrogen turnover in variably saturated soils

    NASA Astrophysics Data System (ADS)

    Batlle-Aguilar, J.; Brovelli, A.; Porporato, A.; Barry, D. A.

    2009-04-01

    Natural ecosystems provide services such as ameliorating the impacts of deleterious human activities on both surface and groundwater. For example, several studies have shown that a healthy riparian ecosystem can reduce the nutrient loading of agricultural wastewater, thus protecting the receiving surface water body. As a result, in order to develop better protection strategies and/or restore natural conditions, there is a growing interest in understanding ecosystem functioning, including feedbacks and nonlinearities. Biogeochemical transformations in soils are heavily influenced by microbial decomposition of soil organic matter. Carbon and nutrient cycles are in turn strongly sensitive to environmental conditions, and primarily to soil moisture and temperature. These two physical variables affect the reaction rates of almost all soil biogeochemical transformations, including microbial and fungal activity, nutrient uptake and release from plants, etc. Soil water saturation and temperature are not constants, but vary both in space and time, thus further complicating the picture. In order to interpret field experiments and elucidate the different mechanisms taking place, numerical tools are beneficial. In this work we developed a 3D numerical reactive-transport model as an aid in the investigation the complex physical, chemical and biological interactions occurring in soils. The new code couples the USGS models (MODFLOW 2000-VSF, MT3DMS and PHREEQC) using an operator-splitting algorithm, and is a further development an existing reactive/density-dependent flow model PHWAT. The model was tested using simplified test cases. Following verification, a process-based biogeochemical reaction network describing the turnover of carbon and nitrogen in soils was implemented. Using this tool, we investigated the coupled effect of moisture content and temperature fluctuations on nitrogen and organic matter cycling in the riparian zone, in order to help understand the relative

  11. Grain coarsening in two-dimensional phase-field models with an orientation field.

    PubMed

    Korbuly, Bálint; Pusztai, Tamás; Henry, Hervé; Plapp, Mathis; Apel, Markus; Gránásy, László

    2017-05-01

    In the literature, contradictory results have been published regarding the form of the limiting (long-time) grain size distribution (LGSD) that characterizes the late stage grain coarsening in two-dimensional and quasi-two-dimensional polycrystalline systems. While experiments and the phase-field crystal (PFC) model (a simple dynamical density functional theory) indicate a log-normal distribution, other works including theoretical studies based on conventional phase-field simulations that rely on coarse grained fields, like the multi-phase-field (MPF) and orientation field (OF) models, yield significantly different distributions. In a recent work, we have shown that the coarse grained phase-field models (whether MPF or OF) yield very similar limiting size distributions that seem to differ from the theoretical predictions. Herein, we revisit this problem, and demonstrate in the case of OF models [R. Kobayashi, J. A. Warren, and W. C. Carter, Physica D 140, 141 (2000)PDNPDT0167-278910.1016/S0167-2789(00)00023-3; H. Henry, J. Mellenthin, and M. Plapp, Phys. Rev. B 86, 054117 (2012)PRBMDO1098-012110.1103/PhysRevB.86.054117] that an insufficient resolution of the small angle grain boundaries leads to a log-normal distribution close to those seen in the experiments and the molecular scale PFC simulations. Our paper indicates, furthermore, that the LGSD is critically sensitive to the details of the evaluation process, and raises the possibility that the differences among the LGSD results from different sources may originate from differences in the detection of small angle grain boundaries.

  12. Grain coarsening in two-dimensional phase-field models with an orientation field

    NASA Astrophysics Data System (ADS)

    Korbuly, Bálint; Pusztai, Tamás; Henry, Hervé; Plapp, Mathis; Apel, Markus; Gránásy, László

    2017-05-01

    In the literature, contradictory results have been published regarding the form of the limiting (long-time) grain size distribution (LGSD) that characterizes the late stage grain coarsening in two-dimensional and quasi-two-dimensional polycrystalline systems. While experiments and the phase-field crystal (PFC) model (a simple dynamical density functional theory) indicate a log-normal distribution, other works including theoretical studies based on conventional phase-field simulations that rely on coarse grained fields, like the multi-phase-field (MPF) and orientation field (OF) models, yield significantly different distributions. In a recent work, we have shown that the coarse grained phase-field models (whether MPF or OF) yield very similar limiting size distributions that seem to differ from the theoretical predictions. Herein, we revisit this problem, and demonstrate in the case of OF models [R. Kobayashi, J. A. Warren, and W. C. Carter, Physica D 140, 141 (2000), 10.1016/S0167-2789(00)00023-3; H. Henry, J. Mellenthin, and M. Plapp, Phys. Rev. B 86, 054117 (2012), 10.1103/PhysRevB.86.054117] that an insufficient resolution of the small angle grain boundaries leads to a log-normal distribution close to those seen in the experiments and the molecular scale PFC simulations. Our paper indicates, furthermore, that the LGSD is critically sensitive to the details of the evaluation process, and raises the possibility that the differences among the LGSD results from different sources may originate from differences in the detection of small angle grain boundaries.

  13. Toward Quantitative Coarse-Grained Models of Lipids with Fluids Density Functional Theory.

    PubMed

    Frink, Laura J Douglas; Frischknecht, Amalie L; Heroux, Michael A; Parks, Michael L; Salinger, Andrew G

    2012-04-10

    We describe methods to determine optimal coarse-grained models of lipid bilayers for use in fluids density functional theory (fluids-DFT) calculations. Both coarse-grained lipid architecture and optimal parametrizations of the models based on experimental measures are discussed in the context of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers in water. The calculations are based on a combination of the modified-iSAFT theory for bonded systems and an accurate fundamental measures theory (FMT) for hard sphere reference fluids. We furthermore discuss a novel approach for pressure control in the fluids-DFT calculations that facilitates both partitioning studies and zero tension control for the bilayer studies. A detailed discussion of the numerical implementations for both solvers and pressure control capabilities are provided. We show that it is possible to develop a coarse-grained lipid bilayer model that is consistent with experimental properties (thickness and area per lipid) of DPPC provided that the coarse-graining is not too extreme. As a final test of the model, we find that the predicted area compressibility moduli and lateral pressure profiles of the optimized models are in reasonable agreement with prior results.

