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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 Central

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

    2003-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  5. Grain metamorphism in polar nitrogen ice on Triton

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

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

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

    PubMed Central

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

    2017-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed

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

    2003-11-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed

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

    2013-05-01

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

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

    PubMed

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

    2010-10-01

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

  12. 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 ...

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

    NASA Astrophysics Data System (ADS)

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

    1994-09-01

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

  14. Stochastic modeling of grain-fabric formation

    NASA Astrophysics Data System (ADS)

    Naruse, H.

    2011-12-01

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

  15. Investigating Nitrogen Pollution: Activities and Models.

    ERIC Educational Resources Information Center

    Green Teacher, 2000

    2000-01-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  17. 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.

  18. 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.

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

    PubMed Central

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

    2016-01-01

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

  20. 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.

  1. 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

  2. Grain Surface Models and Data for Astrochemistry

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

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

    PubMed

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

    2016-11-01

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

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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

  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. 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.

  11. 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...

  12. 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

  13. 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.

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

    EPA Pesticide Factsheets

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

  15. Numerical Investigation of Grain Coarsening and Coalescence Model

    NASA Astrophysics Data System (ADS)

    Muradova, Aliki D.; Hristopulos, Dionisios T.

    2015-01-01

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

  16. Next Generation Carbon-Nitrogen Dynamics Model

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  17. 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.

  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 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

  19. 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

  20. 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.

  1. 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.

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

    PubMed

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

    2017-01-23

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

  3. 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

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

    NASA Astrophysics Data System (ADS)

    Hoang, Thiem; Lazarian, A.

    2016-11-01

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

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

    NASA Technical Reports Server (NTRS)

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

    2004-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Ahmed, Karim E.

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

  8. 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.

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

    ERIC Educational Resources Information Center

    Miller, Jeff; Ulrich, Rolf

    2003-01-01

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

  10. 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

  11. Film grain noise modeling in advanced video coding

    NASA Astrophysics Data System (ADS)

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

    2007-01-01

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

  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. 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.

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

    PubMed Central

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

    2017-01-01

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

  15. 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.

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

    PubMed

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

    2015-01-01

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

  17. Nitrogen Controls on Climate Model Evapotranspiration.

    NASA Astrophysics Data System (ADS)

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

    2002-02-01

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

  18. Absorbing ice model of interstellar grains.

    NASA Technical Reports Server (NTRS)

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

    1971-01-01

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

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

    PubMed

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

    2010-07-01

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

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

    PubMed

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

    2008-11-30

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

  2. Kinetic model of particle-inhibited grain growth

    NASA Astrophysics Data System (ADS)

    Thompson, Gary Scott

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

  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. 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

  5. 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.

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

    PubMed

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

    2005-10-01

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

  7. [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.

  8. A coarse grain model for DNA.

    PubMed

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

    2007-02-28

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

  9. A coarse grain model for DNA

    NASA Astrophysics Data System (ADS)

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

    2007-02-01

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

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

    PubMed

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

    2005-11-01

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

  11. 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).

  12. 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.

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

    PubMed

    Español, Pep; Zúñiga, Ignacio

    2011-06-14

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

  14. 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.

  15. 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.

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

    PubMed

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

    1991-01-01

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

  17. Time Dependent Models of Grain Formation Around Carbon Stars

    NASA Technical Reports Server (NTRS)

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

    1996-01-01

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

  18. Toward a mechanistic modeling of nitrogen limitation for photosynthesis

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

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

    PubMed

    Choi, Eunsong; Mondal, Jagannath; Yethiraj, Arun

    2014-01-09

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

  20. 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.

  1. 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

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

    PubMed

    Yang, Tiejun; Yang, Na; Zhu, Chunhua

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-09-01

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

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

    PubMed Central

    Kar, Parimal; Feig, Michael

    2017-01-01

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

  6. 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

  7. 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...

  8. 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 ‘...

  9. Coarse-Grained Model of SNARE-Mediated Docking

    PubMed Central

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

    2015-01-01

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

  10. 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

  11. 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.

  12. 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

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

    EPA Pesticide Factsheets

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

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

    NASA Astrophysics Data System (ADS)

    Dorfman, Kevin; Linak, Margaret; Tourdot, Richard

    2012-02-01

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

  15. 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.

  16. 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

  17. 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

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

    PubMed

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

    2015-08-01

    The Chesapeake Bay plays an important role in transforming riverine nutrients before they are exported to the adjacent continental shelf. Although the mean nitrogen budget of the Chesapeake Bay has been previously estimated from observations, uncertainties associated with interannually varying hydrological conditions remain. In this study, a land-estuarine-ocean biogeochemical modeling system is developed to quantify Chesapeake riverine nitrogen inputs, within-estuary nitrogen transformation processes and the ultimate export of nitrogen to the coastal ocean. Model skill was evaluated using extensive in situ and satellite-derived data, and a simulation using environmental conditions for 2001-2005 was conducted to quantify the Chesapeake Bay nitrogen budget. The 5 year simulation was characterized by large riverine inputs of nitrogen (154 × 10(9) g N yr(-1)) split roughly 60:40 between inorganic:organic components. Much of this was denitrified (34 × 10(9) g N yr(-1)) and buried (46 × 10(9) g N yr(-1)) within the estuarine system. A positive net annual ecosystem production for the bay further contributed to a large advective export of organic nitrogen to the shelf (91 × 10(9) g N yr(-1)) and negligible inorganic nitrogen export. Interannual variability was strong, particularly for the riverine nitrogen fluxes. In years with higher than average riverine nitrogen inputs, most of this excess nitrogen (50-60%) was exported from the bay as organic nitrogen, with the remaining split between burial, denitrification, and inorganic export to the coastal ocean. In comparison to previous simulations using generic shelf biogeochemical model formulations inside the estuary, the estuarine biogeochemical model described here produced more realistic and significantly greater exports of organic nitrogen and lower exports of inorganic nitrogen to the shelf.

  19. [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.

  20. 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.

  1. 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.

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

    PubMed

    Wei, Shuai; Knotts, Thomas A

    2013-09-07

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

  3. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. [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.

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

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

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

    NASA Astrophysics Data System (ADS)

    Paulsen, Hanna; Ilyina, Tatiana; Six, Katharina

    2015-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

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

    PubMed

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

    2017-01-28

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

  16. 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.

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

    PubMed

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

    2015-06-25

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

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

    Deng, Mingsen; Shen, Hujun

    2016-02-04

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

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

    PubMed

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

    2008-01-01

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

  9. 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...

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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.

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

    PubMed

    Clementi, Cecilia

    2008-02-01

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

  16. 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.

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

    PubMed

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

    2016-09-01

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

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

    PubMed

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

    2012-06-01

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

  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 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

  20. 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

  1. 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.

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

    NASA Astrophysics Data System (ADS)

    Kovacs, G. J.

    2003-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Guardiani, Carlo; Cencini, Massimo; Cecconi, Fabio

    2014-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  5. 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

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

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

    NASA Technical Reports Server (NTRS)

    Housley, R. M.

    1980-01-01

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

  8. 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.

  9. 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.

  10. 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.

  11. 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...

  12. 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.

  13. 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.

  14. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  16. 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

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

    SciTech Connect

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

    2013-01-01

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

  18. Modeling of grain boundary stresses in Alloy 600

    SciTech Connect

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

    1995-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Kuroboshi, Y.; Takemura, K.

    2016-12-01

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

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

    PubMed

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

    2008-11-01

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

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

    NASA Technical Reports Server (NTRS)

    Hiroi, T.; Pieters, Carle M.

    1991-01-01

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

  2. 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.

  3. 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.

  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. 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.

  7. Modelling Ontogenetic Changes of Nitrogen and Water Content in Lettuce

    PubMed Central

    SEGINER, IDO; BLEYAERT, PETER; BREUGELMANS, MAAIKE

    2004-01-01

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

  8. 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.

  9. 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.

  10. 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.

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

    PubMed

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

    2014-02-01

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

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

    DOE PAGES

    Biner, S. B.

    2016-03-16

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  14. 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

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

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

  16. 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.

  17. 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.

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

    SciTech Connect

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

    2016-02-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  20. [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

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

    PubMed

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

    2006-05-01

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

  2. 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

  3. 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

  4. Parametrizing coarse grained models for molecular systems at equilibrium

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  5. 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).

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

    NASA Astrophysics Data System (ADS)

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

    2012-06-01

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

  7. 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.

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

    PubMed

    Simsek, Halis

    2016-11-01

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

  9. 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.

  10. 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

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

    PubMed

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

    2013-03-01

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

  12. 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.

  13. 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.

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

    PubMed

    Invernizzi, Michele; Valsson, Omar; Parrinello, Michele

    2017-03-28

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

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

    PubMed Central

    Invernizzi, Michele; Valsson, Omar; Parrinello, Michele

    2017-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

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

    EPA Science Inventory

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

  18. Modeling nitrogen plasmas produced by intense electron beams

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  2. 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.

  3. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

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

    SciTech Connect

    Radhakrishnan, Balasubramaniam; Gorti, Sarma B

    2009-01-01

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

  6. 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.

  7. Modeling of Ultrasonic Propagation in a Coarse Grain Structure

    NASA Astrophysics Data System (ADS)

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

    2009-03-01

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

  8. Responses of Super Rice (Oryza sativa L.) to Different Planting Methods for Grain Yield and Nitrogen-Use Efficiency in the Single Cropping Season

    PubMed Central

    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. PMID:25111805

  9. 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.

  10. 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.

  11. 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.

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

    PubMed Central

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

    2017-01-01

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

  13. Modeling organic nitrogen conversions in activated sludge bioreactors.

    PubMed

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

    2011-01-01

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

  14. 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.

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

    PubMed Central

    2015-01-01

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

  16. 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.

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

    NASA Astrophysics Data System (ADS)

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

    1983-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-10-01

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

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

    NASA Astrophysics Data System (ADS)

    Kovács, Géza J.

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

  20. 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

  1. 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.

  2. 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.

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

    PubMed

    Hyeon, Changbong; Thirumalai, D

    2011-09-27

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

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

    NASA Astrophysics Data System (ADS)

    Munafò, A.; Liu, Y.; Panesi, M.

    2015-12-01

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

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

    SciTech Connect

    Munafò, A.; Liu, Y.; Panesi, M.

    2015-12-15

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

  6. 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.

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

    DOE PAGES

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

    2017-01-01

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

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

    SciTech Connect

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

    2017-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

  10. 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.

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

    PubMed Central

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

    2008-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2004-12-01

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

  13. Modeling of Nitrogen Oxides Emissions from CFB Combustion

    NASA Astrophysics Data System (ADS)

    Kallio, S.; Keinonen, M.

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

  14. 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.

  15. Mathematical modeling of grain boundary hardening in two-phase materials

    NASA Astrophysics Data System (ADS)

    Ozernykh, Vladimir S.; Volegov, Pavel S.

    2016-11-01

    In this paper, we consider such an important physical mechanism of hardening in polycrystalline metals as hardening due to the interaction of dislocations and grain boundaries. A mathematical model of inelastic deformation for the polycrystalline representative volume with consideration for dislocation hardening on the phase boundary is proposed. Numerical experiments are carried out with different phase parameters. We study the influence of the average grain size of the polycrystalline material and statistical distribution of the grain size on the deformation behavior. A submodel that describes the additional hardening phenomenon due to the interaction of intragranular and grain boundary dislocations is proposed. Numerical experiments under different schemes of material loading are carried out; deformation curves are constructed and analyzed.

  16. 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.

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

    PubMed

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

    2012-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Ruiz, Franklin J.

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

  19. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2006-06-01

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

  1. 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.

  2. 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.

  3. 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.

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

    NASA Astrophysics Data System (ADS)

    Shimizu, Ichiko

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

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

    SciTech Connect

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

    2014-06-01

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

  6. 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.

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

    PubMed

    Zimmermann, Eva; Seifert, Udo

    2015-02-01

    Many single-molecule experiments for molecular motors comprise not only the motor but also large probe particles coupled to it. The theoretical analysis of these assays, however, often takes into account only the degrees of freedom representing the motor. We present a coarse-graining method that maps a model comprising two coupled degrees of freedom which represent motor and probe particle to such an effective one-particle model by eliminating the dynamics of the probe particle in a thermodynamically and dynamically consistent way. The coarse-grained rates obey a local detailed balance condition and reproduce the net currents. Moreover, the average entropy production as well as the thermodynamic efficiency is invariant under this coarse-graining procedure. Our analysis reveals that only by assuming unrealistically fast probe particles, the coarse-grained transition rates coincide with the transition rates of the traditionally used one-particle motor models. Additionally, we find that for multicyclic motors the stall force can depend on the probe size. We apply this coarse-graining method to specific case studies of the F(1)-ATPase and the kinesin motor.

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

    SciTech Connect

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

    2013-02-01

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

  9. 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.

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

    SciTech Connect

    Eckersten, H.

    1985-05-01

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

  11. 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...

  12. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  14. 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.

  15. 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.

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

    PubMed

    Liu, T; Zhang, Z

    2004-03-30

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

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

    NASA Astrophysics Data System (ADS)

    Zhu, Q.; Zhuang, Q.

