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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

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

    2003-12-01

    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.

  2. 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.

  3. Grain metamorphism in polar nitrogen ice on triton

    SciTech Connect

    Zent, A.P.; McKay, C.P.; Pollack, J.B.; Cruikshank, D.P. )

    1989-08-01

    The authors calculate the rate of nitrogen grain growth on putative N{sub 2}-rich polar caps on Triton. For most plausible assumptions of independent variables, mean grain sizes in polar N{sub 2} 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 many require long path length through condensed N{sub 2}, possibly due to grain growth. Upcoming Voyager data may clarify the situation, although possible complications in detecting a glaze of N{sub 2} ice exist.

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

    PubMed

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

    1993-01-01

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

  5. Influence of nitrogen-induced grain refinement on mechanical properties of nitrogen alloyed type 316LN stainless steel

    NASA Astrophysics Data System (ADS)

    Kim, Dae Whan

    2012-01-01

    Tensile, fatigue, and creep tests were conducted to investigate the effect of grain refinement by the addition of nitrogen on mechanical properties of nitrogen alloyed type 316LN stainless steel. Grain size was reduced from 100 μm to 47 μm as nitrogen concentration was increased from 0.04% (N04) to 0.10% (N10). When nitrogen concentration was increased, there was a 20% increase in yield stress and a 14% increase in UTS, respectively. Elongation was not significantly changed with increasing nitrogen concentration. As nitrogen concentration was increased, there was a 41% increase in fatigue life and an approximately sixfold increase in the time to rupture. As grain size was reduced from 100 μm to 47 μm, there was an 8% increase in yield stress and a 3% increase in UTS, respectively. Elongation was little changed with decreasing grain size. As grain size was reduced from 100 μm to 47 μm, there was a 9% increase in fatigue life and a 23% increase in the time to rupture. The grain refinement achieved by the addition of nitrogen improved the high temperature mechanical properties of nitrogen alloyed type 316LN stainless steel but was not the main mechanism for improvement of mechanical properties.

  6. Microbial numbers, rumen fermentation, and nitrogen utilization of steers fed wet or dried brewers' grains.

    PubMed

    Rogers, J A; Conrad, H R; Dehority, B A; Grubb, J A

    1986-03-01

    Holstein steers were fed corn silage supplemented with either wet or dried brewers' grains to determine effects of heat drying commercial brewers' grains. Four rumen-fistulated steers were fed a 12.5% crude protein diet in a single reversal design experiment. Brewers' grains supplied 45% of the protein of the diet. Bacterial numbers, concentration of ciliated protozoa, and ammonia concentration in the rumen were higher, and rumen pH was lower, for steers fed wet brewers' grains. Concentrations of rumen volatile fatty acids were similar for both diets. Ruminal digestibility of dry matter decreased when wet versus dried brewers' grains were fed (56.9 versus 39.3%). The rate of dry matter passage from the rumen was faster with wet brewers' grains. In Experiment 2, 12 steers were in a 2 X 2 factorial design. Diets contained wet or dried brewers' grains supplemented at 22 or 40% of the diet dry matter (12.5 and 14.5% crude protein). Nitrogen retention was increased in steers fed the higher crude protein diet. Apparent digestible nitrogen, acid detergent fiber nitrogen, and nitrogen retention were higher with wet versus dried brewers' grains. Plasma essential and nonessential amino acids were also higher in steers fed wet brewers' grains. Alteration in microbial numbers, fermentation measurements, and nitrogen utilization were associated with more soluble nitrogen with wet (13.4%) versus dried (3.3%) brewers' grains.

  7. 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.

  8. 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 ...

  9. 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

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

    NASA Astrophysics Data System (ADS)

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

    2012-02-01

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

  11. 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…

  12. 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.

  13. Genotypic variation in the uptake, partitioning and remobilisation of nitrogen during grain-filling in wheat☆

    PubMed Central

    Barraclough, Peter B.; Lopez-Bellido, Rafael; Hawkesford, Malcolm J.

    2014-01-01

    Twenty elite varieties of wheat (Triticum aestivum L.), primarily winter wheat, were grown with low and high supplies of nitrogen (N) in a field experiment at Rothamsted, southern England, in the season 2004–05. The aim was to quantify genetic variation in the uptake, partitioning and remobilisation of N in individual plant organs at extreme rates of N supply. The biggest contibutor to variation in plant and crop performance was ‘N-rate’ followed by ‘growth stage’ and then ‘genotype’. At both N-rates, there was significant genetic variation in crop performance (grain yield, grain %N, total N-uptake and post-anthesis N-uptake), and in N contents of individual organs at anthesis and maturity, and in N remobilised from individual vegetative organs to the grain during grain-fill. Nitrogen was remobilised from all vegetative organs with very high levels of efficiency by all varieties (80–85%). Stem-N was a major N pool at anthesis probably due to the amounts of soluble N compounds in transit in the vascular system at this time. Despite the genetic variation in N-related plant parameters including stem-N, there were no strong correlations with grain yield and grain %N at a given N-rate. This was probably due to the narrow gene pool employed in this single-season study. PMID:26412936

  14. 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.

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

    PubMed

    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 (>R (2) 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

  16. 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.

  17. 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

  18. 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.

  19. Coarse-Grain Modeling of Energetic Materials

    NASA Astrophysics Data System (ADS)

    Brennan, John

    2015-06-01

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

  20. Effect of nitrogen fertilization and cover cropping systems on sorghum grain characteristics.

    PubMed

    Kaufman, R C; Wilson, J D; Bean, S R; Presley, D R; Blanco-Canqui, H; Mikha, M

    2013-06-19

    Cover crop treatments and nitrogen (N) fertilization rates were investigated for their impact on sorghum grain quality attributes. Sorghum was planted in field plots treated with differing cover cropping systems and fertilization rates. The size (weight and diameter) and hardness of the kernels were influenced by both the cover crop and N rates. The protein content increased as the N rate increased and also with the addition of cover crops to the system. The protein digestibility values and starch granule size distributions were not affected by N rate or the cover cropping treatments. Soil properties were tested to determine relationships with grain quality attributes. The utilization of cover crops appears to increase the protein content without causing a deleterious effect on protein digestibility. The end-product quality is not hampered by the use of beneficial cropping systems necessary for sustainable agriculture.

  1. 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

  2. [Effects of different irrigation modes on winter wheat grain yield and water- and nitrogen use efficiency].

    PubMed

    Men, Hong-wen; Zhang, Qiu; Dai, Xing-long; Cao, Qian; Wang, Cheng-yu; Zhou, Xiao-hu; He, Ming-rong

    2011-10-01

    Taking the widely planted winter wheat cultivar Tainong 18 as test material, a field experiment was conducted to study the effects of different irrigation modes on the winter wheat grain yield and water- and nitrogen use efficiency in drier year (2009-2010) in Tai' an City of Shandong Province, China. Five treatments were installed, i. e., irrigation before sowing (CK), irrigation before sowing and at jointing stage (W1), irrigation before sowing and at jointing stages and at over-wintering stage with alternative irrigation at milking stage (W2), irrigation before sowing and at jointing and flowering stages (optimized traditional irrigation mode, W3), and irrigation before sowing and at over-wintering, jointing, and milking stages (traditional irrigation mode, W4). The irrigation amount was 600 m3 hm(-2) one time. Under the condition of 119.7 mm precipitation in the winter wheat growth season, no significant difference was observed in the grain yield between treatments W2 and W4, but the water use efficiency was significantly higher in W2 than in W4. Comparing with treatment W3, treatments W2 and W4 had obviously higher grain yield, but the water use efficiency had no significant difference. The partial factor productivity from N fertilization was the highest in W2 and W4, and the NO3(-)-N accumulation amount in 0-100 cm soil layer at harvest was significantly higher in W2 than in W3 and W4, suggesting that W2 could reduce NO3(-)-N leaching loss. Under the conditions of our experiment, irrigation before sowing and jointing stages and at over-wintering stage with alternative irrigation at milking stage was the optimal irrigation mode in considering both the grain yield and the water- and nitrogen use efficiency.

  3. Coarse-grained modeling of DNA curvature

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. 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

  10. 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...

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. 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

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

    PubMed

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  20. 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

  1. 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

  2. [Effects of atmospheric CO2 concentration enhancement and nitrogen application rate on wheat grain yield and quality].

    PubMed

    Cui, Hao; Shi, Zu-liang; Cai, Jian; Jiang, Dong; Cao, Wei-xing; Dai, Ting-bo

    2011-04-01

    FACE platform was applied to study the effects of elevated atmospheric CO2 concentration on wheat grain yield and quality under two nitrogen (N) application rates. Elevated atmospheric CO2 concentration and applying N increased the grain yield, spike number, grain number per spike, and biomass significantly, but elevated CO2 concentration had no significant effects on harvest index (HI). Under elevated CO2 concentration, there was a significant decrease in the protein, gliadin, gluteinin, and glutein contents of the grain and the sedimentation value of the flour, and a significant increase in the starch and its components contents of the grain; under N application, an inverse was observed. The dough stability time and the dough viscosity characteristics, such as peak viscosity, final viscosity, and setback value, increased significantly under elevated CO2 concentration and high N application rate. The interaction of atmospheric CO2 concentration and N application rate had significantly positive effects on wheat grain yield and biomass, but less effect on grain quality. Therefore, with elevated atmospheric CO2 concentration in the future, maintaining a higher N application level would benefit wheat grain yield and paste characteristics, and mitigate the decline of grain quality.

  3. 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.

  4. 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.

  5. 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

  6. 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.

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

    PubMed

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

    2009-01-01

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

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

    PubMed

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

    2016-01-01

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

  9. 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

  10. Lattice Boltzmann models for the grain growth in polycrystalline systems

    NASA Astrophysics Data System (ADS)

    Zheng, Yonggang; Chen, Cen; Ye, Hongfei; Zhang, Hongwu

    2016-08-01

    In the present work, lattice Boltzmann models are proposed for the computer simulation of normal grain growth in two-dimensional systems with/without immobile dispersed second-phase particles and involving the temperature gradient effect. These models are demonstrated theoretically to be equivalent to the phase field models based on the multiscale expansion. Simulation results of several representative examples show that the proposed models can effectively and accurately simulate the grain growth in various single- and two-phase systems. It is found that the grain growth in single-phase polycrystalline materials follows the power-law kinetics and the immobile second-phase particles can inhibit the grain growth in two-phase systems. It is further demonstrated that the grain growth can be tuned by the second-phase particles and the introduction of temperature gradient is also an effective way for the fabrication of polycrystalline materials with grained gradient microstructures. The proposed models are useful for the numerical design of the microstructure of materials and provide effective tools to guide the experiments. Moreover, these models can be easily extended to simulate two- and three-dimensional grain growth with considering the mobile second-phase particles, transient heat transfer, melt convection, etc.

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

    PubMed

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

    2015-09-01

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

  12. [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.

  13. 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.

  14. 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

  15. A Phase-Field Model for Grain Growth

    SciTech Connect

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

    1998-12-23

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

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

    NASA Astrophysics Data System (ADS)

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

    2007-12-01

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

  17. Defect redistribution within a continuum grain boundary plasticity model

    NASA Astrophysics Data System (ADS)

    van Beers, P. R. M.; Kouznetsova, V. G.; Geers, M. G. D.

    2015-10-01

    The mechanical response of polycrystalline metals is significantly affected by the behaviour of grain boundaries, in particular when these interfaces constitute a relatively large fraction of the material volume. One of the current challenges in the modelling of grain boundaries at a continuum (polycrystalline) scale is the incorporation of the many different interaction mechanisms between dislocations and grain boundaries, as identified from fine-scale experiments and simulations. In this paper, the objective is to develop a model that accounts for the redistribution of the defects along the grain boundary in the context of gradient crystal plasticity. The proposed model incorporates the nonlocal relaxation of the grain boundary net defect density. A numerical study on a bicrystal specimen in simple shear is carried out, showing that the spreading of the defect content has a clear influence on the macroscopic response, as well as on the microscopic fields. This work provides a basis that enables a more thorough analysis of the plasticity of polycrystalline metals at the continuum level, where the plasticity at grain boundaries matters.

  18. 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.

  19. Overexpression of a NAC transcription factor delays leaf senescence and increases grain nitrogen concentration in wheat.

    PubMed

    Zhao, D; Derkx, A P; Liu, D-C; Buchner, P; Hawkesford, M J

    2015-07-01

    Increasing the duration of leaf photosynthesis during grain filling using slow-senescing functional stay-green phenotypes is a possible route for increasing grain yields in wheat (Triticum aestivum L.). However, delayed senescence may negatively affect nutrient remobilisation and hence reduce grain protein concentrations and grain quality. A novel NAC1-type transcription factor (hereafter TaNAC-S) was identified in wheat, with gene expression located primarily in leaf/sheath tissues, which decreased during post-anthesis leaf senescence. Expression of TaNAC-S in the second leaf correlated with delayed senescence in two doubled-haploid lines of an Avalon × Cadenza population (lines 112 and 181), which were distinct for leaf senescence. Transgenic wheat plants overexpressing TaNAC-S resulted in delayed leaf senescence (stay-green phenotype). Grain yield, aboveground biomass, harvest index and total grain N content were unaffected, but NAC over-expressing lines had higher grain N concentrations at similar grain yields compared to non-transgenic controls. These results indicate that TaNAC-S is a negative regulator of leaf senescence, and that delayed leaf senescence may lead not only to increased grain yields but also to increased grain protein concentrations.

  20. 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.

  1. 3D reconstruction of grains in polycrystalline materials using a tessellation model with curved grain boundaries

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2006-03-01

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

  3. 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.

  4. 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.

  5. 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.

  6. 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

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

    PubMed

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

    2016-01-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  9. 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.

  10. [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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  12. Soil organic carbon, total nitrogen and grain yields under long-term fertilizations in the upland red soil of Southern China

    NASA Astrophysics Data System (ADS)

    Zhang, W.; Xu, M.; Wang, B.; Wang, X.

    2008-12-01

    A long-term experiment with various fertilizations was carried out during 1990-2006 in a double cropping system rotated with wheat and corn in the red soil of southern China. Applications of manure significantly increased soil organic carbon (SOC) and total nitrogen contents. Applications of inorganic fertilizers without manure showed small influences on SOC, but resulted in declines of soil total nitrogen over the long-term experiment. Grain yields were more than doubled under fertilizations for both wheat and corn. Long-term cropping practices without fertilization or with unbalanced fertilizations (e.g., NP and PK) caused low grain yields. While the balanced NPK fertilization increased grain yields, such practice was not able to maintain high grain yields during the last few years of experiment. Our analyses indicate that both wheat and corn grain yields are significantly correlated with SOC, total and available nitrogen and phosphorus. However, the relationships are stronger with total nitrogen (r = 0.5-0.6) than with available nitrogen (r = 0.26-0.3), indicating the importance of maintaining soil total nitrogen in agricultural practice.

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

    PubMed

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

    2013-09-01

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

  14. 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).

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

    PubMed

    Choi, Eunsong; Mondal, Jagannath; Yethiraj, Arun

    2014-01-01

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

  16. Two-temperature models for nitrogen dissociation

    NASA Astrophysics Data System (ADS)

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

    2007-12-01

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

  17. 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.

  18. 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.

  19. 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

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

    PubMed Central

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

    2011-01-01

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

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

    PubMed

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

    2016-08-25

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

  2. [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.

  3. 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.

  4. 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

  5. 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.

  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. 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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  9. 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

  10. 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

  11. Evolution of 2D Potts Model Grain Microstructures from an Initial Hillert Size Distribution

    SciTech Connect

    Battaile, C.C.; Holm E.A.

    1998-10-19

    Grain growth experiments and simulations exhibit self-similar grain size distributions quite different from that derived via a mean field approach by Hillert [ 1]. To test whether this discrepancy is due to insufficient anneal times, two different two-dimensional grain structures with realistic topologies and Hillert grain size distributions are generated and subjected to grain growth via the Monte Carlo Potts Model (MCPM). In both cases, the observed self-similar grain size distributions deviate from the initial Hillert form and conform instead to that observed in MCPM grain growth simulations that start from a random microstructure. This suggests that the Hillert grain size distribution is not an attractor.

  12. 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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  14. Modeling Nitrogen Species as Pollutants: Thermochemical Influences.

    PubMed

    Bugler, John; Somers, Kieran P; Simmie, John M; Güthe, Felix; Curran, Henry J

    2016-09-15

    To simulate emissions of nitrogen-containing compounds in practical combustion environments, it is necessary to have accurate values for their thermochemical parameters, as well as accurate kinetic values to describe the rates of their formation and decomposition. Significant disparity is observed in the literature for the former, and we therefore present herein high-accuracy ab initio gas-phase thermochemistry for 60 nitrogenous compounds, many of which are important in the formation and consumption chemistry of NOx species. Several quantum-chemical composite methods (CBS-APNO, G3, and G4) were utilized to derive enthalpies of formation via the atomization method. Entropies and heat capacities were calculated from traditional statistical thermodynamics, with oscillators treated as anharmonic based on ro-vibrational property analyses carried out at the B3LYP/cc-pVTZ level of theory. The use of quantum chemical methods, along with the treatments of anharmonicities and hindered rotors, ensures accurate enthalpy of formation, entropy, and heat capacity values across the temperature range 298.15-3000 K. The implications of these results for atmospheric and combustion modeling are discussed. PMID:27547977

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

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

    NASA Astrophysics Data System (ADS)

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

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

  2. 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.

  3. 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

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

    PubMed

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

    2009-11-01

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

  5. [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.

  6. 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

  7. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  9. 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.

  10. 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.

  11. Stress transmission through a model system of cohesionless elastic grains

    NASA Astrophysics Data System (ADS)

    Da Silva, Miguel; Rajchenbach, Jean

    2000-08-01

    Understanding the mechanical properties of granular materials is important for applications in civil and chemical engineering, geophysical sciences and the food industry, as well as for the control or prevention of avalanches and landslides. Unlike continuous media, granular materials lack cohesion, and cannot resist tensile stresses. Current descriptions of the mechanical properties of collections of cohesionless grains have relied either on elasto-plastic models classically used in civil engineering, or on a recent model involving hyperbolic equations. The former models suggest that collections of elastic grains submitted to a compressive load will behave elastically. Here we present the results of an experiment on a two-dimensional model system-made of discrete square cells submitted to a point load-in which the region in which the stress is confined is photoelastically visualized as a parabola. These results, which can be interpreted within a statistical framework, demonstrate that the collective response of the pile contradicts the standard elastic predictions and supports a diffusive description of stress transmission. We expect that these findings will be applicable to problems in soil mechanics, such as the behaviour of cohesionless soils or sand piles.

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

    NASA Astrophysics Data System (ADS)

    Suweis, Samir; Rinaldo, Andrea; Maritan, Amos

    2012-07-01

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

  13. DNA Duplex Formation with a Coarse-Grained Model

    PubMed Central

    2015-01-01

    A middle-resolution coarse-grained model of DNA is proposed. The DNA chain is built of spherical and planar rigid bodies connected by elastic virtual bonds. The bonded part of the potential energy function is fit to potentials of mean force of model systems. The rigid bodies are sets of neutral, charged, and dipolar beads. Electrostatic and van der Waals interactions are parametrized by our recently developed procedure [Maciejczyk, M.; Spasic, A.; Liwo, A.; Scheraga, H.A. J. Comp. Chem.2010, 31, 1644]. Interactions with the solvent and an ionic cloud are approximated by a multipole–multipole Debye–Hückel model. A very efficient R-RATTLE algorithm, for integrating the movement of rigid bodies, is implemented. It is the first coarse-grained model, in which both bonded and nonbonded interactions were parametrized ab initio and which folds stable double helices from separated complementary strands, with the final conformation close to the geometry of experimentally determined structures. PMID:25400520

  14. 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

  15. Recent advances in transferable coarse-grained modeling of proteins.

    PubMed

    Kar, Parimal; Feig, Michael

    2014-01-01

    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 is 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 multiscale hybrid all-atom/CG simulations of proteins.

  16. 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

  17. Models of Polarized Emission from Interstellar Dust Grains

    NASA Astrophysics Data System (ADS)

    Draine, Bruce

    2015-04-01

    Nonspherical aligned dust grains produce strong linearly-polarized thermal emission at submm and microwave frequencies, with polarized fractions exceeding 20% in some parts of the high-latitude sky. Observations of emission, absorption, and scattering by dust, together with our knowledge of the abundances of elements out of which dust grains can be formed, impose many constraints on dust modelers. The dust is in large part composed of amorphous silicates, but with a substantial component of carbonaceous materials, including nanoparticles of polycyclic aromatic hydrocarbons. The smallest particles radiate thermally in the mid-IR following single-photon heating, and also produce rotational emission at microwave frequencies. This rotational emission may account for the so-called Anomalous Microwave Emission. Iron contributes about 25% of the total mass of interstellar dust, but what form the Fe is in is largely unknown; much of the Fe could be in ferromagnetic or ferrimagnetic materials that could emit magnetic dipole radiation at microwave frequencies. I will review the observational constraints on dust models, the current state of our physical models, and prospects for further progress.

  18. 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.

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

    PubMed

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

    2010-06-01

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

  20. 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.

  1. 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.

  2. COARSE-GRAINED MODELING OF PROTEIN UNFOLDING DYNAMICS*

    PubMed Central

    DENG, MINGGE

    2014-01-01

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

  3. 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.

  4. 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

  5. [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.

  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. 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.

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

    PubMed

    Gardner, Jennifer B; Drinkwater, Laurie E

    2009-12-01

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

  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. 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

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

    PubMed Central

    Chakraborty, Promita; Zuckermann, Ronald N.

    2013-01-01

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

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

    PubMed

    Deng, Mingsen; Shen, Hujun

    2016-02-01

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

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

    SciTech Connect

    Zeng, P.; Tikare, V.

    1998-09-01

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

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

    SciTech Connect

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

    2015-03-31

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  16. Predicting the Sensitivity of Multiscale Coarse-Grained Models to their Underlying Fine-Grained Model Parameters.

    PubMed

    Wagner, Jacob W; Dama, James F; Voth, Gregory A

    2015-08-11

    The sensitivity of a coarse-grained (CG) force field to changes in the underlying fine-grained (FG) model from which it was derived provides modeling insight for improving transferability across interaction parameters, transferability across temperature, and the calculation of thermodynamic derivatives. Methods in the literature, such as multi-trajectory finite differences and reweighted finite differences, are either too computationally demanding to calculate within acceptable noise tolerances or are too biased for practical accuracy. This work presents a new reweighting-free, single-simulation formula that allows for practical, high signal-to-noise calculations of CG model sensitivity with respect to FG model interaction parameters and thermodynamic state points. This formula, the self-consistent basis (SCB) single point formula, determines the many-body sensitivity in a single step by approximating the derivative of the many-body potential projected onto the same set of trial functions as the sensitivity. A related diagnostic formula also derived in this paper is the self-consistent iterative (SCI) single point formula, which is useful for identifying the importance of many-body sources of error and verifying CG representability of observables. The SCI formula determines the many-body sensitivity iteratively via a series of partially self-consistent, variational approximations to the complete many-body sensitivity. The new, computationally efficient SCB formula shows substantially less noise than previous methods when applied to single site methanol and solvent-free sodium chloride CG models, though bias can remain a problem. It represents a novel method for calculating alchemical transferability across interaction parameters at low computational cost and with high fidelity, and the results point to new understanding of the current limits of CG model transferability.

  17. Coarse-grained rigid blob model for soft matter simulations

    NASA Astrophysics Data System (ADS)

    Chao, Sheng D.; Kress, Joel D.; Redondo, Antonio

    2005-06-01

    We have developed a coarse-grained multiscale molecular simulation method for soft matter systems that directly incorporates stereochemical information. We divide the material into disjoint groups of atoms or particles that move as separate rigid bodies; we call these groups "rigid blobs," hence the name coarse-grained rigid blob model. The method is enabled by the construction of transferable interblob potentials that approximate the net intermolecular interactions, as obtained from ab initio electronic structure calculations, other all-atom empirical potentials, experimental data, or any combination of the above. We utilize a multipolar expansion to obtain the interblob potential-energy functions. The series, which contains controllable approximations that allow us to estimate the errors, approaches the original intermolecular potential as the number of terms increases. Using a novel numerical algorithm, we can calculate the interblob potentials very efficiently in terms of a few interaction moment tensors. This reduces the labor well beyond what is required in standard molecular-dynamics calculations and allows large-scale simulations for temporal scales commensurate with characteristic times of nano- and mesoscale systems. A detailed derivation of the formulas is presented, followed by illustrative applications to several systems showing that the method can effectively capture realistic microscopic details and can easily extend to large-scale simulations.

  18. 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

  19. A course-grained model for polyethylene glycol polymer

    SciTech Connect

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

    2011-01-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  1. 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.

  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. Multiscale model of metal alloy oxidation at grain boundaries.

    PubMed

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

    2015-06-01

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

  4. Multiscale model of metal alloy oxidation at grain boundaries

    SciTech Connect

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

    2015-06-07

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

  5. Multiscale model of metal alloy oxidation at grain boundaries

    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

  6. 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.

  7. 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.

  8. Modeling the secondary emission yield of salty ice dust grains

    NASA Astrophysics Data System (ADS)

    Richterová, I.; Němeček, Z.; Pavlů, J.; Beránek, M.; Šafránková, J.

    2011-03-01

    Secondary emission is one of important processes leading to dust grain charging in many plasma environments. The secondary yield varies with the grain material, shape, and size. Several experiments confirmed that the yield of small grains differs from that of planar samples. Among other materials, ices of different compositions can be frequently found in the interplanetary space and/or planetary magnetospheres. However, the admixtures can significantly influence the inner structure of such materials and thus may change their yield. We present numerical simulations that provide a realistic description of the secondary emission process from water ice grains. The simulations reveal that the secondary emission yield increases as the grain dimension decreases to tens of nanometers. The yield of backscattered primary electrons approaches unity and the grain can be charged to high positive potentials under these conditions. We found that any reasonable admixture of NaCl does not alter secondary electron emission properties significantly.

  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. AquaCrop model simulation under different irrigation water and nitrogen strategies.

    PubMed

    Khoshravesh, Mojtaba; Mostafazadeh-Fard, Behrouz; Heidarpour, Manouchehr; Kiani, Ali-Reza

    2013-01-01

    On a global scale, irrigated agriculture consumes about 72% of available freshwater resources. Deficit irrigation can be applied in the field to save irrigation water and still lead to acceptable crop production. The AquaCrop model is a simulation model for management of irrigation and nitrogen fertilizer. This model is a new model that is accurate, robust and requires fewer data inputs compared with the other models. The purpose of this study was to simulate canopy cover, grain yield and water use efficiency (WUE) for soybean using the AquaCrop model. A field line source sprinkler irrigation system was conducted under full and deficit irrigation using different nitrogen fertilizer applications during two cropping seasons for soybean at Gorgan province in Iran. The simulation results showed a reasonably accurate prediction of yield, canopy cover and WUE in all cases (error less than 23%). The simulated pattern of canopy progression over time was close to measured values, with Willmott's index of agreement for all the cases being ≥0.95 for different parameters. The AquaCrop model has the ability to simulate the WUE of soybean under different irrigation water and nitrogen applications. This model is a useful tool for managing the crop water productivity.

  12. AquaCrop model simulation under different irrigation water and nitrogen strategies.

    PubMed

    Khoshravesh, Mojtaba; Mostafazadeh-Fard, Behrouz; Heidarpour, Manouchehr; Kiani, Ali-Reza

    2013-01-01

    On a global scale, irrigated agriculture consumes about 72% of available freshwater resources. Deficit irrigation can be applied in the field to save irrigation water and still lead to acceptable crop production. The AquaCrop model is a simulation model for management of irrigation and nitrogen fertilizer. This model is a new model that is accurate, robust and requires fewer data inputs compared with the other models. The purpose of this study was to simulate canopy cover, grain yield and water use efficiency (WUE) for soybean using the AquaCrop model. A field line source sprinkler irrigation system was conducted under full and deficit irrigation using different nitrogen fertilizer applications during two cropping seasons for soybean at Gorgan province in Iran. The simulation results showed a reasonably accurate prediction of yield, canopy cover and WUE in all cases (error less than 23%). The simulated pattern of canopy progression over time was close to measured values, with Willmott's index of agreement for all the cases being ≥0.95 for different parameters. The AquaCrop model has the ability to simulate the WUE of soybean under different irrigation water and nitrogen applications. This model is a useful tool for managing the crop water productivity. PMID:23128644

  13. 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.

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

    NASA Astrophysics Data System (ADS)

    Six, Katharina; Hense, Inga; Ilyina, Tatiana

    2015-04-01

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

  15. 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

  16. Modeling the flow properties of distillers dried grains with solubles

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Distillers dried grains with solubles (DDGS) are an excellent source of energy, minerals, and bypass protein for ruminants, and are also used in monogastric rations as well. With the remarkable growth of the US fuel ethanol industry in the past decade, large quantities of distillers grains are now b...

  17. 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.

  18. 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.