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

    SciTech Connect

    Sussman, Roberto A.; Gaspar, I. Delgado; Hidalgo, Juan Carlos E-mail: ismael.delgadog@uaem.edu.mx

    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.

  15. Modeling the effects of organic nitrogen uptake by plants on the carbon cycling of boreal ecosystems

    NASA Astrophysics Data System (ADS)

    Zhu, Q.; Zhuang, Q.

    2013-08-01

    Boreal forest and tundra are the major ecosystems in the northern high latitudes in which a large amount of carbon is stored. These ecosystems are nitrogen-limited due to slow mineralization rate of the soil organic nitrogen. Recently, abundant field studies have found that organic nitrogen is another important nitrogen supply for boreal ecosystems. In this study, we incorporated a mechanism that allowed boreal plants to uptake small molecular amino acids into a process-based biogeochemical model, the Terrestrial Ecosystem Model (TEM), to evaluate the impact of organic nitrogen uptake on ecosystem carbon cycling. The new version of the model was evaluated at both boreal forest and tundra sites. We found that the modeled organic nitrogen uptake accounted for 36-87% of total nitrogen uptake by plants in tundra ecosystems and 26-50% for boreal forests, suggesting that tundra ecosystem might have more relied on the organic form of nitrogen than boreal forests. The simulated monthly gross ecosystem production (GPP) and net ecosystem production (NEP) tended to be larger with the new version of the model since the plant uptake of organic nitrogen alleviated the soil nitrogen limitation especially during the growing season. The sensitivity study indicated that the most important factors controlling the plant uptake of organic nitrogen were the maximum root uptake rate (Imax) and the radius of the root (r0) in our model. The model uncertainty due to uncertain parameters associated with organic nitrogen uptake at tundra ecosystem was larger than at boreal forest ecosystems. This study suggests that considering the organic nitrogen uptake by plants is important to boreal ecosystem carbon modeling.

  16. Modelling of aflatoxin G1 reduction by kefir grain using response surface methodology.

    PubMed

    Ansari, Farzaneh; Khodaiyan, Faramarz; Rezaei, Karamatollah; Rahmani, Anosheh

    2015-01-01

    Aflatoxin G1 (AFG1) is one of the main toxic contaminants in pistachio nuts and causes potential health hazards. Hence, AFG1 reduction is one of the main concerns in food safety. Kefir-grains contain symbiotic association of microorganisms well known for their aflatoxin decontamination effects. In this study, a central composite design (CCD) using response surface methodology (RSM) was applied to develop a model in order to predict AFG1 reduction in pistachio nuts by kefir-grain (already heated at 70 and 110°C). The independent variables were: toxin concentration (X1: 5, 10, 15, 20 and 25 ng/g), kefir-grain level (X2: 5, 10, 20, 10 and 25%), contact time (X3: 0, 2, 4, 6 and 8 h), and incubation temperature (X4: 20, 30, 40, 50 and 60°C). There was a significant reduction in AFG1 (p < 0.05) when pre-heat-treated kefir-grain used. The variables including X1, X3 and the interactions between X2-X4 as well as X3-X4 have significant effects on AFG1 reduction. The model provided a good prediction of AFG1 reduction under the assay conditions. Optimization was used to enhance the efficiency of kefir-grain on AFG1 reduction. The optimum conditions for the highest AFG1 reduction (96.8%) were predicted by the model as follows: toxin concentration = 20 ng/g, kefir-grain level = 10%, contact time = 6 h, and incubation temperature = 30°C which validated practically in six replications.

  17. Fast coarse-grained model for RNA titration

    NASA Astrophysics Data System (ADS)

    Barroso da Silva, Fernando Luís; Derreumaux, Philippe; Pasquali, Samuela

    2017-01-01

    A new numerical scheme for RNA (ribonucleic acid) titration based on the Debye-Hückel framework for the salt description is proposed in an effort to reduce the computational costs for further applications to study protein-RNA systems. By means of different sets of Monte Carlo simulations, we demonstrated that this new scheme is able to correctly reproduce the experimental titration behavior and salt pKa shifts. In comparison with other theoretical approaches, similar or even better outcomes are achieved at much lower computational costs. The model was tested on the lead-dependent ribozyme, the branch-point helix, and the domain 5 from Azotobacter vinelandii Intron 5.

  18. Grain Size and Parameter Recovery with TIMSS and the General Diagnostic Model

    ERIC Educational Resources Information Center

    Skaggs, Gary; Wilkins, Jesse L. M.; Hein, Serge F.

    2016-01-01

    The purpose of this study was to explore the degree of grain size of the attributes and the sample sizes that can support accurate parameter recovery with the General Diagnostic Model (GDM) for a large-scale international assessment. In this resampling study, bootstrap samples were obtained from the 2003 Grade 8 TIMSS in Mathematics at varying…

  19. Orientation-field models for polycrystalline solidification: Grain coarsening and complex growth forms

    NASA Astrophysics Data System (ADS)

    Korbuly, Bálint; Pusztai, Tamás; Tóth, Gyula I.; Henry, Hervé; Plapp, Mathis; Gránásy, László

    2017-01-01

    We compare two versions of the phase-field theory for polycrystalline solidification, both relying on the concept of orientation fields: one by Kobayashi et al. [Physica D 140 (2000) 141] [15] and the other by Henry et al. [Phys. Rev. B 86 (2012) 054117] [22]. Setting the model parameters so that the grain boundary energies and the time scale of grain growth are comparable in the two models, we first study the grain coarsening process including the limiting grain size distribution, and compare the results to those from experiments on thin films, to the models of Hillert, and Mullins, and to predictions by multiphase-field theories. Next, following earlier work by Gránásy et al. [Phys. Rev. Lett. 88 (2002) 206105; Phys. Rev. E 72 (2005) 011605] [17,21], we extend the orientation field to the liquid state, where the orientation field is made to fluctuate in time and space, and employ the model for describing of multi-dendritic solidification, and polycrystalline growth, including the formation of "dizzy" dendrites disordered via the interaction with foreign particles.