    2013-08-01

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

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

    SciTech Connect

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

    2016-03-01

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

  19. A new constitutive model for nitrogen austenitic stainless steel

    NASA Astrophysics Data System (ADS)

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

    2003-09-01

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

  20. 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.

  1. Fast coarse-grained model for RNA titration

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

  2. 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…

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

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

  4. 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.

  5. Coarse-grained models for interacting, flapping swimmers

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-05-01

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

  7. 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

  8. 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.

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

    PubMed

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

    2016-08-10

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

  10. 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

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

    NASA Astrophysics Data System (ADS)

    Savelyev, Alexey; Papoian, Garegin

    2008-03-01

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

  12. 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.

  13. 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.

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

    NASA Astrophysics Data System (ADS)

    Holtzman, R.; Juanes, R.

    2009-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Johnson, Kevin David

    2000-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  17. 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.

  18. 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.

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

    PubMed

    Srivastava, Anand; Voth, Gregory A

    2013-01-08

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

  20. Evolutionary models of the Earth with a grain size-dependent rheology

    NASA Astrophysics Data System (ADS)

    Rozel, Antoine; Golabek, Gregor; Tackley, Paul

    2015-04-01

    Thermodynamically consistent models of single phase grain size evolution have been proposed in the past years [Austin and Evans (2007), Ricard and Bercovici (2009), Rozel et al. (2011), Rozel (2012)]. Following the same physical approach, the mechanics of two-phase grain aggregates has been formulated [Bercovici and Ricard (2012a)]. Several non-linear mechanisms such as dynamic recrystallization or Zener pinning are now available in a single non-equilibrium formulation of grain size distributions evolution. The self-consistent generation of localized plate boundaries is predicted in [Bercovici and Ricard (2012b)] using this model, but it has not been tested in a dynamically consistent way. Our preliminary results have shown that out of equilibrium grain size dynamics leads to localization of deformation below the lithosphere rather than subduction initiation. Yet this result was obtained assuming indealized conditions. We study here, for the first time, the evolution of grain size in the mantle and lithosphere in evolutionary models, starting from a just-frozen magma ocean until the present day situation. Following complexities are considered in these models: melting, phase transitions, compressible convection, and different pressure-temperature-dependent composite rheologies in upper and lower mantles. We use a visco-plastic rheology in which the viscous strain rate is obtained by summation of dislocation and diffusion creep. Pressure and velocity fields are solved on a staggered grid using a SIMPLER-like method. Multigrid W-cycles and extra coarse-grid relaxations are employed to enhance the convergence of Stokes and continuity equations. The grain size is stored on a large number of tracers advected through the computational domain (a 2D spherical annulus), which prevent numerical diffusion and allows a high resolution. We also describe the physical formalism itself and derive a set of free parameters for the model. The results show that Normal growth, dynamic

  1. 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.

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

    NASA Astrophysics Data System (ADS)

    Weik, Florian; Kesselheim, Stefan; Holm, Christian

    2016-11-01

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

  3. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2011-11-01

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

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

    PubMed Central

    Wei, Zonghui

    2015-01-01

    All-atom molecular dynamics simulations can provide insight into the properties of polymeric gene-delivery carriers by elucidating their interactions and detailed binding patterns with nucleic acids. However, to explore nanoparticle formation through complexation of these polymers and nucleic acids and study their behavior at experimentally relevant time and length scales, a reliable coarse-grained model is needed. Here, we systematically develop such a model for the complexation of small interfering RNA (siRNA) and grafted polyethyleneimine copolymers, a promising candidate for siRNA delivery. We compare the predictions of this model with all-atom simulations and demonstrate that it is capable of reproducing detailed binding patterns, charge characteristics, and water release kinetics. Since the coarse-grained model accelerates the simulations by one to two orders of magnitude, it will make it possible to quantitatively investigate nanoparticle formation involving multiple siRNA molecules and cationic copolymers. PMID:26723631

  6. 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.

  7. 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

  8. Only pick the right grains: Modelling the bias due to subjective grain-size interval selection for chronometric and fingerprinting approaches.

    NASA Astrophysics Data System (ADS)

    Dietze, Michael; Fuchs, Margret; Kreutzer, Sebastian

    2016-04-01

    Many modern approaches of radiometric dating or geochemical fingerprinting rely on sampling sedimentary deposits. A key assumption of most concepts is that the extracted grain-size fraction of the sampled sediment adequately represents the actual process to be dated or the source area to be fingerprinted. However, these assumptions are not always well constrained. Rather, they have to align with arbitrary, method-determined size intervals, such as "coarse grain" or "fine grain" with partly even different definitions. Such arbitrary intervals violate principal process-based concepts of sediment transport and can thus introduce significant bias to the analysis outcome (i.e., a deviation of the measured from the true value). We present a flexible numerical framework (numOlum) for the statistical programming language R that allows quantifying the bias due to any given analysis size interval for different types of sediment deposits. This framework is applied to synthetic samples from the realms of luminescence dating and geochemical fingerprinting, i.e. a virtual reworked loess section. We show independent validation data from artificially dosed and subsequently mixed grain-size proportions and we present a statistical approach (end-member modelling analysis, EMMA) that allows accounting for the effect of measuring the compound dosimetric history or geochemical composition of a sample. EMMA separates polymodal grain-size distributions into the underlying transport process-related distributions and their contribution to each sample. These underlying distributions can then be used to adjust grain-size preparation intervals to minimise the incorporation of "undesired" grain-size fractions.

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

    PubMed Central

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

    2009-01-01

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

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  12. 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.

  13. 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.

  14. The ATAMM procedure model for concurrent processing of large grained control and signal processing algorithms

    NASA Technical Reports Server (NTRS)

    Stoughton, John W.; Mielke, Roland R.

    1988-01-01

    An overview is presented of a model for describing data and control flow associated with the execution of large-grained, decision-free algorithms in a special distributed computer environment. The ATAMM (Algorithm-To-Architecture Mapping Model) model provides a basis for relating an algorithm to its execution in a dataflow multicomputer environment. The ATAMM model features a marked graph Petri net description of the algorithm behavior with regard to both data and control flow. The model provides an analytical basis for calculating performance bounds on throughput characteristics which are demonstrated here.

  15. 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.

  16. 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

  17. 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.

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

    NASA Astrophysics Data System (ADS)

    Daming, Nie; Zhen, Lu; Kaifeng, Zhang

    2017-02-01

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

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

    SciTech Connect

    Helgee, Edit E.; Isacsson, Andreas

    2016-01-15

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

  20. 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.

  1. 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.

  2. 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.

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

    PubMed

    Wang, Yusong; Licht, Louis; Just, Craig

    2016-01-01

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

  4. 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

  5. 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.

  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. Quantification of Epistemic Uncertainty in Grain Attachment Models for Equiaxed Solidification

    NASA Astrophysics Data System (ADS)

    Plotkowski, A.; Krane, M. J. M.

    2017-02-01

    Recent work has investigated various schemes for the attachment of free-floating grains in models of equiaxed solidification in multicomponent alloys. However, these models are deterministic in nature, and simply investigating their differences for a limited number of results would not constitute an adequate comparison of their predictions. Instead, the models are compared in the context of the uncertainty in the most important input parameters. This approach is especially important in light of the effort required to implement a new model. If the predictions are essentially the same, then either model will suffice, or one may be selected for ease of implementation, numerical robustness, or computational efficiency. If, however, the models are significantly different, then the most accurate should be selected. In order to investigate the effects of input uncertainty on the output of grain attachment models, the PRISM Uncertainty Quantification framework was employed. The three models investigated were a constant packing fraction (CPF) scheme, an average solid velocity method (AVM), and a continuum attachment approach. Comparisons were made between the CPF and AVM models to estimate the importance of the local velocity field and between the CPF and continuum models to determine the sensitivity of the macrosegregation to new parameters unique to the continuum model.

  8. 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.

  9. Ultra-Fine Grain Structures Of Model Al-Mg-Si Alloys Produced By Hydrostatic Extrusion

    NASA Astrophysics Data System (ADS)

    Adamczyk-Cieślak, Bogusława; Mizera, Jarosław

    2011-01-01

    Microstructure and mechanical properties were studied in model Al-Mg-Si alloys (Al-1 % Mg-0.8% Si and Al-0.5% Mg-0.3% Si-wt %) deformed by hydrostatic extrusion (HE) to strains of 1.4 and 3.8. In these alloys the different percentage of two hardening second-phase precipitates (Mg2Si and Si) were observed. The microstructure was characterized by transmission electron microscopy and optical microscopy. The microstructure of the alloys in the initial state was built of coarse grains of an average diameter of ˜30 rim. The refined microstructure was examined qualitatively and quantitatively using the stereological method and a computer image analysis. The deformation-processed structures evolved very rapidly, forming ultrafine grained (UFG) materials with grains of about 0.4 μm. In addition, the grain refinement in the HE-treated materials has a substantial effect on their properties, such as the mechanical strength and micro-hardness which increase significantly. It has been found that, after ɛ = 3.8 in the Al-1% Mg-0.8% Si alloy, the micro-hardness increases approximately twofold. The yield stress is more than four times higher in the UFG alloys, in comparison to the initial state. Similar results were identified in the Al-0.5% Mg-0.3% Si. This is due to the very rapid refinement of the microstructure during the deformation and presence of second-phase particles.

  10. Ultra-Fine Grain Structures Of Model Al-Mg-Si Alloys Produced By Hydrostatic Extrusion

    SciTech Connect

    Adamczyk-Cieslak, Boguslawa; Mizera, Jaroslaw

    2011-01-17

    Microstructure and mechanical properties were studied in model Al-Mg-Si alloys (Al-1 % Mg-0.8% Si and Al-0.5% Mg-0.3% Si-wt %) deformed by hydrostatic extrusion (HE) to strains of 1.4 and 3.8. In these alloys the different percentage of two hardening second-phase precipitates (Mg{sub 2}Si and Si) were observed. The microstructure was characterized by transmission electron microscopy and optical microscopy. The microstructure of the alloys in the initial state was built of coarse grains of an average diameter of {approx}30 rim. The refined microstructure was examined qualitatively and quantitatively using the stereological method and a computer image analysis. The deformation-processed structures evolved very rapidly, forming ultrafine grained (UFG) materials with grains of about 0.4 {mu}m. In addition, the grain refinement in the HE-treated materials has a substantial effect on their properties, such as the mechanical strength and micro-hardness which increase significantly. It has been found that, after {epsilon} = 3.8 in the Al-1% Mg-0.8% Si alloy, the micro-hardness increases approximately twofold. The yield stress is more than four times higher in the UFG alloys, in comparison to the initial state. Similar results were identified in the Al-0.5% Mg-0.3% Si. This is due to the very rapid refinement of the microstructure during the deformation and presence of second-phase particles.

  11. 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.

  12. 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

  13. Models performance and robustness for simulating drainage and nitrate-nitrogen fluxes without recalibration

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Intensively grazed pastures generate nitrate-nitrogen (NO3-N) contaminated groundwater creating grave environmental concern. Computer models simulate and forecast appropriate agricultural practices to reduce environmental impact. Model validation is an essential process in evaluation and field appli...

  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. MODELING NANOCRYSTALLINE GRAIN GROWTH DURING THE PULSED ELECTRODEPOSITION OF GOLD-COPPER

    SciTech Connect

    Jankowski, A F

    2005-10-27

    The process parameters of current density, pulse duration, and cell potential affect both the structure and composition of electrodeposits. The mechanism for nucleation and growth as determined from current transients yield relationships for nucleus density and nucleation rate. To develop an understanding of the role of the process parameters on grain size, as a design structural parameter to control strength for example, a formulation is presented to model the affects of the deposition energy on grain size and morphology. An activation energy for the deposition process is modeled that reveals different growth mechanisms, wherein nucleation and diffusion effects are each dominant as dependent upon pulse duration. A diffusion coefficient common for each of the pulsed growth modes demarcates an observed transition in growth from smooth to rough surfaces.

  18. Phase-field modeling of grain-boundary premelting using obstacle potentials.

    PubMed

    Bhogireddy, V Sai Pavan Kumar; Hüter, C; Neugebauer, J; Steinbach, I; Karma, A; Spatschek, R

    2014-07-01

    We investigate the multiorder parameter phase field model of Steinbach and Pezzolla [Physica D 134, 385 (1999)] concerning its ability to describe grain boundary premelting. For a single order parameter situation solid-melt interfaces are always attractive, which allows us to have (unstable) equilibrium solid-melt-solid coexistence above the bulk melting point. The temperature-dependent melt layer thickness and the disjoining potential, which describe the interface interaction, are affected by the choice of the thermal coupling function and the measure to define the amount of the liquid phase. Due to the strictly finite interface thickness the interaction range also is finite. For a multiorder parameter model we find either purely attractive or purely repulsive finite-ranged interactions. The premelting transition is then directly linked to the ratio of the grain boundary and solid-melt interfacial energy.