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

    PubMed

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

    2016-01-01

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

  20. 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

  1. Modelling of porphyroclasts in simple shear and the role of stress variations at grain boundaries

    NASA Astrophysics Data System (ADS)

    Wilson, Christopher J. L.; Evans, Lynn; Delle Piane, Claudio

    2009-11-01

    Grain-scale numerical experiments involving simple shear of a two-phase non-linear viscous material are described and compared with mineral fish or lozenge-shaped porphyroclasts, such as muscovite. Two types of 2D models are considered; either a single elongate grain or two parallel elongate grains, in both cases supported by a weaker polygonal grain matrix. The relative viscosities of the contrasting grain structures were systematically varied, allowing us to observe the effects of non-linear viscous rheology on the resulting microstructure and flow patterns. The results show that the finite rotation of the hard elongate grain was similar within any one experiment, but was largely influenced by viscosity contrast, the geometry of the model and the imposed shear strain. Models involving single elongate hard grains show increasing instability at their ends and less strain compatibility with the deforming matrix grains, as the viscosity contrast is increased. In the paired grain models the greatest variation in the matrix grain microstructure is seen in the region where the two hard grains are oriented at a high-angle to the direction of shear. Finally, we consider the changes in intragranular stress by comparing microstructural observations using different viscosities with the distribution of stress in space and during progressive shear. In the plane approximately parallel to the maximum principal stress direction ( σ1), a localised change of stress occurs across and along the interface between the hard and soft grains. Variations in the mean stress at these boundaries are directly attributable to changes in the minimum principal stress. We propose that with shear strains greater than γ = 2 it is the minimum principal stress that can control diffusion processes at the grain boundary rather than mean stress. In conclusion we suggest that our models have the potential for providing useful insights into why metamorphic reactions can occur at the interface between a

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. A model of grain refinement and strengthening of Al alloys due to cold severe plastic deformation

    NASA Astrophysics Data System (ADS)

    Qiao, Xiao Guang; Gao, Nong; Starink, Marco J.

    2012-02-01

    This paper presents a model which quantitatively predicts grain refinement and strength/hardness of Al alloys after very high levels of cold deformation through processes including cold rolling, equal channel angular pressing (ECAP), multiple forging (MF), accumulative roll bonding (ARB) and embossing. The model deals with materials in which plastic deformation is exclusively due to dislocation movement within grains, which is in good approximation the case for many metallic alloys at low temperature, for instance aluminium alloys. In the early stages of deformation, the generated dislocations are stored in grains and contribute to overall strength. With increase in strain, excess dislocations form and/or move to new cell walls/grain boundaries and grains are refined. We examine this model using both our own data as well as the data in the literature. It is shown that grain size and strength/hardness are predicted to a good accuracy.

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

    NASA Astrophysics Data System (ADS)

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

    2007-10-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  9. Grain Boundary Percolation Modeling of Fission Gas Release in Oxide Fuels

    SciTech Connect

    Paul C. Millett; Michael R. Tonks; S. B. Biner

    2012-05-01

    We present a new approach to fission gas release modeling in oxide fuels based on grain boundary network percolation. The method accounts for variability in the bubble growth and coalescence rates on individual grain boundaries, and the resulting effect on macroscopic fission gas release. Two-dimensional representa- tions of fuel pellet microstructures are considered, and the resulting gas release rates are compared with traditional two-stage Booth models, which do not account for long-range percolation on grain boundary net- works. The results show that the requirement of percolation of saturated grain boundaries can considerably reduce the total gas release rates, particularly when gas resolution is considered.

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

    PubMed

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

    2001-10-30

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

  11. 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.

  12. Probing model interstellar grain surfaces with small molecules

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  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]. PMID:23918962

  14. 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

  15. Complexity and Uncertainty in Soil Nitrogen Modeling

    NASA Astrophysics Data System (ADS)

    Ajami, N. K.; Gu, C.

    2009-12-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed

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

    2016-05-16

    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.

  18. 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

  19. Modelling the size and composition of fruit, grain and seed by process-based simulation models.

    PubMed

    Martre, Pierre; Bertin, Nadia; Salon, Christophe; Génard, Michel

    2011-08-01

    Understanding what determines the size and composition of fruit, grain and seed in response to the environment and genotype is challenging, as these traits result from several linked processes controlled at different levels of organization, from the subcellular to the crop level, with subtle interactions occurring at or between the levels of organization. Process-based simulation models (PBSMs) implement algorithms to simulate metabolic and biophysical aspects of cell, tissue and organ behaviour. In this review, fruit, grain and seed PBSMs describing the main phases of growth, development and storage metabolism are discussed. From this concurrent work, it is possible to identify generic storage organ processes which can be modelled similarly for fruit, grain and seed. Spatial heterogeneity at the tissue and whole-plant level is found to be a key consideration in modelling the effects of the environment and genotype on fruit, grain and seed end-use value. In the future, PBSMs may well become the main link between studies at the molecular and whole-plant levels. To bridge this phenotype-to-genotype gap, future models need to remain plastic without becoming overparameterized.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  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

    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

  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 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

  6. 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.

  7. 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

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

    DOE PAGESBeta

    Biner, S. B.

    2016-03-16

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  10. 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

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

    PubMed

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

    2016-01-01

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

  12. Ab initio modelling of UN grain boundary interfaces

    NASA Astrophysics Data System (ADS)

    Kotomin, E. A.; Zhukovkii, Yu F.; Bocharov, D.; Gryaznov, D.

    2012-08-01

    The uranium mononitride (UN) is a material considered as a promising candidate for Generation-IV nuclear reactor fuels. Unfortunately, oxygen in air affects UN fuel performance and stability. Therefore, it is necessary to understand the mechanism of oxygen adsorption and further UN oxidation in the bulk and at surface. Recently, we performed a detailed study on oxygen interaction with UN surface using density functional theory (DFT) calculations. We were able to identify an atomistic mechanism of UN surface oxidation consisting of several important steps, starting with the oxygen molecule dissociation and finishing with oxygen atom incorporation into vacancies on the surface. However, in reality most of processes occur at the interfaces and on UN grain boundaries. In this study, we present the results of first DFT calculations on O behaviour inside UN grain boundaries performed using GGA exchange-correlation functional PW91 as implemented into the VASP computer code. We consider a simple interface (310)[001](36.8°) tilt grain boundary. The N vacancy formation energies and energies of O incorporation into pre-existing vacancies in the grain boundaries as well as O solution energies were compared with those obtained for the UN (001) and (110) surfaces

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

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

    PubMed

    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

    2013-06-01

    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.

  1. Studying Amphiphilic Self-assembly with Soft Coarse-Grained Models

    NASA Astrophysics Data System (ADS)

    Müller, Marcus

    2011-11-01

    Highly coarse-grained models for investigating the self-assembly of lipids and copolymer materials are discussed. Soft interactions between segments that represent many atoms naturally arise in the course of systematic coarse-graining, and they are necessary for modeling fluctuation effects whose strengths is dictated by a large invariant degree of polymerization. The soft non-bonded interactions of the coarse-grained models are related to the excess free-energy functional of an equivalent field-theoretic description. The connection between the particle-based model and the field-theoretic description helps to identify the physical significance of the model interactions. Non-bonded interactions, which describe the complex phase behavior of compressible mixtures or include local fluid-like packing effects of the coarse-grained segments, can be systematically constructed based on liquid-state theory or classical density functional theory. Details of the computational implementation and limitations of soft coarse-grained models are discussed. Two computational techniques—field-theoretic force-matching and umbrella sampling—are devised for computing a free-energy functional from a particle-based description. They can be employed to (i) derive the non-bonded free-energy functional of a soft coarse-grained model from a more detailed computational model or to (ii) derive a field-theoretic description from a particle-based model. Moreover, different strategies for accurately calculating free energies of self-assembled systems are described and selected applications presented.

  2. 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).

  3. 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.

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

    SciTech Connect

    Moresco, R.F.

    1985-01-01

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

  5. 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.

  6. 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

  7. 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

  8. Idealized model of nitrogen recycling in marine sediments

    SciTech Connect

    Billen, G.

    1982-04-01

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

  9. [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

  10. [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

  11. 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.

  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. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

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

    PubMed

    Simsek, Halis

    2016-11-01

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

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

    PubMed

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

    2006-10-01

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

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

    PubMed Central

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

    2015-01-01

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

  2. 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.

  3. 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

  4. 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.

  5. Modeling uncertainties for tropospheric nitrogen dioxide columns affecting satellite-based inverse modeling of nitrogen oxides emissions

    NASA Astrophysics Data System (ADS)

    Lin, J.-T.; Liu, Z.; Zhang, Q.; Liu, H.; Mao, J.; Zhuang, G.

    2012-12-01

    Errors in chemical transport models (CTMs) interpreting the relation between space-retrieved tropospheric column densities of nitrogen dioxide (NO2) and emissions of nitrogen oxides (NOx) have important consequences on the inverse modeling. They are however difficult to quantify due to lack of adequate in situ measurements, particularly over China and other developing countries. This study proposes an alternate approach for model evaluation over East China, by analyzing the sensitivity of modeled NO2 columns to errors in meteorological and chemical parameters/processes important to the nitrogen abundance. As a demonstration, it evaluates the nested version of GEOS-Chem driven by the GEOS-5 meteorology and the INTEX-B anthropogenic emissions and used with retrievals from the Ozone Monitoring Instrument (OMI) to constrain emissions of NOx. The CTM has been used extensively for such applications. Errors are examined for a comprehensive set of meteorological and chemical parameters using measurements and/or uncertainty analysis based on current knowledge. Results are exploited then for sensitivity simulations perturbing the respective parameters, as the basis of the following post-model linearized and localized first-order modification. It is found that the model meteorology likely contains errors of various magnitudes in cloud optical depth, air temperature, water vapor, boundary layer height and many other parameters. Model errors also exist in gaseous and heterogeneous reactions, aerosol optical properties and emissions of non-nitrogen species affecting the nitrogen chemistry. Modifications accounting for quantified errors in 10 selected parameters increase the NO2 columns in most areas with an average positive impact of 18% in July and 8% in January, the most important factor being modified uptake of the hydroperoxyl radical (HO2) on aerosols. This suggests a possible systematic model bias such that the top-down emissions will be overestimated by the same magnitude

  6. 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.

  7. 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.

  8. 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.

  9. 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.

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

    PubMed Central

    Hämmerle, Martin; Höfle, Bernhard

    2014-01-01

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

  11. 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.

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

    PubMed

    Hämmerle, Martin; Höfle, Bernhard

    2014-01-01

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

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

    PubMed

    Janner, A

    2016-05-01

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

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. A pressure-transferable coarse-grained potential for modeling the shock Hugoniot of polyethylene

    NASA Astrophysics Data System (ADS)

    Agrawal, Vipin; Peralta, Pedro; Li, Yiyang; Oswald, Jay

    2016-09-01

    We investigate the thermomechanical response of semi-crystalline polyethylene under shock compression by performing molecular dynamics (MD) simulations using a new coarse-graining scheme inspired by the embedded atom method. The coarse-graining scheme combines the iterative Boltzmann inversion method and least squares optimization to parameterize interactions between coarse-grained sites, including a many-body potential energy designed to improve the representability of the model across a wide range of thermodynamic states. We demonstrate that a coarse-grained model of polyethylene, calibrated to match target structural and thermodynamic data generated from isothermal MD simulations at different pressures, can also accurately predict the shock Hugoniot response. Analysis of the rise in temperature along the shock Hugoniot and comparison with analytical predictions from the Mie-Grüneisen equation of state are performed to thoroughly explore the thermodynamic consistency of the model. As the coarse-graining model affords nearly two orders of magnitude reduction in simulation time compared to all-atom MD simulations, the proposed model can help identify how nanoscale structure in semi-crystalline polymers, such as polyethylene, influences mechanical behavior under extreme loading.

  20. A pressure-transferable coarse-grained potential for modeling the shock Hugoniot of polyethylene.

    PubMed

    Agrawal, Vipin; Peralta, Pedro; Li, Yiyang; Oswald, Jay

    2016-09-14

    We investigate the thermomechanical response of semi-crystalline polyethylene under shock compression by performing molecular dynamics (MD) simulations using a new coarse-graining scheme inspired by the embedded atom method. The coarse-graining scheme combines the iterative Boltzmann inversion method and least squares optimization to parameterize interactions between coarse-grained sites, including a many-body potential energy designed to improve the representability of the model across a wide range of thermodynamic states. We demonstrate that a coarse-grained model of polyethylene, calibrated to match target structural and thermodynamic data generated from isothermal MD simulations at different pressures, can also accurately predict the shock Hugoniot response. Analysis of the rise in temperature along the shock Hugoniot and comparison with analytical predictions from the Mie-Grüneisen equation of state are performed to thoroughly explore the thermodynamic consistency of the model. As the coarse-graining model affords nearly two orders of magnitude reduction in simulation time compared to all-atom MD simulations, the proposed model can help identify how nanoscale structure in semi-crystalline polymers, such as polyethylene, influences mechanical behavior under extreme loading. PMID:27634275

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

    PubMed

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

    2011-02-14

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

  2. An algorithm for the grain-level modelling of a dry sand particulate system

    NASA Astrophysics Data System (ADS)

    Fang, Qin; Zhang, Jinhua; Chen, Li; Liu, Jinchun; Fan, Junyu; Zhang, Yadong

    2014-07-01

    This paper is composed of two parts: the generation of the sand particulate system and insights into the grain-level response under static and dynamic loadings. First, the algorithms for the generation of sand particles are presented, considering the randomness in their shape and distribution. Improvements to the robustness of the algorithms are obtained using controlling parameters. Second, we employ the take-and-place algorithm, placing sand grains into the specimen and checking how they overlap to form the initial model. In order to improve the porosity of the specimen, we develop the compaction algorithm: self-compaction by gravity and artificial compaction by mechanical vibration and pressure. The steps for the generation of a finite element grid are also introduced. Third, the grain-level configurations of the dry sand particulate system (aspects such as porosity, friction and contact) are taken into account in modelling. Results show that the grain-level responses of grains, i.e. deformation, fracture and damage of sand grains, impose significant effects on the mechanical behavior of dry sand under static and dynamic loadings.

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

    USGS Publications Warehouse

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

    2002-01-01

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

  4. 3-D and quasi-2-D discrete element modeling of grain commingling in a bucket elevator boot system

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  5. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  7. 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.

  8. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-05-01

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

  10. Multiresolution Modeling of Polymer Solutions: Wavelet-Based Coarse-Graining and Reverse-Mapping

    NASA Astrophysics Data System (ADS)

    Ismail, Ahmed; Adorf, Carl Simon; Agarwal, Animesh; Iacovella, Christopher R.

    2014-03-01

    Unlike multiscale methods, which encompass multiple simulation techniques, multiresolution models uses one modeling technique at different length and time scales. We present a combined coarse-graining and reverse-mapping framework for modeling of semidilute polymer solutions, based on the wavelet-accelerated Monte Carlo (WAMC) method, which forms a hierarchy of resolutions to model polymers at length scales that cannot be reached via atomistic or even ``standard'' coarse-grained simulations. A universal scaling function is obtained so that potentials do not need to be recomputed as the scale of the system is changed. We show that coarse-grained polymer solutions can reproduce results obtained from the simulations of the more detailed atomistic system to a reasonable degree of accuracy. Reverse mapping proceeds similarly: using probability distributions obtained from coarse-graining the bond lengths, angles, torsions, and the non-bonded potentials, we can reconstruct a more detailed polymer consistent with both geometric constraints and energetic considerations. Using a ``convergence factor'' within a Monte Carlo-based energy optimization scheme, we can successfully reconstruct entire atomistic configurations from coarse-grained descriptions.

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  12. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  15. 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.

  16. An implicit solvent coarse-grained lipid model with correct stress profile

    NASA Astrophysics Data System (ADS)

    Sodt, Alex J.; Head-Gordon, Teresa

    2010-05-01

    We develop a coarse-grained parametrization strategy for lipid membranes that we illustrate for a dipalmitoylphosphatidylcholine bilayer. Our coarse-graining approach eliminates the high cost of explicit solvent but maintains more lipid interaction sites. We use a broad attractive tail-tail potential and extract realistic bonded potentials of mean force from all-atom simulations, resulting in a model with a sharp gel to fluid transition, a correct bending modulus, and overall very reasonable dynamics when compared with experiment. We also determine a quantitative stress profile and correct breakdown of contributions from lipid components when compared with detailed all-atom simulation benchmarks, which has been difficult to achieve for implicit membrane models. Such a coarse-grained lipid model will be necessary for efficiently simulating complex constructs of the membrane, such as protein assembly and lipid raft formation, within these nonaqueous chemical environments.

  17. 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.

  18. Use of Spectral Radiance to Estimate In-Season Biomass and Grain Yield in Nitrogen- and Water-Stressed Corn.

    PubMed

    Osborne, S. L.; Schepers, J. S.; Francis, D. D.; Schlemmer, M. R.

    2002-01-01

    Current technologies for measuring plant water status are limited, while recently remote sensing techniques for estimating N status have increased with limited research on the interaction between the two stresses. Because plant water status methods are time-consuming and require numerous observations to characterize a field, managers could benefit from remote sensing techniques to assist in irrigation and N management decisions. A 2-yr experiment was initiated to determine specific wavelengths and/or combinations of wavelengths indicative of water stress and N deficiencies, and to evaluate these wavelengths for estimating in-season biomass and corn (Zea mays L.) grain yield. The experiment was a split-plot design with three replications. The treatment structure had five N rates (0, 45, 90, 134, and 269 kg N ha(-1)) and three water treatments [dryland, 0.5 evapotranspiration (ET), and full ET]. Canopy spectral radiance measurements (350-2500 nm) were taken at various growth stages (V6-V7, V13-V16, and V14-R1). Specific wavelengths for estimating crop biomass, N concentration, grain yield, and chlorophyll meter readings changed with growth stage and sampling date. Changes in total N and biomass in the presence of a water stress were estimated using near-infrared (NIR) reflectance and the water absorption bands. Reflectance in the green and NIR regions were used to estimate total N and biomass without water stress. Reflectance at 510, 705, and 1135 nm were found for estimating chlorophyll meter readings regardless of year or sampling date.

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

    PubMed

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

    2016-04-01

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

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

    SciTech Connect

    Michael R Tonks; Yongfeng Zhang; Xianming Bai

    2014-06-01

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

  1. 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.

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

    PubMed

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

    2016-04-01

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

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

    SciTech Connect

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

    1995-11-01

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

  4. Collisional radiative coarse-grain model for ionization in air

    NASA Astrophysics Data System (ADS)

    Panesi, Marco; Lani, Andrea

    2013-05-01

    We present a reduced kinetic mechanism for the modeling of the behavior of the electronic states of the atomic species in air mixtures. The model is built by lumping the electronically excited states of the atomic species and by performing Maxwell-Boltzmann averages of the rate constants describing the elementary kinetic processes of the individual states within each group. The necessary reaction rate coefficients are taken from the model compiled by Bultel et al. ["Collisional-radiative model in air for earth re-entry problems," Phys. Plasmas 13, 043502 (2006), 10.1063/1.2194827]. The reduced number of pseudo-states considered leads to a significant reduction of the computational cost, thus enabling the application of the state of the art collisional radiative models to bi-dimensional and three-dimensional problems. The internal states of the molecular species are assumed to be in equilibrium. The rotational energy mode is assumed to quickly equilibrate with the translational energy mode at the kinetic temperature of the heavy species as opposed to the electronic and the vibrational modes, assumed to be in Maxwell-Boltzmann equilibrium at a common temperature TV. In a first step we validate the model by using simple zero- and one-dimensional test cases for which the full kinetic mechanism can be run efficiently. Finally, the reduced kinetic model is used to analyze the strong non-equilibrium flow surrounding the FIRE II flight experiment during the early part of its re-entry trajectory. It is found that the reduced kinetic mechanism is capable of reproducing the ionizational non-equilibrium phenomena, responsible for the drastic reduction of the radiative heat loads on the space capsules during the re-entry phase.

  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. 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.

  7. 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.

  8. Coarse grain modeling of imperfect networks and gels

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

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

    PubMed

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

    2006-01-01

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

  10. 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.

  11. Fabrication and optimization of a conducting polymer sensor array using stored grain model volatiles.

    PubMed

    Hossain, Md Eftekhar; Rahman, G M Aminur; Freund, Michael S; Jayas, Digvir S; White, Noel D G; Shafai, Cyrus; Thomson, Douglas J

    2012-03-21

    During storage, grain can experience significant degradation in quality due to a variety of physical, chemical, and biological interactions. Most commonly, these losses are associated with insects or fungi. Continuous monitoring and an ability to differentiate between sources of spoilage are critical for rapid and effective intervention to minimize deterioration or losses. Therefore, there is a keen interest in developing a straightforward, cost-effective, and efficient method for monitoring of stored grain. Sensor arrays are currently used for classifying liquors, perfumes, and the quality of food products by mimicking the mammalian olfactory system. The use of this technology for monitoring of stored grain and identification of the source of spoilage is a new application, which has the potential for broad impact. The main focus of the work described herein is on the fabrication and optimization of a carbon black (CB) polymer sensor array to monitor stored grain model volatiles associated with insect secretions (benzene derivatives) and fungi (aliphatic hydrocarbon derivatives). Various methods of statistical analysis (RSD, PCA, LDA, t test) were used to select polymers for the array that were optimum for distinguishing between important compound classes (quinones, alcohols) and to minimize the sensitivity for other parameters such as humidity. The performance of the developed sensor array was satisfactory to demonstrate identification and separation of stored grain model volatiles at ambient conditions.

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  14. 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.

  15. 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.

  16. Modeling Nitrogen Processing in Northeast US River Networks

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  17. 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…

  18. Field Emission at Grain Boundaries: Modeling the Conductivity in Highly Doped Polycrystalline Semiconductors

    NASA Astrophysics Data System (ADS)

    Sommer, Nicolas; Hüpkes, Jürgen; Rau, Uwe

    2016-02-01

    In this contribution, we elaborate a conductivity model for highly doped polycrystalline semiconductors. The prominent feature of the model is the description of grain-boundary scattering by field emission, i.e., quantum-mechanical tunneling of electrons through potential barriers at grain boundaries. For this purpose, we adapt a theory of Stratton [Theory of field emission from semiconductors, Phys. Rev. 125, 67 (1962)] to double Schottky barriers at grain boundaries. We provide strong evidence that field emission rather than the predominantly applied thermionic emission is the dominant transport path across grain boundaries in semiconductors with carrier concentrations exceeding approximately 1019 cm-3 . We obtain a comprehensive conductivity model for highly doped polycrystalline semiconductors by combining field emission with two intragrain scattering mechanisms, that are ionized-impurity and electron-phonon scattering. The model is applied to a wide range of literature data in order to show its applicability and explanatory power. The literature data comprise, in particular, transparent conductive oxides with a special emphasis on aluminum-doped ZnO.

  19. Crystallographic study of grain refinement in aluminum alloys using the edge-to-edge matching model

    SciTech Connect

    Zhang, M.-X. . E-mail: m.zhang@minmet.uq.edu.au; Kelly, P.M.; Easton, M.A.; Taylor, J.A.

    2005-03-01

    The edge-to-edge matching model for describing the interfacial crystallographic characteristics between two phases that are related by reproducible orientation relationships has been applied to the typical grain refiners in aluminum alloys. Excellent atomic matching between Al{sub 3}Ti nucleating substrates, known to be effective nucleation sites for primary Al, and the Al matrix in both close packed directions and close packed planes containing these directions have been identified. The crystallographic features of the grain refiner and the Al matrix are very consistent with the edge-to-edge matching model. For three other typical grain refiners for Al alloys, TiC (when a = 0.4328 nm), TiB{sub 2} and AlB{sub 2}, the matching only occurs between the close packed directions in both phases and between the second close packed plane of the Al matrix and the second close packed plane of the refiners. According to the model, it is predicted that Al{sub 3}Ti is a more powerful nucleating substrate for Al alloy than TiC, TiB{sub 2} and AlB{sub 2}. This agrees with the previous experimental results. The present work shows that the edge-to-edge matching model has the potential to be a powerful tool in discovering new and more powerful grain refiners for Al alloys.

  20. 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.

  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. PMID:27196963

  2. 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

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

    PubMed

    Genheden, Samuel; Essex, Jonathan W

    2015-10-13

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

  5. 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.

  6. Grain boundaries

    SciTech Connect

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

    1991-01-01

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

  7. Grain-boundary-controlled impedances of electroceramics: Generalized effective-medium approach and brick-layer model

    NASA Astrophysics Data System (ADS)

    Nan, Ce Wen; Zhou, Xisong; Nan, Jun; Wu, Junbo

    2001-04-01

    In every electroceramic there exist variations throughout the microstructure of both grain size (and shape) and electrical properties of individual grain boundaries. To calculate the effects of such microstructural variations on the frequency-dependent impedance/dielectric behavior, we describe a generalized statistical effective-medium approach based on effective-medium theory. To illustrate the predictions of the approach, the effect of various distributions in the grain boundary conductivity and the grain size, as well as the grain shape and porosity, are considered. The calculations show that such variations lead to depression of the boundary arc and deviations of the impedance spectra from the well-known brick-layer model with an idealized microstructure consisting of identical grains and grain boundaries.

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

    PubMed

    Kerpedjiev, Peter; Höner Zu Siederdissen, Christian; Hofacker, Ivo L

    2015-06-01

    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

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

    PubMed

    Kerpedjiev, Peter; Höner Zu Siederdissen, Christian; Hofacker, Ivo L

    2015-06-01

    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.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. Interstellar grains

    NASA Technical Reports Server (NTRS)

    Snow, T. P.

    1986-01-01

    There are few aspects of interstellar grains that can be unambiguously defined. Very little can be said that is independent of models or presuppositions; hence issues are raised and questions categorized, rather than providing definitive answers. The questions are issues fall into three general areas; the general physical and chemical nature of the grains; the processes by which they are formed and destroyed; and future observational approaches.

  18. 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.

  19. 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.

  20. 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

  1. 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.

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2015-03-01

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

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

    PubMed

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

    2001-12-11

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

  5. 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

  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

    2016-01-01

    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

  7. 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.

  8. Fracture of granular materials composed of arbitrary grain shapes: A new cohesive interaction model

    NASA Astrophysics Data System (ADS)

    Neveu, A.; Artoni, R.; Richard, P.; Descantes, Y.

    2016-10-01

    Discrete Element Methods (DEM) are a useful tool to model the fracture of cohesive granular materials. For this kind of application, simple particle shapes (discs in 2D, spheres in 3D) are usually employed. However, dealing with more general particle shapes allows to account for the natural heterogeneity of grains inside real materials. We present a discrete model allowing to mimic cohesion between contacting or non-contacting particles whatever their shape in 2D and 3D. The cohesive interactions are made of cohesion points placed on interacting particles, with the aim of representing a cohesive phase lying between the grains. Contact situations are solved according to unilateral contact and Coulomb friction laws. In order to test the developed model, 2D unixial compression simulations are performed. Numerical results show the ability of the model to mimic the macroscopic behavior of an aggregate grain subject to axial compression, as well as fracture initiation and propagation. A study of the influence of model and sample parameters provides important information on the ability of the model to reproduce various behaviors.

  9. On the representability problem and the physical meaning of coarse-grained models

    NASA Astrophysics Data System (ADS)

    Wagner, Jacob W.; Dama, James F.; Durumeric, Aleksander E. P.; Voth, Gregory A.

    2016-07-01

    In coarse-grained (CG) models where certain fine-grained (FG, i.e., atomistic resolution) observables are not directly represented, one can nonetheless identify indirect the CG observables that capture the FG observable's dependence on CG coordinates. Often, in these cases it appears that a CG observable can be defined by analogy to an all-atom or FG observable, but the similarity is misleading and significantly undermines the interpretation of both bottom-up and top-down CG models. Such problems emerge especially clearly in the framework of the systematic bottom-up CG modeling, where a direct and transparent correspondence between FG and CG variables establishes precise conditions for consistency between CG observables and underlying FG models. Here we present and investigate these representability challenges and illustrate them via the bottom-up conceptual framework for several simple analytically tractable polymer models. The examples provide special focus on the observables of configurational internal energy, entropy, and pressure, which have been at the root of controversy in the CG literature, as well as discuss observables that would seem to be entirely missing in the CG representation but can nonetheless be correlated with CG behavior. Though we investigate these problems in the framework of systematic coarse-graining, the lessons apply to top-down CG modeling also, with crucial implications for simulation at constant pressure and surface tension and for the interpretations of structural and thermodynamic correlations for comparison to experiment.

  10. On the representability problem and the physical meaning of coarse-grained models.

    PubMed

    Wagner, Jacob W; Dama, James F; Durumeric, Aleksander E P; Voth, Gregory A

    2016-07-28

    In coarse-grained (CG) models where certain fine-grained (FG, i.e., atomistic resolution) observables are not directly represented, one can nonetheless identify indirect the CG observables that capture the FG observable's dependence on CG coordinates. Often, in these cases it appears that a CG observable can be defined by analogy to an all-atom or FG observable, but the similarity is misleading and significantly undermines the interpretation of both bottom-up and top-down CG models. Such problems emerge especially clearly in the framework of the systematic bottom-up CG modeling, where a direct and transparent correspondence between FG and CG variables establishes precise conditions for consistency between CG observables and underlying FG models. Here we present and investigate these representability challenges and illustrate them via the bottom-up conceptual framework for several simple analytically tractable polymer models. The examples provide special focus on the observables of configurational internal energy, entropy, and pressure, which have been at the root of controversy in the CG literature, as well as discuss observables that would seem to be entirely missing in the CG representation but can nonetheless be correlated with CG behavior. Though we investigate these problems in the framework of systematic coarse-graining, the lessons apply to top-down CG modeling also, with crucial implications for simulation at constant pressure and surface tension and for the interpretations of structural and thermodynamic correlations for comparison to experiment. PMID:27475349

  11. Genomic prediction models for grain yield of spring bread wheat in diverse agro-ecological zones

    PubMed Central

    Saint Pierre, C.; Burgueño, J.; Crossa, J.; Fuentes Dávila, G.; Figueroa López, P.; Solís Moya, E.; Ireta Moreno, J.; Hernández Muela, V. M.; Zamora Villa, V. M.; Vikram, P.; Mathews, K.; Sansaloni, C.; Sehgal, D.; Jarquin, D.; Wenzl, P.; Singh, Sukhwinder

    2016-01-01

    Genomic and pedigree predictions for grain yield and agronomic traits were carried out using high density molecular data on a set of 803 spring wheat lines that were evaluated in 5 sites characterized by several environmental co-variables. Seven statistical models were tested using two random cross-validations schemes. Two other prediction problems were studied, namely predicting the lines’ performance at one site with another (pairwise-site) and at untested sites (leave-one-site-out). Grain yield ranged from 3.7 to 9.0 t ha−1 across sites. The best predictability was observed when genotypic and pedigree data were included in the models and their interaction with sites and the environmental co-variables. The leave-one-site-out increased average prediction accuracy over pairwise-site for all the traits, specifically from 0.27 to 0.36 for grain yield. Days to anthesis, maturity, and plant height predictions had high heritability and gave the highest accuracy for prediction models. Genomic and pedigree models coupled with environmental co-variables gave high prediction accuracy due to high genetic correlation between sites. This study provides an example of model prediction considering climate data along-with genomic and pedigree information. Such comprehensive models can be used to achieve rapid enhancement of wheat yield enhancement in current and future climate change scenario. PMID:27311707

  12. 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.