  20. Grain Size and Parameter Recovery with TIMSS and the General Diagnostic Model

    ERIC Educational Resources Information Center

    Skaggs, Gary; Wilkins, Jesse L. M.; Hein, Serge F.

    2016-01-01

    The purpose of this study was to explore the degree of grain size of the attributes and the sample sizes that can support accurate parameter recovery with the General Diagnostic Model (GDM) for a large-scale international assessment. In this resampling study, bootstrap samples were obtained from the 2003 Grade 8 TIMSS in Mathematics at varying…

  1. 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.

  2. Discrete Element Modeling of Oscillatory Sheet Flow Using Medium and Coarse Spherical Sand Grains.

    NASA Astrophysics Data System (ADS)

    Cobb, M. M.; Calantoni, J.; Holland, T.; Odonoghue, T.

    2006-12-01

    Oscillatory wave-driven sheet flow transports large quantities of surf and swash zone sediment and is fundamental to understanding the redistribution of sediments during the morphodynamic evolution of wave dominated sandy beaches. In order to better understand sheet flow processes and their sensitivity to grain size distributions sediment transport simulations that explicitly describe the small-scale grain-fluid interactions are performed. In this study asymmetric second order stokes wave oscillatory sheet flow is investigated using a discrete element model (DEM). We examine the time averaged total transport, time-dependent transport with depth, and time-dependent concentration with depth for second order stokes waves with periods of 5 and 7.5 seconds and amplitudes of 1 and 1.5 meters, respectively, over beds with medium (D50 = 0.28 mm) and coarse (D50 = 0.51 mm) grains. Direct comparisons are made between model results and data taken at the Aberdeen Oscillatory Flow Tunnel. For coarse grain cases the model predictions are 15-25% greater than the measured total transport in the experiments. Model-data comparisons of the time dependent concentration as a function of depth reveal good agreement within the bedload layer, suggesting that the DEM is successfully describing the same physical processes involved in the sheet flow transport. In addition, correlations between the time-dependent concentrations at different depths indicate that the model has the same spatio-temporal structure exhibited by the laboratory measurements. However, the DEM, which is coupled to a simple one-dimensional mixing length fluid model, underpredicts total transport for medium grains since it cannot account for the substantial amount of suspended sediment that most likely contributes to the measured total transport.

  3. Coarse-grained models for interacting, flapping swimmers

    NASA Astrophysics Data System (ADS)

    Oza, Anand; Ristroph, Leif; Shelley, Michael; Courant Institute Applied Math Lab Collaboration

    2016-11-01

    We present the results of a theoretical investigation into the dynamics of interacting flapping swimmers. Our study is motivated by ongoing experiments in the NYU Applied Math Lab, in which freely-translating, heaving airfoils interact hydrodynamically to choose their relative positions and velocities. We develop a discrete dynamical system in which flapping swimmers shed point vortices during each flapping cycle, which in turn exert forces on the swimmers. We present a framework for finding exact solutions to the evolution equations and for assessing their stability, giving physical insight into the preference for certain observed "schooling states". The model may be extended to arrays of flapping swimmers, and configurations in which the swimmers' flapping frequencies are incommensurate. Generally, our results indicate how hydrodynamics may mediate schooling and flocking behavior in biological contexts. A. Oza acknowledges the support of the NSF Mathematical Sciences Postdoctoral Fellowship.

  4. Quantifying nitrogen losses in oil palm plantations: models and challenges

    NASA Astrophysics Data System (ADS)

    Pardon, Lénaïc; Bessou, Cécile; Saint-Geours, Nathalie; Gabrielle, Benoît; Khasanah, Ni'matul; Caliman, Jean-Pierre; Nelson, Paul N.

    2016-09-01

    Oil palm is the most rapidly expanding tropical perennial crop. Its cultivation raises environmental concerns, notably related to the use of nitrogen (N) fertilisers and the associated pollution and greenhouse gas emissions. While numerous and diverse models exist to estimate N losses from agriculture, very few are currently available for tropical perennial crops. Moreover, there is a lack of critical analysis of their performance in the specific context of tropical perennial cropping systems. We assessed the capacity of 11 models and 29 sub-models to estimate N losses in a typical oil palm plantation over a 25-year growth cycle, through leaching and runoff, and emissions of NH3, N2, N2O, and NOx. Estimates of total N losses were very variable, ranging from 21 to 139 kg N ha-1 yr-1. On average, 31 % of the losses occurred during the first 3 years of the cycle. Nitrate leaching accounted for about 80 % of the losses. A comprehensive Morris sensitivity analysis showed the most influential variables to be soil clay content, rooting depth, and oil palm N uptake. We also compared model estimates with published field measurements. Many challenges remain in modelling processes related to the peculiarities of perennial tropical crop systems such as oil palm more accurately.

  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. Challenges in Modeling the Fate of Nitrogen Applied to Forests

    NASA Astrophysics Data System (ADS)

    Amatya, Devendra; Trettin, C.; Vance, Eric; Nettles, Jami; Skaggs, Wayne

    2008-06-01

    Development of a Comprehensive Forest Nutrient Cycle and Export Modeling Package; Cordesville, South Carolina, 6-7 March 2008; Nitrogen (N) fertilizer is commonly applied to increase productivity of forest plantations, and the extent and intensity of forest fertilizer use could increase in the future as a way of enhancing forest productivity to meet demands for both traditional products and emerging markets for energy and biomaterials. While much of the applied N remains in the soil-plant system, there are concerns about leaching losses and effects on surface water quality. However, understanding the fate of fertilizer N and its potential environmental impacts is particularly complex due to a wide range of abiotic and biotic factors affecting its forms and movement.