  19. A Numerical Model of Anisotropic Mass Transport Through Grain Boundary Networks

    NASA Astrophysics Data System (ADS)

    Wang, Yibo

    Tin (Sn) thin films are commonly used in electronic circuit applications as coatings on contacts and solders for joining components. It is widely observed, for some such system, that whiskers---long, thin crystalline structures---emerge and grow from the film. The Sn whisker phenomenon has become a highly active research area since Sn whiskers have caused a large amount of damage and loss in manufacturing, military, medical and power industries. Though lead (Pb) addition to Sn has been used to solve this problem for over five decades, the adverse environmental and health effects of Pb have motivated legislation to severely constrain Pb use in society. People are researching and seeking the reasons which cause whiskers and corresponding methods to solve the problem. The contributing factors to cause a Sn whisker are potentially many and much still remains unknown. Better understanding of fundamental driving forces should point toward strategies to improve (a) the accuracy with which we can predict whisker formation, and (b) our ability to mitigate the phenomenon. This thesis summarizes recent important research achievements in understanding Sn whisker formation and growth, both experimentally and theoretically. Focus is then placed on examining the role that anisotropy in grain boundary diffusivity plays in determining whisker characteristics (specifically, whether they form and, if so, where on a surface). To study this aspect of the problem and to enable future studies on stress driven grain boundary diffusion, this thesis presents a numerical anisotropic mass transport model. In addition to presenting details of the model and implementation, model predictions for a set of increasingly complex grain boundary networks are discussed. Preliminary results from the model provide evidence that anisotropic grain boundary diffusion may be a primary driving mechanism in whisker formation.

  20. 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.

  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. 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.

  3. A coarse-grained model for amorphous and crystalline fatty acids

    PubMed Central

    Hadley, K. R.; McCabe, C.

    2010-01-01

    Fatty acids constitute one of the main components of the lipid lamellae in the top layer of the skin, known as the stratum corneum, which acts as a barrier to foreign substances entering the body and to water leaving the body. To better understand the mechanics of the skin, a molecular-level understanding of the structure of the lamellae needs to be investigated. As a first step toward this goal, the current work involves the development of a coarse-grained model for fatty acids in an amorphous and a crystalline state. In order to retain the structural details of the atomistic molecules, radial distribution functions have been used to provide target data against which the coarse-grained force field is optimized. The optimization was achieved using the method developed by Reith, Pütz, and Müller-Plathe with a damping factor introduced into the updating scheme to facilitate the convergence against the crystalline radial distribution functions. Using this approach, a transferable force field has been developed for both crystalline and amorphous systems that can be used to describe fatty acids of different chain lengths. We are unaware of any other coarse-grained model in the literature that has been developed to study solid phases. Additionally, the amorphous force field has been shown to accurately model mixtures of different free fatty acids based on the potentials derived from pure lipid systems. PMID:20387939

  4. 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.

  5. Lattice model for the calculation of the angle of repose from microscopic grain properties

    NASA Astrophysics Data System (ADS)

    Alonso, J. J.; Hovi, J.-P.; Herrmann, H. J.

    1998-07-01

    We study a simple lattice model for granular heap, which aims at calculating the macroscopic angle of repose from the microscopic grain properties. The model includes the effects of dissipation of the energy in the particle-particle collisions, and sticking of the particles to the pile. We obtain that, due to the discretization of the space, the angle of repose of the pile behaves as a complete devil's staircase as a function of the model parameters. We present numerical and analytical considerations which characterize the properties of this staircase.

  6. 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

  7. 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...

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

    EPA Science Inventory

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

  9. 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.

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

    SciTech Connect

    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 spatial 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 spatial 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.

  11. Pelagic nitrogen cycling in Jiaozhou Bay, a model study I: The conceptual model

    NASA Astrophysics Data System (ADS)

    Ren, Ling; Zhang, Manping; Brockmann, Uwe H.; Feng, Shizuo

    2003-12-01

    A zero-dimensional box model (PNCMjzb) with six state variables (ammonium, nitrate, dissolved organic nitrogen, phytoplankton, zooplankton and detritus) was developed to study nitrogen cycling in the Jiaozhou Bay pelagic ecosystem. The dominant processes within these compartments are considered with nitrogen as flow currency. Phytoplankton and zooplankton are treated as separate state variables, assuming that the species composition was dominated by two or three species the dynamic constants of which are similar and that they represent the entire plankton community. The microbial loop has not been integrated explicitly in the model. The turnover of bacteria is included implicitly in processes such as detritus decomposition, DON remineralization, pelagic nitrification and denitrification. The model is driven by two forcing variables, viz. water temperature and light intensity. Historical data from the 1980s and 1990s were compiled and used for model calibration. In this paper (part I), the consideration of every main compartment in the model is interpreted in detail. And the applied equations and parameters are presented. The main results from the simulations together with discussion about phytoplankton dynamics and primary production in Jiaozhou Bay are presented in the next paper (part II).

  12. Refining the Treatment of Membrane Proteins by Coarse-Grained Models

    PubMed Central

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

    2015-01-01

    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. PMID:26531155

  13. 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.

  14. Final report: Constructing comprehensive models of grain boundaries using high-throughput experiments

    SciTech Connect

    Demkowicz, Michael; Schuh, Christopher; Marzouk, Youssef

    2016-08-29

    This is the final report on project DE-SC0008926. The goal of this project was to create capabilities for constructing, analyzing, and modeling experimental databases of the crystallographic characters and physical properties of thousands of individual grain boundaries (GBs) in polycrystalline metals. This project focused on gallium permeation through aluminum (Al) GBs and hydrogen uptake into nickel (Ni) GBs as model problems. This report summarizes the work done within the duration of this project (including the original three-year award and the subsequent one-year renewal), i.e. from August 1, 2012 until April 30, 2016.

  15. 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.

  16. Modeling and Simulation - The Effects of Grain Coarsening on Local Stresses and Strains in Solder Microstructure

    SciTech Connect

    Chanchani, R.

    1999-01-21

    A critical issue in the long-term reliability of solder connections used in electronic packages is the joint failure during thermal cycling. Presently in most finite element analysis to predict the solder joint fatigue failures, solder is assumed as a homogeneous single-phase metal. However in the last decade, several metallurgical studies have shown that solder microstructure may have a role in early solder joint failures (ref 1). Investigators have observed (ref 1) that solder microstructure coarsens in local bands during aging and during thermal cycle fatigue. In a failed solder joint, the fatigue cracks are found in these bands of coarse grains. It is speculated that the grain coarsening increases the local strains within the microstructure, thereby increasing the likelihood for a crack to initiate. The objective of this study is to model and simulate the effect of grain coarsening on local stresses and strains. During solidification of eutectic Pb/Sn solder, two types of microstructure form, namely lamellar and equiaxed. In this study, I have developed a computer code to generate both types of microstructures of varying grain coarseness. This code is incorporated into the finite element (FE) code that analyzes the local stresses and strains within the computer-generated microstructure. The FE code, specifically developed for this study, uses an algorithm involving the sparse matrix and iterative solver. This code on a typical single-processor machine will allow the analyst to use over 1 million degrees of freedom. For higher number of degrees of freedom, we have also developed a code to run on a parallel machine using message passing interface. The data reported in this paper were obtained using the single-processor code. The solder microstructure, if assumed to be homogeneous single phase, has gradual variation in local stresses and strains. In 2-phase solder, von mises stresses and strains are heterogeneously distributed. In general, the maximum von mises

  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. 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.

  19. Large Extent Spatial Models of Grain Yield: Where Are the Marginal Areas?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Landscapes marginal for grain productivity are those having low or negative profitability due to lower grain yield or high risk of crop failure. These are the first acres to come into production when cost and price changes increase profitability. Food grain, biofuel grain and potential cellulosic bi...

  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. Computational methods toward accurate RNA structure prediction using coarse-grained and all-atom models.

    PubMed

    Krokhotin, Andrey; Dokholyan, Nikolay V

    2015-01-01

    Computational methods can provide significant insights into RNA structure and dynamics, bridging the gap in our understanding of the relationship between structure and biological function. Simulations enrich and enhance our understanding of data derived on the bench, as well as provide feasible alternatives to costly or technically challenging experiments. Coarse-grained computational models of RNA are especially important in this regard, as they allow analysis of events occurring in timescales relevant to RNA biological function, which are inaccessible through experimental methods alone. We have developed a three-bead coarse-grained model of RNA for discrete molecular dynamics simulations. This model is efficient in de novo prediction of short RNA tertiary structure, starting from RNA primary sequences of less than 50 nucleotides. To complement this model, we have incorporated additional base-pairing constraints and have developed a bias potential reliant on data obtained from hydroxyl probing experiments that guide RNA folding to its correct state. By introducing experimentally derived constraints to our computer simulations, we are able to make reliable predictions of RNA tertiary structures up to a few hundred nucleotides. Our refined model exemplifies a valuable benefit achieved through integration of computation and experimental methods.

  2. 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.

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

    PubMed

    Li, He; Lykotrafitis, George

    2012-01-04

    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.

  5. 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.

  6. Influence of grain size and exchange interaction on the LLB modeling procedure

    NASA Astrophysics Data System (ADS)

    Vogler, Christoph; Abert, Claas; Bruckner, Florian; Suess, Dieter; Praetorius, Dirk

    2016-12-01

    Reliably predicting bit-error rates in realistic heat-assisted magnetic recording simulations is a challenging task. Integrating the Landau-Lifshitz-Bloch (LLB) equation, within a coarse graining approach, can reduce the computational effort to determine the magnetization dynamics in the vicinity of the Curie temperature, compared to solving the atomistic Landau-Lifshitz-Gilbert equation. If the aim is that the dynamics of both approaches coincide, temperature dependent material functions, such as the zero-field equilibrium magnetization as well as the parallel and normal susceptibilities, must be modeled carefully in order to use them as input in the LLB equation. We present an extensive study on how these functions depend on grain size and exchange interactions. We show that, if the size or the exchange constant of a reference grain is modified, the material functions can be scaled, according to the changed Curie temperature, yielding negligible errors. This is shown to be valid for volume changes of up to ±40% and variations of the exchange constant of up to ±10%. Besides the temperature dependent material curves, computed switching probabilities also agree well with probabilities separately determined for each system. Our study suggests that there is no need to recalculate the required LLB input functions for each particle. Within the presented limits, it is sufficient to scale them to the Curie temperature of the altered system.

  7. Characterization and Modeling of Grain Boundary Chemistry Evolution in Ferritic Steels under Irradiation

    SciTech Connect

    Marquis, Emmanuelle; Wirth, Brian; Was, Gary

    2016-03-28

    Ferritic/martensitic (FM) steels such as HT-9, T-91 and NF12 with chromium concentrations in the range of 9-12 at.% Cr and high Cr ferritic steels (oxide dispersion strengthened steels with 12-18% Cr) are receiving increasing attention for advanced nuclear applications, e.g. cladding and duct materials for sodium fast reactors, pressure vessels in Generation IV reactors and first wall structures in fusion reactors, thanks to their advantages over austenitic alloys. Predicting the behavior of these alloys under radiation is an essential step towards the use of these alloys. Several radiation-induced phenomena need to be taken into account, including phase separation, solute clustering, and radiation-induced segregation or depletion (RIS) to point defect sinks. RIS at grain boundaries has raised significant interest because of its role in irradiation assisted stress corrosion cracking (IASCC) and corrosion of structural materials. Numerous observations of RIS have been reported on austenitic stainless steels where it is generally found that Cr depletes at grain boundaries, consistently with Cr atoms being oversized in the fcc Fe matrix. While FM and ferritic steels are also subject to RIS at grain boundaries, unlike austenitic steels, the behavior of Cr is less clear with significant scatter and no clear dependency on irradiation condition or alloy type. In addition to the lack of conclusive experimental evidence regarding RIS in F-M alloys, there have been relatively few efforts at modeling RIS behavior in these alloys. The need for predictability of materials behavior and mitigation routes for IASCC requires elucidating the origin of the variable Cr behavior. A systematic detailed high-resolution structural and chemical characterization approach was applied to ion-implanted and neutron-irradiated model Fe-Cr alloys containing from 3 to 18 at.% Cr. Atom probe tomography analyses of the microstructures revealed slight Cr clustering and segregation to dislocations and

  8. 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.

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

    PubMed

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

    2016-08-07

    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.

  10. 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

  11. Coarse-grained model of conformation-dependent electrophoretic mobility and its influence on DNA dynamics

    NASA Astrophysics Data System (ADS)

    Pandey, Harsh; Underhill, Patrick T.

    2015-11-01

    The electrophoretic mobility of molecules such as λ -DNA depends on the conformation of the molecule. It has been shown that electrohydrodynamic interactions between parts of the molecule lead to a mobility that depends on conformation and can explain some experimental observations. We have developed a new coarse-grained model that incorporates these changes of mobility into a bead-spring chain model. Brownian dynamics simulations have been performed using this model. The model reproduces the cross-stream migration that occurs in capillary electrophoresis when pressure-driven flow is applied parallel or antiparallel to the electric field. The model also reproduces the change of mobility when the molecule is stretched significantly in an extensional field. We find that the conformation-dependent mobility can lead to a new type of unraveling of the molecule in strong fields. This occurs when different parts of the molecule have different mobilities and the electric field is large.

  12. Predicting Bed Grain Size in Threshold Channels Using Lidar Digital Elevation Models

    NASA Astrophysics Data System (ADS)

    Snyder, N. P.; Nesheim, A. O.; Wilkins, B. C.; Edmonds, D. A.