  13. 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.

  14. Contact Mechanics of Naturally Occurring Grains: Experiments and Discrete Element Modeling

    NASA Astrophysics Data System (ADS)

    Cole, David M.; Hopkins, Mark A.

    2009-06-01

    Application of the discrete element method to engineering problems involving naturally occurring granular materials requires knowledge of the contact mechanics of the particles and a realistic treatment of particle shapes. This paper presents results from on-going work that addresses these two fundamental issues of granular media mechanics. Grain-scale laboratory experiments are being conducted to provide the needed contact relationships. A concurrent discrete element modeling effort is under way to implement the experimentally determined contact relationships and employ realistic particle shapes. The experiments determine the stiffness and frictional behavior of normal and sliding contacts of observed for spherical specimens of gneiss. Stiffness in the normal mode is seen to range from 0.1 to 15 MN m-1 depending on force level. Shear stiffness is on the order of the normal stiffness, but only for relatively low shear force levels (or shear deformations). Frictional energy losses are observed to varying degrees under virtually all experimental conditions. The discrete element modeling effort simulates the triaxial response of the spherical grains enclosed in a membrane and implements the experimentally determined contact relationships for normal and sliding contact behavior. Inclusion of the full frictional behavior prior to macroscopic sliding is under development. Some aspects of the simulations of the triaxial deformation of spherical grains of gneiss are presented and compared with the grain-scale experimental data. The simulations are seen to capture the key features of the experimental observations.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. Consistent and transferable coarse-grained model for semidilute polymer solutions in good solvent.

    PubMed

    D'Adamo, Giuseppe; Pelissetto, Andrea; Pierleoni, Carlo

    2012-07-14

    We present a coarse-grained model for linear polymers with a tunable number of effective atoms (blobs) per chain interacting by intra- and intermolecular potentials obtained at zero density. We show how this model is able to accurately reproduce the universal properties of the underlying solution of athermal linear chains at various levels of coarse-graining and in a range of chain densities which can be widened by increasing the spatial resolution of the multiblob representation, i.e., the number of blobs per chain. The present model is unique in its ability to quantitatively predict thermodynamic and large scale structural properties of polymer solutions deep in the semidilute regime with a very limited computational effort, overcoming most of the problems related to the simulations of semidilute polymer solutions in good solvent conditions.

  1. 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.

  2. Subsurface Gas Flow and Ice Grain Acceleration within Enceladus and Europa Fissures: 2D DSMC Models

    NASA Astrophysics Data System (ADS)

    Tucker, O. J.; Combi, M. R.; Tenishev, V.

    2014-12-01

    The ejection of material from geysers is a ubiquitous occurrence on outer solar system bodies. Water vapor plumes have been observed emanating from the southern hemispheres of Enceladus and Europa (Hansen et al. 2011, Roth et al. 2014), and N2plumes carrying ice and ark particles on Triton (Soderblom et al. 2009). The gas and ice grain distributions in the Enceladus plume depend on the subsurface gas properties and the geometry of the fissures e.g., (Schmidt et al. 2008, Ingersoll et al. 2010). Of course the fissures can have complex geometries due to tidal stresses, melting, freezing etc., but directly sampled and inferred gas and grain properties for the plume (source rate, bulk velocity, terminal grain velocity) can be used to provide a basis to constrain characteristic dimensions of vent width and depth. We used a 2-dimensional Direct Simulation Monte Carlo (DSMC) technique to model venting from both axi-symmetric canyons with widths ~2 km and narrow jets with widths ~15-40 m. For all of our vent geometries, considered the water vapor source rates (1027­ - 1028 s-1) and bulk gas velocities (~330 - 670 m/s) obtained at the surface were consistent with inferred values obtained by fits of the data for the plume densities (1026 - 1028 s-1, 250 - 1000 m/s) respectively. However, when using the resulting DSMC gas distribution for the canyon geometries to integrate the trajectories of ice grains we found it insufficient to accelerate submicron ice grains to Enceladus' escape speed. On the other hand, the gas distributions in the jet like vents accelerated grains > 10 μm significantly above Enceladus' escape speed. It has been suggested that micron-sized grains are ejected from the vents with speeds comparable to the Enceladus escape speed. Here we report on these results including comparisons to results obtained from 1D models as well as discuss the implications of our plume model results. We also show preliminary results for similar considerations applied to Europa

  3. Adaptive resolution simulation of polarizable supramolecular coarse-grained water models

    SciTech Connect

    Zavadlav, Julija; Praprotnik, Matej; Melo, Manuel N.; Marrink, Siewert J.

    2015-06-28

    Multiscale simulations methods, such as adaptive resolution scheme, are becoming increasingly popular due to their significant computational advantages with respect to conventional atomistic simulations. For these kind of simulations, it is essential to develop accurate multiscale water models that can be used to solvate biophysical systems of interest. Recently, a 4-to-1 mapping was used to couple the bundled-simple point charge water with the MARTINI model. Here, we extend the supramolecular mapping to coarse-grained models with explicit charges. In particular, the two tested models are the polarizable water and big multiple water models associated with the MARTINI force field. As corresponding coarse-grained representations consist of several interaction sites, we couple orientational degrees of freedom of the atomistic and coarse-grained representations via a harmonic energy penalty term. This additional energy term aligns the dipole moments of both representations. We test this coupling by studying the system under applied static external electric field. We show that our approach leads to the correct reproduction of the relevant structural and dynamical properties.

  4. Apoplastic infusion of sucrose into stem internodes during female flowering does not increase grain yield in maize plants grown under nitrogen-limiting conditions.

    PubMed

    Peng, Yunfeng; Li, Chunjian; Fritschi, Felix B

    2013-08-01

    Nitrogen (N) limitation reduces leaf growth and photosynthetic rates of maize (Zea mays), and constrains photosynthate translocation to developing ears. Additionally, the period from about 1 week before to 2 weeks after silking is critical for establishing the reproductive sink capacity necessary to attain maximum yield. To investigate the influence of carbohydrate availability in plants of differing N status, a greenhouse study was performed in which exogenous sucrose (Suc) was infused around the time of silking into maize stems grown under different N regimes. N deficiency significantly reduced leaf area, leaf longevity, leaf chlorophyll content and photosynthetic rate. High N-delayed leaf senescence, particularly of the six uppermost leaves, compared to the other two N treatments. While N application increased ear leaf soluble protein concentration, it did not influence glucose and suc concentrations. Interestingly, ear leaf starch concentration decreased with increasing N application. Infusion of exogenous suc tended to increase non-structural carbohydrate concentrations in the developing ears of all N treatments at silking and 6 days after silking. However, leaf photosynthetic rates were not affected by suc infusion, and suc infusion failed to increase grain yield in any N treatment. The lack of an effect of suc infusion on ear growth and the high ear leaf starch concentration of N-deficient maize, suggest that yield reduction under N deficiency may not be due to insufficient photosynthate availability to the developing ear during silking, and that yield reduction under N deficiency may be determined at an earlier growth stage.

  5. Cometary grains

    NASA Technical Reports Server (NTRS)

    Baum, William A.; Kreidl, Tobias J.; Schleicher, David G.

    1992-01-01

    CCD observations of cometary comas in the spectral continuum are reported. Radial brightness profiles of 14 comets and isophotal maps of three are presented. For 10 of the 14, the azimuthally averaged brightness in the vicinity of the nucleus falls off faster than rho exp -1, where rho is the projected radial distance from the nucleus in the plane of the sky. Simple modeling is used to show that radiation pressure alone cannot account for the observed departures from rho exp -1; it is postulated that the grains fade, i.e., decrease in albedo or size, while they glow outward. For only three of the comets no evidence was found of any grain fading at all. Cases with the most rapid grain fading occurred at small heliocentric distances, but so did some of the cases with no fading, from which large intrinsic differences from comet to comet in the nature of the grain population are inferred.

  6. RedMDStream: Parameterization and Simulation Toolbox for Coarse-Grained Molecular Dynamics Models

    PubMed Central

    Leonarski, Filip; Trylska, Joanna

    2015-01-01

    Coarse-grained (CG) models in molecular dynamics (MD) are powerful tools to simulate the dynamics of large biomolecular systems on micro- to millisecond timescales. However, the CG model, potential energy terms, and parameters are typically not transferable between different molecules and problems. So parameterizing CG force fields, which is both tedious and time-consuming, is often necessary. We present RedMDStream, a software for developing, testing, and simulating biomolecules with CG MD models. Development includes an automatic procedure for the optimization of potential energy parameters based on metaheuristic methods. As an example we describe the parameterization of a simple CG MD model of an RNA hairpin. PMID:25902423

  7. 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.

  8. Derivation of free energy expressions for tube models from coarse-grained slip-link models.

    PubMed

    Steenbakkers, Rudi J A; Schieber, Jay D

    2012-07-21

    We present the free energy of a single-chain mean-field model for polymer melt dynamics, which uses a continuous (tube-like) approximation to the discrete entanglements with surrounding chains, but, in contrast to previous tube models, includes fluctuations in the number density of Kuhn steps along the primitive path and in the degree of entanglement. The free energy is obtained from that of the slip-link model with fluctuating entanglement positions [J. D. Schieber and K. Horio, J. Chem. Phys. 132, 074905 (2010)] by taking the continuous limit of (functions of) the discrete Kuhn-step numbers and end-to-end vectors of the strands between entanglements. This coarse-graining from a more-detailed level of description has the advantage that no ad hoc arguments need to be introduced. Moreover, the thermodynamic consistency of the slip-link model [J. D. Schieber, J. Non-Equilib. Thermodyn. 28, 179 (2003)] can be preserved. Fluctuations in the positions of entanglements lead to a harmonic bending term in the free energy of the continuous chain, similar to that derived by Read et al. [Macromolecules 41, 6843 (2008)] starting from a modified GLaMM model [R. S. Graham, A. E. Likhtman, T. C. B. McLeish, and S. T. Milner, J. Rheol. 47, 1171 (2003)]. If these fluctuations are set to zero, the free energy becomes purely Gaussian and corresponds to the continuous limit of the original slip-link model, with affinely moving entanglements [J. D. Schieber, J. Chem. Phys. 118, 5162 (2003)]. The free energy reduces to that of Read et al. under their assumptions of a homogeneous Kuhn-step number density and a constant degree of entanglement. Finally, we show how a transformation of the primitive-path coordinate can be applied to make the degree of entanglement an outcome of the model instead of a variable. In summary, this paper constitutes a first step towards a unified mathematical formulation of tube models. The next step will be to formulate the dynamics of the primitive

  9. Derivation of free energy expressions for tube models from coarse-grained slip-link models

    NASA Astrophysics Data System (ADS)

    Steenbakkers, Rudi J. A.; Schieber, Jay D.

    2012-07-01

    We present the free energy of a single-chain mean-field model for polymer melt dynamics, which uses a continuous (tube-like) approximation to the discrete entanglements with surrounding chains, but, in contrast to previous tube models, includes fluctuations in the number density of Kuhn steps along the primitive path and in the degree of entanglement. The free energy is obtained from that of the slip-link model with fluctuating entanglement positions [J. D. Schieber and K. Horio, J. Chem. Phys. 132, 074905 (2010)], 10.1063/1.3314727 by taking the continuous limit of (functions of) the discrete Kuhn-step numbers and end-to-end vectors of the strands between entanglements. This coarse-graining from a more-detailed level of description has the advantage that no ad hoc arguments need to be introduced. Moreover, the thermodynamic consistency of the slip-link model [J. D. Schieber, J. Non-Equilib. Thermodyn. 28, 179 (2003)], 10.1515/JNETDY.2003.010 can be preserved. Fluctuations in the positions of entanglements lead to a harmonic bending term in the free energy of the continuous chain, similar to that derived by Read et al. [Macromolecules 41, 6843 (2008)], 10.1021/ma8009855 starting from a modified GLaMM model [R. S. Graham, A. E. Likhtman, T. C. B. McLeish, and S. T. Milner, J. Rheol. 47, 1171 (2003)], 10.1122/1.1595099. If these fluctuations are set to zero, the free energy becomes purely Gaussian and corresponds to the continuous limit of the original slip-link model, with affinely moving entanglements [J. D. Schieber, J. Chem. Phys. 118, 5162 (2003)], 10.1063/1.1553764. The free energy reduces to that of Read et al. under their assumptions of a homogeneous Kuhn-step number density and a constant degree of entanglement. Finally, we show how a transformation of the primitive-path coordinate can be applied to make the degree of entanglement an outcome of the model instead of a variable. In summary, this paper constitutes a first step towards a unified mathematical

  10. Multiscale Modeling of Grain Boundary Segregation and Embrittlement in Tungsten for Mechanistic Design of Alloys for Coal Fired Plants

    SciTech Connect

    Luo, Jian; Tomar, Vikas; Zhou, Naixie; Lee, Hongsuk

    2013-06-30

    Based on a recent discovery of premelting-like grain boundary segregation in refractory metals occurring at high temperatures and/or high alloying levels, this project investigated grain boundary segregation and embrittlement in tungsten (W) based alloys. Specifically, new interfacial thermodynamic models have been developed and quantified to predict high-temperature grain boundary segregation in the W-Ni binary alloy and W-Ni-Fe, W-Ni-Ti, W-Ni-Co, W-Ni-Cr, W-Ni-Zr and W-Ni-Nb ternary alloys. The thermodynamic modeling results have been experimentally validated for selected systems. Furthermore, multiscale modeling has been conducted at continuum, atomistic and quantum-mechanical levels to link grain boundary segregation with embrittlement. In summary, this 3-year project has successfully developed a theoretical framework in combination with a multiscale modeling strategy for predicting grain boundary segregation and embrittlement in W based alloys.

  11. Optimized parallel computing for cellular automaton-finite element modeling of solidification grain structures

    NASA Astrophysics Data System (ADS)

    Carozzani, T.; Gandin, Ch-A.; Digonnet, H.

    2014-01-01

    A numerical implementation of a three-dimensional (3D) cellular automaton (CA)-finite element (FE) model has been developed for the prediction of solidification grain structures. For the first time, it relies on optimized parallel computation to solve industrial-scale problems (centimeter to meter long) while using a sufficiently small CA grid size to predict representative structures. Several algorithm modifications and strategies to maximize parallel efficiency are introduced. Improvements on a real case simulation are measured and discussed. The CA-FE implementation here is demonstrated using 32 computing units to predict grain structure in a 2.08 m × 0.382 m × 0.382 m ingot involving 4.9 billion cells and 1.6 million grains. These numerical improvements permit tracking of local changes in texture and grain size over real-cast parts while integrating interactions with macrosegregation, heat flow and fluid flow. Full 3D is essential in all these analyses, and can be dealt with successfully using the implementation presented here.

  12. Pairwise energies for polypeptide coarse-grained models derived from atomic force fields

    NASA Astrophysics Data System (ADS)

    Betancourt, Marcos R.; Omovie, Sheyore J.

    2009-05-01

    The energy parametrization of geometrically simplified versions of polypeptides, better known as polypeptide or protein coarse-grained models, is obtained from molecular dynamics and statistical methods. Residue pairwise interactions are derived by performing atomic-level simulations in explicit water for all 210 pairs of amino acids, where the amino acids are modified to closer match their structure and charges in polypeptides. Radial density functions are computed from equilibrium simulations for each pair of residues, from which statistical energies are extracted using the Boltzmann inversion method. The resulting models are compared to similar potentials obtained by knowledge based methods and to hydrophobic scales, resulting in significant similarities in spite of the model simplicity. However, it was found that glutamine, asparagine, lysine, and arginine are more attractive to other residues than anticipated, in part, due to their amphiphilic nature. In addition, equally charged residues appear more repulsive than expected. Difficulties in the calculation of knowledge based potentials and hydrophobicity scale for these cases, as well as sensitivity of the force field to polarization effects are suspected to cause this discrepancy. It is also shown that the coarse-grained model can identify native structures in decoy databases nearly as well as more elaborate knowledge based methods, in spite of its resolution limitations. In a test conducted with several proteins and corresponding decoys, the coarse-grained potential was able to identify the native state structure but not the original atomic force field.

  13. Pairwise energies for polypeptide coarse-grained models derived from atomic force fields.

    PubMed

    Betancourt, Marcos R; Omovie, Sheyore J

    2009-05-21

    The energy parametrization of geometrically simplified versions of polypeptides, better known as polypeptide or protein coarse-grained models, is obtained from molecular dynamics and statistical methods. Residue pairwise interactions are derived by performing atomic-level simulations in explicit water for all 210 pairs of amino acids, where the amino acids are modified to closer match their structure and charges in polypeptides. Radial density functions are computed from equilibrium simulations for each pair of residues, from which statistical energies are extracted using the Boltzmann inversion method. The resulting models are compared to similar potentials obtained by knowledge based methods and to hydrophobic scales, resulting in significant similarities in spite of the model simplicity. However, it was found that glutamine, asparagine, lysine, and arginine are more attractive to other residues than anticipated, in part, due to their amphiphilic nature. In addition, equally charged residues appear more repulsive than expected. Difficulties in the calculation of knowledge based potentials and hydrophobicity scale for these cases, as well as sensitivity of the force field to polarization effects are suspected to cause this discrepancy. It is also shown that the coarse-grained model can identify native structures in decoy databases nearly as well as more elaborate knowledge based methods, in spite of its resolution limitations. In a test conducted with several proteins and corresponding decoys, the coarse-grained potential was able to identify the native state structure but not the original atomic force field.

  14. Cross-Species Extrapolation of Prediction Models for Cadmium Transfer from Soil to Corn Grain

    PubMed Central

    Yang, Hua; Li, Zhaojun; Lu, Lu; Long, Jian; Liang, Yongchao

    2013-01-01

    Cadmium (Cd) is a highly toxic heavy metal for both plants and animals. The presence of Cd in agricultural soils is of great concern regarding its transfer in the soil-plant system. This study investigated the transfer of Cd (exogenous salts) from a wide range of Chinese soils to corn grain (Zhengdan 958). Through multiple stepwise regressions, prediction models were developed, with the combination of Cd bioconcentration factor (BCF) of Zhengdan 958 and soil pH, organic matter (OM) content, and cation exchange capacity (CEC). Moreover, these prediction models from Zhengdan 958 were applied to other non-model corn species through cross-species extrapolation approach. The results showed that the pH of the soil was the most important factor that controlled Cd uptake and lower pH was more favorable for Cd bioaccumulation in corn grain. There was no significant difference among three prediction models in the different Cd levels. When the prediction models were applied to other non-model corn species, the ratio ranges between the predicted BCF values and the measured BCF values were within an interval of 2 folds and close to the solid line of 1∶1 relationship. Furthermore, these prediction models also reduced the measured BCF intra-species variability for all non-model corn species. Therefore, the prediction models established in this study can be applied to other non-model corn species and be useful for predicting the Cd bioconcentration in corn grain and assessing the ecological risk of Cd in different soils. PMID:24324636

  15. Dynamic force matching: A method for constructing dynamical coarse-grained models with realistic time dependence

    SciTech Connect

    Davtyan, Aram; Dama, James F.; Voth, Gregory A.; Andersen, Hans C.

    2015-04-21

    Coarse-grained (CG) models of molecular systems, with fewer mechanical degrees of freedom than an all-atom model, are used extensively in chemical physics. It is generally accepted that a coarse-grained model that accurately describes equilibrium structural properties (as a result of having a well constructed CG potential energy function) does not necessarily exhibit appropriate dynamical behavior when simulated using conservative Hamiltonian dynamics for the CG degrees of freedom on the CG potential energy surface. Attempts to develop accurate CG dynamic models usually focus on replacing Hamiltonian motion by stochastic but Markovian dynamics on that surface, such as Langevin or Brownian dynamics. However, depending on the nature of the system and the extent of the coarse-graining, a Markovian dynamics for the CG degrees of freedom may not be appropriate. In this paper, we consider the problem of constructing dynamic CG models within the context of the Multi-Scale Coarse-graining (MS-CG) method of Voth and coworkers. We propose a method of converting a MS-CG model into a dynamic CG model by adding degrees of freedom to it in the form of a small number of fictitious particles that interact with the CG degrees of freedom in simple ways and that are subject to Langevin forces. The dynamic models are members of a class of nonlinear systems interacting with special heat baths that were studied by Zwanzig [J. Stat. Phys. 9, 215 (1973)]. The properties of the fictitious particles can be inferred from analysis of the dynamics of all-atom simulations of the system of interest. This is analogous to the fact that the MS-CG method generates the CG potential from analysis of equilibrium structures observed in all-atom simulation data. The dynamic models generate a non-Markovian dynamics for the CG degrees of freedom, but they can be easily simulated using standard molecular dynamics programs. We present tests of this method on a series of simple examples that demonstrate that

  16. Dynamic force matching: A method for constructing dynamical coarse-grained models with realistic time dependence

    NASA Astrophysics Data System (ADS)

    Davtyan, Aram; Dama, James F.; Voth, Gregory A.; Andersen, Hans C.

    2015-04-01

    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. In this paper, we consider the problem of constructing dynamic CG models within the context of the Multi-Scale Coarse-graining (MS-CG) method of Voth and coworkers. We propose a method of converting a MS-CG model into a dynamic CG model by adding degrees of freedom to it in the form of a small number of fictitious particles that interact with the CG degrees of freedom in simple ways and that are subject to Langevin forces. The dynamic models are members of a class of nonlinear systems interacting with special heat baths that were studied by Zwanzig [J. Stat. Phys. 9, 215 (1973)]. The properties of the fictitious particles can be inferred from analysis of the dynamics of all-atom simulations of the system of interest. This is analogous to the fact that the MS-CG method generates the CG potential from analysis of equilibrium structures observed in all-atom simulation data. The dynamic models generate a non-Markovian dynamics for the CG degrees of freedom, but they can be easily simulated using standard molecular dynamics programs. We present tests of this method on a series of simple examples that demonstrate that

  17. 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.

  18. 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.

  19. Dynamic and impact contact mechanics of geologic materials: Grain-scale experiments and modeling

    SciTech Connect

    Cole, David M.; Hopkins, Mark A.; Ketcham, Stephen A.

    2013-06-18

    High fidelity treatments of the generation and propagation of seismic waves in naturally occurring granular materials is becoming more practical given recent advancements in our ability to model complex particle shapes and their mechanical interaction. Of particular interest are the grain-scale processes that are activated by impact events and the characteristics of force transmission through grain contacts. To address this issue, we have developed a physics based approach that involves laboratory experiments to quantify the dynamic contact and impact behavior of granular materials and incorporation of the observed behavior indiscrete element models. The dynamic experiments do not involve particle damage and emphasis is placed on measured values of contact stiffness and frictional loss. The normal stiffness observed in dynamic contact experiments at low frequencies (e.g., 10 Hz) are shown to be in good agreement with quasistatic experiments on quartz sand. The results of impact experiments - which involve moderate to extensive levels of particle damage - are presented for several types of naturally occurring granular materials (several quartz sands, magnesite and calcium carbonate ooids). Implementation of the experimental findings in discrete element models is discussed and the results of impact simulations involving up to 5 Multiplication-Sign 105 grains are presented.

  20. Grain-scale modeling of arbitrary fluid saturation in random packings.

    PubMed

    Melnikov, Konstantin; Mani, Roman; Wittel, Falk K; Thielmann, Marcel; Herrmann, Hans J

    2015-08-01

    We propose a model for increasing liquid saturation in a granular packing, which can account for liquid redistribution at saturation levels beyond the well-studied capillary bridge regime. The model is capable of resolving and combining capillary bridges, menisci, and fully saturated pores to form local liquid clusters of any shape. They can exchange volume due to the local Laplace pressure gradient via a liquid film on the surfaces of grains. Local instabilities such as Haines jumps trigger the discontinuous evolution of the liquid front. The applicability of the model is demonstrated and compared to benchmark experiments on the level of individual liquid structures as well as on larger systems.

  1. Computer simulation of topological evolution in 2-d grain growth using a continuum diffuse-interface field model

    SciTech Connect

    Fan, D.; Geng, C.; Chen, L.Q.

    1997-03-01

    The local kinetics and topological phenomena during normal grain growth were studied in two dimensions by computer simulations employing a continuum diffuse-interface field model. The relationships between topological class and individual grain growth kinetics were examined, and compared with results obtained previously from analytical theories, experimental results and Monte Carlo simulations. It was shown that both the grain-size and grain-shape (side) distributions are time-invariant and the linear relationship between the mean radii of individual grains and topological class n was reproduced. The moments of the shape distribution were determined, and the differences among the data from soap froth. Potts model and the present simulation were discussed. In the limit when the grain size goes to zero, the average number of grain edges per grain is shown to be between 4 and 5, implying the direct vanishing of 4- and 5-sided grains, which seems to be consistent with recent experimental observations on thin films. Based on the simulation results, the conditions for the applicability of the familiar Mullins-Von Neumann law and the Hillert`s equation were discussed.

  2. Coarse-graining molecular dynamics models using an extended Galerkin method

    NASA Astrophysics Data System (ADS)

    Li, Xiantao

    2013-03-01

    I will present a systematic approach to coarse-grain molecular dynamics models for solids. The coarse-grained models are derived by Galerkin projection to a sequence of Krylov subspaces. On the coarsest space, the model corresponds to a finite element discretization of the continuum elasto-dynamics model. On the other hand, the projection to the finest space yields the full molecular dynamics description. The models in between serve as a smooth transition between the two scales. We start with a molecular dynamics (MD) model, mix¨i = -∂V/∂xi . First, let Y0 be the approximation space for the continuum model. By projecting the MD model onto the subspace, we obtain a coarse-grained model, M q ¨ = F (q) . Using the Cauchy-Born approximation, this model can be shown to coincide with the finite element representation of the continuum elastodynamics model. This model has limited accuracy near lattice defects. One natural idea is to switch to the MD model in regions surround local defect. As a result, one creates an interface between the continuum and atomistic description, where coupling conditions are needed. Direct coupling methods may involve enforcing constraints or mixing the energy or forces. Such an approach may suffer from large phonon reflections at the interface, and introduce large modeling error. In order to seamlessly couple this model to MD, we successively expand the approximation space to the Krylov spaces, Kl =Y0 + AY0 + ⋯ +AlY0 . Here A is the force constant matrix, computed from the atomistic model. Due to the translational invariance, only a smaller number of such matrices need to be computed. By projecting the MD model onto this new subspace, we obtain an extended system, M q .. =F0 (q ,ξ1 , ... ,ξl) ,ξ̈1 =F1 (q ,ξ1 , ... ,ξl) , ... ... ,ξ̈l =Fl (q ,ξ1 , ... ,ξl) . The additional variables ξj represent the coefficients in the extended approximation space. Using this systematic approach, one can build a hierarchy of models with

  3. Polymer-solid contacts described by soft, coarse-grained models.

    PubMed

    Müller, Marcus; Steinmüller, Birger; Daoulas, Kostas Ch; Ramírez-Hernández, Abelardo; de Pablo, Juan J

    2011-06-14

    The ability of soft, coarse-grained models to describe the narrow interface of a nearly incompressible polymer melt in contact with a solid is explored by numerical self-consistent field calculations and Monte-Carlo simulations. We investigate the effect of the discreteness of the bead-spring architecture by quantitatively comparing the results of a bead-spring model with different number of beads, N, but identical end-to-end distance, R(e), and a continuous Gaussian-thread model. If the width, ξ, of the narrow polymer-solid contact is smaller or comparable to the length of a statistical segment, b=R(e)/√N-1, strong differences in the interface tension and the density profiles between the two models are observed, and strategies for compensating the discrete nature of the bead-spring model are investigated. Compensating the discretization of the chain contour in the bead-spring model by applying an external segment-solid potential, we simultaneously adjust the interface tension and the density profile to the predictions of the Gaussian-thread model. We suggest that the geometry of the polymer-solid contact and the interface tension are relevant characteristics that a coarse-grained model of polymer-solid contacts must reproduce in order to establish a quantitative relationship to an experimental system.

  4. a Nonequilibrium Plasmadynamics Model for Nitrogen/hydrogen Arcjets

    NASA Astrophysics Data System (ADS)

    Megli, Thomas W.

    Electrothermal arcjets offer significant cost advantage over conventional satellite propulsion systems. In these devices, the propellant is electrically heated, allowing for higher temperatures and specific impulse than chemical rockets. Despite the relative simplicity of the basic design, many complex physical processes are poorly understood. Less than 50% of the electrical power is converted to thrust kinetic power. A numerical model is developed to study arcjet plasma flowfields. The model employs a modified set of Navier-Stokes equations, which includes separate energy equations for the electrons and heavy species. A thermal nonequilibrium, chemical equilibrium model is first developed, and then generalized to chemical nonequilibrium. A seven -species plasma of molecules, atoms, and ions is assumed for a variable mixture ratio of nitrogen and hydrogen. This permits simulation of various propellants, including hydrogen, ammonia, and hydrazine. Equations for charge continuity and Ohm's Law are employed to predict the arc current distribution. A thermal model for the nozzle is also included. The combined features of thermal nonequilibrium, chemical nonequilibrium, and propellant flexibility distinguish this model from previous research efforts. Model calculations are presented for 1-2 kW-class arcjets operating with hydrogen and hydrazine propellants. Thermal equilibrium is predicted in the highly ionized arc core, while electron temperatures near the electrodes are an order of magnitude greater than heavy species temperatures. The thermal nonequilibrium enhances ionization and electrical conductivity, and thus governs the current attachment to the nozzle. A comparison of chemical equilibrium and nonequilibrium simulations indicates that ambipolar diffusion of electrons and ions also controls the current conduction. The model is compared with experimental measurements. Respective calculations for specific impulse and exhaust velocities are within approximately 5

  5. Water films at grain-grain contacts: Debye-Hueckel, osmotic model of stress, salinity, and mineralogy dependence

    SciTech Connect

    Renard, F.; Ortoleva, P.