  7. Can knowledge-based N management produce more staple grain with lower greenhouse gas emission and reactive nitrogen pollution? A meta-analysis.

    PubMed

    Xia, Longlong; Lam, Shu Kee; Chen, Deli; Wang, Jinyang; Tang, Quan; Yan, Xiaoyuan

    2017-05-01

    Knowledge-based nitrogen (N) management, which is designed for a better synchronization of crop N demand with N supply, is critical for global food security and environmental sustainability. Yet, a comprehensive assessment on how these N management practices affect food production, greenhouse gas emission (GHG), and N pollution in China is lacking. We compiled the results of 376 studies (1166 observations) to evaluate the overall effects of seven knowledge-based N management practices on crop productivity, nitrous oxide (N2 O) emission, and major reactive N (Nr) losses (ammonia, NH3 ; N leaching and runoff), for staple grain (rice, wheat, and corn) production in China. These practices included the application of controlled-release N fertilizer, nitrification inhibitor (NI) and urease inhibitor (UI), higher splitting frequency of fertilizer N application, lower basal N fertilizer (BF) proportion, deep placement of N fertilizer, and optimal N rate based on soil N test. Our results showed that, compared to traditional N management, these knowledge-based N practices significantly increased grain yields by 1.3-10.0%, which is attributed to the higher aboveground N uptake (5.1-12.1%) and N use efficiency in grain (8.0-48.2%). Moreover, these N management practices overall reduced GHG emission and Nr losses, by 5.4-39.8% for N2 O emission, 30.7-61.5% for NH3 emission (except for the NI application), 13.6-37.3% for N leaching, and 15.5-45.0% for N runoff. The use of NI increased NH3 emission by 27.5% (9.0-56.0%), which deserves extra-attention. The cost and benefit analysis indicated that the yield profit of these N management practices exceeded the corresponding input cost, which resulted in a significant increase of the net economic benefit by 2.9-12.6%. These results suggest that knowledge-based N management practice can be considered an effective way to ensure food security and improve environmental sustainability, while increasing economic return. © 2016 John Wiley

  8. Effect of rice bran as a replacement for oat grain in energy and nitrogen balance, methane emissions, and milk performance of Murciano-Granadina goats.

    PubMed

    Criscioni, P; Fernández, C

    2016-01-01

    The objective of this experiment was to study the effects of substituting oat grain with rice bran on energy, nitrogen and carbon balance, methane emissions, and milk performance in dairy goats. Ten Murciano-Granadina dairy goats in late lactation (46.1 ± 3.07 kg) were assigned to 2 treatments in a crossover design, where each goat received both treatments in 2 periods. One group of 5 goats was fed a mixed ration with 379 g of oat grain/kg of dry matter (O diet) and the other group of 5 goats was fed a diet that replaced oat grain with 379 g/kg dry matter of rice bran (RB diet). Diets were formulated to be isoenergetic and isoproteic, so bypass fat was added to reach the same amount of energy in both diets. The goats were allocated to individual metabolism cages. After 14 d of adaptation, feed intake, total fecal and urine outputs, and milk yield were recorded daily over a 5-d period. Then, gas exchange measurements were recorded individually by a mobile open-circuit indirect calorimetry system using a head box. Dry matter intake was different for both diets [1.83 ± 0.11 vs. 1.61 ± 0.08 (means ± SD), for O and RB, respectively]. Metabolizable energy intake and heat production were not significantly different between diets, with average values of 1,254 [standard error of the mean (SEM) = 110.0] and 640 (SEM = 21.0) kJ/kg of BW(0.75), respectively. Significant differences were found in milk fat content (5.3 and 6.9%, SEM = 0.36; for O and RB, respectively) and milk fatty acids: medium-chain fatty acids (17.17 vs. 12.90 g/100g, SEM = 0.969; for O and RB, respectively) and monounsaturated fatty acids (20.63 vs. 28.29 g/100g, SEM = 1.973; for O and RB, respectively). Enteric CH4 emission was lower for the RB diet (23.2 vs. 30.1g/d, SEM = 2.14; for O and RB, respectively), probably because of the higher lipid content in RB diets than O diets (11.7 vs. 4.1%, respectively). Lactating goats utilized RB without detrimental effects on energy metabolism. Higher milk fat

  9. 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

  10. 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.

  11. Modelling grain alignment by radiative torques and hydrogen formation torques in reflection nebula

    NASA Astrophysics Data System (ADS)

    Hoang, Thiem; Lazarian, A.; Andersson, B.-G.

    2015-04-01

    Reflection nebulae - dense cores - illuminated by surrounding stars offer a unique opportunity to directly test our quantitative model of grain alignment based on radiative torques (RATs) and to explore new effects arising from additional torques. In this paper, we first perform detailed modelling of grain alignment by RATs for the IC 63 reflection nebula illuminated both by a nearby γ Cas star and the diffuse interstellar radiation field. We calculate linear polarization pλ of background stars by radiatively aligned grains and explore the variation of fractional polarization (pλ/AV) with visual extinction AV across the cloud. Our results show that the variation of pV/AV versus AV from the dayside of IC 63 to its centre can be represented by a power law (p_V/A_V∝ A_V^{η }) with different slopes depending on AV. We find a shallow slope η ˜ -0.1 for AV < 3 and a very steep slope η ˜ -2 for AV > 4. We then consider the effects of additional torques due to H2 formation and model grain alignment by joint action of RATs and H2 torques. We find that pV/AV tends to increase with an increasing magnitude of H2 torques. In particular, the theoretical predictions obtained for pV/AV and peak wavelength λmax in this case show an improved agreement with the observational data. Our results reinforce the predictive power of the RAT alignment mechanism in a broad range of environmental conditions and show the effect of pinwheel torques in environments with efficient H2 formation. Physical parameters involved in H2 formation may be constrained using detailed modelling of grain alignment combined with observational data. In addition, we discuss implications of our modelling for interpreting latest observational data by Planck and other ground-based instruments.