    2011-12-01

    Over the past 20 years, researchers have developed GIS-based algorithms to extract channel networks and measure longitudinal profiles from digital elevation models (DEMs), and have used these to study stream morphology in relation to tectonics, climate and ecology. The accuracy of stream elevations from traditional DEMs (10-50 m pixels) is typically limited by the contour interval (3-20 m) of the rasterized topographic map source. This is a particularly severe limitation in low-relief watersheds, where 3 m of channel elevation change may occur over several km. Lidar DEMs (~1 m pixels) allow researchers to resolve channel elevation changes of ~0.5 m, enabling reach-scale calculations of gradient, which is the most important parameter for understanding channel processes at that scale. Lidar DEMs have the additional advantage of allowing users to make estimates of channel width. We present a process-based model that predicts median bed grain size in threshold gravel-bed channels from lidar slope and width measurements using the Shields and Manning equations. We compare these predictions to field grain size measurements in segments of three Maine rivers. Like many paraglacial rivers, these have longitudinal profiles characterized by relatively steep (gradient >0.002) and flat (gradient <0.0005) segments, with length scales of several km. This heterogeneity corresponds to strong variations in channel form, sediment supply, bed grain size, and aquatic habitat characteristics. The model correctly predicts bed sediment size within a factor of two in ~70% of the study sites. The model works best in single-thread channels with relatively low sediment supply, and poorly in depositional, multi-thread and/or fine (median grain size <20 mm) reaches. We evaluate the river morphology (using field and lidar measurements) in the context of the Parker et al. (2007) hydraulic geometry relations for single-thread gravel-bed rivers, and find correspondence in the locations where both

  13. A texture-component Avrami model for predicting recrystallization textures, kinetics and grain size

    NASA Astrophysics Data System (ADS)

    Raabe, Dierk

    2007-03-01

    The study presents an analytical model for predicting crystallographic textures and the final grain size during primary static recrystallization of metals using texture components. The kinetics is formulated as a matrix variant of the Johnson-Mehl-Avrami-Kolmogorov equation. The matrix form is required since the kinetic and crystallographic evolution of the microstructure is described in terms of a limited set of growing (recrystallizing) and swept (deformed) texture components. The number of components required (5-10) defines the order of the matrix since the kinetic coupling occurs between all recrystallizing and all deformed components. Each such couple is characterized by corresponding values for the nucleation energy and grain boundary mobility. The values of these parameters can be obtained by analytical or numerical coarse graining according to a renormalization scheme which replaces many individual grains which grow via recrystallization in a deformed texture component by a single equivalent recrystallization texture component or by fitting to experimental data. Each deformed component is further characterized by an average stored deformation energy. Each element of the kinetic matrix, reflecting one of the possible couplings between a deformed and a recrystallizing texture component, is then derived in each time step by a set of two differential equations. The first equation describes the thermally activated nucleation and growth processes for the expanded (free) volume for a particular couple of a deformed and a recrystallizing texture component and the second equation is used for calculating the constrained (real) volume for that couple which corrects the free volume for those portions of the deformation component which were already swept. The new method is particularly developed for the fast and physically based process simulation of recrystallization textures with respect to processing. The present paper introduces the method and applies it to the

  14. 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.

  15. 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 ...

  16. A SIMPLE MODEL OF THE EFFECTS OF NITROGEN LOADING, FRESHWATER RESIDENCE TIME, AND INTERNAL LOSSES ON THE NITROGEN CONCENTRATIONS AND EXPORT IN ESTUARIES

    EPA Science Inventory

    This simple model uses the annual loading rate of total nitrogen (TN) and the water residence time to calculate average annual TN concentration and internal loss rates (e.g. denitrification and incorporation in sediments) in an estuary, and rate of nitrogen export across the seaw...

  17. 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.

  18. 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.

  19. Random polycrystals of grains containing cracks: Model of quasistatic elastic behavior for fractured systems

    NASA Astrophysics Data System (ADS)

    Berryman, James G.; Grechka, Vladimir

    2006-12-01

    A model study on fractured systems was performed using a concept that treats isotropic cracked systems as ensembles of cracked grains by analogy to isotropic polycrystalline elastic media. The approach has two advantages: (a) Averaging performed is ensemble averaging, thus avoiding the criticism legitimately leveled at most effective medium theories of quasistatic elastic behavior for cracked media based on volume concentrations of inclusions. Since crack effects are largely independent of the volume they occupy in the composite, such a non-volume-based method offers an appealingly simple modeling alternative. (b) The second advantage is that both polycrystals and fractured media are stiffer than might otherwise be expected, due to natural bridging effects of the strong components. These same effects have also often been interpreted as crack-crack screening in high-crack-density fractured media, but there is no inherent conflict between these two interpretations of this phenomenon. Results of the study are somewhat mixed. The spread in elastic constants observed in a set of numerical experiments is found to be very comparable to the spread in values contained between the Reuss and Voigt bounds for the polycrystal model. Unfortunately, computed Hashin-Shtrikman bounds are much too tight to be in agreement with the numerical data, showing that polycrystals of cracked grains tend to violate some implicit assumptions of the Hashin-Shtrikman bounding approach. However, the self-consistent estimates obtained for the random polycrystal model are nevertheless very good estimators of the observed average behavior.

  20. 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.

  1. pOsNAR2.1:OsNAR2.1 expression enhances nitrogen uptake efficiency and grain yield in transgenic rice plants.

    PubMed

    Chen, Jingguang; Fan, Xiaoru; Qian, Kaiyun; Zhang, Yong; Song, Miaoquan; Liu, Yu; Xu, Guohua; Fan, Xiaorong

    2017-02-22

    The nitrate (NO3-) transporter has been selected as an important gene maker in the process of environmental adoption in rice cultivars. In this work, we transferred another native OsNAR2.1 promoter with driving OsNAR2.1 gene into rice plants. The transgenic lines with exogenous pOsNAR2.1:OsNAR2.1 constructs showed enhanced OsNAR2.1 expression level, compared with wild type (WT), and (15) N influx in roots increased 21%-32% in response to 0.2 mm and 2.5 mm 15NO3- and 1.25 mm (15) NH4(15) NO3 . Under these three N conditions, the biomass of the pOsNAR2.1:OsNAR2.1 transgenic lines increased 143%, 129% and 51%, and total N content increased 161%, 242% and 69%, respectively, compared to WT. Furthermore in field experiments we found the grain yield, agricultural nitrogen use efficiency (ANUE), and dry matter transfer of pOsNAR2.1:OsNAR2.1 plants increased by about 21%, 22% and 21%, compared to WT. We also compared the phenotypes of pOsNAR2.1:OsNAR2.1 and pOsNAR2.1:OsNRT2.1 transgenic lines in the field, found that postanthesis N uptake differed significantly between them, and in comparison with the WT. Postanthesis N uptake (PANU) increased approximately 39% and 85%, in the pOsNAR2.1:OsNAR2.1 and pOsNAR2.1:OsNRT2.1 transgenic lines, respectively, possibly because OsNRT2.1 expression was less in the pOsNAR2.1:OsNAR2.1 lines than in the pOsNAR2.1:OsNRT2.1 lines during the late growth stage. These results show that rice NO3(-) uptake, yield and NUE were improved by increased OsNAR2.1 expression via its native promoter.

  2. 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

  3. 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

  4. Spatially resolved modeling of the combined effect of dislocations and grain boundaries on minority carrier lifetime in multicrystalline silicon

    NASA Astrophysics Data System (ADS)

    Stokkan, G.; Riepe, S.; Lohne, O.; Warta, W.

    2007-03-01

    A model for the combined effect of dislocations and grain boundaries on minority carrier lifetime has been developed. Lifetime varies with dislocation density, grain boundary misorientation, and the coincidence site lattice (CSL) nature of the boundaries. Minority carrier lifetime was measured with high spatial resolution (50 μm) using the carrier density imaging (CDI) technique on a silicon nitride passivated multicrystalline sample. Dislocation density was measured on the same sample by image recognition of optical microscope pictures of a Secco etched surface. Grain boundaries were then mapped and characterized by electron backscatter diffraction (EBSD). Lifetime was simulated based on the dislocation and grain boundary measurements. Parameters were chosen to match closely the simulated and measured maps. Very good two-dimensional (2D) correlation was obtained by assigning roughly equal importance to recombination at dislocations and grain boundaries. The value for the capture cross section, which gives the best correlation, is 4×10-14 cm-3. This is in the range of values reported for interstitial transition metals like, for instance, iron. It appears necessary to include also the effect of grain boundaries to explain recombination in low lifetime areas. Sub grain boundaries were particularly recombination active and are dominating the number of active grain boundaries.

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  6. Physical integrated diffusion-oxidation model for implanted nitrogen in silicon

    NASA Astrophysics Data System (ADS)

    Adam, Lahir Shaik; Law, Mark E.; Dokumaci, Omer; Hegde, Suri

    2002-02-01

    Scaling the gate oxide thickness is one of many process development challenges facing device engineers today. Nitrogen implantation has been used to control gate oxide thickness. By varying the dose of the nitrogen implant, process engineers can have multiple gate oxide thicknesses in the same process. Although it has been observed that nitrogen retards gate oxidation kinetics, the physics of how this occurs is not yet well understood. Since the retardation in oxide growth is due to the diffusion of nitrogen and its subsequent incorporation at the silicon/silicon oxide interface, the study of the diffusion behavior of nitrogen in silicon becomes important. Further, it is also necessary to study how this diffusion behavior impacts oxide growth. Models have been developed to explore these issues. The diffusion model is based on ab initio results and is compared to experimental results at two temperatures. The oxide reduction model is based on the diffusion of nitrogen to the surface. The surface nitrogen is coupled to the surface reaction rate of silicon and oxygen to moderate oxide growth.

  7. Automated Optimization of Water–Water Interaction Parameters for a Coarse-Grained Model

    PubMed Central

    2015-01-01

    We have developed an automated parameter optimization software framework (ParOpt) that implements the Nelder–Mead simplex algorithm and applied it to a coarse-grained polarizable water model. The model employs a tabulated, modified Morse potential with decoupled short- and long-range interactions incorporating four water molecules per interaction site. Polarizability is introduced by the addition of a harmonic angle term defined among three charged points within each bead. The target function for parameter optimization was based on the experimental density, surface tension, electric field permittivity, and diffusion coefficient. The model was validated by comparison of statistical quantities with experimental observation. We found very good performance of the optimization procedure and good agreement of the model with experiment. PMID:24460506

  8. 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.

  9. Autocorrelation study of the Θ transition for a coarse-grained polymer model.

    PubMed

    Qi, Kai; Bachmann, Michael

    2014-08-21

    By means of Metropolis Monte Carlo simulations of a coarse-grained model for flexible polymers, we investigate how the integrated autocorrelation times of different energetic and structural quantities depend on the temperature. We show that, due to critical slowing down, an extremal autocorrelation time can also be considered as an indicator for the collapse transition that helps to locate the transition point. This is particularly useful for finite systems, where response quantities such as the specific heat do not necessarily exhibit clear indications for pronounced thermal activity.

  10. 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.

  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. 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

  13. 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.

  14. Grain-Size Based Additivity Models for Scaling Multi-rate Uranyl Surface Complexation in Subsurface Sediments

    SciTech Connect

    Zhang, Xiaoying; Liu, Chongxuan; Hu, Bill X.; Hu, Qinhong

    2015-09-28

    This study statistically analyzed a grain-size based additivity model that has been proposed to scale reaction rates and parameters from laboratory to field. The additivity model assumed that reaction properties in a sediment including surface area, reactive site concentration, reaction rate, and extent can be predicted from field-scale grain size distribution by linearly adding reaction properties for individual grain size fractions. This study focused on the statistical analysis of the additivity model with respect to reaction rate constants using multi-rate uranyl (U(VI)) surface complexation reactions in a contaminated sediment as an example. Experimental data of rate-limited U(VI) desorption in a stirred flow-cell reactor were used to estimate the statistical properties of multi-rate parameters for individual grain size fractions. The statistical properties of the rate constants for the individual grain size fractions were then used to analyze the statistical properties of the additivity model to predict rate-limited U(VI) desorption in the composite sediment, and to evaluate the relative importance of individual grain size fractions to the overall U(VI) desorption. The result indicated that the additivity model provided a good prediction of the U(VI) desorption in the composite sediment. However, the rate constants were not directly scalable using the additivity model, and U(VI) desorption in individual grain size fractions have to be simulated in order to apply the additivity model. An approximate additivity model for directly scaling rate constants was subsequently proposed and evaluated. The result found that the approximate model provided a good prediction of the experimental results within statistical uncertainty. This study also found that a gravel size fraction (2-8mm), which is often ignored in modeling U(VI) sorption and desorption, is statistically significant to the U(VI) desorption in the sediment.

  15. A Model-Based Analysis of Nitrogen Deposition: Effects on Forest Carbon Sequestration

    NASA Astrophysics Data System (ADS)

    Dezi, S.; Medlyn, B. E.; Tonon, G.; Magnani, F.