    1997-05-01

    Water film diffusion is one of the mechanisms proposed to explain the deformation of rocks by pressure-solution during geological processes in the upper crust. This mechanism assumes that matter is dissolved inside the contact between two grains. The resulting solutes are transported in the pore fluid through diffusion in an adsorbed water film. The main problem of this theory is that it requires the presence of a water film that is believed to be stable under large deviatoric stresses inside the contact between two grains. In this paper, we show that the electrically charged surface of a mineral can attract counter-ions from the pore and, by the related change of osmotic pressure, keep water within the contact. This is due to the counter ions in the water film that increase the salinity in the film relative to that in the pore. This lowers the free energy of water in the contact zone to a degree that balances the increase in free energy of water due to the elevated pressure in the film. These notions are made more precise by combining the theory of the Debye-Hueckle double layer with equations of osmotic pressure. The resulting D-H/O theory predicts the dependence of the water film thickness on stress across the contact, composition of the pore fluid, and the identity of the minerals involved. 33 refs., 4 figs., 1 tab.

  6. Effect of grain morphology on gas bubble swelling in UMo fuels - A 3D microstructure dependent Booth model

    NASA Astrophysics Data System (ADS)

    Hu, Shenyang; Burkes, Douglas; Lavender, Curt A.; Joshi, Vineet

    2016-11-01

    A three dimensional microstructure dependent swelling model is developed for studying the fission gas swelling kinetics in irradiated nuclear fuels. The model is extended from the Booth model [1] in order to investigate the effect of heterogeneous microstructures on gas bubble swelling kinetics. As an application of the model, the effect of grain morphology, fission gas diffusivity, and spatially dependent fission rate on swelling kinetics are simulated in UMo fuels. It is found that the decrease of grain size, the increase of grain aspect ratio for the grain having the same volume, and the increase of fission gas diffusivity (fission rate) cause the increase of swelling kinetics. Other heterogeneities such as second phases and spatially dependent thermodynamic properties including diffusivity of fission gas, sink and source strength of defects could be naturally integrated into the model to enhance the model capability.

  7. Physics-Based Reactive Burn Model: Grain size effects and binder effects

    NASA Astrophysics Data System (ADS)

    Lu, Xia; Hamate, Yuichio; Horie, Yasuyuki

    2007-06-01

    We have been developing a physics-based reactive burn (PBRB) model aiming at expanding predictive capability. The PBRB model was formulated based on the concept of a statistical hot spot cell. In the model, thermomechanics and physiochemical features are explicitly modeled. In this paper, we have extended the statistical hot spot model to explicitly describe the ignition and growth of hot spots. In particular, grain size effects are explicitly delineated through introduction of a size-dependent thickness of the hot-region thickness, a size-dependent energy deposition criterion, and a specific surface area. Besides the linear relationships between the run distance to detonation and critical diameter with the reciprocal specific surface area of HE, as discussed in a parallel paper in this meeting, parametric studies have also shown that the PBRB can predict a non-monotonous variation of shock sensitivity with grain size, as observed by Moulard et al. The purpose of this work is to extend the model to include the effects of explosive binders explicitly. As a first step we investigate the thermomechanical effects of a binder by using direct mesoscale simulations. The results will be used in the extending the PBRB model to include binder thermomechanics explicitly.

  8. Refining the treatment of membrane proteins by coarse-grained models.

    PubMed

    Vorobyov, Igor; Kim, Ilsoo; Chu, Zhen T; Warshel, Arieh

    2016-01-01

    Obtaining a quantitative description of the membrane proteins stability is crucial for understanding many biological processes. However the advance in this direction has remained a major challenge for both experimental studies and molecular modeling. One of the possible directions is the use of coarse-grained models but such models must be carefully calibrated and validated. Here we use a recent progress in benchmark studies on the energetics of amino acid residue and peptide membrane insertion and membrane protein stability in refining our previously developed coarse-grained model (Vicatos et al., Proteins 2014;82:1168). Our refined model parameters were fitted and/or tested to reproduce water/membrane partitioning energetics of amino acid side chains and a couple of model peptides. This new model provides a reasonable agreement with experiment for absolute folding free energies of several β-barrel membrane proteins as well as effects of point mutations on a relative stability for one of those proteins, OmpLA. The consideration and ranking of different rotameric states for a mutated residue was found to be essential to achieve satisfactory agreement with the reference data.

  9. Modelling nitrogen and carbon interactions in composting of animal manure in naturally aerated piles.

    PubMed

    Oudart, D; Robin, P; Paillat, J M; Paul, E

    2015-12-01

    Composting animal manure with natural aeration is a low-cost and low-energy process that can improve nitrogen recycling in millions of farms world-wide. Modelling can decrease the cost of choosing the best options for solid manure management in order to decrease the risk of loss of fertilizer value and ammonia emission. Semi-empirical models are suitable, considering the scarce data available in farm situations. Eleven static piles of pig or poultry manure were monitored to identify the main processes governing nitrogen transformations and losses. A new model was implemented to represent these processes in a pile considered as homogeneous. The model is based on four modules: biodegradation, nitrogen transformations and volatilization, thermal exchanges, and free air space evolution. When necessary, the parameters were calibrated with the data set. The results showed that microbial growth could reduce ammonia volatilization. Greatest nitrogen conservation is achieved when microbial growth was limited by nitrogen availability.

  10. Modelling nitrogen and carbon interactions in composting of animal manure in naturally aerated piles.

    PubMed

    Oudart, D; Robin, P; Paillat, J M; Paul, E

    2015-12-01

    Composting animal manure with natural aeration is a low-cost and low-energy process that can improve nitrogen recycling in millions of farms world-wide. Modelling can decrease the cost of choosing the best options for solid manure management in order to decrease the risk of loss of fertilizer value and ammonia emission. Semi-empirical models are suitable, considering the scarce data available in farm situations. Eleven static piles of pig or poultry manure were monitored to identify the main processes governing nitrogen transformations and losses. A new model was implemented to represent these processes in a pile considered as homogeneous. The model is based on four modules: biodegradation, nitrogen transformations and volatilization, thermal exchanges, and free air space evolution. When necessary, the parameters were calibrated with the data set. The results showed that microbial growth could reduce ammonia volatilization. Greatest nitrogen conservation is achieved when microbial growth was limited by nitrogen availability. PMID:26403389

  11. Coarse-graining to the meso and continuum scales with molecular-dynamics-like models

    NASA Astrophysics Data System (ADS)

    Plimpton, Steve

    Many engineering-scale problems that industry or the national labs try to address with particle-based simulations occur at length and time scales well beyond the most optimistic hopes of traditional coarse-graining methods for molecular dynamics (MD), which typically start at the atomic scale and build upward. However classical MD can be viewed as an engine for simulating particles at literally any length or time scale, depending on the models used for individual particles and their interactions. To illustrate I'll highlight several coarse-grained (CG) materials models, some of which are likely familiar to molecular-scale modelers, but others probably not. These include models for water droplet freezing on surfaces, dissipative particle dynamics (DPD) models of explosives where particles have internal state, CG models of nano or colloidal particles in solution, models for aspherical particles, Peridynamics models for fracture, and models of granular materials at the scale of industrial processing. All of these can be implemented as MD-style models for either soft or hard materials; in fact they are all part of our LAMMPS MD package, added either by our group or contributed by collaborators. Unlike most all-atom MD simulations, CG simulations at these scales often involve highly non-uniform particle densities. So I'll also discuss a load-balancing method we've implemented for these kinds of models, which can improve parallel efficiencies. From the physics point-of-view, these models may be viewed as non-traditional or ad hoc. But because they are MD-style simulations, there's an opportunity for physicists to add statistical mechanics rigor to individual models. Or, in keeping with a theme of this session, to devise methods that more accurately bridge models from one scale to the next.

  12. Folding of small knotted proteins: Insights from a mean field coarse-grained model

    SciTech Connect

    Najafi, Saeed; Potestio, Raffaello

    2015-12-28

    A small but relevant number of proteins whose native structure is known features nontrivial topology, i.e., they are knotted. Understanding the process of folding from a swollen unknotted state to the biologically relevant native conformation is, for these proteins, particularly difficult, due to their rate-limiting topological entanglement. To shed some light into this conundrum, we introduced a structure-based coarse-grained model of the protein, where the information about the folded conformation is encoded in bonded angular interactions only, which do not favor the formation of native contacts. A stochastic search scheme in parameter space is employed to identify a set of interactions that maximizes the probability to attain the knotted state. The optimal knotting pathways of the two smallest knotted proteins, obtained through this approach, are consistent with the results derived by means of coarse-grained as well as full atomistic simulations.

  13. The effect of free air carbon dioxide enrichment and nitrogen fertilisation on the chemical composition and nutritional value of wheat and barley grain.

    PubMed

    Wroblewitz, Stefanie; Hüther, Liane; Manderscheid, Remy; Weigel, Hans-Joachim; Wätzig, Hermann; Dänicke, Sven

    2013-08-01

    A rising atmospheric CO2 concentration might influence the nutrient composition of feedstuffs and consequently the nutritional value for livestock. The present study investigates the effects of atmospheric CO2 enrichment on the chemical composition and nutritional value of winter wheat cv. "Batis" and winter barley cv. "Theresa". Both cereals were grown at two different atmospheric CO2 concentrations (ambient CO2 [AMBI]: 380 ppm and enriched CO2 [free air carbon dioxide enrichment, FACE]: 550 ppm) for two growing seasons. The influence of two different nitrogen (N) fertilisation levels (adequate N supply [N100] and nearly 50% of adequate N supply [N50]) were studied as well. A significant effect was observed for the crude protein content, which declined at FACE condition in a range of 8-16 g kg(-1) in wheat and of 10-20 g kg(-1) in barley. A reduced N fertilisation level resulted in a strong reduction of crude protein concentration in both cereal species. In wheat, a decrease in N supply significantly enhanced the concentration of starch and crude fibre. In barley, only the concentration of fructose increased under FACE condition and reduced N fertilisation. The FACE did not have major effects on the concentrations of minerals, while the influence of N fertilisation was different for both cereals. Whereas no effects could be observed for barley, a reduced N supply caused a significant reduction in concentrations of zinc, manganese and iron in wheat. Furthermore, an undirected effect of atmospheric CO2 and N fertilisation levels were found for the amino acid concentrations. Based on these results, future scenarios of climate change would have an impact on the nutritional value of cereal grains.

  14. How well does end-member modelling analysis of grain size data work?

    NASA Astrophysics Data System (ADS)

    Schulte, Philipp; Dietze, Michael; Dietze, Elisabeth

    2014-05-01

    End-member modelling analysis (EMMA) is a powerful and flexible statistic approach to identify and quantify generic sediment transport processes from multimodal grain-size distributions. EMMA has been introduced over 15 years ago and is now available in different approaches as encapsulated FORTRAN code (Weltje, 1997), Matlab-script (Dietze et al., 2012) and the R-package EMMAgeo (Dietze and Dietze, 2013). EMMA was mainly used to reconstruct past sedimentation processes in a variety of sedimentary environments (marine, aeolian, lacustrine). Typically, it is rather difficult to assess how meaningful and well the model performs in a certain environment, since neither the actual process end-members (generic grain-size distributions sorted by a certain sediment transport) nor their individual contributions to each sample are known a priori. To allow a comprehensive performance test, we sampled a set of four known process end-members: alluvial sand (main mode: 0.70±0.55 φ), dune sand (main mode: 1.35±0.60 φ), loess (main mode: 4.71±0.65 φ) and overbank deposit (main mode: 5.81±1.62 φ). High resolution grain-size information is based on laser-diffraction analysis (116 classes). The four process end-members were artificially mixed with random, but known proportions to yield 100 samples. This mixed data set was measured again with the laser particle size analyser and served as input for EMMA within the R-package EMMAgeo. This contribution discusses the ability of EMMA to identify and characterise the four distinct process end-members and quantify their contributions to each sample. Different ways to estimate uncertainties are presented. Further evaluations focus on the influence of numbers of included samples, numbers of grain-size classes, vertical mixing of samples (simulating turbation) and self-similarity of process end-members. Dietze E, et al. 2012. An end-member algorithm for deciphering modern detrital processes from lake sediments of Lake Donggi Cona, NE

  15. Construction of Coarse-Grained Models by Reproducing Equilibrium Probability Density Function

    NASA Astrophysics Data System (ADS)

    Lu, Shi-Jing; Zhou, Xin

    2015-01-01

    The present work proposes a novel methodology for constructing coarse-grained (CG) models, which aims at minimizing the difference between CG model and the corresponding original system. The difference is defined as a functional of their equilibrium conformational probability densities, then is estimated from equilibrium averages of many independent physical quantities denoted as basis functions. An orthonormalization strategy is adopted to get the independent basis functions from sufficiently preselected interesting physical quantities of the system. Thus the current method is named as probability density matching coarse-graining (PMCG) scheme, which effectively takes into account the overall characteristics of the original systems to construct CG model, and it is a natural improvement of the usual CG scheme wherein some physical quantities are intuitively chosen without considering their correlations. We verify the general PMCG framework in constructing a one-site CG water model from TIP3P model. Both structure of liquids and pressure of the TIP3P water system are found to be well reproduced at the same time in the constructed CG model.

  16. Denitrification, leaching, and river nitrogen export in the Community Earth System Model

    NASA Astrophysics Data System (ADS)

    Nevison, Cynthia; Hess, Peter; Riddick, Stuart; Ward, Dan

    2016-03-01

    River nitrogen export is simulated within the Community Earth System Model (CESM) by coupling nitrogen leaching and runoff fluxes from the Community Land Model (CLM) to the River Transport Model (RTM). The coupled CLM-RTM prognostically simulates the downstream impact of human N cycle perturbation on coastal areas. It also provides a framework for estimating denitrification fluxes of N2 and associated trace gases like N2O in soils and river sediments. An important limitation of the current model is that it only simulates dissolved inorganic nitrogen (DIN) river export, due to the lack of dissolved organic nitrogen (DON) and particulate nitrogen (PN) leaching fluxes in CLM. In addition, the partitioning of soil N loss in CLM between the primary loss pathways of denitrification and N leaching/runoff appears heavily skewed toward denitrification compared to other literature estimates, especially in nonagricultural regions, and also varies considerably among the four model configurations presented here. River N export is generally well predicted in the model configurations that include midlatitude crops, but tends to be underpredicted in rivers that are less perturbed by human agriculture. This is especially true in the tropics, where CLM likely underestimates leaching and runoff of all forms of nitrogen. River export of DIN is overpredicted in some relatively unperturbed Arctic rivers, which may result from excessive N inputs to those regions in CLM. Better representation of N loss in CLM can improve confidence in model results with respect to the core model objective of simulating nitrogen limitation of the carbon cycle.

  17. Atomic structures and energies of grain boundaries in Mg2SiO4 forsterite from atomistic modeling

    NASA Astrophysics Data System (ADS)

    Adjaoud, Omar; Marquardt, Katharina; Jahn, Sandro

    2012-10-01

    Grain boundaries influence many physical and chemical properties of crystalline materials. Here, we perform molecular dynamics simulations to study the structure of a series of [100] symmetric tilt grain boundaries in Mg2SiO4 forsterite. The present results show that grain boundary energies depend significantly on misorientation angle. For small misorientation angles (up to 22°), grain boundary structures consist of an array of partial edge dislocations with Burgers vector 1/2[001] associated with stacking faults and their energies can be readily fit with a model which adds the Peach-Koehler equation to the Read-Shockley dislocation model for grain boundaries. The core radius of partial dislocations and the spacing between the partials derived from grain boundary energies show that the transition from low- to high-angle grain boundaries occurs for a misorientation angle between 22° and 32°. For high misorientation angles (32.1° and 60.8°), the cores of dislocations overlap and form repeated structural units. Finally, we use a low energy atomic configuration obtained by molecular dynamics for the misorientation of 12.18° as input to simulate a high-resolution transmission electron microscopy (HRTEM) image. The simulated image is in good agreement with an observed HRTEM image, which indicates the power of the present approach to predict realistic atomic structures of grain boundaries in complex silicates.

  18. Nitrogen transformations in a wetland receiving lagoon effluent: sequential model and implications for water reuse.

    PubMed

    Gerke, S; Baker, L A; Xu, Y

    2001-11-01

    Constructed wetlands could be components of low-tech systems to treat and reuse wastewater in arid region. A key function of the wetland would be to provide additional N removal. To improve design criteria, a sequential model of nitrogen transformations (organic N --> ammonium: ammonium --> nitrate: nitrate --> nitrogen gas) was successfully calibrated and verified for a wetland in Kingman, Arizona. A sequential model has the ability to "recognize" species of nitrogen in the influent and predict species of nitrogen in the effluent. Model scenarios show that increasing nitrification rates in the summer and denitrification rates in the winter would improve nitrogen removal efficiencies. Several lines of evidence suggest that wintertime denitrification may be limited by carbon supply. Winter carbon supply could be augmented by routing a portion of the water through channels planted with dryland vegetation.

  19. Two-Component Coarse-Grained Molecular-Dynamics Model for the Human Erythrocyte Membrane

    PubMed Central

    Li, He; Lykotrafitis, George

    2012-01-01

    We present a two-component coarse-grained molecular-dynamics model for simulating the erythrocyte membrane. The proposed model possesses the key feature of combing the lipid bilayer and the erythrocyte cytoskeleton, thus showing both the fluidic behavior of the lipid bilayer and the elastic properties of the erythrocyte cytoskeleton. In this model, three types of coarse-grained particles are introduced to represent clusters of lipid molecules, actin junctions, and band-3 complexes, respectively. The proposed model facilitates simulations that span large length scales (approximately micrometers) and timescales (approximately milliseconds). By tuning the interaction potential parameters, we were able to control the diffusivity and bending rigidity of the membrane model. We studied the membrane under shearing and found that at a low shear strain rate, the developed shear stress was due mainly to the spectrin network, whereas the viscosity of the lipid bilayer contributed to the resulting shear stress at higher strain rates. In addition, we investigated the effects of a reduced spectrin network connectivity on the shear modulus of the membrane. PMID:22225800

  20. A coarse-grained model to study calcium activation of the cardiac thin filament

    NASA Astrophysics Data System (ADS)

    Zhang, Jing; Schwartz, Steven

    2015-03-01

    Familial hypertrophic cardiomyopathy (FHC) is one of the most common heart disease caused by genetic mutations. Cardiac muscle contraction and relaxation involve regulation of crossbridge binding to the cardiac thin filament, which regulates actomyosin interactions through calcium-dependent alterations in the dynamics of cardiac troponin (cTn) and tropomyosin (Tm). An atomistic model of cTn complex interacting with Tm has been studied by our group. A more realistic model requires the inclusion of the dynamics of actin filament, which is almost 6 times larger than cTn and Tm in terms of atom numbers, and extensive sampling of the model becomes very resource-demanding. By using physics-based protein united-residue force field, we introduce a coarse-grained model to study the calcium activation of the thin filament resulting from cTn's allosteric regulation of Tm dynamics on actin. The time scale is much longer than that of all-atom molecular dynamics simulation because of the reduction of the degrees of freedom. The coarse-grained model is a good template for studying cardiac thin filament mutations that cause FHC, and reduces the cost of computational resources.

  1. Parameterizing the Morse potential for coarse-grained modeling of blood plasma

    SciTech Connect

    Zhang, Na; Zhang, Peng; Kang, Wei; Bluestein, Danny; Deng, Yuefan

    2014-01-15

    Multiscale simulations of fluids such as blood represent a major computational challenge of coupling the disparate spatiotemporal scales between molecular and macroscopic transport phenomena characterizing such complex fluids. In this paper, a coarse-grained (CG) particle model is developed for simulating blood flow by modifying the Morse potential, traditionally used in Molecular Dynamics for modeling vibrating structures. The modified Morse potential is parameterized with effective mass scales for reproducing blood viscous flow properties, including density, pressure, viscosity, compressibility and characteristic flow dynamics of human blood plasma fluid. The parameterization follows a standard inverse-problem approach in which the optimal micro parameters are systematically searched, by gradually decoupling loosely correlated parameter spaces, to match the macro physical quantities of viscous blood flow. The predictions of this particle based multiscale model compare favorably to classic viscous flow solutions such as Counter-Poiseuille and Couette flows. It demonstrates that such coarse grained particle model can be applied to replicate the dynamics of viscous blood flow, with the advantage of bridging the gap between macroscopic flow scales and the cellular scales characterizing blood flow that continuum based models fail to handle adequately.

  2. Two-component coarse-grained molecular-dynamics model for the human erythrocyte membrane.

    PubMed

    Li, He; Lykotrafitis, George

    2012-01-01

    We present a two-component coarse-grained molecular-dynamics model for simulating the erythrocyte membrane. The proposed model possesses the key feature of combing the lipid bilayer and the erythrocyte cytoskeleton, thus showing both the fluidic behavior of the lipid bilayer and the elastic properties of the erythrocyte cytoskeleton. In this model, three types of coarse-grained particles are introduced to represent clusters of lipid molecules, actin junctions, and band-3 complexes, respectively. The proposed model facilitates simulations that span large length scales (approximately micrometers) and timescales (approximately milliseconds). By tuning the interaction potential parameters, we were able to control the diffusivity and bending rigidity of the membrane model. We studied the membrane under shearing and found that at a low shear strain rate, the developed shear stress was due mainly to the spectrin network, whereas the viscosity of the lipid bilayer contributed to the resulting shear stress at higher strain rates. In addition, we investigated the effects of a reduced spectrin network connectivity on the shear modulus of the membrane.

  3. Cross-Species Extrapolation of Models for Predicting Lead Transfer from Soil to Wheat Grain

    PubMed Central

    Liu, Ke; Lv, Jialong; Dai, Yunchao; Zhang, Hong; Cao, Yingfei

    2016-01-01

    The transfer of Pb from the soil to crops is a serious food hygiene security problem in China because of industrial, agricultural, and historical contamination. In this study, the characteristics of exogenous Pb transfer from 17 Chinese soils to a popular wheat variety (Xiaoyan 22) were investigated. In addition, bioaccumulation prediction models of Pb in grain were obtained based on soil properties. The results of the analysis showed that pH and OC were the most important factors contributing to Pb uptake by wheat grain. Using a cross-species extrapolation approach, the Pb uptake prediction models for cultivar Xiaoyan 22 in different soil Pb levels were satisfactorily applied to six additional non-modeled wheat varieties to develop a prediction model for each variety. Normalization of the bioaccumulation factor (BAF) to specific soil physico-chemistry is essential, because doing so could significantly reduce the intra-species variation of different wheat cultivars in predicted Pb transfer and eliminate the influence of soil properties on ecotoxicity parameters for organisms of interest. Finally, the prediction models were successfully verified against published data (including other wheat varieties and crops) and used to evaluate the ecological risk of Pb for wheat in contaminated agricultural soils. PMID:27518712

  4. Cross-Species Extrapolation of Models for Predicting Lead Transfer from Soil to Wheat Grain.

    PubMed

    Liu, Ke; Lv, Jialong; Dai, Yunchao; Zhang, Hong; Cao, Yingfei

    2016-01-01

    The transfer of Pb from the soil to crops is a serious food hygiene security problem in China because of industrial, agricultural, and historical contamination. In this study, the characteristics of exogenous Pb transfer from 17 Chinese soils to a popular wheat variety (Xiaoyan 22) were investigated. In addition, bioaccumulation prediction models of Pb in grain were obtained based on soil properties. The results of the analysis showed that pH and OC were the most important factors contributing to Pb uptake by wheat grain. Using a cross-species extrapolation approach, the Pb uptake prediction models for cultivar Xiaoyan 22 in different soil Pb levels were satisfactorily applied to six additional non-modeled wheat varieties to develop a prediction model for each variety. Normalization of the bioaccumulation factor (BAF) to specific soil physico-chemistry is essential, because doing so could significantly reduce the intra-species variation of different wheat cultivars in predicted Pb transfer and eliminate the influence of soil properties on ecotoxicity parameters for organisms of interest. Finally, the prediction models were successfully verified against published data (including other wheat varieties and crops) and used to evaluate the ecological risk of Pb for wheat in contaminated agricultural soils. PMID:27518712

  5. Linking Agricultural Crop Management and Air Quality Models for Regional to National-Scale Nitrogen Assessments

    EPA Science Inventory

    While nitrogen (N) is an essential element for life, human population growth and demands for energy, transportation and food can lead to excess nitrogen in the environment. A modeling framework is described and implemented to promote a more integrated, process-based and system le...

  6. EFFECT OF RESIDENCE TIME ON ANNUAL EXPORT AND DENITRIFICATION OF NITROGEN IN ESTUARIES: A MODEL ANALYSIS

    EPA Science Inventory

    A simple model of annual average response of an estuary to mean nitrogen loading rate and freshwater residence time was developed and tested. It uses nitrogen inputs from land, deposition from the atmosphere, and first-order calculations of internal loss rate and export to perfor...

  7. [Model designing for suitable nitrogen index dynamics of rice and wheat].

    PubMed

    Cao, Jing; Liu, Xiao-Jun; Tang, Liang; Cao, Wei-Xing; Zhu, Yan

    2010-02-01

    By analyzing and extracting the quantitative relationships of suitable nitrogen index dynamics of rice and wheat to their cultivar types, cultural techniques, and eco-environments, a design model for the suitable nitrogen index dynamics of rice and wheat was developed. The model was driven by the physiological development time-based relative growing degree days, with the relative nitrogen indices as modeling parameters, and could be used to generate the time-course indices such as the nitrogen accumulation and concentration of rice and wheat under different growth conditions. Case studies with the datasets from 3-year field experiments in Nanjing showed that the average RMSEs of the simulated to measured plant nitrogen accumulation and concentration were 0.1245 and 0.1316 for rice, and 0.1166 and 0.1301 for wheat, respectively. It was suggested that this model could reliably guide the dynamics of major nitrogen indices of rice and wheat, which would help with the quantitative nitrogen diagnosis and precision nitrogen management of rice and wheat under different eco-environments, cultivar types, and production conditions.

  8. Models of compacted fine-grained soils used as mineral liner for solid waste

    NASA Astrophysics Data System (ADS)

    Sivrikaya, Osman

    2008-02-01

    To prevent the leakage of pollutant liquids into groundwater and sublayers, the compacted fine-grained soils are commonly utilized as mineral liners or a sealing system constructed under municipal solid waste and other containment hazardous materials. This study presents the correlation equations of the compaction parameters required for construction of a mineral liner system. The determination of the characteristic compaction parameters, maximum dry unit weight ( γ dmax) and optimum water content ( w opt) requires considerable time and great effort. In this study, empirical models are described and examined to find which of the index properties correlate well with the compaction characteristics for estimating γ dmax and w opt of fine-grained soils at the standard compactive effort. The compaction data are correlated with different combinations of gravel content ( G), sand content ( S), fine-grained content (FC = clay + silt), plasticity index ( I p), liquid limit ( w L) and plastic limit ( w P) by performing multilinear regression (MLR) analyses. The obtained correlations with statistical parameters are presented and compared with the previous studies. It is found that the maximum dry unit weight and optimum water content have a considerably good correlation with plastic limit in comparison with liquid limit and plasticity index.

  9. Systematic coarse-graining of spectrin-level red blood cell models

    PubMed Central

    Fedosov, Dmitry A.; Caswell, Bruce; Karniadakis, George Em

    2013-01-01

    We present a rigorous procedure to derive coarse-grained red blood cell (RBC) models, which yield accurate mechanical response. Based on a semi-analytic theory the linear and nonlinear elastic properties of healthy and infected RBCs in malaria can be matched with those obtained in optical tweezers stretching experiments. The present analysis predicts correctly the membrane Young’s modulus in contrast to about 50% error in predictions by previous models. In addition, we develop a stress-free model which avoids a number of pitfalls of existing RBC models, such as non-smooth or poorly controlled equilibrium shape and dependence of the mechanical properties on the initial triangulation quality. Here we employ dissipative particle dynamics for the implementation but the proposed model is general and suitable for use in many existing continuum and particle-based numerical methods. PMID:24353352

  10. Development of DPD coarse-grained models: From bulk to interfacial properties.

    PubMed

    Solano Canchaya, José G; Dequidt, Alain; Goujon, Florent; Malfreyt, Patrice

    2016-08-01

    A new Bayesian method was recently introduced for developing coarse-grain (CG) force fields for molecular dynamics. The CG models designed for dissipative particle dynamics (DPD) are optimized based on trajectory matching. Here we extend this method to improve transferability across thermodynamic conditions. We demonstrate the capability of the method by developing a CG model of n-pentane from constant-NPT atomistic simulations of bulk liquid phases and we apply the CG-DPD model to the calculation of the surface tension of the liquid-vapor interface over a large range of temperatures. The coexisting densities, vapor pressures, and surface tensions calculated with different CG and atomistic models are compared to experiments. Depending on the database used for the development of the potentials, it is possible to build a CG model which performs very well in the reproduction of the surface tension on the orthobaric curve. PMID:27497539

  11. A polarizable coarse-grained protein model for dissipative particle dynamics.

    PubMed

    Peter, Emanuel K; Lykov, Kirill; Pivkin, Igor V

    2015-10-01

    We present a new coarse-grained polarizable protein model for dissipative particle dynamics (DPD) method. This method allows large timesteps in particle-based systems and speeds up sampling by many orders of magnitude. Our new model is based on the electrostatic polarization of the protein backbone and a detailed representation of the sidechains in combination with a polarizable water model. We define our model parameters using the experimental structures of two proteins, TrpZip2 and TrpCage. Backmapping and subsequent short replica-exchange molecular dynamics runs verify our approach and show convergence to the experimental structures on the atomistic level. We validate our model on five different proteins: GB1, the WW-domain, the B-domain of Protein A, the peripheral binding subunit and villin headpiece. PMID:26339692

  12. Development of DPD coarse-grained models: From bulk to interfacial properties

    NASA Astrophysics Data System (ADS)

    Solano Canchaya, José G.; Dequidt, Alain; Goujon, Florent; Malfreyt, Patrice

    2016-08-01

    A new Bayesian method was recently introduced for developing coarse-grain (CG) force fields for molecular dynamics. The CG models designed for dissipative particle dynamics (DPD) are optimized based on trajectory matching. Here we extend this method to improve transferability across thermodynamic conditions. We demonstrate the capability of the method by developing a CG model of n-pentane from constant-NPT atomistic simulations of bulk liquid phases and we apply the CG-DPD model to the calculation of the surface tension of the liquid-vapor interface over a large range of temperatures. The coexisting densities, vapor pressures, and surface tensions calculated with different CG and atomistic models are compared to experiments. Depending on the database used for the development of the potentials, it is possible to build a CG model which performs very well in the reproduction of the surface tension on the orthobaric curve.