  12. Thermodynamics of atomistic and coarse-grained models of water on nonpolar surfaces

    NASA Astrophysics Data System (ADS)

    Ardham, Vikram Reddy; Leroy, Frédéric

    2017-08-01

    In order to study the phenomena where interfaces play a dominant role through molecular simulations, the proper representation of the interfacial thermodynamic properties of a given model is of crucial importance. The use of coarse-grained rather than atomistic models makes it possible to simulate interfacial systems with larger time and length scales. In the present work, we compare the structure and thermodynamic behavior of one atomistic and two single-site coarse-grained models of water on nonpolar surfaces, namely, graphite and the basal plane of molybdenum disulfide. The three models interact with the surfaces through Lennard-Jones potentials parametrized to reproduce recent experimental contact angle measurements. The models form a layered structure close to the surface, which is usually observed on sufficiently attractive nonpolar substrates. However, differences in the structure and thermodynamic behavior are observed between the models. These differences are explained by certain features of the water models, such as short range tetrahedral order and liquid density fluctuations. Besides these results, the approach employed in the present study may be used to assess the ability of coarse-grained models for solid-liquid systems to represent consistent interfacial thermodynamics.

  13. 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.

  14. Hydrate Formation in Gas-Rich Marine Sediments: A Grain-Scale Model

    NASA Astrophysics Data System (ADS)

    Holtzman, R.; Juanes, R.

    2009-12-01

    We present a grain-scale model of marine sediment, which couples solid- and multiphase fluid-mechanics together with hydrate kinetics. The model is applied to investigate the spatial distribution of the different methane phases - gas and hydrate - within the hydrate stability zone. Sediment samples are generated from three-dimensional packs of spherical grains, mapping the void space into a pore network by tessellation. Gas invasion into the water-saturated sample is simulated by invasion-percolation, coupled with a discrete element method that resolves the grain mechanics. The coupled model accounts for forces exerted by the fluids, including cohesion associated with gas-brine surface tension. Hydrate growth is represented by a hydrate film along the gas-brine interface, which increases sediment cohesion by cementing the grain contacts. Our model of hydrate growth includes the possible rupture of the hydrate layer, which leads to the creation of new gas-water interface. In previous work, we have shown that fine-grained sediments (FGS) exhibit greater tendency to fracture, whereas capillary invasion is the preferred mode of methane gas transport in coarse-grained sediments (CGS). The gas invasion pattern has profound consequences on the hydrate distribution: a larger area-to-volume ratio of the gas cluster leads to a larger drop in gas pressure inside the growing hydrate shell, causing it to rupture. Repeated cycles of imbibition and hydrate growth accompanied by trapping of gas allow us to determine the distribution of hydrate and gas within the sediment as a function of time. Our pore-scale model suggests that, even when film rupture takes place, the conversion of gas to hydrate is slow. This explains two common field observations: the coexistence of gas and hydrate within the hydrate stability zone in CGS, and the high methane fluxes through fracture conduits in FGS. These results demonstrate the importance of accounting for the strong coupling among multiphase

  15. 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

  16. 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

  17. Toward multiscale modeling of the chromatin fiber: a coarse grain model for DNA

    NASA Astrophysics Data System (ADS)

    Savelyev, Alexey; Papoian, Garegin

    2008-03-01

    In eukaryotic cells DNA is compacted a million-fold into a chromatin. Understanding the mechanism of chromatin folding is of great biological importance. All-atom Molecular Dynamics (MD) simulations could provide crucial insights into the electrostatic and structural mechanisms of chromatin folding. However, because of the enormous size of even short chromatin fiber segment and long folding time-scales, atomistic simulations are computationally impractical. Our long-term aim is to build an accurate coarse-grain (CG) model of the chromatin, derived systematically from all-atom simulations of its smaller parts. Here we report the development of the CG model for a linear DNA chain, playing the role of a linker DNA segment in the chromatin. We derived CG inter-DNA electrostatic potential from atomistic simulations with explicit solvent and mobile ions, instead of relying on the standard models of continuum electrostatics, which are inadequate at small intermolecular distances. In addition, we used the ideas of renormalization group theory to construct an optimization scheme for parameterizing the CG force field. This novel approach is designed to accurately reproduce correlations among various CG degrees of freedom. The implementation of these correlations was left as an open question in the prior studies of CG polymer models.

  18. An investigation of nanoscale grain boundary electrical activity and electrical properties in a model electroceramic: Niobium-doped strontium titanate

    NASA Astrophysics Data System (ADS)

    Johnson, Kevin David

    2000-12-01

    This thesis presents an integrated approach towards understanding grain boundary electrical properties in electroceramics by examining the effects of doping and annealing conditions on macroscopic electrical measurements, nanoscale potentials, and defect distributions at grain boundaries. The varistor behavior of a model electroceramic system, bicrystals of Nb bulk doped SrTiO 3, has been investigated as a basis for correlating grain boundary properties through a simplified microstructure. Although these bicrystals only have a single grain boundary, AC and DC electrical measurements have revealed a four order of magnitude increase in resistance for the isolated grain boundary. Characteristic of varistor behavior, this grain boundary resistance was demonstrated to rapidly decline above a switch-on voltage, indicating nonlinear grain boundary barrier breakdown. For the same bicrystals that showed varistor behavior, the characteristics of the grain boundary barrier were examined as a function of doping and heat treatment. SrTiO3 bicrystals, doped with donors (Nb) and acceptors (Mn), were examined with high resolution transmission electron microscopy techniques to observe changes in the local grain boundary chemistry and structure. Although Nb does not strongly segregate, through a Mn grain boundary doping procedure, highly doped grain boundaries were achieved. In both cases, electron holograms revealed the presence of potentials at these grain boundaries, indicative of the underlying charge density distributions. Another major contribution of this research has been the development of a unique procedure for incorporating in situ applied current with electron holography. This approach has enabled for the first time dynamic changes in grain boundary potentials to be directly observed as a function of applied bias. Although there remain many open-ended questions regarding the electrical activity of grain boundaries in even this simple electroceramic system, the thesis