    2009-04-01

    Over the last 150 years nitrogen deposition has increased, especially in the northern hemisphere, mainly due to the use of fossil fuels, deforestation and agricultural practices. Although the impact of this increase on the terrestrial carbon cycle is still uncertain, it is likely that this large perturbation of the global nitrogen cycle will have important effects on carbon cycling, particularly via impacts on forest carbon storage. In the present work we investigated qualitatively the overall response of forest carbon sequestration to nitrogen deposition, and the relative importance of different mechanisms that bring about this response. For this purpose we used the G'DAY forest carbon-nitrogen cycling model (Comins and McMurtrie 1993), introducing some new assumptions which focus on the effect of nitrogen deposition. Specifically the new assumptions are: (i) foliar litterfall and specific leaf area (SLA) are functions of leaf nitrogen concentration; (ii) belowground C allocation is a function of net primary production (NPP); (iii) forest canopies can directly take up nitrogen; (iv) management of forests occurs; (v) leaching occurs only for nitrate nitrogen. We investigated the effect of each assumption on net ecosystem production (NEP), with a step increase in nitrogen deposition from a steady state of 0.4 gN m-2 yr-1 to 2 gN m-2 yr-1, and then running the old and new model versions for different nitrogen deposition levels. Our analysis showed that nitrogen deposition can have a large effect on forest carbon storage at ecosystem level. In particular the effect of the assumptions (ii), (iii) and (iv) seem to be of greater importance, giving rise to a markedly higher level of forest carbon sequestration than in their absence. On the contrary assumptions (i) and (v) seem not to have any particular effect on the NEP simulated. Finally, running the models for different levels of nitrogen deposition showed that estimating forest carbon exchange without taking into

  16. An integrated model for simulating nitrogen trading in an agricultural catchment with complex hydrogeology.

    PubMed

    Cox, T J; Rutherford, J C; Kerr, S C; Smeaton, D C; Palliser, C C

    2013-09-30

    Nitrogen loads to several New Zealand lakes are dominated by nonpoint runoff from pastoral farmland which adversely affects lake water quality. A 'cap and trade' scheme is being considered to help meet targets set for nitrogen loads to Lake Rotorua, and a numerical model, NTRADER, has been developed to simulate and compare alternative schemes. NTRADER models both the geophysics of nitrogen generation and transport, including groundwater lag times, and the economics of 'cap and trade' schemes. It integrates the output from several existing models, including a farm-scale nitrogen leaching and abatement model, a farm-scale management economic model, and a catchment-scale nitrogen transport model. This paper details modeling methods and compares possible trading program design features for the Lake Rotorua catchment. Model simulations demonstrate how a cap and trade program could be used to effectively achieve challenging environmental goals in the targeted catchment. However, results also show that, due to complex hydrogeology, satisfactory environmental outcomes may be not achieved unless groundwater lag times are incorporated into the regulatory scheme. One way to do this, as demonstrated here, would be to explicitly include lag times in the cap and trade program. The utility of the model is further demonstrated by quantifying relative differences in abatement costs across potential regulatory schemes.

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

    PubMed

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

    2016-09-07

    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

  18. 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

  19. Development of a new model for vibration-dissociation coupling in nitrogen

    NASA Technical Reports Server (NTRS)

    Landrum, D. B.; Candler, Graham V.

    1992-01-01

    A new model for vibration-dissociation coupling is derived using knowledge obtained from a simulation of the vibrational relaxation of heated nitrogen by collisional processes. This bilevel model is based on the assumption that nitrogen can be represented by two molecular species. The vibrational energy relaxation is represented by a modified form of the Landau-Teller equation. The effects of the bilevel model on a typical hypervelocity flowfield computation are examined and compared to the Park TTv model. Specifically, it is found that the bilevel model exhibits a decreased dissociation rate. This is believed to be due to the inhibition of dissociation by nonequilibrium vibrational relaxation.

  20. Modelling Nitrogen Cycling in a Mariculture Ecosystem as a Tool to Evaluate its Outflow

    NASA Astrophysics Data System (ADS)

    Lefebvre, S.; Bacher, C.; Meuret, A.; Hussenot, J.

    2001-03-01

    A model was constructed to describe an intensive mariculture ecosystem growing sea bass ( Dicentrarchus labrax), located in the salt marshes of the Fiers d'Ars Bay on the French Atlantic coast, in order to assess nitrogen cycling within the system and nitrogen outflow from the system. The land-based system was separated into three main compartments: a seawater reservoir, fish ponds and a lagoon (sedimentation pond). Three submodels were built for simulation purposes: (1) a hydrological submodel which simulated water exchange; (2) a fish growth and excretion bioenergetic submodel; and (3) a nitrogen compound transformation and loss submodel (i.e. ammonification, nitrification and assimilation processes). A two-year sampling period of nitrogen water quality concentrations and fish growth was used to validate the model. The model fitted the observations of dissolved nitrogen components, fish growth and water fluxes on a daily basis in all the compartments. The dissolved inorganic nitrogen ranged widely and over time from 0·5 to 9 g N m -3within the system, depending on seawater supply and water temperature, without affecting fish growth. Fish feed was the most important input of nitrogen into the system. The mean average input of nitrogen in the feed was 205 kg N day -1, of which 19% was retained by fish, 4% accumulated in the sediment and 61% flowed from the system as dissolved components. The farm represented about 25% of the total dissolved nitrogen export from the bay, although the farm surface area was 100 times smaller than that of the bay.

  1. Developing ISM Dust Grain Models with Precision Elemental Abundances from IXO

    NASA Technical Reports Server (NTRS)

    Valencic, L. A.; Smith, R. K.; Juet, A.

    2009-01-01

    The exact nature of interstellar dust grains in the Galaxy remains mysterious, despite their ubiquity. Many viable models exist, based on available IR-UV data and assumed elemental abundances. However, the abundances, which are perhaps the most stringent constraint, are not well known: modelers must use proxies in the absence of direct measurements for the diffuse interstellar medium (ISM). Recent revisions of these proxy values have only added to confusion over which is the best representative for the diffuse ISM, and highlighted the need for direct, high signal-to-noise measurements from the ISM itself. The International X-ray Observatory's superior facilities will enable high-precision elemental abundance measurements. We ill show how these results will measure both the overall ISM abundances and challenge dust models, allowing us to construct a more realistic picture of the ISM.

  2. 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.

  3. A unique Critical State two-surface hyperplasticity model for fine-grained particulate media

    NASA Astrophysics Data System (ADS)

    Coombs, W. M.; Crouch, R. S.; Augarde, C. E.

    2013-01-01

    Even mild compression can cause re-arrangement of the internal structure of clay-like geomaterials, whereby clusters of particles rotate and collapse as face-to-face contacts between the constituent mineral platelets increase at the expense of edge-to-face (or edge-to-edge) contacts. The collective action of local particle re-orientation ultimately leads to path-independent isochoric macroscopic deformation under continuous shearing. This asymptotic condition is the governing feature of Critical State elasto-plasticity models. Unlike earlier formulations, the two-surface anisotropic model proposed herein is able to reproduce a unique isotropic Critical State stress envelope which agrees well with test data. Material point predictions are compared against triaxial experimental results and five other existing constitutive models. The hyperplastic formulation is seen to offer a significantly improved descriptor of the anisotropic behaviour of fine-grained particulate materials.

  4. 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

  5. Analytical modeling for bridging stress function involving grain size distribution in a polycrystalline alumina

    NASA Astrophysics Data System (ADS)

    Sohn, Kee-Sun; Lee, Sunghak; Baik, Sunggi

    1995-05-01

    In order to investigate the microstructural effect on the R-curve behavior in a polycrystalline alumina, an analytical model has been proposed based on the relationship between bridging stress and crack opening displacement. The crack opening displacement was measured using an in situ SEM fracture method, and then used for a fitting procedure to obtain the bridging stress distribution. The results indicated that the bridging stress function and the R-curve computed by the current model were consistent with those computed by the power-law relation, and that the grain size distribution was closely related to the bridging stress. Thus, the current model explained well the correlation between the bridging stress distribution and the local-fracture-controlling microstructural parameter to interpret the microfracture mechanism, including the R-curve behavior.

  6. Insights from Coarse-GrainedModels for Protein Folding and Dynamics

    PubMed Central

    Hills, Ronald D.; Brooks, Charles L.

    2009-01-01

    Exploring the landscape of large scale conformational changes such as protein folding at atomistic detail poses a considerable computational challenge. Coarse-grained representations of the peptide chain have therefore been developed and over the last decade have proved extremely valuable. These include topology-based Gō models, which constitute a smooth and funnel-like approximation to the folding landscape. We review the many variations of the Gō model that have been employed to yield insight into folding mechanisms. Their success has been interpreted as a consequence of the dominant role of the native topology in folding. The role of local contact density in determining protein dynamics is also discussed and is used to explain the ability of Gō-like models to capture sequence effects in folding and elucidate conformational transitions. PMID:19399227

  7. Acoustics of marine sediment under compaction: binary grain-size model and viscoelastic extension of Biot's theory.

    PubMed

    Leurer, Klaus C; Brown, Colin

    2008-04-01

    This paper presents a model of acoustic wave propagation in unconsolidated marine sediment, including compaction, using a concept of a simplified sediment structure, modeled as a binary grain-size sphere pack. Compressional- and shear-wave velocities and attenuation follow from a combination of Biot's model, used as the general framework, and two viscoelastic extensions resulting in complex grain and frame moduli, respectively. An effective-grain model accounts for the viscoelasticity arising from local fluid flow in expandable clay minerals in clay-bearing sediments. A viscoelastic-contact model describes local fluid flow at the grain contacts. Porosity, density, and the structural Biot parameters (permeability, pore size, structure factor) as a function of pressure follow from the binary model, so that the remaining input parameters to the acoustic model consist solely of the mass fractions and the known mechanical properties of each constituent (e.g., carbonates, sand, clay, and expandable clay) of the sediment, effective pressure, or depth, and the environmental parameters (water depth, salinity, temperature). Velocity and attenuation as a function of pressure from the model are in good agreement with data on coarse- and fine-grained unconsolidated marine sediments.

  8. A coarse-grained model for synergistic action of multiple enzymes on cellulose

    SciTech Connect

    Asztalos, Andrea; Daniels, Marcus; Sethi, Anurag; Shen, Tongye; Langan, Paul; Redondo, Antonio; Gnanakaran, Sandrasegaram

    2012-08-01

    In this study, degradation of cellulose to glucose requires the cooperative action of three classes of enzymes, collectively known as cellulases. Endoglucanases randomly bind to cellulose surfaces and generate new chain ends by hydrolyzing -1,4-D-glycosidic bonds. Exoglucanases bind to free chain ends and hydrolyze glycosidic bonds in a processive manner releasing cellobiose units. Then, -glucosidases hydrolyze soluble cellobiose to glucose. Optimal synergistic action of these enzymes is essential for efficient digestion of cellulose. Experiments show that as hydrolysis proceeds and the cellulose substrate becomes more heterogeneous, the overall degradation slows down. As catalysis occurs on the surface of crystalline cellulose, several factors affect the overall hydrolysis. Therefore, spatial models of cellulose degradation must capture effects such as enzyme crowding and surface heterogeneity, which have been shown to lead to a reduction in hydrolysis rates. As a result, we present a coarse-grained stochastic model for capturing the key events associated with the enzymatic degradation of cellulose at the mesoscopic level. This functional model accounts for the mobility and action of a single cellulase enzyme as well as the synergy of multiple endo- and exo-cellulases on a cellulose surface. The quantitative description of cellulose degradation is calculated on a spatial model by including free and bound states of both endo- and exo-cellulases with explicit reactive surface terms (e.g., hydrogen bond breaking, covalent bond cleavages) and corresponding reaction rates. The dynamical evolution of the system is simulated by including physical interactions between cellulases and cellulose. In conclusion, our coarse-grained model reproduces the qualitative behavior of endoglucanases and exoglucanases by accounting for the spatial heterogeneity of the cellulose surface as well as other spatial factors such as enzyme crowding. Importantly, it captures the endo

  9. A Direct Method for Incorporating Experimental Data into Multiscale Coarse-Grained Models.

    PubMed

    Dannenhoffer-Lafage, Thomas; White, Andrew D; Voth, Gregory A

    2016-05-10

    To extract meaningful data from molecular simulations, it is necessary to incorporate new experimental observations as they become available. Recently, a new method was developed for incorporating experimental observations into molecular simulations, called experiment directed simulation (EDS), which utilizes a maximum entropy argument to bias an existing model to agree with experimental observations while changing the original model by a minimal amount. However, there is no discussion in the literature of whether or not the minimal bias systematically and generally improves the model by creating agreement with the experiment. In this work, we show that the relative entropy of the biased system with respect to an ideal target is always reduced by the application of a minimal bias, such as the one utilized by EDS. Using all-atom simulations that have been biased with EDS, one can then easily and rapidly improve a bottom-up multiscale coarse-grained (MS-CG) model without the need for a time-consuming reparametrization of the underlying atomistic force field. Furthermore, the improvement given by the many-body interactions introduced by the EDS bias can be maintained after being projected down to effective two-body MS-CG interactions. The result of this analysis is a new paradigm in coarse-grained modeling and simulation in which the "bottom-up" and "top-down" approaches are combined within a single, rigorous formalism based on statistical mechanics. The utility of building the resulting EDS-MS-CG models is demonstrated on two molecular systems: liquid methanol and ethylene carbonate.