  13. Coarse-grained simulations of polyelectrolyte complexes: MARTINI models for poly(styrene sulfonate) and poly(diallyldimethylammonium)

    SciTech Connect

    Vögele, Martin; Holm, Christian; Smiatek, Jens

    2015-12-28

    We present simulations of aqueous polyelectrolyte complexes with new MARTINI models for the charged polymers poly(styrene sulfonate) and poly(diallyldimethylammonium). Our coarse-grained polyelectrolyte models allow us to study large length and long time scales with regard to chemical details and thermodynamic properties. The results are compared to the outcomes of previous atomistic molecular dynamics simulations and verify that electrostatic properties are reproduced by our MARTINI coarse-grained approach with reasonable accuracy. Structural similarity between the atomistic and the coarse-grained results is indicated by a comparison between the pair radial distribution functions and the cumulative number of surrounding particles. Our coarse-grained models are able to quantitatively reproduce previous findings like the correct charge compensation mechanism and a reduced dielectric constant of water. These results can be interpreted as the underlying reason for the stability of polyelectrolyte multilayers and complexes and validate the robustness of the proposed models.

  14. Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism.

    PubMed

    Li, Zhen; Bian, Xin; Li, Xiantao; Karniadakis, George Em

    2015-12-28

    The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables, and the memory kernel is evaluated directly from microscopic dynamics. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons between the CG models with Markovian and non-Markovian approximations indicate that including the memory effects using NM-DPD yields similar results as the Markovian-based DPD if the system has clear time scale separation. However, for systems with small separation of time scales, NM-DPD can reproduce correct short-time properties that are related to how the system responds to high-frequency disturbances, which cannot be captured by the Markovian-based DPD model. PMID:26723613

  15. Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism

    NASA Astrophysics Data System (ADS)

    Li, Zhen; Bian, Xin; Li, Xiantao; Karniadakis, George Em

    2015-12-01

    The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables, and the memory kernel is evaluated directly from microscopic dynamics. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons between the CG models with Markovian and non-Markovian approximations indicate that including the memory effects using NM-DPD yields similar results as the Markovian-based DPD if the system has clear time scale separation. However, for systems with small separation of time scales, NM-DPD can reproduce correct short-time properties that are related to how the system responds to high-frequency disturbances, which cannot be captured by the Markovian-based DPD model.

  16. Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism

    SciTech Connect

    Li, Zhen; Bian, Xin; Karniadakis, George Em; Li, Xiantao

    2015-12-28

    The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables, and the memory kernel is evaluated directly from microscopic dynamics. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons between the CG models with Markovian and non-Markovian approximations indicate that including the memory effects using NM-DPD yields similar results as the Markovian-based DPD if the system has clear time scale separation. However, for systems with small separation of time scales, NM-DPD can reproduce correct short-time properties that are related to how the system responds to high-frequency disturbances, which cannot be captured by the Markovian-based DPD model.

  17. A sandpile model of grain blocking and consequences for sediment dynamics in step-pool streams

    NASA Astrophysics Data System (ADS)

    Molnar, P.

    2012-04-01

    Coarse grains (cobbles to boulders) are set in motion in steep mountain streams by floods with sufficient energy to erode the particles locally and transport them downstream. During transport, grains are often blocked and form width-spannings structures called steps, separated by pools. The step-pool system is a transient, self-organizing and self-sustaining structure. The temporary storage of sediment in steps and the release of that sediment in avalanche-like pulses when steps collapse, leads to a complex nonlinear threshold-driven dynamics in sediment transport which has been observed in laboratory experiments (e.g., Zimmermann et al., 2010) and in the field (e.g., Turowski et al., 2011). The basic question in this paper is if the emergent statistical properties of sediment transport in step-pool systems may be linked to the transient state of the bed, i.e. sediment storage and morphology, and to the dynamics in sediment input. The hypothesis is that this state, in which sediment transporting events due to the collapse and rebuilding of steps of all sizes occur, is analogous to a critical state in self-organized open dissipative dynamical systems (Bak et al., 1988). To exlore the process of self-organization, a cellular automaton sandpile model is used to simulate the processes of grain blocking and hydraulically-driven step collapse in a 1-d channel. Particles are injected at the top of the channel and are allowed to travel downstream based on various local threshold rules, with the travel distance drawn from a chosen probability distribution. In sandpile modelling this is a simple 1-d limited non-local model, however it has been shown to have nontrivial dynamical behaviour (Kadanoff et al., 1989), and it captures the essence of stochastic sediment transport in step-pool systems. The numerical simulations are used to illustrate the differences between input and output sediment transport rates, mainly focussing on the magnification of intermittency and

  18. Chemistry in disks. IV. Benchmarking gas-grain chemical models with surface reactions

    NASA Astrophysics Data System (ADS)

    Semenov, D.; Hersant, F.; Wakelam, V.; Dutrey, A.; Chapillon, E.; Guilloteau, St.; Henning, Th.; Launhardt, R.; Piétu, V.; Schreyer, K.

    2010-11-01

    Context. We describe and benchmark two sophisticated chemical models developed by the Heidelberg and Bordeaux astrochemistry groups. Aims: The main goal of this study is to elaborate on a few well-described tests for state-of-the-art astrochemical codes covering a range of physical conditions and chemical processes, in particular those aimed at constraining current and future interferometric observations of protoplanetary disks. Methods: We considered three physical models: a cold molecular cloud core, a hot core, and an outer region of a T Tauri disk. Our chemical network (for both models) is based on the original gas-phase osu_03_2008 ratefile and includes gas-grain interactions and a set of surface reactions for the H-, O-, C-, S-, and N-bearing molecules. The benchmarking was performed with the increasing complexity of the considered processes: (1) the pure gas-phase chemistry, (2) the gas-phase chemistry with accretion and desorption, and (3) the full gas-grain model with surface reactions. The chemical evolution is modeled within 109 years using atomic initial abundances with heavily depleted metals and hydrogen in its molecular form. Results: The time-dependent abundances calculated with the two chemical models are essentially the same for all considered physical cases and for all species, including the most complex polyatomic ions and organic molecules. This result, however, required a lot of effort to make all necessary details consistent through the model runs, e.g., definition of the gas particle density, density of grain surface sites, or the strength and shape of the UV radiation field. Conclusions: The reference models and the benchmark setup, along with the two chemical codes and resulting time-dependent abundances are made publicly available on the internet. This will facilitate and ease the development of other astrochemical models and provide nonspecialists with a detailed description of the model ingredients and requirements to analyze the cosmic

  19. The referential grain size and effective porosity in the Kozeny-Carman model

    NASA Astrophysics Data System (ADS)

    Urumović, Kosta; Urumović, Kosta, Sr.

    2016-05-01

    In this paper, the results of permeability and specific surface area analyses as functions of granulometric composition of various sediments (from silty clays to very well graded gravels) are presented. The effective porosity and the referential grain size are presented as fundamental granulometric parameters expressing an effect of the forces operating on fluid movement through the saturated porous media. This paper suggests procedures for calculating referential grain size and determining effective (flow) porosity, which result in parameters that reliably determine the specific surface area and permeability. These procedures ensure the successful application of the Kozeny-Carman model up to the limits of validity of Darcy's law. The value of effective porosity in the referential mean grain size function was calibrated within the range of 1.5 µm to 6.0 mm. The reliability of the parameters applied in the KC model was confirmed by a very high correlation between the predicted and tested hydraulic conductivity values (R2 = 0.99 for sandy and gravelly materials; R2 = 0.70 for clayey-silty materials). The group representation of hydraulic conductivity (ranging from 10-12 m s-1 up to 10-2 m s-1) presents a coefficient of correlation of R2 = 0.97 for a total of 175 samples of various deposits. These results present new developments in the research of the effective porosity, the permeability and the specific surface area distributions of porous materials. This is important because these three parameters are critical conditions for successful groundwater flow modeling and contaminant transport. Additionally, from a practical viewpoint, it is very important to identify these parameters swiftly and very accurately.

  20. Coarse-grained particle model for pedestrian flow using diffusion maps

    NASA Astrophysics Data System (ADS)

    Marschler, Christian; Starke, Jens; Liu, Ping; Kevrekidis, Ioannis G.

    2014-01-01

    Interacting particle systems constitute the dynamic model of choice in a variety of application areas. A prominent example is pedestrian dynamics, where good design of escape routes for large buildings and public areas can improve evacuation in emergency situations, avoiding exit blocking and the ensuing panic. Here we employ diffusion maps to study the coarse-grained dynamics of two pedestrian crowds trying to pass through a door from opposite sides. These macroscopic variables and the associated smooth embeddings lead to a better description and a clearer understanding of the nature of the transition to oscillatory dynamics. We also compare the results to those obtained through intuitively chosen macroscopic variables.

  1. Sediment transport modelling based on grain size trend analysis in Augusta Harbour (Sicily)

    NASA Astrophysics Data System (ADS)

    Barbera, Giuseppe; Feo, Roberto; Freni, Gabriele

    2015-12-01

    To support marine civil engineer in pollutant studies, sediment management or dredging operations, is useful to know how the sediments move in accumulation basin. This paper investigates the dynamic of the sediment path using a two-dimensional numeric model: the Grain Size Trend Analysis (GSTA). The GSTA was applied using GiSedTrend plugin, under GIS software. The case study is the Augusta Harbour, which is one of the most polluted Italian harbours. It is the marine part of the Site of National Interest (SNI) of Priolo Gargallo (Siracusa, Italy) and it can be hydrodynamically considered as a lagoon. Two scenarios were obtained by using different geostatistical criteria.

  2. Asymmetric impact of rainfall on India's food grain production: evidence from quantile autoregressive distributed lag model

    NASA Astrophysics Data System (ADS)

    Pal, Debdatta; Mitra, Subrata Kumar

    2016-10-01

    This study used a quantile autoregressive distributed lag (QARDL) model to capture asymmetric impact of rainfall on food production in India. It was found that the coefficient corresponding to the rainfall in the QARDL increased till the 75th quantile and started decreasing thereafter, though it remained in the positive territory. Another interesting finding is that at the 90th quantile and above the coefficients of rainfall though remained positive was not statistically significant and therefore, the benefit of high rainfall on crop production was not conclusive. However, the impact of other determinants, such as fertilizer and pesticide consumption, is quite uniform over the whole range of the distribution of food grain production.

  3. Nitrogen feedbacks increase future terrestrial ecosystem carbon uptake in an individual-based dynamic vegetation model

    NASA Astrophysics Data System (ADS)

    Wårlind, D.; Smith, B.; Hickler, T.; Arneth, A.

    2014-11-01

    Recently a considerable amount of effort has been put into quantifying how interactions of the carbon and nitrogen cycle affect future terrestrial carbon sinks. Dynamic vegetation models, representing the nitrogen cycle with varying degree of complexity, have shown diverging constraints of nitrogen dynamics on future carbon sequestration. In this study, we use LPJ-GUESS, a dynamic vegetation model employing a detailed individual- and patch-based representation of vegetation dynamics, to evaluate how population dynamics and resource competition between plant functional types, combined with nitrogen dynamics, have influenced the terrestrial carbon storage in the past and to investigate how terrestrial carbon and nitrogen dynamics might change in the future (1850 to 2100; one representative "business-as-usual" climate scenario). Single-factor model experiments of CO2 fertilisation and climate change show generally similar directions of the responses of C-N interactions, compared to the C-only version of the model as documented in previous studies using other global models. Under an RCP 8.5 scenario, nitrogen limitation suppresses potential CO2 fertilisation, reducing the cumulative net ecosystem carbon uptake between 1850 and 2100 by 61%, and soil warming-induced increase in nitrogen mineralisation reduces terrestrial carbon loss by 31%. When environmental changes are considered conjointly, carbon sequestration is limited by nitrogen dynamics up to the present. However, during the 21st century, nitrogen dynamics induce a net increase in carbon sequestration, resulting in an overall larger carbon uptake of 17% over the full period. This contrasts with previous results with other global models that have shown an 8 to 37% decrease in carbon uptake relative to modern baseline conditions. Implications for the plausibility of earlier projections of future terrestrial C dynamics based on C-only models are discussed.

  4. Polarizable Water Model for the Coarse-Grained MARTINI Force Field

    PubMed Central

    Sengupta, Durba; Marrink, Siewert J.

    2010-01-01

    Coarse-grained (CG) simulations have become an essential tool to study a large variety of biomolecular processes, exploring temporal and spatial scales inaccessible to traditional models of atomistic resolution. One of the major simplifications of CG models is the representation of the solvent, which is either implicit or modeled explicitly as a van der Waals particle. The effect of polarization, and thus a proper screening of interactions depending on the local environment, is absent. Given the important role of water as a ubiquitous solvent in biological systems, its treatment is crucial to the properties derived from simulation studies. Here, we parameterize a polarizable coarse-grained water model to be used in combination with the CG MARTINI force field. Using a three-bead model to represent four water molecules, we show that the orientational polarizability of real water can be effectively accounted for. This has the consequence that the dielectric screening of bulk water is reproduced. At the same time, we parameterized our new water model such that bulk water density and oil/water partitioning data remain at the same level of accuracy as for the standard MARTINI force field. We apply the new model to two cases for which current CG force fields are inadequate. First, we address the transport of ions across a lipid membrane. The computed potential of mean force shows that the ions now naturally feel the change in dielectric medium when moving from the high dielectric aqueous phase toward the low dielectric membrane interior. In the second application we consider the electroporation process of both an oil slab and a lipid bilayer. The electrostatic field drives the formation of water filled pores in both cases, following a similar mechanism as seen with atomistically detailed models. PMID:20548957

  5. Secondary emission from dust grains with a surface layer: comparison between experimental and model results

    NASA Astrophysics Data System (ADS)

    Richterová, I.; Pavlů, J.; Němeček, Z.; Šafránková, J.; Žilavý, P.

    2006-01-01

    The motion, coalescence, and other processes in dust clouds are determined by the dust charge. Since dust grains in the space are bombarded by energetic electrons, the secondary emission is an important process contributing to their charge. It is generally expected that the secondary emission yield is related to surface properties of the bombarded body. However, it is well known that secondary emission from small bodies is determined not only by their composition but an effect of dimension can be very important when the penetration depth of primary electrons is comparable with the grain size. It implies that the secondary emission yield can be influenced by the substrate material if the surface layer is thin enough. We have developed a simple Monte Carlo model of secondary emission that was successfully applied on the dust stimulants from glass and melamine formaldehyde (MF) resin and matched very well experimental results. In order to check the influence of surface layers, we have modified the model for spheres covered by a layer with different material properties. The results of model simulations are compared with measurements on MF spheres covered by a nickel layer.

  6. Coarse-grained model for the interconversion between different crystalline cellulose allomorphs

    SciTech Connect

    Langan, Paul

    2012-01-01

    We present the results of Langevin dynamics simulations on a coarse grained model for crystalline cellulose. In particular, we analyze two different cellulose crystalline forms: cellulose I (the natural form of cellulose) and cellulose IIII (obtained after cellulose I is treated with anhydrous liquid ammonia). Cellulose IIII has been the focus of wide interest in the field of cellulosic biofuels as it can be efficiently hydrolyzed to glucose (its enzymatic degradation rates are up to 5 fold higher than those of cellulose I ). In turn, glucose can eventually be fermented into fuels. The coarse-grained model presented in this study is based on a simplified geometry and on an effective potential mimicking the changes in both intracrystalline hydrogen bonds and stacking interactions during the transition from cellulose I to cellulose IIII. The model accurately reproduces both structural and thermomechanical properties of cellulose I and IIII. The work presented herein describes the structural transition from cellulose I to cellulose IIII as driven by the change in the equilibrium state of two degrees of freedom in the cellulose chains. The structural transition from cellulose I to cellulose IIII is essentially reduced to a search for optimal spatial arrangement of the cellulose chains.

  7. A Comparison of Process-Scale Modeling and Measurements of Atmosphere-Snowpack Exchange of Nitrogen Oxides at Summit, Greenland

    NASA Astrophysics Data System (ADS)

    Murray, K. A.; Helmig, D.; Kramer, L. J.; Doskey, P. V.; Van Dam, B. A.; Seok, B.; Ganzeveld, L.

    2015-12-01

    Snowpack over glacial ice is a reservoir for reactive nitrogen gases. Previous studies indicate nitrogen oxides (NOx) are generated in snowpack interstitial air through photolysis of nitrate (NO3-). Gradients in NOx mixing ratios between snowpack interstitial air and the overlying atmosphere regulate NOx surface exchange, which affects the Arctic ozone budget and climate. To better understand the dynamics of cryosphere-atmosphere exchange of NOx in the Arctic, we use a 1-D process-scale model to evaluate measurements of NOxin and above the snowpack during March-May 2009 at Summit, Greenland. The model is based upon the processes previously presented in the snowpack chemistry and physics model, MISTRA-SNOW, which represents snow grains as spheres with surfaces uniformly coated by an aqueous phase. Modeled profiles of NO, NO2, and O3 up to ~ 2 meters deep into the snowpack for March-May 2009 have been compared to measured profiles and will be presented. During the March-May time period at Summit, low irradiances are observed during March, diurnal irradiance profiles are observed during April, and the sun never sets in May. The model results suggest a key chemical pathway for the formation of NO2 during "nighttime" that was previously unexplained. In addition, modeled 24-hour NOx fluxes are compared to measured NOx fluxes from a MET tower at Summit. Modeled fluxes of NOx in April 2009 are the same order of magnitude as the measurements; however, modeled fluxes of NOx deviate up to one order of magnitude from measurements in May 2009. A detailed analysis of the modeled/measured flux comparison will be presented.

  8. Box-modelling of the impacts of atmospheric nitrogen deposition and benthic remineralisation on the nitrogen cycle of the eastern tropical South Pacific

    NASA Astrophysics Data System (ADS)

    Su, Bei; Pahlow, Markus; Oschlies, Andreas

    2016-09-01

    Both atmospheric deposition and benthic remineralisation influence the marine nitrogen cycle, and hence ultimately also marine primary production. The biological and biogeochemical relations in the eastern tropical South Pacific (ETSP) among nitrogen deposition, benthic denitrification and phosphorus regeneration are analysed in a prognostic box model of the oxygen, nitrogen and phosphorus cycles in the ETSP. Atmospheric nitrogen deposition ( ≈ 1.5 Tg N yr-1 for the years 2000-2009) is offset by half in the model by reduced N2 fixation, with the other half transported out of the model domain. Model- and data-based benthic denitrification in our model domain are responsible for losses of 0.19 and 1.0 Tg Tg N yr-1, respectively, and both trigger nitrogen fixation, partly compensating for the NO3- loss. Model- and data-based estimates of enhanced phosphate release via sedimentary phosphorus regeneration under suboxic conditions are 0.062 and 0.11 Tg N yr-1, respectively. Since phosphate is the ultimate limiting nutrient in the model, even very small additional phosphate inputs stimulate 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 remineralisation indicates dominant stabilising 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 for by increased nitrogen fixation; enhanced nitrogen fixation stimulated by phosphate regeneration is partly counteracted by stronger water-column denitrification. Even though the water column in our model domain acts as a NO3- source, the ETSP including benthic denitrification might be a NO3- sink.

  9. Coarse-grained Brownian ratchet model of membrane protrusion on cellular scale.

    PubMed

    Inoue, Yasuhiro; Adachi, Taiji

    2011-07-01

    Membrane protrusion is a mechanochemical process of active membrane deformation driven by actin polymerization. Previously, Brownian ratchet (BR) was modeled on the basis of the underlying molecular mechanism. However, because the BR requires a priori load that cannot be determined without information of the cell shape, it cannot be effective in studies in which resultant shapes are to be solved. Other cellular-scale models describing the protrusion have also been suggested for modeling a whole cell; however, these models were not developed on the basis of coarse-grained physics representing the underlying molecular mechanism. Therefore, to express the membrane protrusion on the cellular scale, we propose a novel mathematical model, the coarse-grained BR (CBR), which is derived on the basis of nonequilibrium thermodynamics theory. The CBR can reproduce the BR within the limit of the quasistatic process of membrane protrusion and can estimate the protrusion velocity consistently with an effective elastic constant that represents the state of the energy of the membrane. Finally, to demonstrate the applicability of the CBR, we attempt to perform a cellular-scale simulation of migrating keratocyte in which the proposed CBR is used for the membrane protrusion model on the cellular scale. The results show that the experimentally observed shapes of the leading edge are well reproduced by the simulation. In addition, The trend of dependences of the protrusion velocity on the curvature of the leading edge, the temperature, and the substrate stiffness also agreed with the other experimental results. Thus, the CBR can be considered an appropriate cellular-scale model to express the membrane protrusion on the basis of its underlying molecular mechanism.

  10. Nitrogen feedbacks increase future terrestrial ecosystem carbon uptake in an individual-based dynamic vegetation model

    NASA Astrophysics Data System (ADS)

    Wårlind, D.; Smith, B.; Hickler, T.; Arneth, A.

    2014-01-01

    Recently a considerable amount of effort has been put into quantifying how interactions of the carbon and nitrogen cycle affect future terrestrial carbon sinks. Dynamic vegetation models, representing the nitrogen cycle with varying degree of complexity, have shown diverging constraints of nitrogen dynamics on future carbon sequestration. In this study, we use the dynamic vegetation model LPJ-GUESS to evaluate how population dynamics and resource competition between plant functional types, combined with nitrogen dynamics, have influenced the terrestrial carbon storage in the past and to investigate how terrestrial carbon and nitrogen dynamics might change in the future (1850 to 2100; one exemplary "business-as-usual" climate scenario). Single factor model experiments of CO2 fertilisation and climate change show generally similar directions of the responses of C-N interactions, compared to the C-only version of the model, as documented in previous studies. Under a RCP 8.5 scenario, nitrogen limitation suppresses potential CO2 fertilisation, reducing the cumulative net ecosystem carbon uptake between 1850 and 2100 by 61%, and soil warming-induced increase in nitrogen mineralisation reduces terrestrial carbon loss by 31%. When environmental changes are considered conjointly, carbon sequestration is limited by nitrogen dynamics until present. However, during the 21st century nitrogen dynamics induce a net increase in carbon sequestration, resulting in an overall larger carbon uptake of 17% over the full period. This contradicts earlier model results that showed an 8 to 37% decrease in carbon uptake, questioning the often stated assumption that projections of future terrestrial C dynamics from C-only models are too optimistic.

  11. Long Mantle Mixing Times for the early Earth Inferred from Convection Models with Grain-Damage

    NASA Astrophysics Data System (ADS)

    Foley, B. J.; Rizo, H.

    2015-12-01

    Mantle dynamics on the Hadean and Archean Earth, particularly whether plate tectonics was in operation or not, is hotly debated. One important constraint comes from evidence for long mantle mixing timescales in the early Earth based on observations of early-formed geochemical heterogeneities. Specifically, 142Nd anomalies recorded in 3.8 to 3.4 Ga rocks from southwest Greenland [e.g. 1] and 2.7 Ga rocks from the Superior Province (Canada) [2] indicate that chemically heterogeneous reservoirs, formed during the first ~ 10-100 million years of Earths' history, survived their remixing into the mantle for over 1 Gyr. Such a long mantle mixing time is difficult to explain with a traditional model of plate tectonics, where plate speeds increase significantly in the past due to a hotter mantle, thus prompting appeals to stagnant lid convection on the early Earth [e.g. 2]. However, a new model for generating plate tectonics from mantle convection based on grainsize reduction (called grain-damage) proposes that plate speeds may have decreased with increasing mantle temperature. Higher mantle temperatures lead to higher grain-growth rates that inhibit the formation of weak lithospheric shear zones. As a result, plate boundaries are more viscous and provide a stronger resistance to plate motions, and thus mantle-mixing times in the mobile lid regime may still be long even at Hadean or Archean mantle temperatures. We use new numerical models of convection with grain-damage to constrain mantle-mixing times for the early Earth with the effects of grainsize variation included. We find that mantle mixing times for mobile lid convection remain long as mantle temperature increases because of faster grain-growth rates in the mantle and lithosphere. Therefore the preservation of chemical heterogeneities for over 1 Gyr in the Hadean-Archean mantle is not inconsistent with the operation of mobile lid convection and subduction at this time. Early Earth subduction may still have differed

  12. Multiobjective Sensitivity Analysis Of Sediment And Nitrogen Processes With A Watershed Model

    EPA Science Inventory

    This paper presents a computational analysis for evaluating critical non-point-source sediment and nutrient (specifically nitrogen) processes and management actions at the watershed scale. In the analysis, model parameters that bear key uncertainties were presumed to reflect the ...

  13. Limited impact of atmospheric nitrogen deposition on marine productivity due to biogeochemical feedbacks in a global ocean model

    NASA Astrophysics Data System (ADS)

    Somes, Christopher J.; Landolfi, Angela; Koeve, Wolfgang; Oschlies, Andreas

    2016-05-01

    The impact of increasing anthropogenic atmospheric nitrogen deposition on marine biogeochemistry is uncertain. We performed simulations to quantify its effect on nitrogen cycling and marine productivity in a global 3-D ocean biogeochemistry model. Nitrogen fixation provides an efficient feedback by decreasing immediately to deposition, whereas water column denitrification increases more gradually in the slowly expanding oxygen deficient zones. Counterintuitively, nitrogen deposition near oxygen deficient zones causes a net loss of marine nitrogen due to the stoichiometry of denitrification. In our idealized atmospheric deposition simulations that only account for nitrogen cycle perturbations, these combined stabilizing feedbacks largely compensate deposition and suppress the increase in global marine productivity to <2%, in contrast to a simulation that neglects nitrogen cycle feedbacks that predicts an increase of >15%. Our study emphasizes including the dynamic response of nitrogen fixation and denitrification to atmospheric nitrogen deposition to predict future changes of the marine nitrogen cycle and productivity.

  14. The heliocentric evolution of cometary infrared spectra - Results from an organic grain model

    NASA Technical Reports Server (NTRS)

    Chyba, Christopher F.; Sagan, Carl; Mumma, Michael J.

    1989-01-01

    An emission feature peaking near 3.4 microns that is typical of C-H stretching in hydrocarbons and which fits a simple, two-component thermal emission model for dust in the cometary coma, has been noted in observations of Comets Halley and Wilson. A noteworthy consequence of this modeling is that, at about 1 AU, emission features at wavelengths longer than 3.4 microns come to be 'diluted' by continuum emission. A quantitative development of the model shows it to agree with observational data for Comet Halley for certain, plausible values of the optical constants; the observed heliocentric evolution of the 3.4-micron feature thereby furnishes information on the composition of the comet's organic grains.

  15. Monte-Carlo simulations of a coarse-grained model for α-oligothiophenes

    NASA Astrophysics Data System (ADS)

    Almutairi, Amani; Luettmer-Strathmann, Jutta

    The interfacial layer of an organic semiconductor in contact with a metal electrode has important effects on the performance of thin-film devices. However, the structure of this layer is not easy to model. Oligothiophenes are small, π-conjugated molecules with applications in organic electronics that also serve as small-molecule models for polythiophenes. α-hexithiophene (6T) is a six-ring molecule, whose adsorption on noble metal surfaces has been studied extensively (see, e.g., Ref.). In this work, we develop a coarse-grained model for α-oligothiophenes. We describe the molecules as linear chains of bonded, discotic particles with Gay-Berne potential interactions between non-bonded ellipsoids. We perform Monte Carlo simulations to study the structure of isolated and adsorbed molecules

  16. Reconciling modeled and observed atmospheric deposition of soluble organic nitrogen at coastal locations

    NASA Astrophysics Data System (ADS)

    Ito, Akinori; Lin, Guangxing; Penner, Joyce E.