  19. Nitrogen loads to estuaries from waste water plumes: Modeling and isotopic approaches

    USGS Publications Warehouse

    Kroeger, K.D.; Cole, Marci L.; York, J.K.; Valiela, I.

    2006-01-01

    We developed, and applied in two sites, novel methods to measure ground water-borne nitrogen loads to receiving estuaries from plumes resulting from land disposal of waste water treatment plant (WWTP) effluent. In addition, we quantified nitrogen losses from WWTP effluent during transport through watersheds. WWTP load to receiving water was estimated as the difference between total measured ground water-transported nitrogen load and modeled load from major nitrogen sources other than the WWTP. To test estimated WWTP loads, we applied two additional methods. First, we quantified total annual waste water nitrogen load from watersheds based on nitrogen stable isotopic signatures of primary producers in receiving water. Second, we used published data on ground water nitrogen concentrations in an array of wells to estimate dimensions of the plume and quantify the annual mass of nitrogen transported within the plume. Loss of nitrogen during transport through the watershed was estimated as the difference between the annual mass of nitrogen applied to watersheds as treatment plant effluent and the estimated nitrogen load reaching receiving water. In one plume, we corroborated our estimated nitrogen loss in watersheds using data from multiple-level sampling wells to calculate the loss of nitrogen relative to a conservative tracer. The results suggest that nitrogen from the plumes is discharging to the estuaries but that substantial nitrogen loss occurs during transport through the watersheds. The measured vs. modeled and stable isotopic approaches, in comparison to the plume mapping approach, may more reliably quantify ground water-transported WWTP loads to estuaries. Copyright ?? 2005 National Ground Water Association.

  20. 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

  1. The Use of a Principal Axis Model to Examine Individual Plant Harvest Index in Four Grain Legumes

    PubMed Central

    AYAZ, S.; MOOT, D. J.; MCKENZIE, B. A.; HILL, G. D.; MCNEIL, D. L.

    2004-01-01

    • Background and Aims A principal axis model (PAM) has been proposed to enable the selection of crop ideotypes. The PAM enables plant-to-plant variability within crops to be quantified and compared. The aim of this paper is to validate the PAM for four grain legumes. • Methods Four grain legumes (Cicer arietinum, Lens culinaris, Lupinus angustifolius, Pisum sativum) were used to quantify the influence of plant-to-plant variability on crop yields. To create variability, populations of 10, 100 and 400 plants m−2 were established ‘on-the-square’ with sowing depths of 2, 5 and 10 cm. Further, a central plant was treated with nitrogen and the impact of this on its four neighbouring plants was examined. Seeds were sown and plants harvested individually by hand. • Key Results Mean individual plant seed weight (SWT) and plant weight (PWT) decreased as plant population increased but there was a consistent and strong (R2 > 0·90) linear relationship between SWT and PWT, with a negative SWT-axis intercept in all species. These components form the basis of the principal axis model (PAM). The PAM was used to summarize the performance of individual plants within a crop and quantify the variability caused by N treatment and the lowest and highest yielding individual plants. A negative SWT-axis intercept indicated that a minimum plant weight (MPW) was required for seed production and therefore the relationship between plant harvest index (PHI) and PWT was asymptotic. The heaviest MPW was calculated for plants grown at the lowest plant population and it was species-dependent, being higher in the larger seeded species. • Conclusions Agronomic or physiological characteristics that lead to variability in PWT within a population will decrease PHI, and crop yield. The PAM may be useful in breeding programmes to identify plant phenotypes that minimize this plant-to-plant variability. PMID:15292041

  2. 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

  3. 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.

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

    PubMed Central

    Wei, Zonghui

    2015-01-01

    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. PMID:26723631

  5. 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.

  6. Diblock copolymer bilayers as model for polymersomes: A coarse grain approach.

    PubMed

    Grillo, Damián A; Albano, Juan M R; Mocskos, Esteban E; Facelli, Julio C; Pickholz, Mónica; Ferraro, Marta B

    2017-06-28

    This paper presents a new model for polymersomes developed using a poly(ethylene oxide)-poly(butadiene) diblock copolymer bilayer. The model is based on a coarse-grained approach using the MARTINI force field. Since no MARTINI parameters exist for poly(butadiene), we have refined these parameters using quantum mechanical calculations and molecular dynamics simulations. The model has been validated using extensive molecular dynamics simulations in systems with several hundred polymer units and reaching up to 6 μs. These simulations show that the copolymer coarse grain model self-assemble into bilayers and that NPT and NPNγT ensemble runs reproduce key structural and mechanical experimental properties for different copolymer length chains with a similar hydrophilic weight fraction.

  7. 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.

  8. Diblock copolymer bilayers as model for polymersomes: A coarse grain approach

    NASA Astrophysics Data System (ADS)

    Grillo, Damián A.; Albano, Juan M. R.; Mocskos, Esteban E.; Facelli, Julio C.; Pickholz, Mónica; Ferraro, Marta B.