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

    SciTech Connect

    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 reduce 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.

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

    DOE PAGES

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

    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

  12. Evaluation of in vitro models for predicting acidosis risk of barley grain in finishing beef cattle.

    PubMed

    Anele, U Y; Swift, M-L; McAllister, T A; Galyean, M L; Yang, W Z

    2015-10-01

    Our objective was to develop a model to predict the acidosis potential of barley based on the in vitro batch culture incubation of 50 samples varying in bulk density, starch content, processing method, growing location, and agronomic practices. The model was an adaptation of the acidosis index (calculated from a combination of in situ and in vitro analyses and from several components of grain chemical composition) developed in Australia for use in the feed industry to estimate the potential for grains to increase the risk of ruminal acidosis. Of the independent variables considered, DM disappearance at 6 h of incubation (DMD6) using reduced-strength (20%) buffer in the batch culture accounted for 90.5% of the variation in the acidosis index with a root mean square error (RMSE) of 4.46%. To evaluate our model using independent datasets (derived from previous batch culture studies using full-strength [100%] buffer), we performed another batch culture study using full-strength buffer. The full-strength buffer model using in vitro DMD6 (DMD6-FS) accounted for 66.5% of the variation in the acidosis index with an RMSE of 8.30%. When the new full-strength buffer model was applied to 3 independent datasets to predict acidosis, it accounted for 20.1, 28.5, and 30.2% of the variation in the calculated acidosis index. Significant ( < 0.001) mean bias was evident in 2 of the datasets, for which the DMD6 model underpredicted the acidosis index by 46.9 and 5.73%. Ranking of samples from the most diverse independent dataset using the DMD6-FS model and the Black (2008) model (calculated using in situ starch degradation) indicated the relationship between the rankings using Spearman's rank correlation was negative (ρ = -0.30; = 0.059). When the reduced-strength buffer model was used, however, there were similarities in the acidosis index ranking of barley samples by the models as shown by the result of a correlation analysis between calculated (using the Australian model) and

  13. 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.

  14. 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.

  15. Integral equation analysis of single-site coarse-grained models for polymer-colloid mixtures

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

    We discuss the reliability of integral equation methods based on several commonly used closure relations in determining the phase diagram of coarse-grained models of soft-matter systems characterised by mutually interacting soft- and hard-core particles. Specifically, we consider a set of potentials appropriate to describe a system of hard-sphere colloids and linear homopolymers in good solvent, and investigate the behaviour when the soft particles are smaller than the colloids, which is the regime of validity of the coarse-grained models. Using computer-simulation results as a benchmark, we find that the hypernetted-chain approximation provides accurate estimates of thermodynamics and structure in the colloid-gas phase in which the density of colloids is small. On the other hand, all closures considered appear to be unable to describe the behaviour of the mixture in the colloid-liquid phase, as they cease to converge at polymer densities significantly smaller than those at the binodal. As a consequence, integral equations appear to be unable to predict a quantitatively correct phase diagram.

  16. 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

    2016-02-09

    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.

  17. 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.

  18. Extension of CAVS coarse-grained model to phospholipid membranes: The importance of electrostatics.

    PubMed

    Shen, Hujun; Deng, Mingsen; Zhang, Yachao

    2017-05-15

    It is evident from experiment that electrostatic potential (or dipole potential) is positive inside PC or PE lipid bilayers in the absence of ions. MARTINI coarse-grained (CG) model, which has been widely used in simulating physical properties of lipid bilayers, fails to reproduce the positive value for the dipole potential in the membrane interior. Although the total dipole potential can be correctly described by the BMW/MARTINI model, the contribution from the ester dipoles, playing a nontrivial role in the electrostatic potential across lipid membranes, is neglected by this hybrid approach. In the ELBA CG model, the role of the ester dipoles is considered, but it is overweighed because various atomistic models have consistently shown that water is actually the leading contributor of dipole potential. Here, we present a CG approach by combining the BMW-like water model (namely CAVS model) with the ELBA-like lipid model proposed in this work. Our CG model was designed not only to correctly reproduce the positive values for the dipole potential inside PC and PE lipid bilayers but also to properly balance the individual contributions from the ester dipoles and water, surmounting the limitations of current CG models in the calculations of dipole potential. © 2017 Wiley Periodicals, Inc.

  19. 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

  20. Modeling Grain-Scale Diffusion Kinetics Controlling Uranium Sorption and Transport in Contaminated Sediments.

    NASA Astrophysics Data System (ADS)

    Hay, M. B.; Stoliker, D. L.; Johnson, K. J.; Curtis, G. P.; Kent, D. B.; Davis, J. A.

    2008-12-01

    The mobility of U(VI) in contaminated aquifers is limited by adsorption to mineral surfaces. While the chemical sorption step proceeds rapidly, the achievement of equilibrium can be kinetically limited by the diffusion of U(VI) through soil aggregates, grain fractures, and mineral coatings. The diffusion kinetics are in turn dependent on the adsorption equilibrium, due to the sorptive retardation effect that occurs within the intragranular diffusion regime. Since adsorption equilibrium is dependent on chemical conditions (e.g., pH, alkalinity, Ca concentration), diffusion of these chemical species as solution conditions change may also affect U(VI) kinetics. These coupled effects are difficult to capture in generic rate models that do not explicitly include a diffusion mechanism, particularly when the diffusion regime is heterogeneous. We present a grain-scale diffusion model for contaminated sediments from Naturita, CO and Hanford, WA, constrained by kinetic U(VI) desorption data and non-reactive tracer uptake and release measurements with tritiated water. Batch and column-scale tracer results are modeled using a multi-rate mass transfer scheme to extract intragranular diffusion parameters. These results suggest a high degree of heterogeneity in the diffusivity of the intragranular pore space, as indicated by a wide, bi/multimodal distribution of mass transfer rates. These results are used to constrain a U(VI) diffusion model with surface complexation and multicomponent diffusion that can be incorporated into field-scale reactive transport models. Preliminary results suggest that the sorptive retardation effect is significant; U(VI) batch-scale diffusion kinetics requiring hundreds to thousands of hours for equilibration appear to be controlled by intragranular pore space that requires less than 24 hours for equilibration of a non-reactive tracer.

  1. Ensemble modelling of nitrogen fluxes: data fusion for a Swedish meso-scale catchment

    NASA Astrophysics Data System (ADS)

    Exbrayat, J.-F.; Viney, N. R.; Seibert, J.; Wrede, S.; Frede, H.-G.; Breuer, L.

    2010-08-01

    Model predictions of biogeochemical fluxes at the landscape scale are highly uncertain, both with respect to stochastic (parameter) and structural uncertainty. In this study 5 different models (LASCAM, LASCAM-S, a self-developed tool, SWAT and HBV-N-D) designed to simulate hydrological fluxes as well as mobilisation and transport of one or several nitrogen species were applied to the mesoscale River Fyris catchment in mid-eastern Sweden. Hydrological calibration against 5 years of recorded daily discharge at two stations gave highly variable results with Nash-Sutcliffe Efficiency (NSE) ranging between 0.48 and 0.83. Using the calibrated hydrological parameter sets, the parameter uncertainty linked to the nitrogen parameters was explored in order to cover the range of possible predictions of exported loads for 3 nitrogen species: nitrate (NO3), ammonium (NH4) and total nitrogen (Tot-N). For each model and each nitrogen species, predictions were ranked in two different ways according to the performance indicated by two different goodness-of-fit measures: the coefficient of determination R2 and the root mean square error RMSE. A total of 2160 deterministic Single Model Ensembles (SME) was generated using an increasing number of members (from the 2 best to the 10 best single predictions). Finally, the best SME for each model, nitrogen species and discharge station were selected and merged into 330 different Multi-Model Ensembles (MME). The evolution of changes in R2 and RMSE was used as a performance descriptor of the ensemble procedure. In each studied case, numerous ensemble merging schemes were identified which outperformed any of their members. Improvement rates were generally higher when worse members were introduced. The highest improvements were achieved for the nitrogen SMEs compiled with multiple linear regression models with R2 selected members, which resulted in the RMSE decreasing by up to 90%.

  2. Ensemble modelling of nitrogen fluxes: data fusion for a Swedish meso-scale catchment

    NASA Astrophysics Data System (ADS)

    Exbrayat, J.-F.; Viney, N. R.; Seibert, J.; Wrede, S.; Frede, H.-G.; Breuer, L.

    2010-12-01

    Model predictions of biogeochemical fluxes at the landscape scale are highly uncertain, both with respect to stochastic (parameter) and structural uncertainty. In this study 5 different models (LASCAM, LASCAM-S, a self-developed tool, SWAT and HBV-N-D) designed to simulate hydrological fluxes as well as mobilisation and transport of one or several nitrogen species were applied to the mesoscale River Fyris catchment in mid-eastern Sweden. Hydrological calibration against 5 years of recorded daily discharge at two stations gave highly variable results with Nash-Sutcliffe Efficiency (NSE) ranging between 0.48 and 0.83. Using the calibrated hydrological parameter sets, the parameter uncertainty linked to the nitrogen parameters was explored in order to cover the range of possible predictions of exported loads for 3 nitrogen species: nitrate (NO3), ammonium (NH4) and total nitrogen (Tot-N). For each model and each nitrogen species, predictions were ranked in two different ways according to the performance indicated by two different goodness-of-fit measures: the coefficient of determination R2 and the root mean square error RMSE. A total of 2160 deterministic Single Model Ensembles (SME) was generated using an increasing number of members (from the 2 best to the 10 best single predictions). Finally the best SME for each model, nitrogen species and discharge station were selected and merged into 330 different Multi-Model Ensembles (MME). The evolution of changes in R2 and RMSE was used as a performance descriptor of the ensemble procedure. In each studied case, numerous ensemble merging schemes were identified which outperformed any of their members. Improvement rates were generally higher when worse members were introduced. The highest improvements were achieved for the nitrogen SMEs compiled with multiple linear regression models with R2 selected members, which resulted in the RMSE decreasing by up to 90%.

  3. Microscale deformation of a tempered martensite ferritic steel: Modelling and experimental study of grain and sub-grain interactions

    NASA Astrophysics Data System (ADS)

    Golden, Brian J.; Li, Dong-Feng; Guo, Yina; Tiernan, Peter; Leen, Sean B.; O'Dowd, Noel P.

    2016-01-01

    In this paper, a finite-element modelling framework is presented with explicit representation of polycrystalline microstructure for a tempered martensite ferritic steel. A miniature notched specimen was manufactured from P91 steel with a 20,000 h service history and tested at room temperature under three point bending. Deformation at the microscale is quantified by electron back scattered diffraction (EBSD) before and after mechanical loading. A representative volume element was developed, based on the initial EBSD scan, and a crystal plasticity model used to account for slip-based inelastic deformation in the material. The model showed excellent correlation with the experimental data when the relevant comparisons were made.

  4. Nitrogen Substituted Phenothiazine Derivatives: Modelling of Molecular Self-Assembling

    PubMed Central

    Bende, Attila; Turcu, Ioan

    2011-01-01

    The study aims to present a detailed theoretical investigation of noncovalent intermolecular interactions between different π–π stacking nitrogen substituted phenothiazine derivatives by applying second-order Møller-Plesset perturbation (MP2), density functional (DFT) and semiempirical theories. The conformational stability of these molecular systems is mainly given by the dispersion-type electron correlation effects. The density functional tight-binding (DFTB) method applied for dimer structures are compared with the results obtained by the higher level theoretical methods. Additionally, the optimal configuration of the investigated supramolecular systems and their self-assembling properties are discussed. PMID:21686172

  5. 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

  6. 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.

  7. Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics.

    PubMed

    Wabik, Jacek; Kmiecik, Sebastian; Gront, Dominik; Kouza, Maksim; Koliński, Andrzej

    2013-05-10

    We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  8. 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.

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

    DOE PAGES

    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

  10. 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.

  11. 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.

  12. 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.