    2014-06-01

    Atmospheric deposition of reactive nitrogen (N) species from air pollutants is a significant source of exogenous nitrogen in marine ecosystems. Here we use an atmospheric chemical transport model to investigate the supply of soluble organic nitrogen (ON) from anthropogenic sources to the ocean. Comparisons of modeled deposition with observations at coastal and marine locations show good overall agreement for inorganic nitrogen and total soluble nitrogen. However, previous modeling approaches result in significant underestimates of the soluble ON deposition if the model only includes the primary soluble ON and the secondary oxidized ON in gases and aerosols. Our model results suggest that including the secondary reduced ON in aerosols as a source of soluble ON contributes to an improved prediction of the deposition rates (g N m-2 yr-1). The model results show a clear distinction in the vertical distribution of soluble ON in aerosols between different processes from the primary sources and the secondary formation. The model results (excluding the biomass burning and natural emission changes) suggest an increase in soluble ON outflow from atmospheric pollution, in particular from East Asia, to the oceans in the twentieth century. These results highlight the necessity of improving the process-based quantitative understanding of the chemical reactions of inorganic nitrogen species with organics in aerosol and cloud water.

  17. A Coupled Land Surface-Subsurface Biogeochemical Model for Aqueous and Gaseous Nitrogen Losses

    NASA Astrophysics Data System (ADS)

    Gu, C.; Maggi, F.; Riley, W.; Pan, L.; Xu, T.; Oldenburg, C.; Miller, N.

    2008-12-01

    In recent years concern has grown over the contribution of nitrogen (N) fertilizers to nitrate (NOB3PB-P) water pollution and atmospheric pollution of nitrous oxide (NB2BO), nitric oxide (NO), and ammonia (NHB3B). Characterizing the amount and species of N losses is therefore essential in developing a strategy to estimate and mitigate N leaching and emission to the atmosphere. Indeed, transformations of nitrogen depend strongly on water content, soil temperature, and nitrogen concentration. Land surface processes therefore have to be taken into account to properly characterize N biogeochemical cycling. However, most current nitrogen biogeochemical models take the land surface as the upper boundary by lumping the complex processes above the surface as known boundary conditions. In this study, an extant subsurface mechanistic N cycle model (TOUGHREACT-N) was coupled with the community land model (CLM). The resulting coupled model extends the modeling capability of TOUGHREACT-N to include the important energy, momentum, and moisture dynamics provided by CLM. The coupled model showed a significant impact of land-surface diurnal forcing on soil temperature and moisture and on nitrogen fluxes. We also discuss field applications of the model and discuss how temporal dynamics of nitrogen fluxes are affected by land surface processes.

  18. Modelling the nitrogen loadings from large yellow croaker (Larimichthys crocea) cage aquaculture.

    PubMed

    Cai, Huiwen; Ross, Lindsay G; Telfer, Trevor C; Wu, Changwen; Zhu, Aiyi; Zhao, Sheng; Xu, Meiying

    2016-04-01

    Large yellow croaker (LYC) cage farming is a rapidly developing industry in the coastal areas of the East China Sea. However, little is known about the environmental nutrient loadings resulting from the current aquaculture practices for this species. In this study, a nitrogenous waste model was developed for LYC based on thermal growth and bioenergetic theories. The growth model produced a good fit with the measured data of the growth trajectory of the fish. The total, dissolved and particulate nitrogen outputs were estimated to be 133, 51 and 82 kg N tonne(-1) of fish production, respectively, with daily dissolved and particulate nitrogen outputs varying from 69 to 104 and 106 to 181 mg N fish(-1), respectively, during the 2012 operational cycle. Greater than 80 % of the nitrogen input from feed was predicted to be lost to the environment, resulting in low nitrogen retention (<20 %) in the fish tissues. Ammonia contributed the greatest proportion (>85 %) of the dissolved nitrogen generated from cage farming. This nitrogen loading assessment model is the first to address nitrogenous output from LYC farming and could be a valuable tool to examine the effects of management and feeding practices on waste from cage farming. The application of this model could help improve the scientific understanding of offshore fish farming systems. Furthermore, the model predicts that a 63 % reduction in nitrogenous waste production could be achieved by switching from the use of trash fish for feed to the use of pelleted feed. PMID:26728289

  19. Coarse-Grained Modeling of Nucleic Acids Using Anisotropic Gay-Berne and Electric Multipole Potentials.

    PubMed

    Li, Guohui; Shen, Hujun; Zhang, Dinglin; Li, Yan; Wang, Honglei

    2016-02-01

    In this work, we attempt to apply a coarse-grained (CG) model, which is based on anisotropic Gay-Berne and electric multipole (EMP) potentials, to the modeling of nucleic acids. First, a comparison has been made between the CG and atomistic models (AMBER point-charge model) in the modeling of DNA and RNA hairpin structures. The CG results have demonstrated a good quality in maintaining the nucleic acid hairpin structures, in reproducing the dynamics of backbone atoms of nucleic acids, and in describing the hydrogen-bonding interactions between nucleic acid base pairs. Second, the CG and atomistic AMBER models yield comparable results in modeling double-stranded DNA and RNA molecules. It is encouraging that our CG model is capable of reproducing many elastic features of nucleic acid base pairs in terms of the distributions of the interbase pair step parameters (such as shift, slide, tilt, and twist) and the intrabase pair parameters (such as buckle, propeller, shear, and stretch). Finally, The GBEMP model has shown a promising ability to predict the melting temperatures of DNA duplexes with different lengths.

  20. Coarse-Grained Modeling of Nucleic Acids Using Anisotropic Gay-Berne and Electric Multipole Potentials.

    PubMed

    Li, Guohui; Shen, Hujun; Zhang, Dinglin; Li, Yan; Wang, Honglei

    2016-02-01

    In this work, we attempt to apply a coarse-grained (CG) model, which is based on anisotropic Gay-Berne and electric multipole (EMP) potentials, to the modeling of nucleic acids. First, a comparison has been made between the CG and atomistic models (AMBER point-charge model) in the modeling of DNA and RNA hairpin structures. The CG results have demonstrated a good quality in maintaining the nucleic acid hairpin structures, in reproducing the dynamics of backbone atoms of nucleic acids, and in describing the hydrogen-bonding interactions between nucleic acid base pairs. Second, the CG and atomistic AMBER models yield comparable results in modeling double-stranded DNA and RNA molecules. It is encouraging that our CG model is capable of reproducing many elastic features of nucleic acid base pairs in terms of the distributions of the interbase pair step parameters (such as shift, slide, tilt, and twist) and the intrabase pair parameters (such as buckle, propeller, shear, and stretch). Finally, The GBEMP model has shown a promising ability to predict the melting temperatures of DNA duplexes with different lengths. PMID:26717419

  1. A Coarse Grained Model for Methylcellulose: Spontaneous Ring Formation at Elevated Temperature

    NASA Astrophysics Data System (ADS)

    Huang, Wenjun; Larson, Ronald

    Methylcellulose (MC) is widely used as food additives and pharma applications, where its thermo-reversible gelation behavior plays an important role. To date the gelation mechanism is not well understood, and therefore attracts great research interest. In this study, we adopted coarse-grained (CG) molecular dynamics simulations to model the MC chains, including the homopolymers and random copolymers that models commercial METHOCEL A, in an implicit water environment, where each MC monomer modeled with a single bead. The simulations are carried using a LAMMPS program. We parameterized our CG model using the radial distribution functions from atomistic simulations of short MC oligomers, extrapolating the results to long chains. We used dissociation free energy to validate our CG model against the atomistic model. The CG model captured the effects of monomer substitution type and temperature from the atomistic simulations. We applied this CG model to simulate single chains up to 1000 monomers long and obtained persistence lengths that are close to those determined from experiment. We observed the chain collapse transition for random copolymer at 600 monomers long at 50C. The chain collapsed into a stable ring structure with outer diameter around 14nm, which appears to be a precursor to the fibril structure observed in the methylcellulose gel observed by Lodge et al. in the recent studies. Our CG model can be extended to other MC derivatives for studying the interaction between these polymers and small molecules, such as hydrophobic drugs.

  2. Order parameter re-mapping algorithm for 3D phase field model of grain growth using FEM

    DOE PAGESBeta

    Permann, Cody J.; Tonks, Michael R.; Fromm, Bradley; Gaston, Derek R.

    2016-01-14

    Phase field modeling (PFM) is a well-known technique for simulating microstructural evolution. To model grain growth using PFM, typically each grain is assigned a unique non-conserved order parameter and each order parameter field is evolved in time. Traditional approaches using a one-to-one mapping of grains to order parameters present a challenge when modeling large numbers of grains due to the computational expense of using many order parameters. This problem is exacerbated when using an implicit finite element method (FEM), as the global matrix size is proportional to the number of order parameters. While previous work has developed methods to reducemore » the number of required variables and thus computational complexity and run time, none of the existing approaches can be applied for an implicit FEM implementation of PFM. Here, we present a modular, dynamic, scalable reassignment algorithm suitable for use in such a system. Polycrystal modeling with grain growth and stress require careful tracking of each grain’s position and orientation which is lost when using a reduced order parameter set. In conclusion, the method presented in this paper maintains a unique ID for each grain even after reassignment, to allow the PFM to be tightly coupled to calculations of the stress throughout the polycrystal. Implementation details and comparative results of our approach are presented.« less

  3. Contrasting Polymer Behavior Under Nanoconfinement using Thermomechanically Consistent Coarse-Grained Models

    NASA Astrophysics Data System (ADS)

    Keten, Sinan; Xia, Wenjie; Hsu, David

    2015-03-01

    We present a systematic, two-bead per monomer coarse graining strategy that simulates the thermomechanical behavior of polymers several hundred times faster than all-atom MD (Hsu et al. JCTC, 2014). The predictive capability of the technique is illustrated here for 5 different methacrylate monomers and polystyrene stereoisomers. The approach involves optimization of analytical bonded potentials from atomistic bonded distributions to emulate local structure, as validated by chain end-to-end length and the radius of gyration comparisons with experiments and random coil theory. Nonbonded Lennard-Jones potentials are tuned to reproduce the elastic modulus (E) and glass transition temperature (Tg) at a single thermodynamic state. Density-corrected parameters capture temperature-modulus dependence in the 150-600 K range. Flory-Fox constants of the CG models are commensurate with all atomistic and experimental results, even though all calibrations are done at a single molecular weight. Finally, we further demonstrate the predictive capabilities of the models by examining thin film nanoconfinement effects for different polymers, film thicknesses, interfacial energies, and molecular weights. Our technique, called thermomechanically consistent coarse graining (TCCG), is demonstrated, using polystyrene and poly(methylmethacrylate) as universal benchmarks, to be a robust and effective technique to understand the thermomechanical behavior of polymers thin films and nanocomposites.

  4. Dynamic implicit-solvent coarse-grained models of lipid bilayer membranes: fluctuating hydrodynamics thermostat.

    PubMed

    Wang, Yaohong; Sigurdsson, Jon Karl; Brandt, Erik; Atzberger, Paul J

    2013-08-01

    We introduce a thermostat based on fluctuating hydrodynamics for dynamic simulations of implicit-solvent coarse-grained models of lipid bilayer membranes. We show our fluctuating hydrodynamics approach captures interesting correlations in the dynamics of lipid bilayer membranes that are missing in simulations performed using standard Langevin dynamics. Our momentum conserving thermostat accounts for solvent-mediated momentum transfer by coupling coarse-grained degrees of freedom to stochastic continuum fields that account for both the solvent hydrodynamics and thermal fluctuations. We present both a general framework and specific methods to couple the particle and continuum degrees of freedom in a manner consistent with statistical mechanics and amenable to efficient computational simulation. For self-assembled vesicles, we study the diffusivity of lipids and their spatial correlations. We find the hydrodynamic coupling yields within the bilayer interesting correlations between diffusing lipids that manifest as a vortex-like structure similar to those observed in explicit-solvent simulations. We expect the introduced fluctuating hydrodynamics methods to provide a way to extend implicit-solvent models for use in a wide variety of dynamic studies.

  5. Multiscale Modeling of Damage Processes in Aluminum Alloys: Grain-Scale Mechanisms

    NASA Technical Reports Server (NTRS)

    Hochhalter, J. D.; Veilleux, M. G.; Bozek, J. E.; Glaessgen, E. H.; Ingraffea, A. R.

    2008-01-01

    This paper has two goals related to the development of a physically-grounded methodology for modeling the initial stages of fatigue crack growth in an aluminum alloy. The aluminum alloy, AA 7075-T651, is susceptible to fatigue cracking that nucleates from cracked second phase iron-bearing particles. Thus, the first goal of the paper is to validate an existing framework for the prediction of the conditions under which the particles crack. The observed statistics of particle cracking (defined as incubation for this alloy) must be accurately predicted to simulate the stochastic nature of microstructurally small fatigue crack (MSFC) formation. Also, only by simulating incubation of damage in a statistically accurate manner can subsequent stages of crack growth be accurately predicted. To maintain fidelity and computational efficiency, a filtering procedure was developed to eliminate particles that were unlikely to crack. The particle filter considers the distributions of particle sizes and shapes, grain texture, and the configuration of the surrounding grains. This filter helps substantially reduce the number of particles that need to be included in the microstructural models and forms the basis of the future work on the subsequent stages of MSFC, crack nucleation and microstructurally small crack propagation. A physics-based approach to simulating fracture should ultimately begin at nanometer length scale, in which atomistic simulation is used to predict the fundamental damage mechanisms of MSFC. These mechanisms include dislocation formation and interaction, interstitial void formation, and atomic diffusion. However, atomistic simulations quickly become computationally intractable as the system size increases, especially when directly linking to the already large microstructural models. Therefore, the second goal of this paper is to propose a method that will incorporate atomistic simulation and small-scale experimental characterization into the existing multiscale

  6. Eastern oyster (Crassostrea virginica) δ15N as a bioindicator of nitrogen sources: Observations and modeling

    PubMed Central

    Fertig, B.; Carruthers, T.J.B.; Dennison, W.C.; Fertig, E.J.; Altabet, M.A.

    2013-01-01

    Stable nitrogen isotopes (δ15N) in bioindicators are increasingly employed to identify nitrogen sources in many ecosystems and biological characteristics of the eastern oyster (Crassostrea virginica) make it an appropriate species for this purpose. To assess nitrogen isotopic fractionation associated with assimilation and baseline variations in oyster mantle, gill, and muscle tissue δ15N, manipulative fieldwork in Chesapeake Bay and corresponding modeling exercises were conducted. This study (1) determined that five individuals represented an optimal sample size; (2) verified that δ15N in oysters from two locations converged after shared deployment to a new location reflecting a change in nitrogen sources; (3) identified required exposure time and temporal integration (four months for muscle, two to three months for gill and mantle); and (4) demonstrated seasonal δ15N increases in seston (summer) and oysters (winter). As bioindicators, oysters can be deployed for spatial interpolation of nitrogen sources, even in areas lacking extant populations. PMID:20381097

  7. Tracer experiment and model evidence for macrofaunal shaping of microbial nitrogen functions along rocky shores

    NASA Astrophysics Data System (ADS)

    Pfister, Catherine A.; Altabet, Mark A.; Pather, Santhiska; Dwyer, Greg

    2016-06-01

    Seawater microbes as well as those associated with macrobiota are increasingly recognized as a key feature affecting nutrient cycling. Tidepools are ideal natural mesocosms to test macrofauna and microbe interactions, and we quantified rates of microbial nitrogen processing using tracer enrichment of ammonium (15NNH4) or nitrate (15NNO3) when tidepools were isolated from the ocean during low intertidal periods. Experiments were conducted during both day and night as well as in control tidepools and those from which mussels had been removed, allowing us to determine the role of both mussels and daylight in microbial nitrogen processing. We paired time series observations of 15N enrichment in NH4+, NO2- and NO3- with a differential equation model to quantify multiple, simultaneous nitrogen transformations. Mussel presence and daylight increased remineralization and photosynthetic nitrogen uptake. When we compared ammonium gain or loss that was attributed to any tidepool microbes vs. photosynthetic uptake, microbes accounted for 32 % of this ammonium flux on average. Microbial transformations averaged 61 % of total nitrate use; thus, microbial activity was almost 3 times that of photosynthetic nitrate uptake. Because it accounted for processes that diluted our tracer, our differential equation model assigned higher rates of nitrogen processing compared to prior source-product models. Our in situ experiments showed that animals alone elevate microbial nitrogen transformations by 2 orders of magnitude, suggesting that coastal macrobiota are key players in complex microbial nitrogen transformations.

  8. Design of a rotamer library for coarse-grained models in protein-folding simulations.

    PubMed

    Larriva, María; Rey, Antonio

    2014-01-27

    Rotamer libraries usually contain geometric information to trace an amino acid side chain, atom by atom, onto a protein backbone. These libraries have been widely used in protein design, structure refinement and prediction, homology modeling, and X-ray and NMR structure validation. However, they usually present too much information and are not always fully compatible with the coarse-grained models of the protein geometry that are frequently used to tackle the protein-folding problem through molecular simulation. In this work, we introduce a new backbone-dependent rotamer library for side chains compatible with low-resolution models in polypeptide chains. We have dispensed with an atomic description of proteins, representing each amino acid side chain by its geometric center (or centroid). The resulting rotamers have been estimated from a statistical analysis of a large structural database consisting of high-resolution X-ray protein structures. As additional information, each rotamer includes the frequency with which it has been found during the statistical analysis. More importantly, the library has been designed with a careful control to ensure that the vast majority of side chains in protein structures (at least 95% of residues) are properly represented. We have tested our library using an independent set of proteins, and our results support a good correlation between the reconstructed centroids from our rotamer library and those in the experimental structures. This new library can serve to improve the definition of side chain centroids in coarse-grained models, avoiding at the same time an excessive additional complexity in a geometric model for the polypeptide chain.

  9. Comparing normal modes across different models and scales: Hessian reduction versus coarse-graining.

    PubMed

    Ghysels, An; Miller, Benjamin T; Pickard, Frank C; Brooks, Bernard R

    2012-10-30

    Dimension reduction is often necessary when attempting to reach longer length and time scales in molecular simulations. It is realized by constraining degrees of freedom or by coarse-graining the system. When evaluating the accuracy of a dimensional reduction, there is a practical challenge: the models yield vectors with different lengths, making a comparison by calculating their dot product impossible. This article investigates mapping procedures for normal mode analysis. We first review a horizontal mapping procedure for the reduced Hessian techniques, which projects out degrees of freedom. We then design a vertical mapping procedure for the "implosion" of the all-atom (AA) Hessian to a coarse-grained scale that is based upon vibrational subsystem analysis. This latter method derives both effective force constants and an effective kinetic tensor. Next, a series of metrics is presented for comparison across different scales, where special attention is given to proper mass-weighting. The dimension-dependent metrics, which require prior mapping for proper evaluation, are frequencies, overlap of normal mode vectors, probability similarity, Hessian similarity, collectivity of modes, and thermal fluctuations. The dimension-independent metrics are shape derivatives, elastic modulus, vibrational free energy differences, heat capacity, and projection on a predefined basis set. The power of these metrics to distinguish between reasonable and unreasonable models is tested on a toy alpha helix system and a globular protein; both are represented at several scales: the AA scale, a Gō-like model, a canonical elastic network model, and a network model with intentionally unphysical force constants.

  10. Material and interaction properties of selected grains and oilseeds for modeling discrete particles

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Experimental investigations of grain flow can be expensive and time-consuming, but computer simulations can reduce the large effort required to evaluate the flow of grain in handling operations. Published data on material and interaction properties of selected grains and oilseeds relevant to Discret...

  11. Measurement and modeling of ozone and nitrogen oxides produced by laser breakdown in oxygen-nitrogen atmospheres.

    PubMed

    Gornushkin, Igor B; Stevenson, Chris L; Galbács, Gábor; Smith, Ben W; Winefordner, James D

    2003-11-01

    The production of ozone nad nitrogen oxides was studied during multiple laser breakdown in oxygen-nitrogen mixtures at atmospheric pressure. About 2000 laser shots at 10(10) W cm-2 were delivered into a sealed reaction chamber. The chamber with a long capillary was designed to measure absorption of O3, NO, and NO2 as a function of the number of laser shots. The light source for absorption measurements was the continuum radiation emitted by the plasma during the first 0.2 microsecond of its evolution. A kinetic model was developed that encompassed the principal chemical reactions between the major atmospheric components and the products of laser breakdown. In the model, the laser plasma was treated as a source of nitric oxide and atomic oxygen, whose rates of production were calculated using measured absorption by NO, NO2, and O3. The calculated concentration profiles for NO, NO2, and O3 were in good agreement with measured profiles over a time scale of 0-200 s. The steady-state concentration of ozone was measured in a flow cell in air. For a single breakdown in air, the estimated steady-state yield of ozone was 2 x 10(12) molecules, which agreed with the model prediction. This study can be of importance for general understanding of laser plasma chemistry and for elucidating the nature of spectral interferences and matrix effects that may take place in applied spectrochemical analysis.

  12. Measurement and modeling of ozone and nitrogen oxides produced by laser breakdown in oxygen-nitrogen atmospheres.

    PubMed

    Gornushkin, Igor B; Stevenson, Chris L; Galbács, Gábor; Smith, Ben W; Winefordner, James D

    2003-11-01

    The production of ozone nad nitrogen oxides was studied during multiple laser breakdown in oxygen-nitrogen mixtures at atmospheric pressure. About 2000 laser shots at 10(10) W cm-2 were delivered into a sealed reaction chamber. The chamber with a long capillary was designed to measure absorption of O3, NO, and NO2 as a function of the number of laser shots. The light source for absorption measurements was the continuum radiation emitted by the plasma during the first 0.2 microsecond of its evolution. A kinetic model was developed that encompassed the principal chemical reactions between the major atmospheric components and the products of laser breakdown. In the model, the laser plasma was treated as a source of nitric oxide and atomic oxygen, whose rates of production were calculated using measured absorption by NO, NO2, and O3. The calculated concentration profiles for NO, NO2, and O3 were in good agreement with measured profiles over a time scale of 0-200 s. The steady-state concentration of ozone was measured in a flow cell in air. For a single breakdown in air, the estimated steady-state yield of ozone was 2 x 10(12) molecules, which agreed with the model prediction. This study can be of importance for general understanding of laser plasma chemistry and for elucidating the nature of spectral interferences and matrix effects that may take place in applied spectrochemical analysis. PMID:14658160

  13. Modeling the influence of bubble pressure on grain boundary separation and fission gas release

    SciTech Connect

    Pritam Chakraborty; Michael R. Tonks; Giovanni Pastore

    2014-09-01

    Grain boundary (GB) separation as a mechanism for fission gas release (FGR), complementary to gas bubble interlinkage, has been experimentally observed in irradiated light water reactor fuel. However there has been limited effort to develop physics-based models incorporating this mechanism for the analysis of FGR. In this work, a computational study is carried out to investigate GB separation in UO2 fuel under the effect of gas bubble pressure and hydrostatic stress. A non-dimensional stress intensity factor formula is obtained through 2D axisymmetric analyses considering lenticular bubbles and Mode-I crack growth. The obtained functional form can be used in higher length-scale models to estimate the contribution of GB separation to FGR.

  14. Coarse-graining intermittent intracellular transport: Two- and three-dimensional models.

    PubMed

    Lawley, Sean D; Tuft, Marie; Brooks, Heather A

    2015-10-01

    Viruses and other cellular cargo that lack locomotion must rely on diffusion and cellular transport systems to navigate through a biological cell. Indeed, advances in single particle tracking have revealed that viral motion alternates between (a) diffusion in the cytoplasm and (b) active transport along microtubules. This intermittency makes quantitative analysis of trajectories difficult. Therefore, the purpose of this paper is to construct mathematical methods to approximate intermittent dynamics by effective stochastic differential equations. The coarse-graining method that we develop is more accurate than existing techniques and applicable to a wide range of intermittent transport models. In particular, we apply our method to two- and three-dimensional cell geometries (disk, sphere, and cylinder) and demonstrate its accuracy. In addition to these specific applications, we also explain our method in full generality for use on future intermittent models.

  15. Multiscale Modeling of Grain Boundaries in ZrB2: Structure, Energetics, and Thermal Resistance

    NASA Technical Reports Server (NTRS)

    Lawson, John W.; Daw, Murray S.; Squire, Thomas H.; Bauschlicher, Charles W., Jr.

    2012-01-01

    A combination of ab initio, atomistic and finite element methods (FEM) were used to investigate the structures, energetics and lattice thermal conductance of grain boundaries for the ultra high temperature ceramic ZrB2. Atomic models of idealized boundaries were relaxed using density functional theory. Information about bonding across the interfaces was determined from the electron localization function. The Kapitza conductance of larger scale versions of the boundary models were computed using non-equilibrium molecular dynamics. The interfacial thermal parameters together with single crystal thermal conductivities were used as parameters in microstructural computations. FEM meshes were constructed on top of microstructural images. From these computations, the effective thermal conductivity of the polycrystalline structure was determined.

  16. Coarse-graining intermittent intracellular transport: Two- and three-dimensional models

    NASA Astrophysics Data System (ADS)

    Lawley, Sean D.; Tuft, Marie; Brooks, Heather A.

    2015-10-01

    Viruses and other cellular cargo that lack locomotion must rely on diffusion and cellular transport systems to navigate through a biological cell. Indeed, advances in single particle tracking have revealed that viral motion alternates between (a) diffusion in the cytoplasm and (b) active transport along microtubules. This intermittency makes quantitative analysis of trajectories difficult. Therefore, the purpose of this paper is to construct mathematical methods to approximate intermittent dynamics by effective stochastic differential equations. The coarse-graining method that we develop is more accurate than existing techniques and applicable to a wide range of intermittent transport models. In particular, we apply our method to two- and three-dimensional cell geometries (disk, sphere, and cylinder) and demonstrate its accuracy. In addition to these specific applications, we also explain our method in full generality for use on future intermittent models.

  17. A temperature-dependent coarse-grained model for the thermoresponsive polymer poly(N-isopropylacrylamide)

    DOE PAGESBeta

    Abbott, Lauren J.; Stevens, Mark J.

    2015-12-22

    In this study, a coarse-grained (CG) model is developed for the thermoresponsive polymer poly(N-isopropylacrylamide) (PNIPAM), using a hybrid top-down and bottom-up approach. Nonbonded parameters are fit to experimental thermodynamic data following the procedures of the SDK (Shinoda, DeVane, and Klein) CG force field, with minor adjustments to provide better agreement with radial distribution functions from atomistic simulations. Bonded parameters are fit to probability distributions from atomistic simulations using multi-centered Gaussian-based potentials. The temperature-dependent potentials derived for the PNIPAM CG model in this work properly capture the coil–globule transition of PNIPAM single chains and yield a chain-length dependence consistent with atomisticmore » simulations.« less

  18. Modelling of c-C2H4O Formation on Grain-Surfaces

    NASA Astrophysics Data System (ADS)

    Occhiogrosso, Angela; Viti, S.; Ward, M. D.; Price, S. D.

    2013-01-01

    Ethylene oxide (c-C2H4O) is a ring-shaped organic compound that may lead to the synthesis of amino acids and the early metabolic pathways in the interstellar medium (ISM) (Cleaves 2003; Miller & Schlesinger 1993). This molecule has been detected towards several high-mass star forming regions (Ikeda et al. 2001) but to date, its observational abundances cannot be reproduced by chemical models. We include new experimental results in the UCL_CHEM chemical model with the aim of reproducing the abundances of ethylene oxide across high-mass sources. In particular, we focused on the solid state reaction investigated by Ward & Price (2011). By comparing our theoretical column densities with those from the observations we found that the reaction between atomic oxygen and ethylene on grains is a viable route of formation for ethylene oxide (Occhiogrosso et al., accepted by MNRAS).

  19. A temperature-dependent coarse-grained model for the thermoresponsive polymer poly(N-isopropylacrylamide)

    SciTech Connect

    Abbott, Lauren J.; Stevens, Mark J.

    2015-12-28

    A coarse-grained (CG) model is developed for the thermoresponsive polymer poly(N-isopropylacrylamide) (PNIPAM), using a hybrid top-down and bottom-up approach. Nonbonded parameters are fit to experimental thermodynamic data following the procedures of the SDK (Shinoda, DeVane, and Klein) CG force field, with minor adjustments to provide better agreement with radial distribution functions from atomistic simulations. Bonded parameters are fit to probability distributions from atomistic simulations using multi-centered Gaussian-based potentials. The temperature-dependent potentials derived for the PNIPAM CG model in this work properly capture the coil–globule transition of PNIPAM single chains and yield a chain-length dependence consistent with atomistic simulations.

  20. A temperature-dependent coarse-grained model for the thermoresponsive polymer poly(N-isopropylacrylamide)

    SciTech Connect

    Abbott, Lauren J.; Stevens, Mark J.

    2015-12-22

    In this study, a coarse-grained (CG) model is developed for the thermoresponsive polymer poly(N-isopropylacrylamide) (PNIPAM), using a hybrid top-down and bottom-up approach. Nonbonded parameters are fit to experimental thermodynamic data following the procedures of the SDK (Shinoda, DeVane, and Klein) CG force field, with minor adjustments to provide better agreement with radial distribution functions from atomistic simulations. Bonded parameters are fit to probability distributions from atomistic simulations using multi-centered Gaussian-based potentials. The temperature-dependent potentials derived for the PNIPAM CG model in this work properly capture the coil–globule transition of PNIPAM single chains and yield a chain-length dependence consistent with atomistic simulations.

  1. Atmospheric Chemistry Transport Modeling of Organic Nitrogen Input to the Ocean

    NASA Astrophysics Data System (ADS)

    Ito, A.; Lin, G.; Penner, J. E.

    2013-12-01

    Atmospheric deposition of reactive nitrogen (N) species from air pollutants is a significant source of exogenous nitrogen in marine ecosystems. Here we use an atmospheric chemical transport model to investigate the supply of soluble organic nitrogen (ON) from anthropogenic sources to the ocean. Comparisons of modeled deposition with observations at coastal and marine locations show good overall agreement for inorganic nitrogen and total soluble nitrogen, but significant underestimates for soluble ON when we include the primary soluble ON from combustion sources and the secondary carbon-containing oxidized N in gases and aerosols. The model results suggest that including the secondary carbon-containing reduced N in aerosols contributes to a better predictive capability of the deposition rates. The model results show a clear distinction in the vertical distribution of soluble ON in aerosols between different processes from the primary sources and the secondary formation. The model results (excluding the biomass burning and natural emission changes) suggest an increase in soluble ON outflow from atmospheric pollution, in particular from East Asia, to the oceans in the twentieth century. These results highlight the necessity of improving the process-based quantitative understanding of the chemical reactions of inorganic nitrogen species with organics in aerosol and cloud water.