    2017-06-01

    This paper presents a new model for polymersomes developed using a poly(ethylene oxide)-poly(butadiene) diblock copolymer bilayer. The model is based on a coarse-grained approach using the MARTINI force field. Since no MARTINI parameters exist for poly(butadiene), we have refined these parameters using quantum mechanical calculations and molecular dynamics simulations. The model has been validated using extensive molecular dynamics simulations in systems with several hundred polymer units and reaching up to 6 μ s. These simulations show that the copolymer coarse grain model self-assemble into bilayers and that NPT and NPNγT ensemble runs reproduce key structural and mechanical experimental properties for different copolymer length chains with a similar hydrophilic weight fraction.

  9. 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.

  10. A coarse-grained DNA model for the prediction of current signals in DNA translocation experiments

    NASA Astrophysics Data System (ADS)

    Weik, Florian; Kesselheim, Stefan; Holm, Christian

    2016-11-01

    We present an implicit solvent coarse-grained double-stranded DNA (dsDNA) model confined to an infinite cylindrical pore that reproduces the experimentally observed current modulations of a KaCl solution at various concentrations. Our model extends previous coarse-grained and mean-field approaches by incorporating a position dependent friction term on the ions, which Kesselheim et al. [Phys. Rev. Lett. 112, 018101 (2014)] identified as an essential ingredient to correctly reproduce the experimental data of Smeets et al. [Nano Lett. 6, 89 (2006)]. Our approach reduces the computational effort by orders of magnitude compared with all-atom simulations and serves as a promising starting point for modeling the entire translocation process of dsDNA. We achieve a consistent description of the system's electrokinetics by using explicitly parameterized ions, a friction term between the DNA beads and the ions, and a lattice-Boltzmann model for the solvent.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. A coupled modeling approach to evaluate nitrogen retention within the Shanmei Reservoir watershed, China

    NASA Astrophysics Data System (ADS)

    Liu, Meibing; Chen, Xingwei; Yao, Huaxia; Chen, Ying

    2015-12-01

    To simulate impacts of nitrogen retention in the reservoir on nitrogen nutrient transported from the upland watershed to the ocean, a coupled watershed-reservoir modeling system, consisting of a watershed distributed model (SWAT) and a two-dimensional water quality model (CE-QUAL-W2), was developed. The coupled modeling system was well calibrated, and simulated values mainly agreed with observed data, demonstrating that the SWAT and CE-QUAL-W2 coupled modeling system can be used to assess hydrodynamic and water quality processes in a complex watershed comprised of an upland watershed and a downstream reservoir. Applying the coupled model, a long time simulation was conducted to analyze the temporal characteristics of nitrogen exported from the watershed and to reveal the effect of nitrogen retention in the reservoir at annual, monthly and daily scales. The results showed that nitrogen export from the watershed is closely associated with precipitation and runoff. The wet season was the critical period of nitrogen loss, whereas the dry season is the critical period for water quality management. The reservoir serves mainly as a nitrogen sink at annual scale due to the effect of nitrogen retention, but within the year, it may act as a sink during the wet season and a source during the dry season, which is significantly influenced by inflow runoff, nitrogen load and reservoir regulation.

  16. 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

  17. 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.

  18. Modeling nitrogen plasmas produced by intense electron beams

    SciTech Connect

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

    2016-05-15

    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/cm{sup 2} 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.

  19. 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.

  20. 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.

  1. 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.

  2. One-dimensional model of the equiaxed grain formation in multi-crystalline silicon

    NASA Astrophysics Data System (ADS)

    Beaudhuin, M.; Duffar, T.; Lemiti, M.; Zaidat, K.

    2011-03-01

    During solidification of low purity silicon for photovoltaic (PV) cells, solute rejection at the growth interface leads to an increase of the carbon concentration in the liquid phase and then to the precipitation of silicon carbide (SiC). When the precipitate radius becomes higher than the silicon critical nucleus radius, SiC can act as a refining agent for the Si and Si equiaxed grains appear in the liquid. The grain structure of the ingot changes from columnar to small grains, also known as grits. We developed a one-dimensional analytical model of this series of phenomena, including C segregation, SiC nucleation and growth, Si nucleation on the SiC precipitates and subsequent growth of the Si equiaxed grains. The equations are implemented under Matlab software in order to predict the columnar to equiaxed transition (CET) during the directional solidification of PV Si. We carried out calculations of the position and thickness of the equiaxed areas and of the number and size of Si grits as a function of the main process parameters: thermal gradient and growth velocity. Recommendations in order to adapt the growth process parameters to the initial carbon content are given. It is expected that coupling this model to global 3D numerical simulation codes could help improving the yield of ingot solidification.

  3. 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.

  4. Adsorption of metal atoms at a buckled graphene grain boundary using model potentials

    SciTech Connect

    Helgee, Edit E.; Isacsson, Andreas

    2016-01-15

    Two model potentials have been evaluated with regard to their ability to model adsorption of single metal atoms on a buckled graphene grain boundary. One of the potentials is a Lennard-Jones potential parametrized for gold and carbon, while the other is a bond-order potential parametrized for the interaction between carbon and platinum. Metals are expected to adsorb more strongly to grain boundaries than to pristine graphene due to their enhanced adsorption at point defects resembling those that constitute the grain boundary. Of the two potentials considered here, only the bond-order potential reproduces this behavior and predicts the energy of the adsorbate to be about 0.8 eV lower at the grain boundary than on pristine graphene. The Lennard-Jones potential predicts no significant difference in energy between adsorbates at the boundary and on pristine graphene. These results indicate that the Lennard-Jones potential is not suitable for studies of metal adsorption on defects in graphene, and that bond-order potentials are preferable.