  13. Representing environment-induced helix-coil transitions in a coarse grained peptide model

    NASA Astrophysics Data System (ADS)

    Dalgicdir, Cahit; Globisch, Christoph; Sayar, Mehmet; Peter, Christine

    2016-10-01

    Coarse grained (CG) models are widely used in studying peptide self-assembly and nanostructure formation. One of the recurrent challenges in CG modeling is the problem of limited transferability, for example to different thermodynamic state points and system compositions. Understanding transferability is generally a prerequisite to knowing for which problems a model can be reliably used and predictive. For peptides, one crucial transferability question is whether a model reproduces the molecule's conformational response to a change in its molecular environment. This is of particular importance since CG peptide models often have to resort to auxiliary interactions that aid secondary structure formation. Such interactions take care of properties of the real system that are per se lost in the coarse graining process such as dihedral-angle correlations along the backbone or backbone hydrogen bonding. These auxiliary interactions may then easily overstabilize certain conformational propensities and therefore destroy the ability of the model to respond to stimuli and environment changes, i.e. they impede transferability. In the present paper we have investigated a short peptide with amphiphilic EALA repeats which undergoes conformational transitions between a disordered and a helical state upon a change in pH value or due to the presence of a soft apolar/polar interface. We designed a base CG peptide model that does not carry a specific (backbone) bias towards a secondary structure. This base model was combined with two typical approaches of ensuring secondary structure formation, namely a C α -C α -C α -C α pseudodihedral angle potential or a virtual site interaction that mimics hydrogen bonding. We have investigated the ability of the two resulting CG models to represent the environment-induced conformational changes in the helix-coil equilibrium of EALA. We show that with both approaches a CG peptide model can be obtained that is environment-transferable and that

  14. Coarse graining approach to First principles modeling of radiation cascade in large Fe super-cells

    NASA Astrophysics Data System (ADS)

    Odbadrakh, Khorgolkhuu; Nicholson, Don; Rusanu, Aurelian; Wang, Yang; Stoller, Roger; Zhang, Xiaoguang; Stocks, George

    2012-02-01

    First principles techniques employed to understand systems at an atomistic level are not practical for large systems consisting of millions of atoms. We present an efficient coarse graining approach to bridge the first principles calculations of local electronic properties to classical Molecular Dynamics (MD) simulations of large structures. Local atomic magnetic moments in crystalline Fe are perturbed by radiation generated defects. The effects are most pronounced near the defect core and decay with distance. We develop a coarse grained 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. This work was supported by the Center for Defect Physics, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences.

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

    NASA Astrophysics Data System (ADS)

    Zhu, Q.; Zhuang, Q.

    2013-12-01

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

  16. Multiscale Modeling at Nanointerfaces: Polymer Thin Film Materials Discovery via Thermomechanically Consistent Coarse Graining

    NASA Astrophysics Data System (ADS)

    Hsu, David D.

    Due to high nanointerfacial area to volume ratio, the properties of "nanoconfined" polymer thin films, blends, and composites become highly altered compared to their bulk homopolymer analogues. Understanding the structure-property mechanisms underlying this effect is an active area of research. However, despite extensive work, a fundamental framework for predicting the local and system-averaged thermomechanical properties as a function of configuration and polymer species has yet to be established. Towards bridging this gap, here, we present a novel, systematic coarse-graining (CG) method which is able to capture quantitatively, the thermomechanical properties of real polymer systems in bulk and in nanoconfined geometries. This method, which we call thermomechanically consistent coarse-graining (TCCG), is a two-bead-per-monomer CG hybrid approach through which bonded interactions are optimized to match the atomistic structure via the Iterative Boltzmann Inversion method (IBI), and nonbonded interactions are tuned to macroscopic targets through parametric studies. We validate the TCCG method by systematically developing coarse-grain models for a group of five specialized methacrylate-based polymers including poly(methyl methacrylate) (PMMA). Good correlation with bulk all-atom (AA) simulations and experiments is found for the temperature-dependent glass transition temperature (Tg) Flory-Fox scaling relationships, self-diffusion coefficients of liquid monomers, and modulus of elasticity. We apply this TCCG method also to bulk polystyrene (PS) using a comparable coarse-grain CG bead mapping strategy. The model demonstrates chain stiffness commensurate with experiments, and we utilize a density-correction term to improve the transferability of the elastic modulus over a 500 K range. Additionally, PS and PMMA models capture the unexplained, characteristically dissimilar scaling of Tg with the thickness of free-standing films as seen in experiments. Using vibrational

  17. Modelling dust processing and the evolution of grain sizes in the ISM using the method of moments

    NASA Astrophysics Data System (ADS)

    Mattsson, Lars

    2016-11-01

    Interstellar dust grains do not have a single well-defined origin. Stars are demonstrably dust producers, but also efficient destroyers of cosmic dust. Dust destruction in the ISM is believed to be the result of SN shocks hitting the ambient ISM gas (and dust) and lead to an increased rate of ion sputtering, which reduces the dust mass. Grains located in cold molecular clouds can on the other hand grow by condensation, thus providing a replenishment mechanism or even a dominant channel of dust formation. In dense environments grains may coagulate and form large composite grains and aggregates and if grains collide with large enough energies they may be shattered, forming a range of smaller debris grains. The present paper presents a statistical modelling approach using the method of moments, which is computationally very inexpensive and may therefore be an attractive option when combining dust processing with, e.g., detailed simulations of interstellar gas dynamics. A solar-neighbourhood-like toy model of interstellar dust evolution is presented as an example.

  18. 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.

  19. 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.

  20. Protein simulation using coarse-grained two-bead multipole force field with polarizable water models

    NASA Astrophysics Data System (ADS)

    Li, Min; Zhang, John Z. H.

    2017-02-01

    A recently developed two-bead multipole force field (TMFF) is employed in coarse-grained (CG) molecular dynamics (MD) simulation of proteins in combination with polarizable CG water models, the Martini polarizable water model, and modified big multipole water model. Significant improvement in simulated structures and dynamics of proteins is observed in terms of both the root-mean-square deviations (RMSDs) of the structures and residue root-mean-square fluctuations (RMSFs) from the native ones in the present simulation compared with the simulation result with Martini's non-polarizable water model. Our result shows that TMFF simulation using CG water models gives much stable secondary structures of proteins without the need for adding extra interaction potentials to constrain the secondary structures. Our result also shows that by increasing the MD time step from 2 fs to 6 fs, the RMSD and RMSF results are still in excellent agreement with those from all-atom simulations. The current study demonstrated clearly that the application of TMFF together with a polarizable CG water model significantly improves the accuracy and efficiency for CG simulation of proteins.

  1. Coarse-grained red blood cell model with accurate mechanical properties, rheology and dynamics.

    PubMed

    Fedosov, Dmitry A; Caswell, Bruce; Karniadakis, George E

    2009-01-01

    We present a coarse-grained red blood cell (RBC) model with accurate and realistic mechanical properties, rheology and dynamics. The modeled membrane is represented by a triangular mesh which incorporates shear inplane energy, bending energy, and area and volume conservation constraints. The macroscopic membrane elastic properties are imposed through semi-analytic theory, and are matched with those obtained in optical tweezers stretching experiments. Rheological measurements characterized by time-dependent complex modulus are extracted from the membrane thermal fluctuations, and compared with those obtained from the optical magnetic twisting cytometry results. The results allow us to define a meaningful characteristic time of the membrane. The dynamics of RBCs observed in shear flow suggests that a purely elastic model for the RBC membrane is not appropriate, and therefore a viscoelastic model is required. The set of proposed analyses and numerical tests can be used as a complete model testbed in order to calibrate the modeled viscoelastic membranes to accurately represent RBCs in health and disease.

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

    PubMed Central

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

    2017-01-01

    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 timescales 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

  3. Root traits explain observed tundra vegetation nitrogen uptake patterns: Implications for trait-based land models

    NASA Astrophysics Data System (ADS)

    Zhu, Qing; Iversen, Colleen M.; Riley, William J.; Slette, Ingrid J.; Vander Stel, Holly M.

    2016-12-01

    Ongoing climate warming will likely perturb vertical distributions of nitrogen availability in tundra soils through enhancing nitrogen mineralization and releasing previously inaccessible nitrogen from frozen permafrost soil. However, arctic tundra responses to such changes are uncertain, because of a lack of vertically explicit nitrogen tracer experiments and untested hypotheses of root nitrogen uptake under the stress of microbial competition implemented in land models. We conducted a vertically explicit 15N tracer experiment for three dominant tundra species to quantify plant N uptake profiles. Then we applied a nutrient competition model (N-COM), which is being integrated into the ACME Land Model, to explain the observations. Observations using an 15N tracer showed that plant N uptake profiles were not consistently related to root biomass density profiles, which challenges the prevailing hypothesis that root density always exerts first-order control on N uptake. By considering essential root traits (e.g., biomass distribution and nutrient uptake kinetics) with an appropriate plant-microbe nutrient competition framework, our model reasonably reproduced the observed patterns of plant N uptake. In addition, we show that previously applied nutrient competition hypotheses in Earth System Land Models fail to explain the diverse plant N uptake profiles we observed. Our results cast doubt on current climate-scale model predictions of arctic plant responses to elevated nitrogen supply under a changing climate and highlight the importance of considering essential root traits in large-scale land models. Finally, we provided suggestions and a short synthesis of data availability for future trait-based land model development.

  4. Harmonized, distributed and nation wide modelling of Nitrogen retention in Danish surface fresh waters

    NASA Astrophysics Data System (ADS)

    Thodsen, Hans; Larsen, Søren E.; Windolf, Jørgen; Bering Ovesen, Niels; Bøgestrand, Jens; Kronvang, Brian

    2010-05-01

    According to the EU Water Framework Directive all freshwater bodies must obtain good ecological status by 2015. In Denmark this means that all lakes with a surface area above 5 ha must be evaluated individually and mitigation measures must be enforced if the ecological status is below "good". In consequence, the nutrient pressures from point and diffuse sources must be assessed based on a quantification of the nutrient loading of each lake. In this study we focus on the loading of nitrogen. Surface water Nitrogen retention is an important parameter in loading estimations of nitrogen to lakes and marine areas. Estimations of the cost, of reducing Nitrogen loadings also largely depends on calculations of surface water retention as large percentages of the load can be removed/ retained in surface waters. Especially the presents of larger lakes on the river network can make a large difference between the loads from different catchments. A standardised calculation on annual (1990 - 2008) Nret percentages has been carried out for all Danish lakes larger than 5 hectares attached to a river network (591 lakes). The Nret calculation is based on water residence time calculations from each lake. A national 3D hydrological model, covering all major parts of the country estimated runoff for lake catchments. The diffuse nitrogen input to each lake was simulated with an empirical nitrogen load model. Where lakes are located upstream/ downstream of each other, a calculation chain involving the nitrogen retention in lakes was created. Harmonized national calculations of river nitrogen retention are carried out on the basis of river length and river width information and information on rivers in forested areas. Each river class is given a specific retention pr. unit area. The total average (1990 - 2008) Nitrogen load to Danish surface waters is modelled to 99000 t/yr. The total surface water retention is estimated to 23700 t/yr (24%). Of the surface water retention, 35% origins from

  5. Optimization of an elastic network augmented coarse grained model to study CCMV capsid deformation.

    PubMed

    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.

  6. 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

  7. Milk production, nitrogen balance, and fiber digestibility prediction of corn, whole plant grain sorghum, and forage sorghum silages in the dairy cow.

    PubMed

    Colombini, S; Galassi, G; Crovetto, G M; Rapetti, L

    2012-08-01

    Total mixed rations containing corn (CS), whole plant grain sorghum (WPGS), or forage sorghum (FS) silages were fed to 6 primiparous Italian Friesian cows to determine the effects on lactation performance, nutrient digestibility, and N balance. Furthermore, the relationship between in vivo total-tract neutral detergent fiber (NDF) digestibility (ttNDFD) and the ttNDFD derived by the Cornell Net Carbohydrate and Protein System (CNCPS) model was assessed. Cows were assigned to 1 of 3 diets in a replicated 3 × 3 Latin square with 28-d periods. The experimental treatment was silage type and 3 different silages were included in the diets. The diets were formulated to be iso-NDF. Accordingly, each diet was formulated to contain 41.5% CS silage, 36.7% WPGS silage, or 28.0% FS silage, on a DM basis. Starch content was balanced by adding the appropriate amount of corn meal. Separate collection of total urine and feces was performed. Dietary forages were analyzed for in vitro NDF digestibility (6 and 24h of incubation) to predict fiber digestion rate with 2 NDF pools (digestible and indigestible). Rumen digestibility of the potentially digestible NDF pool was predicted using CNCPS version 6.1, using the in vitro forage fiber digestion rate. The ttNDFD was predicted assuming that intestinal digestibility of the NDF amount escaping rumen digestion was 20%, according to the CNCPS model. Dry matter intake was decreased by approximately 1.8 kg/d in cows fed the FS diet compared with the other diets, probably for the greater particle size of FS diet. Hence, milk yield (kg/d) was lowest for FS (23.6), intermediate for WPGS (24.6), and highest for the CS diet (25.4). Milk urea N (mg/dL) was highest for FS (12.9), intermediate for WPGS (11.9), and lowest for CS (10.7) diet. In vivo ttNDFD (%) was 51.4 (CS), 48.6 (WPGS), and 54.1 (FS); this was probably due to a higher retention time of FS diet in the rumen rather than to a better quality of the FS silage, as confirmed by in situ and

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    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+] = 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.

  9. 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.

  10. 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.

  11. 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.

  12. A mechanistic treatment of the dominant soil nitrogen cycling processes: Model development, testing, and application

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The development and initial application of a mechanistic model (TOUGHREACT-N) designed to characterize soil nitrogen (N) cycling and losses are described. The model couples advective and diffusive nutrient transport, multiple microbial biomass dynamics, and equilibrium and kinetic chemical reactions...

  13. Tidal Prism Modeling of Phytoplankton and Nitrogen Concentrations in Narragansett Bay and its Sub-Embayments

    EPA Science Inventory

    A tidal prism model was developed to calculate temporal changes in the spatially averaged concentration of three state variables: phytoplankton, dissolved inorganic nitrogen, and detritus. Our main objective was to develop a model to help us understand the causes of phytoplankton...