  2. Improving dynamic phytoplankton reserve-utilization models with an indirect proxy for internal nitrogen.

    PubMed

    Malerba, Martino E; Heimann, Kirsten; Connolly, Sean R

    2016-09-01

    Ecologists have often used indirect proxies to represent variables that are difficult or impossible to measure directly. In phytoplankton, the internal concentration of the most limiting nutrient in a cell determines its growth rate. However, directly measuring the concentration of nutrients within cells is inaccurate, expensive, destructive, and time-consuming, substantially impairing our ability to model growth rates in nutrient-limited phytoplankton populations. The red chlorophyll autofluorescence (hereafter "red fluorescence") signal emitted by a cell is highly correlated with nitrogen quota in nitrogen-limited phytoplankton species. The aim of this study was to evaluate the reliability of including flow cytometric red fluorescence as a proxy for internal nitrogen status to model phytoplankton growth rates. To this end, we used the classic Quota model and designed three approaches to calibrate its model parameters to data: where empirical observations on cell internal nitrogen quota were used to fit the model ("Nitrogen-Quota approach"), where quota dynamics were inferred only from changes in medium nutrient depletion and population density ("Virtual-Quota approach"), or where red fluorescence emission of a cell was used as an indirect proxy for its internal nitrogen quota ("Fluorescence-Quota approach"). Two separate analyses were carried out. In the first analysis, stochastic model simulations were parameterized from published empirical relationships and used to generate dynamics of phytoplankton communities reared under nitrogen-limited conditions. Quota models were fitted to the dynamics of each simulated species with the three different approaches and the performance of each model was compared. In the second analysis, we fit Quota models to laboratory time-series and we calculate the ability of each calibration approach to describe the observed trajectories of internal nitrogen quota in the culture. Results from both analyses concluded that the

  3. Improving dynamic phytoplankton reserve-utilization models with an indirect proxy for internal nitrogen.

    PubMed

    Malerba, Martino E; Heimann, Kirsten; Connolly, Sean R

    2016-09-01

    Ecologists have often used indirect proxies to represent variables that are difficult or impossible to measure directly. In phytoplankton, the internal concentration of the most limiting nutrient in a cell determines its growth rate. However, directly measuring the concentration of nutrients within cells is inaccurate, expensive, destructive, and time-consuming, substantially impairing our ability to model growth rates in nutrient-limited phytoplankton populations. The red chlorophyll autofluorescence (hereafter "red fluorescence") signal emitted by a cell is highly correlated with nitrogen quota in nitrogen-limited phytoplankton species. The aim of this study was to evaluate the reliability of including flow cytometric red fluorescence as a proxy for internal nitrogen status to model phytoplankton growth rates. To this end, we used the classic Quota model and designed three approaches to calibrate its model parameters to data: where empirical observations on cell internal nitrogen quota were used to fit the model ("Nitrogen-Quota approach"), where quota dynamics were inferred only from changes in medium nutrient depletion and population density ("Virtual-Quota approach"), or where red fluorescence emission of a cell was used as an indirect proxy for its internal nitrogen quota ("Fluorescence-Quota approach"). Two separate analyses were carried out. In the first analysis, stochastic model simulations were parameterized from published empirical relationships and used to generate dynamics of phytoplankton communities reared under nitrogen-limited conditions. Quota models were fitted to the dynamics of each simulated species with the three different approaches and the performance of each model was compared. In the second analysis, we fit Quota models to laboratory time-series and we calculate the ability of each calibration approach to describe the observed trajectories of internal nitrogen quota in the culture. Results from both analyses concluded that the

  4. Coarse-graining polymer solutions: A critical appraisal of single- and multi-site models

    NASA Astrophysics Data System (ADS)

    D'Adamo, G.; Menichetti, R.; Pelissetto, A.; Pierleoni, C.

    2015-09-01

    We critically discuss and review the general ideas behind single- and multi-site coarse-grained (CG) models as applied to macromolecular solutions in the dilute and semi-dilute regime. We first consider single-site models with zero-density and density-dependent pair potentials. We highlight advantages and limitations of each option in reproducing the thermodynamic behavior and the large-scale structure of the underlying reference model. As a case study we consider solutions of linear homopolymers in a solvent of variable quality. Secondly, we extend the discussion to multi-component systems presenting, as a test case, results for mixtures of colloids and polymers. Specifically, we found the CG model with zero-density potentials to be unable to predict fluid-fluid demixing in a reasonable range of densities for mixtures of colloids and polymers of equal size. For larger colloids, the polymer volume fractions at which phase separation occurs are largely overestimated. CG models with density-dependent potentials are somewhat less accurate than models with zero-density potentials in reproducing the thermodynamics of the system and, although they present a phase separation, they significantly underestimate the polymer volume fractions along the binodal. Finally, we discuss a general multi-site strategy, which is thermodynamically consistent and fully transferable with the number of sites, and that allows us to overcome most of the limitations discussed for single-site models.

  5. Effect of subsoiling in fallow period on soil water storage and grain protein accumulation of dryland wheat and its regulatory effect by nitrogen application.

    PubMed

    Sun, Min; Gao, ZhiQiang; Zhao, WeiFeng; Deng, LianFeng; Deng, Yan; Zhao, HongMei; Ren, AiXia; Li, Gang; Yang, ZhenPing

    2013-01-01

    To provide a new way to increase water storage and retention of dryland wheat, a field study was conducted at Wenxi experimental site of Shanxi Agricultural University. The effect of subsoiling in fallow period on soil water storage, accumulation of proline, and formation of grain protein after anthesis were determined. Our results showed that subsoiling in fallow period could increase water storage in the 0-300 cm soil at pre-sowing stage and at anthesis stage with low or medium N application, especially for the 60-160 cm soil. However, the proline content, glutamine synthetase (GS) activity, glutamate dehydrogenase (GDH) activity in flag leaves and grains were all decreased by subsoiling in fallow period. In addition, the content of albumin, gliadin, and total protein in grains were also decreased while globulin content, Glu/Gli, protein yield, and glutelin content were increased. With N application increasing, water storage of soil layers from 20 to 200 cm was decreased at anthesis stage. High N application resulted in the increment of proline content and GS activity in grains. Besides, correlation analysis showed that soil storage in 40-160 cm soil was negatively correlated with proline content in grains; proline content in grains was positively correlated with GS and GDH activity in flag leaves. Contents of albumin, globulin and total protein in grains were positively correlated with proline content in grains and GDH activity in flag leaves. In conclusion, subsoiling in fallow period, together with N application at 150 kg·hm(-2), was beneficial to increase the protein yield and Glu/Gli in grains which improve the quality of wheat.

  6. Effect of subsoiling in fallow period on soil water storage and grain protein accumulation of dryland wheat and its regulatory effect by nitrogen application.

    PubMed

    Sun, Min; Gao, ZhiQiang; Zhao, WeiFeng; Deng, LianFeng; Deng, Yan; Zhao, HongMei; Ren, AiXia; Li, Gang; Yang, ZhenPing

    2013-01-01

    To provide a new way to increase water storage and retention of dryland wheat, a field study was conducted at Wenxi experimental site of Shanxi Agricultural University. The effect of subsoiling in fallow period on soil water storage, accumulation of proline, and formation of grain protein after anthesis were determined. Our results showed that subsoiling in fallow period could increase water storage in the 0-300 cm soil at pre-sowing stage and at anthesis stage with low or medium N application, especially for the 60-160 cm soil. However, the proline content, glutamine synthetase (GS) activity, glutamate dehydrogenase (GDH) activity in flag leaves and grains were all decreased by subsoiling in fallow period. In addition, the content of albumin, gliadin, and total protein in grains were also decreased while globulin content, Glu/Gli, protein yield, and glutelin content were increased. With N application increasing, water storage of soil layers from 20 to 200 cm was decreased at anthesis stage. High N application resulted in the increment of proline content and GS activity in grains. Besides, correlation analysis showed that soil storage in 40-160 cm soil was negatively correlated with proline content in grains; proline content in grains was positively correlated with GS and GDH activity in flag leaves. Contents of albumin, globulin and total protein in grains were positively correlated with proline content in grains and GDH activity in flag leaves. In conclusion, subsoiling in fallow period, together with N application at 150 kg·hm(-2), was beneficial to increase the protein yield and Glu/Gli in grains which improve the quality of wheat. PMID:24098371

  7. Coarse Grained Approach to First Principles Modeling of Radiation Cascade in Large Fe Supercells

    NASA Astrophysics Data System (ADS)

    Odbadrakh, Kh; Nicholson, D. M.; Rusanu, A.; Samolyuk, G. D.; Stoller, R. E.; Zhang, X.-G.; Stocks, G. M.

    2012-12-01

    Classical Molecular Dynamics (MD) simulations characterizing dislocations and radiation damage typically treat 105-107 atoms. First principles techniques employed to understand systems at an atomistic level are not practical for such large systems consisting of millions of atoms. We present an efficient coarse grained (CG) approach to calculate local electronic and magnetic properties of large MD-generated structures from the first principles. Local atomic magnetic moments in crystalline Fe are perturbed by the presence of radiation generated vacancies and interstitials. The effects are most pronounced near the defect cores and decay slowly as the strain field of the defects decrease with distance. We develop the CG technique based on the Locally Self-consistent Multiple Scattering (LSMS) method that exploits the near-sightedness of the electron Green function. The atomic positions were determined by MD with an embedded atom force field. The local moments in the neighborhood of the defect cores are calculated with first-principles based on full local structure information. Atoms in the rest of the system are modeled by representative atoms with approximated properties. The calculations result in local moments near the defect centers with first-principles accuracy, while capturing coarse-grained details of local moments at greater length scales. This CG approach makes these large scale structures amenable to first principles study.

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

    SciTech Connect

    Palmer, T A

    2001-08-17

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

  9. A coarse-grained α-carbon protein model with anisotropic hydrogen-bonding

    PubMed Central

    Yap, Eng-Hui; Fawzi, Nicolas Lux; Head-Gordon, Teresa

    2012-01-01

    We develop a sequence based α-carbon model to incorporate a mean field estimate of the orientation dependence of the polypeptide chain that gives rise to specific hydrogen bond pairing to stabilize α-helices and β-sheets. We illustrate the success of the new protein model in capturing thermodynamic measures and folding mechanism of proteins L and G. Compared to our previous coarse-grained model, the new model shows greater folding cooperativity and improvements in designability of protein sequences, as well as predicting correct trends for kinetic rates and mechanism for proteins L and G. We believe the model is broadly applicable to other protein folding and protein–protein co-assembly processes, and does not require experimental input beyond the topology description of the native state. Even without tertiary topology information, it can also serve as a mid-resolution protein model for more exhaustive conformational search strategies that can bridge back down to atomic descriptions of the polypeptide chain. PMID:17879350

  10. Modeling sediment resuspension-induced DO variation in fine-grained streams.

    PubMed

    Zahraeifard, Vahid; Deng, Zhiqiang

    2012-12-15

    Dissolved Oxygen (DO) levels in streams with nutrient enriched fine-grained sediment are highly affected by sediment resuspension. This paper presents a new model, called VART-DOS model, for simulation of instream DO transport, DO exchanges across water-sediment and water-air interfaces, and DO variation in response to sediment resuspension. The sediment resuspension effect is described by introducing a lumped term as a product of DO concentration and a rate of sediment resuspension-induced DO consumption (Λ). The rate parameter Λ is defined as a nonlinear function of average summer temperature of water and several sediment erosion-related parameters. This is a novel and unique feature of the VART-DOS model. Based on sensitivity analysis, effects of BOD and Sediment Oxygen Demand (SOD) on DO consumption are not so important as compared to sediment resuspension which can cause up to 83% reduction in DO level during high flow. The VART-DOS model was applied to the Lower Amite River in Louisiana, USA to perform continuous simulations of DO fluctuations in the winter month January and the summer month July involving several flood-induced sediment resuspension events. Simulation results indicate that the VART-DOS model is capable of capturing overall variation trends in DO concentration. The Normalized Root Mean Square Error (RMSE) between VART-DOS simulated and observed DO levels was 0. 42 for January and 0.23 for July, demonstrating the efficacy of the VART-DOS model. PMID:23137983

  11. Universal and non-universal features in coarse-grained models of flow in disordered solids.

    PubMed

    Nicolas, Alexandre; Martens, Kirsten; Bocquet, Lydéric; Barrat, Jean-Louis

    2014-07-14

    We study the two-dimensional (2D) shear flow of amorphous solids within variants of an elastoplastic model, paying particular attention to spatial correlations and time fluctuations of, e.g., local stresses. The model is based on the local alternation between an elastic regime and plastic events during which the local stress is redistributed. The importance of a fully tensorial description of the stress and of the inclusion of (coarse-grained) convection in the model is investigated; scalar and tensorial models yield similar results, while convection enhances fluctuations and breaks the spurious symmetry between the flow and velocity gradient directions, for instance when shear localisation is observed. Besides, correlation lengths measured with diverse protocols are discussed. One class of such correlation lengths simply scale with the spacing between homogeneously distributed, simultaneous plastic events. This leads to a scaling of the correlation length with the shear rate as γ̇(-1/2) in 2D in the athermal regime, regardless of the details of the model. The radius of the cooperative disk, defined as the near-field region in which plastic events induce a stress redistribution that is not amenable to a mean-field treatment, notably follows this scaling. On the other hand, the cooperative volume measured from the four-point stress susceptibility and its dependence on the system size and the shear rate are model-dependent.

  12. A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition

    SciTech Connect

    Dalgicdir, Cahit; Sensoy, Ozge; Sayar, Mehmet; Peter, Christine

    2013-12-21

    One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties.

  13. A Model to Predict Nitrogen Losses in Advanced Soil-Based Wastewater Treatment Systems

    NASA Astrophysics Data System (ADS)

    Morales, I.; Cooper, J.; Loomis, G.; Kalen, D.; Amador, J.; Boving, T. B.

    2014-12-01

    Most of the non-point source Nitrogen (N) load in rural areas is attributed to onsite wastewater treatment systems (OWTS). Nitrogen compounds are considered environmental pollutants because they deplete the oxygen availability in water bodies and produce eutrophication. The objective of this study was to simulate the fate and transport of Nitrogen in OWTS. The commercially-available 2D/3D HYDRUS software was used to develop a transport and fate model. Experimental data from a laboratory meso-cosm study included the soil moisture content, NH4 and NO3- data. That data set was used to calibrate the model. Three types of OWTS were simulated: (1) pipe-and-stone (P&S), (2) advanced soil drainfields, pressurized shallow narrow drainfield (SND) and (3) Geomat (GEO), a variation of SND. To better understand the nitrogen removal mechanism and the performance of OWTS technologies, replicate (n = 3) intact soil mesocosms were used with 15N-labelled nitrogen inputs. As a result, it was estimated that N removal by denitrification was predominant in P&S. However, it is suggested that N was removed by nitrification in SND and GEO. The calibrated model was used to estimate Nitrogen fluxes for both conventional and advanced OWTS. Also, the model predicted the N losses from nitrification and denitrification in all OWTS. These findings help to provide practitioners with guidelines to estimate N removal efficiencies for OWTS, and predict N loads and spatial distribution for identifying non-point sources.

  14. The heliocentric evolution of cometary infrared spectra: results from an organic grain model.

    PubMed

    Chyba, C F; Sagan, C; Mumma, M J

    1989-01-01

    Observations of Comets Halley and Wilson reveal an emission feature peaking near 3.4 micrometers, characteristic of C-H stretching in hydrocarbons. We have previously (Chyba and Sagan 1987a, Nature (London) 330, 350-353) fit this feature with a simple two-component thermal emission model for dust in the cometary coma (one component corresponding to large, cool, optically thick particles, the other due to smaller, hotter, organic grains) by employing laboratory spectra of the organic residue produced by the irradiation of carbon-bearing ices. This procedure yields optical depths in agreement with limits from spacecraft data. One remarkable result of such modeling is that at approximately 1 AU emission features at wavelengths longer than 3.4 micrometers are largely overwhelmed (or "diluted") by continuum emission. The large particle optical depth is approximately 10(2) times that of the emitting organics, so that, relative to the continuum, only near the continuum minimum can the emitting organics make a significant contribution. At approximately 1 AU, the 3.4-micrometers feature is the sole feature near that minimum, lying at the intersection of the curves for particle thermal emission and scattered sunlight. Thus, since as a comet moves away from perihelion the intersection of the scattered solar spectrum and the comet's thermal emission spectrum will move to longer wavelengths, we predicted (Chyba and Sagan 1987a) that the 3.4-micrometers feature is diluted while those at longer wavelengths are progressively revealed--so long as the comet retains its coma. We now quantitatively develop this model and find agreement with observational data for Comet Halley for certain plausible values of optical constants. Thus the observed heliocentric evolution of the 3.4-micrometers feature provides information on the composition, and perhaps structure, of the organic grains in Comet Halley. In addition, we argue that the heliocentric evolution of organic features will differ in

  15. A Coarse-Grained Model of Stratum Corneum Lipids: Free Fatty Acids and Ceramide NS.

    PubMed

    Moore, Timothy C; Iacovella, Christopher R; Hartkamp, Remco; Bunge, Annette L; McCabe, Clare

    2016-09-22

    Ceramide (CER)-based biological membranes are used both experimentally and in simulations as simplified model systems of the skin barrier. Molecular dynamics studies have generally focused on simulating preassembled structures using atomistically detailed models of CERs, which limit the system sizes and time scales that can practically be probed, rendering them ineffective for studying particular phenomena, including self-assembly into bilayer and lamellar superstructures. Here, we report on the development of a coarse-grained (CG) model for CER NS, the most abundant CER in human stratum corneum. Multistate iterative Boltzmann inversion is used to derive the intermolecular pair potentials, resulting in a force field that is applicable over a range of state points and suitable for studying ceramide self-assembly. The chosen CG mapping, which includes explicit interaction sites for hydroxyl groups, captures the directional nature of hydrogen bonding and allows for accurate predictions of several key structural properties of CER NS bilayers. Simulated wetting experiments allow the hydrophobicity of CG beads to be accurately tuned to match atomistic wetting behavior, which affects the whole system, since inaccurate hydrophobic character is found to unphysically alter the lipid packing in hydrated lamellar states. We find that CER NS can self-assemble into multilamellar structures, enabling the study of lipid systems more representative of the multilamellar lipid structures present in the skin barrier. The coarse-grained force field derived herein represents an important step in using molecular dynamics to study the human skin barrier, which gives a resolution not available through experiment alone. PMID:27564869

  16. Optimization of an Elastic Network Augmented Coarse Grained Model to Study CCMV Capsid Deformation

    PubMed Central

    Globisch, Christoph; Krishnamani, Venkatramanan; Deserno, Markus; Peter, Christine

    2013-01-01

    The major protective coat of most viruses is a highly symmetric protein capsid that forms spontaneously from many copies of identical proteins. Structural and mechanical properties of such capsids, as well as their self-assembly process, have been studied experimentally and theoretically, including modeling efforts by computer simulations on various scales. Atomistic models include specific details of local protein binding but are limited in system size and accessible time, while coarse grained (CG) models do get access to longer time and length scales but often lack the specific local interactions. Multi-scale models aim at bridging this gap by systematically connecting different levels of resolution. Here, a CG model for CCMV (Cowpea Chlorotic Mottle Virus), a virus with an icosahedral shell of 180 identical protein monomers, is developed, where parameters are derived from atomistic simulations of capsid protein dimers in aqueous solution. In particular, a new method is introduced to combine the MARTINI CG model with a supportive elastic network based on structural fluctuations of individual monomers. In the parametrization process, both network connectivity and strength are optimized. This elastic-network optimized CG model, which solely relies on atomistic data of small units (dimers), is able to correctly predict inter-protein conformational flexibility and properties of larger capsid fragments of 20 and more subunits. Furthermore, it is shown that this CG model reproduces experimental (Atomic Force Microscopy) indentation measurements of the entire viral capsid. Thus it is shown that one obvious goal for hierarchical modeling, namely predicting mechanical properties of larger protein complexes from models that are carefully parametrized on elastic properties of smaller units, is achievable. PMID:23613730

  17. Optimality-based modeling of nitrogen allocation and photoacclimation in photosynthesis

    NASA Astrophysics Data System (ADS)

    Armstrong, Robert A.

    2006-03-01

    The ability to predict phytoplankton growth rates under light and nutrient limitation is fundamental to modeling the ocean carbon cycle. Equally fundamental is the ability to predict chlorophyll:carbon ratios, since satellite-based chlorophyll estimates are one of the few data sets to which model output can be compared globally. Because the Geider et al. [Geider, R.J., MacIntyre, H.L., Kana, T.M., 1998. A dynamic regulatory model of phytoplanktonic acclimation to light, nutrients, and temperature. Limnology and Oceanography 43, 679-694] model addresses both desiderata, it has become the model of choice for representing photosynthesis in a wide range of ecosystem models. The Geider et al. [Geider, R.J., MacIntyre, H.L., Kana, T.M., 1998. A dynamic regulatory model of phytoplanktonic acclimation to light, nutrients, and temperature. Limnology and Oceanography 43, 679-694] model follows previous models in positing that maximum photosynthetic rate can be reached only when nitrogen cell quota (nitrogen:carbon ratio) reaches a fixed maximum value qN,maxC. Empirically, this assumption is contradicted by the extremely thorough data set of Laws and Bannister [Laws, E.A., Bannister, T.T., 1980. Nutrient- and light-limited growth of Thalassiosira fluviatilis in continuous culture, with implications for phytoplankton growth in the ocean. Limnology and Oceanography 25, 457-473] and by other studies: maximum growth rate does not seem to require maximum nitrogen cell quota. To the extent that existing models do not reflect this key characteristic, they may fail to yield reliable predictions of chlorophyll:carbon ratios as functions of nitrogen:carbon ratios. They also may fail to reflect differences in growth rates of competing phytoplankton species, an essential feature of state-of-the-art ecosystem models used in biogeochemistry simulations. In the present paper I replace the nitrogen limitation function of previous models by one that does not require maximum nitrogen cell

  18. Modeling riparian soil nitrogen removal based on a modified SWAT model coupled with remote sensing data

    NASA Astrophysics Data System (ADS)

    Wang, Xuelei; Yang, Shengtian; Mannaerts, Chris M.; Zeng, Hongjuan; Zheng, Donghai

    2010-11-01

    Riparian zone, as the interlaced zone between land and water, plays an important role in society, landscape and environmental quality. Riparian ecosystems have critical impacts on controlling the non-point source pollution (NPSP) and maintaining the health of aquatic ecosystems, especially on nitrogen (N) removal. The processes that affect N removal in riparian ecological system mainly include soil nitrous gas emission, plant uptake and sediment retention, of which nitrous gas release by soil denitrification is one of the most important functions for riparian system. Therefore, it's critical to build an N removal model including soil denitrification, nitrification and ammonium volatilization to evaluate the riparian ecological function and management practice. In this study, the Soil and Water Assessment Tool (SWAT) was extended with algorithms from a simple soil denitrification model and remote sensing data to enhance the model performance with regard to predicting soil N removal in the Guanting reservoir riparian catchment. The N removal model is based on chemical and physical relationships that govern soil heat, moisture and nitrogen movement. Processes considered include denitrification, nitrification and ammonia (NH3) volatilization. SPOT-5 and Landsat5-TM satellite data were used to interpret the spatial land surface information and derive model parameters. Results of laboratory-scale anaerobic incubation experiment were applied to estimate the soil denitrification model parameters for the different soil types. In an in situ field-scale experiment conducted to calibrate and validate models and an indirect method was used to test simulated N removal load in the Guanting reservoir riparian catchment. Results showed that the process-based model performed well and produced sound simulation results for the riparian reservoir catchment, with the coefficient of determination (R2) between the simulated and observed values being 0.71.

  19. Modeling riparian soil nitrogen removal based on a modified SWAT model coupled with remote sensing data

    NASA Astrophysics Data System (ADS)

    Wang, Xuelei; Yang, Shengtian; Mannaerts, Chris M.; Zeng, Hongjuan; Zheng, Donghai

    2009-09-01

    Riparian zone, as the interlaced zone between land and water, plays an important role in society, landscape and environmental quality. Riparian ecosystems have critical impacts on controlling the non-point source pollution (NPSP) and maintaining the health of aquatic ecosystems, especially on nitrogen (N) removal. The processes that affect N removal in riparian ecological system mainly include soil nitrous gas emission, plant uptake and sediment retention, of which nitrous gas release by soil denitrification is one of the most important functions for riparian system. Therefore, it's critical to build an N removal model including soil denitrification, nitrification and ammonium volatilization to evaluate the riparian ecological function and management practice. In this study, the Soil and Water Assessment Tool (SWAT) was extended with algorithms from a simple soil denitrification model and remote sensing data to enhance the model performance with regard to predicting soil N removal in the Guanting reservoir riparian catchment. The N removal model is based on chemical and physical relationships that govern soil heat, moisture and nitrogen movement. Processes considered include denitrification, nitrification and ammonia (NH3) volatilization. SPOT-5 and Landsat5-TM satellite data were used to interpret the spatial land surface information and derive model parameters. Results of laboratory-scale anaerobic incubation experiment were applied to estimate the soil denitrification model parameters for the different soil types. In an in situ field-scale experiment conducted to calibrate and validate models and an indirect method was used to test simulated N removal load in the Guanting reservoir riparian catchment. Results showed that the process-based model performed well and produced sound simulation results for the riparian reservoir catchment, with the coefficient of determination (R2) between the simulated and observed values being 0.71.

  20. Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models.

    PubMed

    Baron, Riccardo; Trzesniak, Daniel; de Vries, Alex H; Elsener, Andreas; Marrink, Siewert J; van Gunsteren, Wilfred F

    2007-02-19

    Thermodynamic data are often used to calibrate or test amomic-level (AL) force fields for molecular dynamics (MD) simulations. In contrast, the majority of coarse-grained (CG) force fields do not rely extensively on thermodynamic quantities. Recently, a CG force field for lipids, hydrocarbons, ions, and water, in which approximately four non-hydrogen atoms are mapped onto one interaction site, has been proposed and applied to study various aspects of lipid systems. To date, no extensive investigation of its capability to describe salvation thermodynamics has been undertaken. In the present study, a detailed picture of vaporization, solvation, and phase-partitioning thermodynamics for liquid hydrocarbons and water was obtained at CG and AL resolutions, in order to compare the two types or models and evaluate their ability to describe thermodynamic properties in the temperature range between 263 and 343 K. Both CG and AL models capture the experimental dependence of the thermodynamic properties on the temperature, albeit a systematically weaker dependence is found for the CG model. Moreover, deviations are found for solvation thermodynamics and for the corresponding enthalpy-entropy compensation for the CG model. Particularly water/oil repulsion seems to be overestimated. However, the results suggest that the thermodynamic properties considered should be reproducible by a CG model provided it is reparametrized on the basis of these liquid-phase properties.

  1. AgRISTARS: Supporting research. Spring small grains planting date distribution model

    NASA Technical Reports Server (NTRS)

    Hodges, T.; Artley, J. A. (Principal Investigator)

    1981-01-01

    A model was developed using 996 planting dates at 51 LANDSAT segments for spring wheat and spring barley in Minnesota, Montana, North Dakota, and South Dakota in 1979. Daily maximum and minimum temperatures and precipitation were obtained from the cooperative weather stations nearest to each segment. The model uses a growing degree day summation modified for daily temperature range to estimate the beginning of planting and uses a soil surface wetness variable to estimate how a fixed number of planting days are distributed after planting begins. For 1979, the model predicts first, median, and last planting dates with root mean square errors of 7.91, 6.61, and 7.09 days, respectively. The model also provides three or four dates to represent periods of planting activity within the planting season. Although the full model was not tested on an independent data set, it may be suitable in areas other than the U.S. Great Plains where spring small grains are planted as soon as soil and air temperatures become warm enough in the spring for plant growth.

  2. Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

    SciTech Connect

    Snodin, Benedict E. K. Mosayebi, Majid; Schreck, John S.; Romano, Flavio; Doye, Jonathan P. K.; Randisi, Ferdinando; Šulc, Petr; Ouldridge, Thomas E.; Tsukanov, Roman; Nir, Eyal; Louis, Ard A.

    2015-06-21

    We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na{sup +}] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.

  3. Improving Model Representation of Reduced Nitrogen in the Greater Yellowstone Area

    NASA Astrophysics Data System (ADS)

    Thompson, T. M.