  5. Grain Size Effect of Commercial Pure Titanium Foils on Mechanical Properties, Fracture Behaviors and Constitutive Models

    NASA Astrophysics Data System (ADS)

    Daming, Nie; Zhen, Lu; Kaifeng, Zhang

    2017-02-01

    The constitutive models based on grain size effect are crucial for analyzing the deformation of metal foils. Previous investigations on the constitutive models concentrate on the foils whose thickness/average grain diameter (T/D) ratios are more than 3. In this study, the commercial pure titanium foils with thickness of 0.1 and 0.2 mm were employed as the experimental materials. The mechanical properties of foils with dimensions of nine different T/D ratios categorized into three ranges (T/D < 1, 1 ≤ T/D < 3, T/D ≥ 3)were tested. Meanwhile, the fracture behaviors and fracture mechanisms of the samples with different T/D ratios were compared and analyzed. Besides, three constitutive models incorporating the surface layer effect and grain boundary strengthening effect were established for the three T/D ratio ranges correspondingly. In these models, the thickness of the surface layers is set T for T/D < 1 foils, D for T/D > 3, and increases with D linearly in 1 ≤ T/D < 3. The results calculated by the three models were compared. The experiments indicate that those models are all in good agreement.

  6. 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

    2016-06-17

    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.

  7. 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

  8. 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.

  9. 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.

  10. Improving representation of nitrogen uptake, allocation, and carbon assimilation in the Community Land Model

    NASA Astrophysics Data System (ADS)

    Ghimire, B.; Riley, W. J.; Koven, C.

    2013-12-01

    Nitrogen is the most important nutrient limiting plant carbon assimilation and growth, and is required for production of photosynthetic enzymes, growth and maintenance respiration, and maintaining cell structure. The forecasted rise in plant available nitrogen through atmospheric nitrogen deposition and the release of locked soil nitrogen by permafrost thaw in high latitude ecosystems is likely to result in an increase in plant productivity. However a mechanistic representation of plant nitrogen dynamics is lacking in earth system models. Most earth system models ignore the dynamic nature of plant nutrient uptake and allocation, and further lack tight coupling of below- and above-ground processes. In these models, the increase in nitrogen uptake does not translate to a corresponding increase in photosynthesis parameters, such as maximum Rubisco capacity and electron transfer rate. We present an improved modeling framework implemented in the Community Land Model version 4.5 (CLM4.5) for dynamic plant nutrient uptake, and allocation to different plant parts, including leaf enzymes. This modeling framework relies on imposing a more realistic flexible carbon to nitrogen stoichiometric ratio for different plant parts. The model mechanistically responds to plant nitrogen uptake and leaf allocation though changes in photosynthesis parameters. We produce global simulations, and examine the impacts of the improved nitrogen cycling. The improved model is evaluated against multiple observations including TRY database of global plant traits, nitrogen fertilization observations and 15N tracer studies. Global simulations with this new version of CLM4.5 showed better agreement with the observations than the default CLM4.5-CN model, and captured the underlying mechanisms associated with plant nitrogen cycle.

  11. 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.

  12. The kinetics of heterogeneous nucleation and growth: an approach based on a grain explicit model

    NASA Astrophysics Data System (ADS)

    Rouet-Leduc, B.; Maillet, J.-B.; Denoual, C.

    2014-04-01

    A model for phase transitions initiated on grain boundaries is proposed and tested against numerical simulations: this approach, based on a grain explicit model, allows us to consider the granular structure, resulting in accurate predictions for a wide span of nucleation processes. Comparisons are made with classical models of homogeneous (JMAK: Johnson and Mehl 1939 Trans. Am. Inst. Min. Eng. 135 416; Avrami 1939 J. Chem. Phys. 7 1103; Kolmogorov 1937 Bull. Acad. Sci. USSR, Mat. Ser. 1 335) as well as heterogeneous (Cahn 1996 Thermodynamics and Kinetics of Phase Transformations Im et al (Pittsburgh: Materials Research Society)) nucleation. A transition scale based on material properties is proposed, allowing us to discriminate between random and site-saturated regimes. Finally, we discuss the relationship between an Avrami-type exponent and the transition regime, establishing conditions for its extraction from experiments.

  13. A coarse-grain three-site-per-nucleotide model for DNA with explicit ions

    NASA Astrophysics Data System (ADS)

    Freeman, Gordon S.; Hinckley, Daniel M.; de Pablo, Juan J.

    2011-10-01

    The "three sites per nucleotide" (3SPN) model provides a coarse-grained representation of nucleic acids for simulation of molecular processes. Previously, this model has relied on an implicit representation of the surrounding ionic environment at the level of Debye-Hückel theory. In this work, we eliminate this limitation and present an explicit representation of ions, both monovalent and divalent. The coarse-grain ion-ion and ion-phosphate potential energy functions are inferred from all-atom simulations and parameterized to reproduce key features of the local structure and organization of ions in bulk water and in the presence of DNA. The resulting model, 3SPN.1-I, is capable of reproducing the local structure observed in detailed atomistic simulations, as well as the experimental melting temperature of DNA for a range of DNA oligonucleotide lengths, CG-content, Na+ concentration, and Mg2 + concentration.

  14. Folding and stability of helical bundle proteins from coarse-grained models.

    PubMed

    Kapoor, Abhijeet; Travesset, Alex

    2013-07-01

    We develop a coarse-grained model where solvent is considered implicitly, electrostatics are included as short-range interactions, and side-chains are coarse-grained to a single bead. The model depends on three main parameters: hydrophobic, electrostatic, and side-chain hydrogen bond strength. The parameters are determined by considering three level of approximations and characterizing the folding for three selected proteins (training set). Nine additional proteins (containing up to 126 residues) as well as mutated versions (test set) are folded with the given parameters. In all folding simulations, the initial state is a random coil configuration. Besides the native state, some proteins fold into an additional state differing in the topology (structure of the helical bundle). We discuss the stability of the native states, and compare the dynamics of our model to all atom molecular dynamics simulations as well as some general properties on the interactions governing folding dynamics. Copyright © 2013 Wiley Periodicals, Inc.

  15. 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