  14. Coarse-grained model of adsorption of blood plasma proteins onto nanoparticles

    NASA Astrophysics Data System (ADS)

    Lopez, Hender; Lobaskin, Vladimir

    2015-12-01

    We present a coarse-grained model for evaluation of interactions of globular proteins with nanoparticles (NPs). The protein molecules are represented by one bead per aminoacid and the nanoparticle by a homogeneous sphere that interacts with the aminoacids via a central force that depends on the nanoparticle size. The proposed methodology is used to predict the adsorption energies for six common human blood plasma proteins on hydrophobic charged or neutral nanoparticles of different sizes as well as the preferred orientation of the molecules upon adsorption. Our approach allows one to rank the proteins by their binding affinity to the nanoparticle, which can be used for predicting the composition of the NP-protein corona. The predicted ranking is in good agreement with known experimental data for protein adsorption on surfaces.

  15. Stratospheric distributions of odd nitrogen and odd hydrogen in a two-dimensional model

    NASA Technical Reports Server (NTRS)

    Prinn, R. G.; Alyea, F. N.; Cunnold, D. M.

    1975-01-01

    A two-dimensional pole-to-pole chemical model of the stratosphere is developed which extends from 8 to 38 km in altitude. Atmospheric motions are simulated by mean vertical and meridional winds and eddy diffusion coefficients. Seasonally averaged distributions of important odd nitrogen (NO, NO2, and HNO3) and odd hydrogen (H, OH, HO2, H2O2) compounds are computed. Photodissociation of N2O leads to production of odd nitrogen in the stratosphere, and the odd nitrogen is ultimately removed by downward transport into the troposphere and by rain-out (modeled by a rain-out lifetime of 30 days below 8-km altitude). Results are presented for a quasi-steady state in which seasonal cycles repeat themselves. These results show significant latitudinal as well as vertical variations in the predicted species which emphasize the need for at least two dimensions in accurate stratospheric modeling. Computed concentrations are compared with observations when they exist.

  16. 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

  17. A coarse-grained model for synergistic action of multiple enzymes on cellulose

    DOE PAGES

    Asztalos, Andrea; Daniels, Marcus; Sethi, Anurag; ...

    2012-08-01

    In this study, degradation of cellulose to glucose requires the cooperative action of three classes of enzymes, collectively known as cellulases. Endoglucanases randomly bind to cellulose surfaces and generate new chain ends by hydrolyzing -1,4-D-glycosidic bonds. Exoglucanases bind to free chain ends and hydrolyze glycosidic bonds in a processive manner releasing cellobiose units. Then, -glucosidases hydrolyze soluble cellobiose to glucose. Optimal synergistic action of these enzymes is essential for efficient digestion of cellulose. Experiments show that as hydrolysis proceeds and the cellulose substrate becomes more heterogeneous, the overall degradation slows down. As catalysis occurs on the surface of crystalline cellulose,more » several factors affect the overall hydrolysis. Therefore, spatial models of cellulose degradation must capture effects such as enzyme crowding and surface heterogeneity, which have been shown to lead to a reduction in hydrolysis rates. As a result, we present a coarse-grained stochastic model for capturing the key events associated with the enzymatic degradation of cellulose at the mesoscopic level. This functional model accounts for the mobility and action of a single cellulase enzyme as well as the synergy of multiple endo- and exo-cellulases on a cellulose surface. The quantitative description of cellulose degradation is calculated on a spatial model by including free and bound states of both endo- and exo-cellulases with explicit reactive surface terms (e.g., hydrogen bond breaking, covalent bond cleavages) and corresponding reaction rates. The dynamical evolution of the system is simulated by including physical interactions between cellulases and cellulose. In conclusion, our coarse-grained model reproduces the qualitative behavior of endoglucanases and exoglucanases by accounting for the spatial heterogeneity of the cellulose surface as well as other spatial factors such as enzyme crowding. Importantly, it captures the endo

  18. The NASA Lightning Nitrogen Oxides Model (LNOM): Application to Air Quality Modeling

    NASA Technical Reports Server (NTRS)

    Koshak, William; Peterson, Harold; Khan, Maudood; Biazar, Arastoo; Wang, Lihua

    2011-01-01

    Recent improvements to the NASA Marshall Space Flight Center Lightning Nitrogen Oxides Model (LNOM) and its application to the Community Multiscale Air Quality (CMAQ) modeling system are discussed. The LNOM analyzes Lightning Mapping Array (LMA) and National Lightning Detection Network(TradeMark)(NLDN) data to estimate the raw (i.e., unmixed and otherwise environmentally unmodified) vertical profile of lightning NO(x) (= NO + NO2). The latest LNOM estimates of lightning channel length distributions, lightning 1-m segment altitude distributions, and the vertical profile of lightning NO(x) are presented. The primary improvement to the LNOM is the inclusion of non-return stroke lightning NOx production due to: (1) hot core stepped and dart leaders, (2) stepped leader corona sheath, K-changes, continuing currents, and M-components. The impact of including LNOM-estimates of lightning NO(x) for an August 2006 run of CMAQ is discussed.

  19. Nitrogen mass transfer models for plasma-based low-energy ion implantation

    SciTech Connect

    Zheng, Bocong; Wang, Kesheng; Zhang, Zhipeng; Che, Honglong; Lei, Mingkai

    2015-03-15

    The nitrogen mass transfer process in plasma-based low-energy ion implantation (PBLEII) is theoretically and experimentally studied in order to explore the process mechanism of PBLEII and therefore to optimize the apparatus design and the process conditions. An electron cyclotron resonance (ECR) microwave discharge generates the nitrogen plasma with a high density of 10{sup 11}–10{sup 12} ions/cm{sup 3}, which diffuses downstream to the process chamber along the divergent magnetic field. The nitrogen ions in the plasma implant into the surface and transport to the matrix of an austenitic stainless steel under the low negative pulsed bias of −2 kV at a process temperature of 400 °C. A global plasma model is used to simulate the ECR microwave plasma discharge for a range of working pressures and microwave powers. The fluid models are adopted to calculate the plasma downstream diffusion, the sheath expansion and the low-energy ion implantation on the surface. A nonlinear kinetic discrete model is established to describe the nitrogen transport in the austenitic stainless steel and the results are compared with the experimental measurements. Under an average implantation current density of 0.3–0.6 mA/cm{sup 2}, the surface nitrogen concentration in the range from 18.5 to 29 at. % is a critical factor for the nitrogen transport in the AISI 304 austenitic stainless steel by PBLEII, which accelerates the implanted nitrogen diffusion inward up to 6–12 μm during a nitriding time of 4 h.

  20. 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.

  1. Prediction of traffic-related nitrogen oxides concentrations using Structural Time-Series models

    NASA Astrophysics Data System (ADS)

    Lawson, Anneka Ruth; Ghosh, Bidisha; Broderick, Brian

    2011-09-01

    Ambient air quality monitoring, modeling and compliance to the standards set by European Union (EU) directives and World Health Organization (WHO) guidelines are required to ensure the protection of human and environmental health. Congested urban areas are most susceptible to traffic-related air pollution which is the most problematic source of air pollution in Ireland. Long-term continuous real-time monitoring of ambient air quality at such urban centers is essential but often not realistic due to financial and operational constraints. Hence, the development of a resource-conservative ambient air quality monitoring technique is essential to ensure compliance with the threshold values set by the standards. As an intelligent and advanced statistical methodology, a Structural Time Series (STS) based approach has been introduced in this paper to develop a parsimonious and computationally simple air quality model. In STS methodology, the different components of a time-series dataset such as the trend, seasonal, cyclical and calendar variations can be modeled separately. To test the effectiveness of the proposed modeling strategy, average hourly concentrations of nitrogen dioxide and nitrogen oxides from a congested urban arterial in Dublin city center were modeled using STS methodology. The prediction error estimates from the developed air quality model indicate that the STS model can be a useful tool in predicting nitrogen dioxide and nitrogen oxides concentrations in urban areas and will be particularly useful in situations where the information on external variables such as meteorology or traffic volume is not available.

  2. 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.

  3. 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.

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

    SciTech Connect

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

    2016-01-07

    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.

  5. 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.

  6. A hybrid modeling approach for estimating reactive nitrogen deposition in Rocky Mountain National Park

    NASA Astrophysics Data System (ADS)

    Malm, William C.; Rodriguez, Marco A.; Schichtel, Bret A.; Gebhart, Kristi A.; Thompson, Tammy M.; Barna, Michael G.; Benedict, Katherine B.; Carrico, Christian M.; Collett, Jeffrey L.

    2016-02-01

    Changes in ecosystem function at Rocky Mountain National Park (RMNP) are occurring because of nitrogen deposition associated with emissions of nitrogen from sources in Colorado as well as other areas of the North American continent and beyond. Nitrogen species are in both reduced and oxidized forms. A year-long monitoring program was initiated to better understand their origins as well as the complex chemistry occurring during transport from source to receptor. Specifically, the goals of the study were to characterize the atmospheric concentrations of nitrogen species in gaseous, particulate, and aqueous phases in RMNP and to identify the emission sources of these various species. The apportionment strategy was designed to focus on differentiating between sources within and outside the state of Colorado and then further differentiate between sources along the Front Range of Colorado and the rest of Colorado. It was also desirous to identify the relative contributions to atmospheric nitrogen species from mobile sources, agricultural activities, and large and small point sources within the state of Colorado. The Particle Source Apportionment Technology (PSAT) module available in the chemical transport model, the Comprehensive Air quality Model with extensions (CAMx), is used to develop first-principle estimates of the contributions from different areas of North America. The CAMx_PSAT results are combined with measured species concentrations in a receptor modeling approach to develop final estimates of source apportionment of the various species' concentrations and deposition.

  7. A dynamic growth model of vegetative soya bean plants: model structure and behaviour under varying root temperature and nitrogen concentration

    NASA Technical Reports Server (NTRS)

    Lim, J. T.; Wilkerson, G. G.; Raper, C. D. Jr; Gold, H. J.

    1990-01-01

    A differential equation model of vegetative growth of the soya bean plant (Glycine max (L.) Merrill cv. Ransom') was developed to account for plant growth in a phytotron system under variation of root temperature and nitrogen concentration in nutrient solution. The model was tested by comparing model outputs with data from four different experiments. Model predictions agreed fairly well with measured plant performance over a wide range of root temperatures and over a range of nitrogen concentrations in nutrient solution between 0.5 and 10.0 mmol NO3- in the phytotron environment. Sensitivity analyses revealed that the model was most sensitive to changes in parameters relating to carbohydrate concentration in the plant and nitrogen uptake rate.

  8. Polycyclic aromatic hydrocarbons in edible grain: a pilot study of agricultural crops as a human exposure pathway for environmental contaminants using wheat as a model crop.

    PubMed

    Kobayashi, Reiko; Okamoto, Robert A; Maddalena, Randy L; Kado, Norman Y

    2008-06-01

    The concentrations of polycyclic aromatic hydrocarbons (PAHs) were investigated in a pilot study of field wheat grain as a model indicator for environmental contamination. The edible grain would serve as a portal for human exposure. Wheat grain was initially studied since it is one of the major food crops consumed internationally by many including infants and children. Wheat grain samples from five different geographical growing locations in California that span approximately 450 km were collected during the same growing season. The same variety of grain was harvested and analyzed for PAHs that ranged from 2- to 6-rings. PAHs were detected in all grain samples and were mainly 2- to 4-ring PAHs with naphthalene the most abundant among them. There were geographical differences in the levels of PAHs in the grain. The sources of the PAHs were not known in this pilot study, but the principal component analysis indicates that the major source is similar in all locations except for naphthalene. Grain naphthalene concentrations may reflect local naphthalene emissions. Diesel-fueled harvesting operations did not appear to contribute to the observed PAH concentrations in the grain. An estimate of naphthalene intake from eating grain compared to inhalation intake demonstrated the potential importance of field contamination of grain as a possible portal of human exposure. The relationship between PAH concentrations in grain and air should be quantitatively investigated to better quantitate exposure and to identify effective measures to lower the risk from PAH exposure through eating grain.

  9. 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

  10. Inversion of coupled carbon-nitrogen model parameters against multiple datasets using Markov chain Monte Carlo methodology

    NASA Astrophysics Data System (ADS)

    Yang, Y.; Zhou, X.; Weng, E.; Luo, Y.

    2010-12-01

    The Markov chain Monte Carlo (MCMC) method has been widely used to estimate terrestrial ecosystem model parameters. However, inverse analysis is now mainly applied to estimate parameters involved in terrestrial ecosystem carbon models, and yet not used to inverse terrestrial nitrogen model parameters. In this study, the Bayesian probability inversion and MCMC technique were applied to inverse model parameters in a coupled carbon-nitrogen model, and then the trained ecosystem model was used to predict nitrogen pool sizes at the Duke Forests FACE site. We used datasets of soil respiration, nitrogen mineralization, nitrogen uptake, carbon and nitrogen pools in wood, foliage, litterfall, microbial, forest floor, and mineral soil under ambient and elevated CO2 plots from 1996-2005. Our results showed that, the initial values of C pools in leaf, wood, root, litter, microbial and forest floor were well constrained. The transfer coefficients from pools of leaf biomass, woody biomass, root biomass, litter, forest floor were also well constrained by the actual measurements. The observed datasets gave moderate info