    2015-12-01

    Human activity, including fossil fuel combustion and agriculture has greatly increased the amount of reactive nitrogen (RN) in the atmosphere and its subsequent deposition to land. Increases in deposition of RN compounds can adversely affect sensitive ecosystems and is a growing problem in many natural areas. The National Park Service in conjunction with Colorado State University researchers and assistance from the Forest Service conducted the Grand Teton Reactive Nitrogen Deposition Study (GrandTReNDS) involving spatially and temporally detailed measurements of RN during spring/summer 2011. In this work it was found that during summer months at the high elevation site Grand Targhee, 62% of the nitrogen deposition was due to reduced nitrogen, about equally split between dry and wet deposition, oxidized nitrogen accounted for 27% of the total, and the remaining was wet deposited organic nitrogen. An important next step to GrandTReNDS is the use of chemical transport models (CTMs) to estimate source contributions to RN in the park. Given the large contribution of reduced nitrogen species to total nitrogen deposition in the park, understanding and properly characterizing ammonia in CTMs is critical to estimating the total nitrogen deposition. A model performance evaluation of the CAMx uni-directional model and CMAQ bi-direction and uni-directional 2011 model simulations versus GrandTReNDS and other datasets was conducted. Preliminary results suggest that, in some areas, model performance of ambient ammonia concentration is more sensitive to the spatial resolution of the model and the accuracy of the spatial representation of emissions than to the incorporation of bi-directional flux. Additional model sensitivity runs, including sensitivity to resolution (with and without bi-directional flux capabilities), changes to model estimated ammonia dry deposition velocities, and improved representation of the spatial distribution of ammonia emissions, are used to identify the

  4. Membrane-Protein Interactions in a Generic Coarse-Grained Model for Lipid Bilayers

    PubMed Central

    West, Beate; Brown, Frank L.H.; Schmid, Friederike

    2009-01-01

    Abstract We study membrane-protein interactions and membrane-mediated protein-protein interactions by Monte Carlo simulations of a generic coarse-grained model for lipid bilayers with cylindrical hydrophobic inclusions. The strength of the hydrophobic force and the hydrophobic thickness of the proteins are systematically varied. The results are compared with analytical predictions of two popular analytical theories: The Landau-de Gennes theory and the elastic theory. The elastic theory provides an excellent description of the fluctuation spectra of pure membranes and successfully reproduces the deformation profiles of membranes around single proteins. However, its prediction for the potential of mean force between proteins is not compatible with the simulation data for large distances. The simulations show that the lipid-mediated interactions are governed by five competing factors: direct interactions; lipid-induced depletion interactions; lipid bridging; lipid packing; and a smooth long-range contribution. The mechanisms leading to hydrophobic mismatch interactions are critically analyzed. PMID:18835907

  5. [Hyperspectral remote sensing diagnosis models of rice plant nitrogen nutritional status].

    PubMed

    Tan, Chang-Wei; Zhou, Qing-Bo; Qi, La; Zhuang, Heng-Yang

    2008-06-01

    The correlations of rice plant nitrogen content with raw hyperspectral reflectance, first derivative hyperspectral reflectance, and hyperspectral characteristic parameters were analyzed, and the hyperspectral remote sensing diagnosis models of rice plant nitrogen nutritional status with these remote sensing parameters as independent variables were constructed and validated. The results indicated that the nitrogen content in rice plant organs had a variation trend of stem < sheath < spike < leaf. The spectral reflectance at visible light bands was leaf < spike < sheath < stem, but that at near-infrared bands was in adverse. The linear and exponential models with the raw hyperspectral reflectance at 796.7 nm and the first derivative hyperspectral reflectance at 738.4 nm as independent variables could better diagnose rice plant nitrogen nutritional status, with the decisive coefficients (R2) being 0.7996 and 0.8606, respectively; while the model with vegetation index (SDr - SDb) / (SDr + SDb) as independent variable, i. e., y = 365.871 + 639.323 ((SDr - SDb) / (SDr + SDb)), was most fit rice plant nitrogen content, with R2 = 0.8755, RMSE = 0.2372 and relative error = 11.36%, being able to quantitatively diagnose the nitrogen nutritional status of rice.

  6. PEATBOG: a biogeochemical model for analyzing coupled carbon and nitrogen dynamics in northern peatlands

    NASA Astrophysics Data System (ADS)

    Wu, Y.; Blodau, C.

    2013-03-01

    Elevated nitrogen deposition and climate change alter the vegetation communities and carbon (C) and nitrogen (N) cycling in peatlands. To address this issue we developed a new process-oriented biogeochemical model (PEATBOG) for analyzing coupled carbon and nitrogen dynamics in northern peatlands. The model consists of four submodels, which simulate: (1) daily water table depth and depth profiles of soil moisture, temperature and oxygen levels; (2) competition among three plants functional types (PFTs), production and litter production of plants; (3) decomposition of peat; and (4) production, consumption, diffusion and export of dissolved C and N species in soil water. The model is novel in the integration of the C and N cycles, the explicit spatial resolution belowground, the consistent conceptualization of movement of water and solutes, the incorporation of stoichiometric controls on elemental fluxes and a consistent conceptualization of C and N reactivity in vegetation and soil organic matter. The model was evaluated for the Mer Bleue Bog, near Ottawa, Ontario, with regards to simulation of soil moisture and temperature and the most important processes in the C and N cycles. Model sensitivity was tested for nitrogen input, precipitation, and temperature, and the choices of the most uncertain parameters were justified. A simulation of nitrogen deposition over 40 yr demonstrates the advantages of the PEATBOG model in tracking biogeochemical effects and vegetation change in the ecosystem.

  7. PEATBOG: a biogeochemical model for analyzing coupled carbon and nitrogen dynamics in northern peatlands

    NASA Astrophysics Data System (ADS)

    Wu, Y.; Blodau, C.

    2013-08-01

    Elevated nitrogen deposition and climate change alter the vegetation communities and carbon (C) and nitrogen (N) cycling in peatlands. To address this issue we developed a new process-oriented biogeochemical model (PEATBOG) for analyzing coupled carbon and nitrogen dynamics in northern peatlands. The model consists of four submodels, which simulate: (1) daily water table depth and depth profiles of soil moisture, temperature and oxygen levels; (2) competition among three plants functional types (PFTs), production and litter production of plants; (3) decomposition of peat; and (4) production, consumption, diffusion and export of dissolved C and N species in soil water. The model is novel in the integration of the C and N cycles, the explicit spatial resolution belowground, the consistent conceptualization of movement of water and solutes, the incorporation of stoichiometric controls on elemental fluxes and a consistent conceptualization of C and N reactivity in vegetation and soil organic matter. The model was evaluated for the Mer Bleue Bog, near Ottawa, Ontario, with regards to simulation of soil moisture and temperature and the most important processes in the C and N cycles. Model sensitivity was tested for nitrogen input, precipitation, and temperature, and the choices of the most uncertain parameters were justified. A simulation of nitrogen deposition over 40 yr demonstrates the advantages of the PEATBOG model in tracking biogeochemical effects and vegetation change in the ecosystem.

  8. Incorporation of Fine-Grained Sediment Erodibility Measurements into Sediment Transport Modeling, Capitol Lake, Washington

    USGS Publications Warehouse

    Stevens, Andrew W.; Gelfenbaum, Guy; Elias, Edwin; Jones, Craig

    2008-01-01

    Capitol Lake was created in 1951 with the construction of a concrete dam and control gate that prevented salt-water intrusion into the newly formed lake and regulated flow of the Deschutes River into southern Puget Sound. Physical processes associated with the former tidally dominated estuary were altered, and the dam structure itself likely caused an increase in retention of sediment flowing into the lake from the Deschutes River. Several efforts to manage sediment accumulation in the lake, including dredging and the construction of sediment traps upriver, failed to stop the lake from filling with sediment. The Deschutes Estuary Feasibility Study (DEFS) was carried out to evaluate the possibility of removing the dam and restoring estuarine processes as an alternative ongoing lake management. An important component of DEFS was the creation of a hydrodynamic and sediment transport model of the restored Deschutes Estuary. Results from model simulations indicated that estuarine processes would be restored under each of four restoration alternatives, and that over time, the restored estuary would have morphological features similar to the predam estuary. The model also predicted that after dam-removal, a large portion of the sediment eroded from the lake bottom would be deposited near the Port of Olympia and a marina located in lower Budd Inlet seaward of the present dam. The volume of sediment transported downstream was a critical piece of information that managers needed to estimate the total cost of the proposed restoration project. However, the ability of the model to predict the magnitude of sediment transport in general and, in particular, the volume of sediment deposition in the port and marina was limited by a lack of information on the erodibility of fine-grained sediments in Capitol Lake. Cores at several sites throughout Capitol Lake were collected between October 31 and November 1, 2007. The erodibility of sediments in the cores was later determined in the

  9. Coarse-grained model of water diffusion and proton conductivity in hydrated polyelectrolyte membrane

    NASA Astrophysics Data System (ADS)

    Lee, Ming-Tsung; Vishnyakov, Aleksey; Neimark, Alexander V.

    2016-01-01

    Using dissipative particle dynamics (DPD), we simulate nanoscale segregation, water diffusion, and proton conductivity in hydrated sulfonated polystyrene (sPS). We employ a novel model [Lee et al. J. Chem. Theory Comput. 11(9), 4395-4403 (2015)] that incorporates protonation/deprotonation equilibria into DPD simulations. The polymer and water are modeled by coarse-grained beads interacting via short-range soft repulsion and smeared charge electrostatic potentials. The proton is introduced as a separate charged bead that forms dissociable Morse bonds with the base beads representing water and sulfonate anions. Morse bond formation and breakup artificially mimics the Grotthuss mechanism of proton hopping between the bases. The DPD model is parameterized by matching the proton mobility in bulk water, dissociation constant of benzenesulfonic acid, and liquid-liquid equilibrium of water-ethylbenzene solutions. The DPD simulations semi-quantitatively predict nanoscale segregation in the hydrated sPS into hydrophobic and hydrophilic subphases, water self-diffusion, and proton mobility. As the hydration level increases, the hydrophilic subphase exhibits a percolation transition from isolated water clusters to a 3D network. The analysis of hydrophilic subphase connectivity and water diffusion demonstrates the importance of the dynamic percolation effect of formation and breakup of temporary junctions between water clusters. The proposed DPD model qualitatively predicts the ratio of proton to water self-diffusion and its dependence on the hydration level that is in reasonable agreement with experiments.

  10. Coarse-grained model of water diffusion and proton conductivity in hydrated polyelectrolyte membrane.

    PubMed

    Lee, Ming-Tsung; Vishnyakov, Aleksey; Neimark, Alexander V

    2016-01-01

    Using dissipative particle dynamics (DPD), we simulate nanoscale segregation, water diffusion, and proton conductivity in hydrated sulfonated polystyrene (sPS). We employ a novel model [Lee et al. J. Chem. Theory Comput. 11(9), 4395-4403 (2015)] that incorporates protonation/deprotonation equilibria into DPD simulations. The polymer and water are modeled by coarse-grained beads interacting via short-range soft repulsion and smeared charge electrostatic potentials. The proton is introduced as a separate charged bead that forms dissociable Morse bonds with the base beads representing water and sulfonate anions. Morse bond formation and breakup artificially mimics the Grotthuss mechanism of proton hopping between the bases. The DPD model is parameterized by matching the proton mobility in bulk water, dissociation constant of benzenesulfonic acid, and liquid-liquid equilibrium of water-ethylbenzene solutions. The DPD simulations semi-quantitatively predict nanoscale segregation in the hydrated sPS into hydrophobic and hydrophilic subphases, water self-diffusion, and proton mobility. As the hydration level increases, the hydrophilic subphase exhibits a percolation transition from isolated water clusters to a 3D network. The analysis of hydrophilic subphase connectivity and water diffusion demonstrates the importance of the dynamic percolation effect of formation and breakup of temporary junctions between water clusters. The proposed DPD model qualitatively predicts the ratio of proton to water self-diffusion and its dependence on the hydration level that is in reasonable agreement with experiments. PMID:26747818

  11. Coarse-grained model of water diffusion and proton conductivity in hydrated polyelectrolyte membrane.

    PubMed

    Lee, Ming-Tsung; Vishnyakov, Aleksey; Neimark, Alexander V

    2016-01-01

    Using dissipative particle dynamics (DPD), we simulate nanoscale segregation, water diffusion, and proton conductivity in hydrated sulfonated polystyrene (sPS). We employ a novel model [Lee et al. J. Chem. Theory Comput. 11(9), 4395-4403 (2015)] that incorporates protonation/deprotonation equilibria into DPD simulations. The polymer and water are modeled by coarse-grained beads interacting via short-range soft repulsion and smeared charge electrostatic potentials. The proton is introduced as a separate charged bead that forms dissociable Morse bonds with the base beads representing water and sulfonate anions. Morse bond formation and breakup artificially mimics the Grotthuss mechanism of proton hopping between the bases. The DPD model is parameterized by matching the proton mobility in bulk water, dissociation constant of benzenesulfonic acid, and liquid-liquid equilibrium of water-ethylbenzene solutions. The DPD simulations semi-quantitatively predict nanoscale segregation in the hydrated sPS into hydrophobic and hydrophilic subphases, water self-diffusion, and proton mobility. As the hydration level increases, the hydrophilic subphase exhibits a percolation transition from isolated water clusters to a 3D network. The analysis of hydrophilic subphase connectivity and water diffusion demonstrates the importance of the dynamic percolation effect of formation and breakup of temporary junctions between water clusters. The proposed DPD model qualitatively predicts the ratio of proton to water self-diffusion and its dependence on the hydration level that is in reasonable agreement with experiments.

  12. Coarse-Grained Structure-Based Model for RNA-Protein Complexes Developed by Fluctuation Matching.

    PubMed

    Hori, Naoto; Takada, Shoji

    2012-09-11

    RNA and RNA-protein complexes have recently been intensively studied in experiments, but the corresponding molecular simulation work is much less abundant, primarily due to its large system size and the long time scale involved. Here, to overcome these bottlenecks, we develop a coarse-grained (CG) structure-based simulation model for RNA and RNA-protein complexes and test it for several molecular systems. The CG model for RNA contains three particles per nucleotide, each for phosphate, sugar, and a base. Focusing on RNA molecules that fold to well-defined native structures, we employed a structure-based potential, which is similar to the Go-like potential successfully used in CG modeling of proteins. In addition, we tested three means to approximate electrostatic interactions. Many parameters involved in the CG potential were determined via a multiscale method: We matched the native fluctuation of the CG model with that by all-atom simulations for 16 RNA molecules and 10 RNA-protein complexes, from which we derived a generic set of CG parameters. We show that the derived parameters can reproduce native fluctuations well for four RNA and two RNA-protein complexes. For tRNA, the native fluctuation in solution includes large-amplitude motions that reach conformations nearly corresponding to the hybrid state P/E and EF-Tu-bound state A/T seen in the complexes with ribosome. Finally, large-amplitude modes of ribosome are briefly described.

  13. Modeling kinetics of aflatoxin production by Aspergillus flavus in maize-based medium and maize grain.

    PubMed

    Garcia, Daiana; Ramos, Antonio J; Sanchis, Vicente; Marín, Sonia

    2013-03-15

    Predictive mycology has dealt mainly with germination, growth and inactivation of fungi while the issue of mycotoxin production remains relatively unexplored. Very few studies provide biomass dry weight/colony size data along with mycotoxin data for the same sample times, thus the ratio mycotoxin accumulation per fungal biomass dry weight/colony size has rarely been reported. For this reason, the objective of the present study was to model the kinetics of mycotoxin production under the assumption of existing both no-growth-associated and growth-associated production. Aspergillus flavus was chosen as a model mycotoxigenic microorganism, and it was grown in maize agar medium and maize grain at 0.90 and 0.99 aw at 25°C. A significant positive correlation (p<0.05) was observed among the biomass responses (colony radius and biomass dry weight) in agar medium and colony radius in maize at both aw levels assayed. The Luedeking-Piret model was used to model AFB1 production and reasonable percentages of variability were explained. Moreover, AFB1 production was in general slightly better predicted through colony area. As conclusion, aflatoxin production may follow a mixed-growth associated trend, confirming that toxin formation does not present a clear delay in relation to growth under certain conditions. PMID:23422844

  14. 2D stochastic-integral models for characterizing random grain noise in titanium alloys

    SciTech Connect

    Sabbagh, Harold A.; Murphy, R. Kim; Sabbagh, Elias H.; Cherry, Matthew; Pilchak, Adam; Knopp, Jeremy S.; Blodgett, Mark P.

    2014-02-18

    We extend our previous work, in which we applied high-dimensional model representation (HDMR) and analysis of variance (ANOVA) concepts to the characterization of a metallic surface that has undergone a shot-peening treatment to reduce residual stresses, and has, therefore, become a random conductivity field. That example was treated as a onedimensional problem, because those were the only data available. In this study, we develop a more rigorous two-dimensional model for characterizing random, anisotropic grain noise in titanium alloys. Such a model is necessary if we are to accurately capture the 'clumping' of crystallites into long chains that appear during the processing of the metal into a finished product. The mathematical model starts with an application of the Karhunen-Loève (K-L) expansion for the random Euler angles, θ and φ, that characterize the orientation of each crystallite in the sample. The random orientation of each crystallite then defines the stochastic nature of the electrical conductivity tensor of the metal. We study two possible covariances, Gaussian and double-exponential, which are the kernel of the K-L integral equation, and find that the double-exponential appears to satisfy measurements more closely of the two. Results based on data from a Ti-7Al sample will be given, and further applications of HDMR and ANOVA will be discussed.

  15. The impact of resolution upon entropy and information in coarse-grained models

    NASA Astrophysics Data System (ADS)

    Foley, Thomas T.; Shell, M. Scott; Noid, W. G.

    2015-12-01

    By eliminating unnecessary degrees of freedom, coarse-grained (CG) models tremendously facilitate numerical calculations and theoretical analyses of complex phenomena. However, their success critically depends upon the representation of the system and the effective potential that governs the CG degrees of freedom. This work investigates the relationship between the CG representation and the many-body potential of mean force (PMF), W, which is the appropriate effective potential for a CG model that exactly preserves the structural and thermodynamic properties of a given high resolution model. In particular, we investigate the entropic component of the PMF and its dependence upon the CG resolution. This entropic component, SW, is a configuration-dependent relative entropy that determines the temperature dependence of W. As a direct consequence of eliminating high resolution details from the CG model, the coarsening process transfers configurational entropy and information from the configuration space into SW. In order to further investigate these general results, we consider the popular Gaussian Network Model (GNM) for protein conformational fluctuations. We analytically derive the exact PMF for the GNM as a function of the CG representation. In the case of the GNM, -TSW is a positive, configuration-independent term that depends upon the temperature, the complexity of the protein interaction network, and the details of the CG representation. This entropic term demonstrates similar behavior for seven model proteins and also suggests, in each case, that certain resolutions provide a more efficient description of protein fluctuations. These results may provide general insight into the role of resolution for determining the information content, thermodynamic properties, and transferability of CG models. Ultimately, they may lead to a rigorous and systematic framework for optimizing the representation of CG models.

  16. The impact of resolution upon entropy and information in coarse-grained models

    SciTech Connect

    Foley, Thomas T.; Shell, M. Scott; Noid, W. G.

    2015-12-28

    By eliminating unnecessary degrees of freedom, coarse-grained (CG) models tremendously facilitate numerical calculations and theoretical analyses of complex phenomena. However, their success critically depends upon the representation of the system and the effective potential that governs the CG degrees of freedom. This work investigates the relationship between the CG representation and the many-body potential of mean force (PMF), W, which is the appropriate effective potential for a CG model that exactly preserves the structural and thermodynamic properties of a given high resolution model. In particular, we investigate the entropic component of the PMF and its dependence upon the CG resolution. This entropic component, S{sub W}, is a configuration-dependent relative entropy that determines the temperature dependence of W. As a direct consequence of eliminating high resolution details from the CG model, the coarsening process transfers configurational entropy and information from the configuration space into S{sub W}. In order to further investigate these general results, we consider the popular Gaussian Network Model (GNM) for protein conformational fluctuations. We analytically derive the exact PMF for the GNM as a function of the CG representation. In the case of the GNM, −TS{sub W} is a positive, configuration-independent term that depends upon the temperature, the complexity of the protein interaction network, and the details of the CG representation. This entropic term demonstrates similar behavior for seven model proteins and also suggests, in each case, that certain resolutions provide a more efficient description of protein fluctuations. These results may provide general insight into the role of resolution for determining the information content, thermodynamic properties, and transferability of CG models. Ultimately, they may lead to a rigorous and systematic framework for optimizing the representation of CG models.

  17. EBSD characterization and modeling of columnar dendritic grains growing in the presence of fluid flow[Electron Backscattered Diffraction

    SciTech Connect

    Takatani, H.; Gandin, C.A.; Rappaz, M.

    2000-02-09

    Columnar dendritic grains of steel growth in the presence of fluid flow (e.g., solidified on turning rolls) have been characterized by Electron Backscattered Diffraction (EBSD) technique. It is shown that grains have a random crystallographic orientation at the surfaces of the sheet in contact with the mould. In the middle of the sheet, the grains which have survived the growth selection mechanisms exhibit a (100) texture in which the average dendrite trunk direction is not exactly aligned with the thermal gradient (i.e., the normal to the surfaces of the sheet). It is tilted by about 15{degree} toward the upstream direction. This deviation is examined by simulations of grain structure formation based on a three-dimensional Cellular Automation (CA)-Finite Element (FE) (3D CAFE) model, which has been modified in order to account for fluid flow effects. The modified Ca algorithm includes a growth kinetics of the dendrites which is a function of both the undercooling and fluid flow direction. It is validated by comparing the predicted shape of an individual grain growing under given thermal and fluid flow conditions with an analytical solution. The 3D CAFE predictions of the columnar grains grown in the presence of fluid flow are in good agreement with the experimental EBSB results.

  18. Calibration and Uncertainty in Scenario Simulations with the HBV-N Nitrogen Model

    NASA Astrophysics Data System (ADS)

    Lindstrom, G.; Arheimer, B.

    2002-12-01

    The HBV model, a Swedish precipitation-runoff model has been used extensively in basins all over Sweden for 30 years. Recently, it has been complemented with routines for nitrogen transformation in groundwater, rivers and lakes. The aim is to develop a decision support tool for evaluation of nitrogen load on recipients due to different management practices and policies. The hydrological submodel has a large number of parameters, which are established by calibration, supported by experience from earlier model applications. The root zone leakage of nitrogen, used as input to the HBV model, is simulated by the SOIL-N model, a model for turnover of water, heat and nitrogen in the unsaturated zone. The nitrogen subroutines introduce additional parameters. It is clear that no unique optimum parameter set can be obtained from a single-site model calibation to runoff and nitrogen measurements. This equifinality results in a wide range of uncertainty in the scenario simulations, when studied by ordinary Monte Carlo simulation and acceptance of all parameter sets that produce a fitness criterion above a chosen limit. This is illustrated in a case study for the R”nne † basin in the agricultural region of southern Sweden. The objective of the uncertainty analysis is to explore the uncertainty in the scenario simulations, and to provide support for decision-makers to choose between measures according to expected results and the reliability of these results. However, an ordinary Monte Carlo simulation in which all parameters are simulated and combined randomly does not take advantage of the experience from earlier applications. Therefore, a method is proposed, in which parameter sets are judged not only according to the fitness to observations but also according to their agreement with earlier model applications and hydrological experience, by use of subjective likelihood weights. The range in the scenario simulations obtained from the combined approach is finally compared

  19. Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations.

    PubMed

    Takada, Shoji; Kanada, Ryo; Tan, Cheng; Terakawa, Tsuyoshi; Li, Wenfei; Kenzaki, Hiroo

    2015-12-15

    Due to hierarchic nature of biomolecular systems, their computational modeling calls for multiscale approaches, in which coarse-grained (CG) simulations are used to address long-time dynamics of large systems. Here, we review recent developments and applications of CG modeling methods, focusing on our methods primarily for proteins, DNA, and their complexes. These methods have been implemented in the CG biomolecular simulator, CafeMol. Our CG model has resolution such that ∼10 non-hydrogen atoms are grouped into one CG particle on average. For proteins, each amino acid is represented by one CG particle. For DNA, one nucleotide is simplified by three CG particles, representing sugar, phosphate, and base. The protein modeling is based on the idea that proteins have a globally funnel-like energy landscape, which is encoded in the structure-based potential energy function. We first describe two representative minimal models of proteins, called the elastic network model and the classic Go̅ model. We then present a more elaborate protein model, which extends the minimal model to incorporate sequence and context dependent local flexibility and nonlocal contacts. For DNA, we describe a model developed by de Pablo's group that was tuned to well reproduce sequence-dependent structural and thermodynamic experimental data for single- and double-stranded DNAs. Protein-DNA interactions are modeled either by the structure-based term for specific cases or by electrostatic and excluded volume terms for nonspecific cases. We also discuss the time scale mapping in CG molecular dynamics simulations. While the apparent single time step of our CGMD is about 10 times larger than that in the fully atomistic molecular dynamics for small-scale dynamics, large-scale motions can be further accelerated by two-orders of magnitude with the use of CG model and a low friction constant in Langevin dynamics. Next, we present four examples of applications. First, the classic Go̅ model was used to

  20. A conceptual model to evaluate potential watershed nitrogen saturation in the Great Smoky Mountains

    SciTech Connect

    Nicholas, N.S.; Van Miegroet, H.; Zucker, S.J.; Rose, A.K.

    1998-12-31

    Even though Title IV of the 1990 Clean Air Act Amendments requires significant reduction in utility nitrogen oxides emissions, the recent 1995 EPA Acid Deposition Standard Feasibility Study Report to Congress assumes that watersheds in the Southern Blue Ridge Province will eventually reach nitrogen saturation given historic and current deposition rates. Because of high atmospheric deposition levels (i.e., N loadings {approximately} 1900 eq/ha/yr 30 kg/ha/yr), much focus has been centered on the high elevation forests in the Southern Appalachians. Most nitrogen saturation scenarios focus on steady state forest conditions with little consideration for the role of natural disturbance regimes. However, in recent years, at least partly due to exotic insect infestation, the high elevation spruce-fir forests (Picea rubens-Abies fraseri) in the Smokies have developed a heterogeneous structure with numerous gaps and a large variation in stand age, number of live and dead standing trees, and amount of coarse woody debris on the forest floor. Assessment of nitrogen saturation status in this type of disturbed system requires more than a simple calculation of nitrogen input and export levels. This multi-year research, which has been funded by the National Park Service, the Tennessee Valley Authority, the US Department of Agriculture, and the US Geological Survey includes measurement of the three categories of factors that control nitrogen saturation including external (atmospheric) inputs, soil properties, and vegetation characteristics. The authors will discuss a conceptual model for a high elevation watershed in the Great Smoky Mountains National Park to examine potential nitrogen saturation in disturbed systems based on soil nitrogen levels, input and output fluxes, and quantification of potential nitrogen source and sink areas within the catchment.

  1. Nitrogen in Ancient Mud: A Biosignature?

    NASA Astrophysics Data System (ADS)

    Stüeken, Eva E.

    2016-09-01

    Nitrogen is an essential nutrient for all life on Earth and possibly elsewhere. Burial of nitrogen bound to organic matter constitutes the major flux of nitrogen into sediments today, which has led to the inference that nitrogen enrichments in sedimentary rocks may be a biosignature. However, abiotic processes such as lightning or volcanism can fix atmospheric N2 and contribute to sedimentary nitrogen burial in the absence of life. It is therefore uncertain whether observed nitrogen enrichments of up to 430 ppm in Paleoarchean metasedimentary biotite grains are indeed biogenic. This study seeks to address that problem with a numerical model. The NH4+ concentration of an abiotic ocean is modeled as a function of source fluxes, pH-dependent NH3 volatilization, and equilibrated adsorption of NH4+ onto clay particles. The results suggest that the observed nitrogen concentrations in Paleoarchean biotite can only be reconciled with purely abiotic processes if the ocean was more acidic (pH <6) and/or if the source fluxes from lightning and volcanism were at least an order of magnitude higher (≥1012 mol/yr) than previously thought. The bulk of the nitrogen is thus most likely of biological origin. While this does not necessitate a particular metabolism such as biological N2 fixation, the data provide evidence of nitrogen utilization back to 3.8 Gyr. Nitrogen abundances could thus provide useful information in extraterrestrial missions.

  2. Effects of air filtration on spring wheat grown in open-top field chambers at a rural site. II. Effects on mineral partitioning, sulphur and nitrogen metabolism and on grain quality.

    PubMed

    Vandermeiren, K; De Temmerman, L; Staquet, A; Baeten, H

    1992-01-01

    In 1988 the effect of ambient levels of air pollutants on the nutrients status and grain quality of spring wheat (Triticum aestivum cv. Pelican) was investigated by comparing plants grown in open-top chambers (OTC) ventilated with ambient air (NF treatments) and charcoal-filtered air (CF treatments) at a rural site (Tervuren, Belgium). Spring wheat cultivated in NF OTC showed only minor differences in the P, K, Ca, Mg, Mn and Na concentrations of the different plant parts at final harvest, as well as organic and inorganic S fractions, compared to those of the plants grown in CF air. The plants' total P content was reduced, as well as the P and K concentration of the flour. The total S concentration of the flour was increased by 4%. Effects on N concentrations and grain quality were much more pronounced. At final harvest the N concentrations of straw and flour of the NF air treated plants were much higher compared to CF air. However, the N content of the aerial biomass and the grain N yield were not significantly affected, implying a reduction of other structual compounds. Nitrogen harvest index (NHI) and the ratio of NHI over grain harvest index (GHI), indicated a significant reduction of N translocation from the above-ground biomass to the grain. Changes in the N status and partitioning of spring wheat had an effect on the baking quality of wheat flour. Several parameters that are commonly used as an indication of baking quality have been significantly increased in the NF treatment: total protein concentration, Zeleny value, dry and wet gluten concentration. A slightly increased Hagberg value indicated a reduced alpha-amylase activity. The possibility of foliar N uptake as an additional N source, especially after anthesis and implications of increased protein production instead of carbohydrate synthesis are discussed.

  3. Effects of air filtration on spring wheat grown in open-top field chambers at a rural site. II. Effects on mineral partitioning, sulphur and nitrogen metabolism and on grain quality.

    PubMed

    Vandermeiren, K; De Temmerman, L; Staquet, A; Baeten, H

    1992-01-01

    In 1988 the effect of ambient levels of air pollutants on the nutrients status and grain quality of spring wheat (Triticum aestivum cv. Pelican) was investigated by comparing plants grown in open-top chambers (OTC) ventilated with ambient air (NF treatments) and charcoal-filtered air (CF treatments) at a rural site (Tervuren, Belgium). Spring wheat cultivated in NF OTC showed only minor differences in the P, K, Ca, Mg, Mn and Na concentrations of